Rapid molecular cytogenetic analysis of X-chromosomal microdeletions: fluorescence in situ hybridization (FISH) for complex glycerol kinase deficiency

Diagnosis of X-chromosomal microdeletions has relied upon the traditional methods of Southern blotting and DNA amplification, with carrier identification requiring time-consuming and unreliable dosage calculations. In this report, we describe rapid molecular cytogenetic identification of deleted DNA in affected males with the Xp21 contiguous gene syndrome (complex glycerol kinase deficiency, CGKD) and female carriers for this disorder. CGKD deletions involve the genes for glycerol kinase, Duchenne muscular dystrophy, and/or adrenal hypoplasia congenita. We report an improved method for diagnosis of deletions in individuals with CGKD and for identification of female carriers within their families, using fluorescence in situ hybridization (FISH) with a cosmid marker (cosmid 35) within the glycerol kinase gene. When used in combination with an Xq control probe, affected males demonstrate a single signal from the control probe, while female carriers demonstrate a normal chromosome with two signals, as well as a deleted chromosome with a single signal from the control probe. FISH analysis for CGKD provides the advantages of speed and accuracy for evaluation of submicroscopic X-chromosomal deletions, particularly in identification of female carriers. In addition to improving carrier evaluation, FISH will make prenatal diagnosis of CGKD more readily available.

Dysmorphic features in patients with complex glycerol kinase deficiency

Complex glycerol kinase deficiency is a contiguous gene syndrome consisting of a deletion of the glycerol kinase locus, together with the genes for adrenal hypoplasia congenita or Duchenne muscular dystrophy or both. We describe an infant with complex glycerol kinase deficiency and mildly dysmorphic features similar to those seen in other patients, including an "hourglass" appearance of the middle of the face; hypertelorism; rounded palpebral fissures; esotropia; wide, flattened earlobes; and a downturned mouth. The combination of medical history and characteristic facies should prompt the request for specific laboratory tests diagnostic for this potentially treatable condition.

Amplification of bacterial DNA using highly conserved sequences: automated analysis and potential for molecular triage of sepsis

OBJECTIVE

The clinical diagnosis of sepsis remains difficult, particularly in the young child, and would be improved by a rapid and reliable method for identification of bacteria in blood and other body fluids. Polymerase chain reaction (PCR) amplification of highly conserved DNA sequences found in all bacteria would permit fast and sensitive determination of the presence of bacteria in clinical specimens.

METHODOLOGY

A primer pair for highly conserved regions of bacterial DNA encoding 16S ribosomal RNA (rDNA) was utilized for PCR amplification. PCR products were analyzed by gel electrophoresis, and, after modification of the primers, by an automated 96-well plate reader.

RESULTS

rDNA was amplified from 12 different species of bacteria, including Gram-negative and -positive organisms. No signal was observed when total human DNA was used as template. Colorimetric analysis of amplified sequences using a 96-well format was also successful.

CONCLUSIONS

We conclude that a single primer pair designed to anneal to a highly conserved region of bacterial DNA can amplify DNA specimens from a variety of different bacteria, while not amplifying human DNA. Such a molecular genetics approach can be fully automated with existing robotic technology. Because of speed, sensitivity, and cost, molecular triage of patients with signs and symptoms of possible bacterial infection will decrease morbidity and mortality among those with unrecognized bacteremia who are managed as outpatients, and will dramatically reduce hospital expenses from individuals who are admitted and are not bacteremic.

Identification of new members of a carbohydrate kinase-encoding gene family

In a sequence database search using the human glycerol kinase-encoding sequence (HUMGLYKINB) as a query, we identified six previously unidentified carbohydrate kinase sequences. Five of the six newly identified sequences appear to be known types of carbohydrate kinases, four are glycerol kinases and one is a gluconokinase. The sixth newly identified sequence, the Caenorhabditis elegans gene, CER08D7.7-CEF59B2.1, shows similarity to the family of carbohydrate kinases including other glycerol kinases, xylulokinases, gluconokinases, ribulokinases, rhamnulokinases, and fucokinases. A phylogenetic comparison of this newly identified Caenorhabditis elegans gene with the other members of the carbohydrate kinase family demonstrated that this sequence cannot be assigned to one of the known classes of carbohydrate kinases.

An unusual member of the nuclear hormone receptor superfamily responsible for X-linked adrenal hypoplasia congenita

X-linked adrenal hypoplasia congenita is a developmental disorder of the human adrenal gland that results in profound hormonal deficiencies and is lethal if untreated. We have isolated the gene responsible for the disease, DAX-1, which is deleted or mutated in X-linked adrenal hypoplasia patients. DAX-1 encodes a new member of the nuclear hormone receptor superfamily displaying a novel DNA-binding domain. The DAX-1 product acts as a dominant negative regulator of transcription mediated by the retinoic acid receptor.

Hexokinase binding in ischemic and reperfused piglet brain

Hexokinase catalyzes the first step in cerebral glucose utilization and is a rate-limiting enzyme in glycolysis. Glucose utilization is tightly coupled to cerebral blood flow so that during ischemia the brain has a decreased supply of glucose, as well as oxygen. We studied hexokinase enzymatic activity in a newborn piglet model of ischemia-reperfusion to determine if any changes in the activity or mitochondrial binding of the enzyme occurred. We observed that mitochondrial binding of cortical HK increased from 55 to 71% with ischemia and returned toward control levels, but did not completely recover, after 2 h of reperfusion.

Hexokinase autophosphorylation: identification of a new dual specificity protein kinase

Hexokinase 1 (HK1) purified from rat brain exhibits protein kinase activity, including autophosphorylation and phosphorylation of other protein substrates. The amino acid specificity of rat brain autophosphorylation was analyzed with monoclonal antibodies directed against phosphotyrosine and by acid hydrolysis of the phosphorylated enzyme. The results show that serine, threonine, and tyrosine residues are phosphorylated after incubation with ATP. The stoichiometry of this phosphorylation was 0.2 mole phosphate per mole hexokinase after 30 min of incubation. Evaluation of freshly isolated HK1 with monoclonal anti-phosphotyrosine antibody indicates that the enzyme is phosphorylated at a basal level in its native state. We concluded that rat brain HK1 is a dual specificity protein kinase that is phosphorylated physiologically.

A dosage sensitive locus at chromosome Xp21 is involved in male to female sex reversal

Male to female sex reversal has been observed in individuals with duplications of the short arm of the X chromosome. Here we demonstrate that sex reversal results from the presence of two active copies of an Xp locus rather than from its rearrangement and that alterations at this locus constitute one of the causes of sex reversal in individuals with a normal 46,XY karyotype. We have named this locus DSS (Dosage Sensitive Sex reversal) and localized it to a 160 kilobase region of chromosome Xp21, adjacent to the adrenal hypoplasia congenita locus. The identification of male individuals deleted for DSS suggests that this locus is not required for testis differentiation. We propose that DSS has a role in ovarian development and/or functions as a link between ovary and testis formation.

Application of molecular genetics in public health: improved follow-up in a neonatal hemoglobinopathy screening program

Newborn screening for the hemoglobinopathies has been shown to reduce morbidity and mortality, particularly for sickle cell anemia, by facilitating initiation of penicillin prophylaxis by 4 months of age. The purpose of the current investigation was to determine whether molecular genetic follow-up testing could be introduced into a neonatal hemoglobinopathy screening program and, if successfully introduced, whether it would reduce time to diagnostic confirmation. Between July 1, 1991, and October 7, 1992, 518 original dried blood specimens were referred from the Texas Department of Health Neonatal Hemoglobinopathy Screening Program for molecular genetic follow-up testing. Allele-specific cleavage (ASC) after amplification with matched and mismatched polymerase chain reaction primers was compared to allele-specific oligonucleotide (ASO) hybridization. By November 2, 1992, molecular genetic analyses were definitive in 506, and agreement was observed between ASC and ASO hybridization in all specimens analyzed. Approximately 13% of those initially screened FS were considered probable S/beta-thal by DNA and RNA testing. Rapid molecular genetic analysis contributed to a substantial reduction of the mean age at confirmation by approximately 50%, to about 2 months of age. ASC is a reliable method for molecular genetic analysis of dried blood specimens, providing methodology which can be readily automated. An automated method is demonstrated that is based on microtiter plate technology and will significantly reduce labor intensity and costs, while increasing sample throughput. Even with current manual testing methods, DNA and RNA analysis of initial newborn screening specimens will reduce the age at confirmation well under 4 months, the age cut-off for effective initiation of penicillin prophylaxis.

Microcompartmentation of energy metabolism at the outer mitochondrial membrane: role in diabetes mellitus and other diseases

Complexes made up of the kinases, hexokinase and glycerol kinase, together with the outer mitochondrial membrane voltage-dependent anion channel (VDAC) protein, porin, and the inner mitochondrial membrane protein, the adenine nucleotide translocator, are involved in tumorigenesis, diabetes mellitus, and central nervous system function. Identification of these two mitochondrial membrane proteins, along with an 18 kD protein, as components of the peripheral benzodiazepine receptor, provides independent confirmation of the interaction of porin and the adenine nucleotide translocator to form functional contact sites between the inner and outer mitochondrial membranes. We suggest that these are dynamic structures, with channel conductances altered by the presence of ATP, and that ligand-mediated conformational changes in the porin-adenine nucleotide translocator complexes may be a general mechanism in signal transduction.

Human genes encoding the voltage-dependent anion channel (VDAC) of the outer mitochondrial membrane: mapping and identification of two new isoforms

The voltage-dependent anion channel of the mitochondrial outer membrane (VDAC) is a small, abundant pore-forming protein found in the outer membranes of all eukaryotic mitochondria. The VDAC protein is believed to form the major pathway for movement of adenine nucleotides through the outer membrane and to be the mitochondrial binding site for hexokinase and glycerol kinase. Previous studies have indicated that at least two human VDAC isoforms are expressed. Here, we report the mapping of VDAC1 to the X chromosome in the interval Xq13-q21 and VDAC2 to chromosome 21 by polymerase chain reaction and restriction analysis of a human/rodent somatic cell mapping panel. In the process of mapping these genes, we identified and mapped two additional sequences highly homologous to VDAC1. VDAC3 maps to chromosome 12 and VDAC4 maps to chromosome 1. The locations of VDAC1 and VDAC4 have been confirmed by fluorescence in situ hybridization analysis. Future studies will be aimed at defining the specific physiological role of each member of this family of channel proteins.

DNA techniques for screening of inborn errors of metabolism

Molecular genetic techniques are being used increasingly in newborn screening programs. Initial applications involved genotypic confirmation of positive screening tests by DNA microextraction or direct amplification from the dried blood spots. More recently we have shown that RNA can be microextracted from newborn screening specimens, treated with reverse transcriptase and amplified by the polymerase chain reaction. Primary DNA screening is being considered for medium chain acyl-CoA dehydrogenase deficiency in an attempt to identify and treat affected children before their first hypoglycemic episodes. An exciting new development is the application of DNA "fingerprinting" to the microorganisms used in the bacterial inhibition assays for quality control of these critical biological reagents. Thus, molecular genetic approaches will be valuable, not only for confirmatory testing, but also for primary newborn screening for inborn errors of metabolism.

Clinical application of gene therapy: emerging opportunities and current limitations

Protocols for human gene therapy have been approved and a number of investigative trials are in place. While somatic gene therapy is favored over germline therapy, it must be recognized that transformation of somatic cells may occur inadvertently. Ex vivo and in vivo approaches offer two different strategies for genetic intervention and are discussed in the context of therapy for inborn errors of metabolism, brain tumors and other neurological diseases, and AIDS and other infectious diseases. Current technology appears quite promising, but serious limitations remain before routine application of gene therapy is possible.

Isolation of a yeast artificial chromosome contig spanning the X chromosomal translocation breakpoint in a patient with Rett syndrome

Rett syndrome is a neurodevelopmental disorder observed exclusively in females. A de novo X;3 translocation was detected in a patient (TH) with Rett syndrome. The X chromosomal breakpoint maps to Xp21.3 between the distal end of the Duchenne muscular dystrophy (DMD) gene and the DXS28 (C7) locus. To determine if this translocation caused the Rett syndrome in this patient, our efforts focused on mapping and cloning of the X chromosomal breakpoint in this patient. Toward these goals, we generated a set of radiation-reduced hybrid cell lines for the short arm of the X chromosome to use as a source for region-specific markers. Using Alu-PCR, 13 new DNA markers were isolated from a radiation-reduced hybrid, which retained both DMD and DXS28. These markers were localized within Xp21 using DNA from males with various interstitial deletions in this region. Two new markers, K23-2p and K23b-1, were found to be closer flanking markers to the X chromosomal breakpoint than DMD and DXS28. Long range restriction mapping using K23-2p and K23b-1 determined that the maximum distance between them was 800 kb. Several of the new markers were developed into sequence tagged-sites and were used to isolate yeast artificial chromosome (YAC) clones. A total of 22 YAC clones was isolated and characterized; these YACs were then developed into 3 large contigs in the Xp21.3 region. This effort resulted in the cloning of the region containing the X chromosomal translocation breakpoint of the Rett syndrome patient in a 170-kb YAC clone.

Negative-configuration electroretinogram in Oregon eye disease. Consistent phenotype in Xp21 deletion syndrome

OBJECTIVE

To determine whether abnormal configurations on electroretinogram were a consistent finding in patients with Xp21 deletion and to characterize the associated ophthalmologic phenotype.

DESIGN

Case series.

SETTING

University hospitals and eye institutes.

PATIENTS

Five patients with complex glycerol kinase deficiency (Duchenne-type or Becker's muscular dystrophy, glycerol kinase deficiency, and congenital adrenal hypoplasia) and demonstrated chromosomal deletions at Xp21. Control patients were matched by age.

MAIN OUTCOME MEASURES

Clinical information was obtained from medical records. Complete ophthalmologic examinations were performed. Electroretinography was performed using a Ganzfeld technique and chloral hydrate sedation.

RESULTS

We report the clinical features and abnormal configurations on electroretinograms of five patients with complex glycerol kinase deficiency, including follow-up studies on a previously described patient. The original patient had ocular hypopigmentation; four, strabismus; two, myopia; three, astigmatism; and one, symptomatic night blindness. All had negative configurations on scotopic electroretinograms showing a reduced-amplitude B wave in the dark-adapted state.

CONCLUSIONS

Our original report suggested a diagnosis of Aland Island eye disease, which appears to be an incomplete form of congenital stationary night blindness. Linkage data place Aland Island eye disease and congenital stationary night blindness at Xp11, whereas our patients had deletions at Xp21. The phenotype reported here may represent the effects of a single gene defect or the compound effects of the Xp21 contiguous gene syndrome (complex glycerol kinase deficiency). The phenotype is referred to as Oregon eye disease.

Unbiased analysis of the frequency of beta-thalassemia point mutations in a population of African-American newborns

OBJECTIVE

To determine frequency of specific beta-thalassemia alleles in the African-American population prospectively, using newborn screening specimens, and to evaluate the need for including these alleles in screening follow-up programs.

DESIGN

Allele-specific oligonucleotide tests were developed and used to analyze African-American newborn screening specimens for beta-thalassemia point mutations to determine their frequency. Direct sequencing of amplified DNA from the dried blood specimens was used to confirm the presence of point mutations.

POPULATION

African-American newborns in Texas.

RESULTS

Allele-specific oligonucleotides identified five newborn specimens carrying beta-thalassemia point mutations among 471 specimens from African-American neonates. Direct sequencing of DNA from the dried blood specimens confirmed that these individuals had a normal and a mutant allele. Five newborn screening specimens in which the results of screening and DNA tests were in disagreement (four with FS by screening and AS by DNA, and one with FC by screening and AC by DNA) were analyzed for these beta-thalassemia point mutations and in each case were found to be S/beta-thalassemia or C/beta-thalassemia compound heterozygotes, respectively.

CONCLUSIONS

Allele-specific oligonucleotides accurately identified newborn specimens carrying beta-thalassemia point mutations. Direct sequencing from dried blood specimens confirmed these results. The A(-29)G allele frequency was 0.003, and the C(-88)T frequency was 0.002. These alleles also were observed among positive samples in a neonatal hemoglobinopathy screening program. Therefore, any newborn screening program with a molecular genetic follow-up component must include testing for these beta-thalassemia alleles to assure timely and appropriate management for affected infants.

X-linked dilated cardiomyopathy. Molecular genetic evidence of linkage to the Duchenne muscular dystrophy (dystrophin) gene at the Xp21 locus

BACKGROUND

X-linked cardiomyopathy (XLCM) is a rapidly progressive primary myocardial disorder presenting in teenage males as congestive heart failure. Manifesting female carriers have later onset (fifth decade) and slower progression. The purpose of this study was to localize the XLCM gene locus in two families using molecular genetic techniques.

METHODS AND RESULTS

Linkage analysis using 60 X-chromosome-specific DNA markers was performed in a previously reported large XLCM pedigree and a smaller new pedigree. Two-point and multipoint linkage was calculated using the LINKAGE computer program package. Deletion analysis included multiplex polymerase chain reaction (PCR). Dystrophin protein was evaluated by Western blotting with N-terminal and C-terminal dystrophin antibody. Linkage of XLCM to the centromeric portion of the dystrophin or Duchenne muscular dystrophy (DMD) locus at Xp21 was demonstrated with combined maximum logarithm of the scores of +4.33, theta = 0 with probe XJ1.1 (DXS206) using two-point linkage and +4.81 at XJ1.1 with multipoint linkage analysis. LOD scores calculated using other proximal DMD genomic and cDNA probes and polymerase chain reaction polymorphisms supported linkage. No deletions were observed. Abnormalities of cardiac dystrophin were shown by Western blotting with N-terminal dystrophin antibody, whereas skeletal muscle dystrophin was normal, suggesting primary involvement of the DMD gene with preferential involvement of cardiac muscle.

CONCLUSIONS

XLCM is due to an abnormality within the centromeric half of the dystrophin genomic region in heart. This abnormality could be due to 1) a point mutation in the 5' region of the DMD coding sequence preferentially affecting cardiac function, 2) a cardiac-specific promoter mutation that alters expression in this tissue, 3) splicing abnormalities, resulting in an abnormal cardiac protein, or 4) deletion mutations undetectable by Southern and multiplex polymerase chain reaction analysis.

Cloning and functional expression in yeast of two human isoforms of the outer mitochondrial membrane channel, the voltage-dependent anion channel

The voltage-dependent anion channel (VDAC) of the outer mitochondrial membrane is a small abundant protein found in all eukaryotic kingdoms which forms a voltage-gated pore when incorporated into planar lipid bilayers. VDAC is also the site of binding of the metabolic enzymes hexokinase and glycerol kinase to the mitochondrion in what may be a significant metabolic regulatory interaction. Recently, there has been speculation that there may be multiple forms of VDAC in mammals which differ in their localization in the outer mitochondrial membrane and in their physiological function. In this report, we describe the identification and characterization of two human cDNAs encoding VDAC homologs (HVDAC1 and HVDAC2). To confirm VDAC function, each human protein has been expressed in yeast lacking the endogenous VDAC gene. Human proteins isolated from yeast mitochondria formed channels with the characteristics expected of VDAC when incorporated into planar lipid bilayers. In addition, expression of the human proteins in such strains can complement phenotypic defects associated with elimination of the endogenous yeast VDAC gene. Since VDAC is the site of binding of hexokinase to the outer mitochondrial membrane, the binding capacity of each VDAC isoform expressed in yeast mitochondria was assessed. When compared with the binding of hexokinase to mitochondria lacking VDAC, the results show that mitochondria expressing HVDAC1 are capable of specifically binding hexokinase, whereas mitochondria expressing HVDAC2 only bind hexokinase at background levels. The expression of each human cDNA has been assessed by Northern blot and polymerase chain reaction techniques. With one exception, each is expressed in all human cell lines and tissues examined.

Xp21 contiguous gene syndromes: deletion quantitation with bivariate flow karyotyping allows mapping of patient breakpoints

Bivariate flow karyotyping was used to estimate the deletion sizes for a series of patients with Xp21 contiguous gene syndromes. The deletion estimates were used to develop an approximate scale for the genomic map in Xp21. The bivariate flow karyotype results were compared with clinical and molecular genetic information on the extent of the patients' deletions, and these various types of data were consistent. The resulting map spans > 15 Mb, from the telomeric interval between DXS41 (99-6) and DXS68 (L1-4) to a position centromeric to the ornithine transcarbamylase locus. The deletion sizing was considered to be accurate to +/- 1 Mb. The map provides information on the relative localization of genes and markers within this region. For example, the map suggests that the adrenal hypoplasia congenita and glycerol kinase genes are physically close to each other, are within 1-2 Mb of the telomeric end of the Duchenne muscular dystrophy (DMD) gene, and are nearer to the DMD locus than to the more distal marker DXS28 (C7). Information of this type is useful in developing genomic strategies for positional cloning in Xp21. These investigations demonstrate that the DNA from patients with Xp21 contiguous gene syndromes can be valuable reagents, not only for ordering loci and markers but also for providing an approximate scale to the map of the Xp21 region surrounding DMD.

Characterization of human genomic yeast artificial chromosome inserts containing hexokinase 1 coding information on chromosome 10

Hexokinase 1 (HK1) is one of four mammalian HK isoenzymes and maps to human chromosome 10. Two yeast artificial chromosomes (YACs) were identified in the Washington University human YAC library using polymerase chain reaction (PCR) primers designed with knowledge of the human HK1 cDNA sequence. YAC B129B12 is 120 kb in length and maps entirely to chromosome 10. YAC A159D5 is 400 kb in length and appears to have resulted from a recombination of chromosome 10 with non-chromosome 10 material. We report these YACs as potential resources for those interested in HK1 gene organization and mapping, as well as those desiring additional genomic information and markers on chromosome 10.

RNA analysis from newborn screening dried blood specimen

We have previously demonstrated that DNA can be extracted from the dried blood specimen of the type used for newborn screening. The technique presented here allows us to extract RNA from newborn screening specimens for cDNA synthesis by reverse transcriptase and amplification by the polymerase chain reaction (PCR). Products of the PCR reaction are then analyzed by restriction enzymes. This method successfully distinguishes beta A and beta S transcripts in unaffected (AA), carrier (AS), and affected (SS) individuals. The value of this approach for identification of a compound heterozygous patient with S/beta-thalassemia, using the original newborn screening specimen, is also demonstrated. This work shows that mRNA is stable in dried blood specimens and that analysis of the mRNA phenotype can be a useful adjunct in the application of molecular genetic technology to newborn screening.