Use of the single strand conformation polymorphism method for rapid screening for mutations in the low density lipoprotein receptor gene in patients with familial hypercholesterolemia: effect on plasma lipid levels of different classes of mutations

The single strand conformational polymorphism (SSCP) method was used to screen patients with familial hypercholesterolemia (FH) for mutations in the 3' part of exon 4 of the low density lipoprotein receptor (LDLR) gene. In 311 patients, six previously described mutations were identified in 29 apparently unrelated individuals (9.3%); three of the mutations are null alleles producing no protein, while the other three lead to production of a defective protein. In the patients where no mutation was detected mean total plasma cholesterol levels were 9.4 mmol/l, compared to 11.3 mmol/l in those individuals with a mutation creating a null allele, and 11.2 mmol/l in those with a mutation that resulted in the production of a defective protein (p < 0.001). These data reinforce observations of others that specific mutations in the LDL receptor gene are associated with different effects on plasma lipids, and indicate that the phenotype is influenced by the genotype.

High throughput modifications of single-strand conformation polymorphism analysis : mutation detection in familial hypercholesterolemia

In most patients with familial hypercholesterolemia (FH) the disorder is caused by a mutation in the gene coding for the low density lipoprotein receptor (LDL-R) (1). The variety of different defects observed in receptor function at the cellular level reflects mutations in different domains of the gene, and there is an increasing number of pointers to suggest that genetic factors influence clinical severity. The diagnosis of FH on clinical grounds is not 100% accurate, and some hypercholesterolemic individuals may not have a mutation in the LDL-R gene, whereas some individuals who would not be included in the clinical criteria do have such a mutation. The purpose of this chapter is to Illustrate the use of the single-strand conformational polymorphism (SSCP) technique for mutation screening in the LDL-R gene and to discuss several adaptations of published methods that improve throughput, and that we believe are appropriate for a disorder such as FH. In the next few years such techniques will help to tackle molecular diagnosis and family tracing in the large number of FH patients present in Europe and North America.

High-throughput method for determination of apolipoprotein E genotypes with use of restriction digestion analysis by microplate array diagonal gel electrophoresis

Molecular epidemiological research has identified the association of a common apolipoprotein E (apo E) isoform (E4 as opposed to E3), with risk both of coronary artery disease and of Alzheimer dementia. In addition, the role of apo E genotype (usually E2/E2) in Type III hyperlipidemia is well known. However, both for diagnostic and research purposes, apo E genotyping is cumbersome. The preferred approach is electrophoretic sizing of restriction digestion fragments, enabling simultaneous analysis of the two codons (112 and 158) that represent the six common genotypes (E2/E2; E2/E3; E2/E4; E3/E3; E3/E4; E4/E4). However, the consequent demands of high-yield PCR, high-resolution, high-throughput electrophoresis, and sufficient detection sensitivity have left shortfalls in published protocols. In conjunction with a high-throughput electrophoresis system we described recently, microplate array diagonal gel electrophoresis (MADGE), we have constructed extensively optimized, simplified protocols for DNA isolation from mouthwash samples for PCR setup and high-yield PCR, for restriction digestion, and for subsequent MADGE gel image analysis. The integral system enables one worker to readily undertake apo E genotyping of as many as hundreds of DNA samples per day, without special equipment.

High-throughput method for determination of apolipoprotein E genotypes with use of restriction digestion analysis by microplate array diagonal gel electrophoresis

Molecular epidemiological research has identified the association of a common apolipoprotein E (apo E) isoform (E4 as opposed to E3), with risk both of coronary artery disease and of Alzheimer dementia. In addition, the role of apo E genotype (usually E2/E2) in Type III hyperlipidemia is well known. However, both for diagnostic and research purposes, apo E genotyping is cumbersome. The preferred approach is electrophoretic sizing of restriction digestion fragments, enabling simultaneous analysis of the two codons (112 and 158) that represent the six common genotypes (E2/E2; E2/E3; E2/E4; E3/E3; E3/E4; E4/E4). However, the consequent demands of high-yield PCR, high-resolution, high-throughput electrophoresis, and sufficient detection sensitivity have left shortfalls in published protocols. In conjunction with a high-throughput electrophoresis system we described recently, microplate array diagonal gel electrophoresis (MADGE), we have constructed extensively optimized, simplified protocols for DNA isolation from mouthwash samples for PCR setup and high-yield PCR, for restriction digestion, and for subsequent MADGE gel image analysis. The integral system enables one worker to readily undertake apo E genotyping of as many as hundreds of DNA samples per day, without special equipment.

High-throughput genotyping using horizontal polyacrylamide gels with wells arranged for microplate array diagonal gel electrophoresis (MADGE)

Genotyping (typing of genetic variation) typically involves PCR followed by an allele-specific oligonucleotide-binding assay, restriction enzyme digest or direct check of the outcome of a PCR designed to distinguish genotype. Electrophoresis can resolve "bound" from "free" oligonucleotide, as well as resolve PCR fragments and digests, but it is traditionally regarded as cumbersome and laborious in comparison with solution assays. Here we describe simple horizontal polyacrylamide gels which can receive a 96-well array of samples directly, which can be stacked in tanks and which are bound to a robust support of glass. The line of electrophoresis is on a 71.6 degree diagonal relative to the columns of the array (microplate array diagonal gel electrophoresis [MADGE]). Several thousand reactions can conveniently be analyzed in a shoebox-sized apparatus in a couple of hours. High resolution is achieved in the range of 20-1000 bp, information processing is simplified and automation is possible.

Patterns of DNA methylation of the parathyroid hormone-related protein gene in human lung carcinoma

Humoral hypercalcaemia of malignancy often results from production of parathyroid hormone-related protein (PTHrP) by the tumour. We have investigated whether malignancy is associated with epigenetic changes in the PTHrP gene in lung. In normal and tumour tissue, there was a general background of nonmethylation in the PTHrP gene. In the 5' region, there appeared to be increased methylation of sites upstream of the promoter, P2. The extent of methylation increased from germ line to normal tissue to tumour tissue to tumour cell line, indicating that new methylation events in this region mark neoplastic change in lung cells.

Electrophoresis for genotyping: temporal thermal gradient gel electrophoresis for profiling of oligonucleotide dissociation

Traditional use of an oligonucleotide probe to determine genotype depends on perfect base pairing to a single-stranded target which is stable to a higher temperature than when imperfect binding occurs due to a mismatch in the target sequence. Bound oligonucleotide is detected at a predetermined single temperature 'snapshot' of the melting profile, allowing the distinction of perfect from imperfect base pairing. In heterozygotes, the presence of the alternative sequence must be verified with a second oligonucleotide complementary to the variant. Here we describe a system of real-time variable temperature electrophoresis during which the oligonucleotide dissociates from its target. In 20% polyacrylamide the target strand has minimal mobility and released oligonucleotide migrates extremely quickly so that the 'freed' rather than the 'bound' is displayed. The full profile of oligonucleotide dissociation during gel electrophoresis is represented along the gel track, and a single oligonucleotide is sufficient to confirm heterozygosity, since the profile displays two separate peaks. Resolution is great, with use of short track lengths enabling analysis of dense arrays of samples. Each gel track can contain a different target or oligonucleotide and the temperature gradient can accommodate oligonucleotides of different melting temperatures. This provides a convenient system to examine the interaction of many different oligonucleotides and target sequences simultaneously and requires no prior knowledge of the mutant sequence(s) nor of oligonucleotide melting temperatures. The application of the technique is described for screening of a hotspot for mutations in the LDL receptor gene in patients with familial hypercholesterolaemia.

Utilities for high throughput use of the single strand conformational polymorphism method: screening of 791 patients with familial hypercholesterolaemia for mutations in exon 3 of the low density lipoprotein receptor gene

We have modified several aspects of the single strand conformational polymorphism (SSCP) method to increase the speed with which the technique can be used for mutation detection. The methods attain high resolution of small mobility differences using long (30 cm) gels and use a modified polymerase reaction to maximise detection sensitivity using a minimised quantity of 32P. By using custom cut "sharktooth" combs (4.5 mm between teeth) as the slot formers, commercially available multichannel pipettes (9 mm tip to tip) can be used to load eight or 12 samples at a time from standard microtitre plates. PCR products that have been prepared and radiolabelled using simplified protocols are loaded on to the gel, and after a precalculated time of electrophoresis another set of samples can be loaded, either with combs moved across 2.25 mm or onto the same gel tracks. The run conditions are calculated so that there is no overlap between the bands produced by the two loadings, thus doubling the amount of information that can be gained from one gel. A computer program has been developed to solve equations to determine suitable timings for repetitive loadings. Finally, a modification of the gel pouring system is described so that two gels can be poured between three standard glass plates, with both gels run simultaneously. Of the order of 1000 PCR reactions can be prepared and analysed in 24 man hours using five 40 cm x 30 cm gel tanks. The application of these techniques is described to detect SSCPs in exon 3 of the low density lipoprotein receptor (LDLR) gene in 791 patients with familial hypercholesterolaemia (FH). Eight different SSCP patterns were seen, one of which was caused by the previously described E80K mutation, which was present in 11 patients (1.4%). In total, 32 patients (4%) were identified with exon 3 mutations.

PGP9.5, a ubiquitin C-terminal hydrolase; pattern of mRNA and protein expression during neural development in the mouse

PGP9.5 is a neurone and neuro-endocrine specific ubiquitin carboxyl terminal hydrolase estimated to form 1-2% of total brain protein. We have examined the temporal and spatial distribution of PGP9.5 mRNA and protein in the developing mouse embryo. These studies show that PGP9.5 is present at high levels in all differentiated neurones throughout the central and peripheral nervous systems at all stages of development. The mRNA is detected in the neural tube 1 day prior to the protein and before neuronal differentiation is underway. Both mRNA and protein are present during the initial appearance of motor and sensory neurones, prior to their peak production. PGP9.5 immunoreactivity was detected using microwave pretreatment of sections in order to unmask epitopes. In general unmasking led to an overall enhancement of immunoreactivity although in some sites, for example the dorsal root and cranial nerve ganglia and the bundle of His, there was evidence for anatomical variation in the distribution of masked versus unmasked protein. The very early expression of PGP9.5 suggests that there is a role for ubiquitin hydrolases in the differentiation of neurone precursors as well as in the differentiated neurone.

Rapid methods for population-scale analysis for gene polymorphisms: the ACE gene as an example

OBJECTIVE

To obtain rapid, high throughput genotyping of the angiotensin converting enzyme (ACE) gene intron 16 insertion/deletion polymorphism.

METHODS

DNA was obtained from whole blood samples by a simple liquid phase methanol extraction procedure. The ACE gene was amplified by the polymerase chain reaction (PCR) using two oligonucleotide primers (ACE1 and ACE3) outside the insertion sequence and one primer (ACE2) inside the sequence. Microtitre array diagonal gel electrophoresis (MADGE) was used to determine genotypes.

RESULTS

84 and 65 bp PCR products indicating the presence of deletion (D) and insertion (I) alleles, respectively, were clearly resolved after electrophoresis on a 7.5% polyacrylamide gel. Up to 480 DNA samples on 5 gels could be genotyped in a single electrophoresis run, or up to 1000 samples in a working day.

CONCLUSIONS

A simplified DNA extraction protocol coupled to the high throughput capability of the MADGE electrophoretic system for genotyping enables analysis of large populations for association studies of ACE genotype with cardiac disease events.

Effect on plasma lipid levels of different classes of mutations in the low-density lipoprotein receptor gene in patients with familial hypercholesterolemia

We used the single-strand conformational polymorphism method to screen 311 patients with familial hypercholesterolemia from London lipid clinics and Southampton and South West Hampshire health district for mutations in the 3' part of exon 4 of the low-density lipoprotein (LDL) receptor gene. This part of the gene codes for repeat 5 of the binding domain of the LDL receptor, which is known to be critical for the receptor-mediated removal of both triglyceride-rich lipoprotein remnants and LDL. Six previously described mutations were identified in 29 apparently unrelated individuals (9.3%), with the mutations all lying within a 50-bp fragment of the gene. Three of the mutations are null alleles producing no protein, and the other three lead to production of a defective protein. The effect of the different gene mutations on lipid levels was examined, after the data were combined with information on previously reported mutations in this patient group. Mean LDL cholesterol levels were highest in those individuals with a mutation creating a null allele (9.54 mmol/L) and were similar to levels in those individuals with a mutation affecting repeat 5 that resulted in the production of a defective protein (9.37 mmol/L). In this sample, previously identified patients with a defective protein mutation outside repeat 5 had lower mean levels of LDL cholesterol (7.78 mmol/L), which were similar to levels seen in patients in whom the specific mutation had not been identified (7.31 mmol/L). Overall, these differences were highly statistically significant (P < .001).(ABSTRACT TRUNCATED AT 250 WORDS)

Electrophoresis for genotyping: microtiter array diagonal gel electrophoresis on horizontal polyacrylamide gels, hydrolink, or agarose

Electrophoresis of DNA has been performed traditionally in either an agarose or acrylamide gel matrix. Considerable effort has been directed to improved quality agaroses capable of high resolution, but for small fragments, such as those from polymerase chain reaction (PCR) and post-PCR digests, acrylamide still offers the highest resolution. Although agarose gels can easily be prepared in an open-faced format to gain the conveniences of horizontal electrophoresis, acrylamide does not polymerize in the presence of air and the usual configurations for gel preparation lead to electrophoresis in the vertical dimension. We describe here a very simple device and method to prepare and manipulate horizontal polyacrylamide gels (H-PAGE). In addition, the open-faced horizontal arrangement enables loading of arrays of wells. Since many procedures are undertaken in standard 96-well microtiter plates, we have also designed a device which preserves the exact configuration of the 8 x 12 array and enables electrophoresis in tracks following a 71.6 degrees diagonal between wells (MADGE, microtiter array diagonal gel electrophoresis), using either acrylamide or agarose. This eliminates almost all of the staff time taken in setup, loading, and recordkeeping and offers high resolution for genotyping pattern recognition. The nature and size of the gels allow direct stacking of gels in one tank, so that a tank used typically to analyze 30-60 samples can readily be used to analyze 1000-2000 samples. The gels would also enable robotic loading. Electrophoresis allows analysis of size and charge, parameters inaccessible to liquid-phase methods: thus, genotyping size patterns, variable length repeats, and haplotypes is possible, as well as adaptability to typing of point variations using protocols which create a difference detectable by electrophoresis.

Mapping of antigenic sites in human neuron-specific enolase by expression subcloning

Human serum neuron-specific enolase (NSE) is a marker of neurons and of small-cell carcinoma of the lung; improved immunoassays of NSE remain an important goal. Here, we used overlapping complementary DNA (cDNA) clones for reconstruction to express full-length recombinant NSE, and also to express a set of cloned subfragments through the prokaryotic expression vectors pUEX and pUBEX. Subfragments expressed as fusion proteins were used to characterize immunogenic and antigenic regions and epitopes and, expressed as affinity matrices, to derive purified, fractionated polyclonal antibodies. NSE epitope data can be visualized with yeast enolase-1 crystal structure coordinates: The two protein sequences align almost perfectly and are 61% identical. This approach demonstrates the complementarity of cDNA expression with techniques of polyclonal antiserum and monoclonal antibody production and with chemical peptide synthesis in the refinement of immunodiagnostic reagents.

Mapping of antigenic sites in human neuron-specific enolase by expression subcloning

Human serum neuron-specific enolase (NSE) is a marker of neurons and of small-cell carcinoma of the lung; improved immunoassays of NSE remain an important goal. Here, we used overlapping complementary DNA (cDNA) clones for reconstruction to express full-length recombinant NSE, and also to express a set of cloned subfragments through the prokaryotic expression vectors pUEX and pUBEX. Subfragments expressed as fusion proteins were used to characterize immunogenic and antigenic regions and epitopes and, expressed as affinity matrices, to derive purified, fractionated polyclonal antibodies. NSE epitope data can be visualized with yeast enolase-1 crystal structure coordinates: The two protein sequences align almost perfectly and are 61% identical. This approach demonstrates the complementarity of cDNA expression with techniques of polyclonal antiserum and monoclonal antibody production and with chemical peptide synthesis in the refinement of immunodiagnostic reagents.

Characterisation of an epitope specific to the neuron-specific isoform of human enolase recognised by a monoclonal antibody raised against a synthetic peptide corresponding to the C-terminus of beta/A4-protein

Antibodies to synthetic peptides corresponding to different regions of beta/A4-protein recognize deposits of amyloid in the brains of patients with Alzheimer's disease. Down's syndrome cases and in the normal ageing brain. We have prepared a monoclonal antibody, mAb 22.212, raised against a synthetic C-terminal peptide of beta/A4 protein (residues 28-40) which labelled senile plaques in Alzheimer's disease after proteolytic treatment of tissue sections. In addition to recognising synthetic beta/A4-peptides that include the C-terminal residues 28-42, the mAb 22.212 was found to cross-react with a soluble, 47 kDa protein found in brain homogenates. This protein was shown, by amino acid sequence analysis and immunoassay, to be neuron-specific enolase (NSE). The mAb 22.212 did not recognize the non-neuronal enolase (NNE) or muscle-specific enolase (MSE) isoforms and its epitope was mapped to a short stretch of amino-acids unique to NSE, near the C-terminus. The cross-reactive NSE epitope is sited between residues 402-423 in NSE and shows no common sequence with beta/A4, perhaps suggesting that it is a conformational epitope. The significance and applications of these findings are discussed.

Methylation patterns in the human muscle-specific enolase gene (ENO3)

The methylation status in the human-muscle enolase gene (ENO3) was assayed. Previous sequence data and MspI cleavage sites indicate the presence of a 5' CpG-rich island of at least 4 kb: none of 22 characterized MspI CCGG sites is methylated in any of muscle, sperm or brain DNA. However a complex pattern of complete and partial methylation of MspI sites that is different between tissues is observed within the ENO3 gene: events at one site may be specific to muscle DNA. The absence of methylation in the promoter region of the ENO3 gene makes it unlikely that methylation plays a causal role either in transcriptional events or in the divergence of enolase-isogene regulation. The role of tissue-specific methylation events within ENO3 remains to be determined.

Analysis of the 5'-AAUAAA motif and its flanking sequence in human RNA: relevance to cDNA library sorting

The motif, N-8..N-1AAUAAAN1..N8 (where N is A, C, G or U), and its flanking sequence in human mRNA were examined by database analysis. Approximately 20% of 5'-AAUAAA in 3'-noncoding regions appear not to direct mRNA cleavage-polyadenylation. In coding regions, Asn-Lys, Ile-Lys and Ile-Asn are proven not to be unfavourable, and AAUAAA is not an unfavourable choice of coding sequence, occurring in 16% of mRNAs. Neither immediate flanking sequence nor associated motifs bear sufficient information content to account for the cleavage specificity observed. The unusual distribution and properties of the motif, AATAAA, in cDNA invite novel strategies for sorting cDNA libraries.

The gene for human neurone specific ubiquitin C-terminal hydrolase (UCHL1, PGP9.5) maps to chromosome 4p14

Ubiquitin carboxy terminal hydrolase 1, UCHL1, is a neurone-specific protein involved in the ubiquitin-mediated proteolytic pathway. The gene for human UCHL1 has been mapped to chromosome 4 using the polymerase chain reaction to amplify specifically the human UCHL1 sequences in rodent/human somatic cell hybrid DNA. A regional assignment of this locus to 4p14 has been made by in situ hybridization to metaphase chromosomes using both tritium and fluorescently labelled probes.

Molecular structure of the human muscle-specific enolase gene (ENO3)

The single human gene for muscle-specific enolase was isolated and its structure was characterized, from which the mature mRNA transcript and encoded protein were also deduced. The gene contains 12 exons, spans approx. 6 kb and encodes a protein of 433 residues. The gene structure is similar to that found for the rat neuron-specific enolase gene, and the deduced protein aligns precisely with other enolase sequences, including the sequence of the only published crystallized enolase, yeast eno-1. The 5' boundary of the gene includes a 5' non-coding exon and is characterized by an upstream TATA-like box and CpG-rich region. This region contains potential recognition motifs for general transcriptional regulation involving Sp1, activator protein 1 and 2, CCAAT box transcription factor/nuclear factor I and cyclic AMP, and for muscle-specific transcriptional regulation involving a CC(A + T-rich)6GG box, M-CAT-box CAATCCT and two myocyte-specific enhancer-binding factor 1 boxes.

The structure of the human gene encoding protein gene product 9.5 (PGP9.5), a neuron-specific ubiquitin C-terminal hydrolase

Database search using a bovine thymus ubiquitin C-terminal hydrolase sequence indicated 54% sequence identity with the abundant human neuron-specific protein gene product 9.5 (PGP9.5), which was then shown to possess the same activity [Wilkinson, Lee, Deshpande, Duerksen-Hughes, Boss & Pohl (1989) Science 246, 670-673]. A yeast counterpart of the enzyme is also known. The human PGP9.5 gene, described here, spans 10 kb, contains nine exons and displays 5' features some common to many genes and some common with neurofilament neuron-specific enolase and Thy-1-antigen gene 5' regions.