Access to a messenger RNA sequence or its protein product is not limited by tissue or species specificity

Regulation and specificity of MNDA expression in monocytes, macrophages, and leukemia/B lymphoma cell lines

The expression of the human myeloid cell nuclear differentiation antigen (MNDA) was observed specifically in cells of the granulocyte-macrophage lineage in our earlier reports. The specificity of MNDA expression for cells in the granulocyte-macrophage lineage was reexamined in cell lines established from patients with Philadelphia chromosome-positive chronic myeloid leukemia. Cell lines that expressed MNDA exhibited myeloid cell features and granulocyte or monocyte differentiation could be induced in vitro, while cell lines exhibiting properties of very early stage cells or multipotential cells did not express MNDA. Cells originating from cases of Burkitt's lymphoma were negative. By contrast, three lymphoblastoid cell lines (immortalized in vitro with Epstein-Barr virus) were weakly positive and MNDA was up-regulated by interferon-alpha (IFN-alpha) treatment. As we reported previously, MNDA mRNA level in adherent monocytes is elevated by IFN-alpha; in this study, we further assessed MNDA expression in in vitro monocyte-derived macrophages. Three additional agents (endotoxin, phytohemagglutinin, and phorbol ester) and other conditions that affect function, cytokine production, differentiation, and/or growth of monocytes were examined for their ability to alter MNDA expression. The results varied with the agent, cell type, and stage of differentiation. Changes in MNDA expression occurred slowly (hours to days), suggesting that MNDA could mediate changes realized over a long period. The results also reveal a discordance in certain MNDA positive cells between steady-state levels or changes in levels of protein and mRNA indicating that the regulation of MNDA expression occurs at more than one point. Changes in MNDA expression are consistent with a role in opposing macrophage differentiation and activation of monocytes/macrophages.

Spontaneous mutations in lacI-containing lambda lysogens derived from transgenic mice: the observed patterns differ in liver and spleen

The pattern of somatic mutation observed in tumor suppressor genes, such as the p53 gene, vary dramatically with tumor type. Some of the observed differences are due to tissue specific effects of mutagens, but it is also possible that some differences may reflect the tissue/cell type specificity of spontaneous mutation. Transgenic mouse models with recombinant shuttle vectors containing the lacI or lacZ target genes may shed light on the extent to which spontaneous mutation displays tissue specificity. Herein we utilize a recently described selectable system to obtain spontaneous mutants for analysis of the molecular lesions. Spontaneous mutations were isolated in the lacI gene recovered from five transgenic mice carrying a lambda shuttle vector. Seventy-three and 67 independent mutations derived from liver and spleen DNA, respectively, were defined in the amino terminal region of lacI. Although technical barriers preclude a direct assessment of the E. coli derived pattern of mutation in this system, five pieces of circumstantial evidence suggest that many of the mutations arose in mouse rather than in E. coli. In DNA from both liver and spleen, mutations at CpG dinucleotides predominate (58% and 51%, respectively). In spleen, most of the mutations at CpG are transitions, while in liver most are transversions. In addition, liver has a higher frequency of GC-->TA transversions at non-CpG dinucleotides while spleen had a higher frequency of deletions and insertions. The data provide evidence that the spontaneous pattern of mutation is tissue specific. In addition, the high frequency of transversions at CpG suggests the need to reevaluate the mechanisms by which mutations occur at this methylated dinucleotide.

Identification of alpha-cardiac myosin heavy chain mRNA and protein in extraocular muscle of the adult rabbit

Extraocular muscles contain both fast-twitch and multiply-innervated, tonic-contracting fibres. In rat, these fibres collectively express numerous myosin heavy chain isoforms including fast-type embryonic and neonatal, adult slow twitch type I and fast twitch type II, and a fast isoform unique to extraocular muscle. Immunocytochemical and Western blotting results are presented which suggest that, in rabbit, an additional species, the alpha-cardiac myosin heavy chain, is present. The immunoreactive species is found in all rabbit extraocular muscles and in the extraocular muscles is expressed in almost all fibres which do not contain a fast myosin heavy chain. Positive identification of this isoform as the alpha-cardiac myosin heavy chain was obtained by sequencing a cloned PCR product derived from extraocular muscle mRNA unique to the 3'-end of rabbit alpha-cardiac myosin heavy chain mRNA. This is the first unequivocal demonstration of alpha-cardiac myosin heavy chain expression in extraocular muscle.

T cell receptor (beta chain) transgenic mice have selective deficits in gamma delta T cell subpopulations

TCR-beta (T cell receptor-beta chain) transgenic mice have altered lymphocyte development. TCR-beta transgenic mice are hyporesponsive to alloantigens in vivo and are deficient in gamma delta T cells. In order to begin a study of the relationship between a deficiency of alloreactive gamma delta cells and the defective function of in vivo alloantigen recognition, we analysed the gamma delta T cell development in TCR-beta mice. The presence of the TCR-V beta 8.2 chain transgene is associated with inhibition of gamma chain gene rearrangement. In order to determine how the presence of the TCR-beta transgene affects gamma delta T cell development, gamma delta T cells were studied in the skin, intestine and spleen. TCR-beta mice have dramatically reduced numbers of gamma delta T cells in the spleen and moderately reduced numbers of gamma delta T cells among intestinal intraepithelial lymphocytes. In contrast, these mice have normal numbers of gamma delta dendritic epidermal cells (DEC). These selective deficits could be due to the developmental regulation of transgene transcription during fetal life. We examined transcription of the TCR-beta transgene in the fetal thymus and found that the TCR-beta transgene is first transcribed at high levels on day 16 of fetal life, after DEC have already migrated from the thymus to the epidermis. Furthermore, mRNA from the transgene was detected in DEC, ruling out the formal possibility that DEC bear a gamma delta receptor only because they are incapable of expressing the transgene.(ABSTRACT TRUNCATED AT 250 WORDS)

Unexpected inactivation of acceptor consensus splice sequence by a -3 C to T transition in intron 2 of the CFTR gene

Cystic fibrosis is caused by mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR). Analysis of DNA from a pancreatic sufficient patient by means of denaturing gradient gel electrophoresis (DGGE) and subsequent DNA sequencing led to the identification of a novel potential splice mutation and a novel missense mutation in the CFTR gene. One C to T substitution (297-3C-->T) was found at the splice acceptor site of intron 2 and a T to C substitution at 1213 was found in exon 7. To determine the effect of the potential splicing mutation on the patient's CFTR transcripts and by taking advantage of the "illegitimate" transcription phenomenon, RNA from EBV-lymphoblastoid cells was reverse transcribed and amplified by the polymerase chain reaction (PCR). Direct sequencing of the PCR product revealed that the transcript from the chromosome with the 297-3C-->T mutation exhibited the skipping of exon 3.

Search for mutations in the beta 1 GABAA receptor subunit gene in patients with schizophrenia

As alterations in GABAergic neurotransmission have been indirectly implicated in the pathogenetics of schizophrenia, GABAA receptor subunit genes are plausible candidate genes for the illness. We undertook a search for sequence variations in the coding region of beta 1 subunit gene by designing intron-based primers to amplify its 9 exons. Using single strand conformation polymorphism (SSCP) analysis, we found an exon 9 variant present in 3 of 86 unrelated schizophrenic cases derived from families having at least 2 first-degree relatives with schizophrenia. Direct sequencing of the SSCP variant revealed a C-->G nucleotide transversion at codon 396 predicting a histidine to glutamine substitution in the beta 1 peptide. The predicted amino acid substitution occurs at a highly conserved site, 9 residues from a cAMP-dependent serine phosphorylation consensus sequence. All known GABAA beta 1 subunit genes including human, bovine, and rat, code for histidine at position 396. Although the variant cosegregated with disease in a family with 2 affected sibs, it was only transmitted to 2 of 3 affected sibs in a multiplex family. The variant was not found in an additional sample comprising 155 unrelated schizophrenics and the sequence variant was present at a low frequency (approximately 1.1%) in control groups. Although these results indicate that the sequence variant is likely to be a natural polymorphism, it is possible that the variant may be a predisposing allele in rare instances. It is also possible that the variant may change the function or regulation of the GABAA receptor complex and it may be of pharmacogenetic relevance.

Distinct vascular lesions in giant cell arteritis share identical T cell clonotypes

Giant cell arteritis (GCA) is a spontaneous vasculitic syndrome that specifically targets the walls of medium and large arteries. Vascular lesions are characterized by patchy granulomatous infiltrates composed of T cells, macrophages, histiocytes, and giant cells. To test the hypothesis that a locally residing antigen recruits T cells into the vessel walls, we have analyzed T cell receptor (TCR) molecules of tissue infiltrating T cells. A total of 638 CD4+ T cell clones were isolated from temporal artery specimens of three patients with GCA. Analysis of TCR molecules for the usage of V beta 1-V beta 20 revealed that all TCR V beta elements were represented, demonstrating that interleukin 2 (IL-2)-responsive T cells infiltrating the tissue are highly diverse. To detect expanded T cell specificities, we made use of the patchy character of the inflammatory disease and compared the TCR repertoire of T cells established from independent vasculitic foci of the same artery. Sequence analysis of TCR V beta chains documented that individual TCR specificities were present in multiple copies, indicating clonal expansion. T cells with identical beta chains were isolated from distinct inflammatory foci of the same patient. These specificities represented only a small fraction of tissue-infiltrating T cells and involved the V beta 5.3 gene segment in the two patients sharing the HLA-DRB1*0401 allele. The third complementarity determining region of clonally expanded TCR beta chains was characterized by a cluster of negatively and positively charged residues, suggesting that the juxtaposed antigenic peptide is charged. The sharing of identical T cell specificities by distinct and independent regions of the granulomatous inflammation suggests that these T cells are disease relevant and that their repertoire is strongly restricted. These data suggest that an antigen residing in the arterial wall is recognized by a small fraction of CD4+ T cells in the inflammatory process characteristic for GCA.

Analysis of the partial nucleotide sequences and deduced primary structures of the protease domains of mammalian blood coagulation factors VII and X

In order to obtain sequence data for the blood coagulation factor VII and factor X in several mammalian species, we amplified and sequenced the DNA segments of exon VIII from each gene by means of the polymerase chain reaction (PCR) method. The DNA segments from the following species were successfully amplified: factor VII from the rhesus monkey and dog, and factor X from the rhesus monkey, Syrian hamster and rat. In each factor, the nucleotide sequences and predicted primary structures of the protease domain showed a high degree of homology among species; amino acid identities of approximately 68%-92% and 80%-98% were demonstrated among species in factor VII and factor X, respectively. The locations of the active site residues and five Cys residues were evolutionarily conserved in both factors. Interestingly, the amino acids involved in the human genetic variants, both factor VII 304-Arg and factor X 326-Arg, were always conserved across species. The data presented here will be helpful for investigating human genetic variants of factor VII or X, and will provide considerable information for constructing in vitro site-specific mutants of these factors.

A comparative study of partial primary structures of the catalytic region of mammalian protein C

Protein C (PROC) is a plasma vitamin K-dependent zymogen of a serine protease which regulates blood-clotting cascade through proteolytic inactivation of the non-enzymatic cofactors of blood coagulation, Va and VIIIa. We characterized the partial nucleotide and amino acid sequences for the catalytic domain of PROC in six mammalian species, rhesus monkey, dog, cat, goat, horse and mouse, and compared these sequences with known ones from humans, the bovine and rat. By using a pair of primers based on the nucleotide sequences from human and bovine PROC cDNA, the PROC gene fragments were enzymatically amplified from their genomic DNAs and were sequenced by the dideoxy-termination method. The cloned PROC gDNA encoded a part of the heavy chain of PROC including the lesions of active site residues corresponding to human PROC Asp-257 and Ser-360. Comparison of the sequences from these species revealed that there was a high degree of homology at the nucleotide and amino acid levels; from 69% to 96% of the amino acids in the catalytic region were identical among the nine species including humans, the bovine and rat. The locations of five Cys residues as well as the putative carbohydrate attachment sites were evolutionally conserved. All the amino acids recognized in the human abnormal PROC variants were conserved across species, suggesting their functional importance, and a comparison of the conserved residues among PROC from multiple species will provide considerable information in the investigations of PROC functions.

Detection of cell specific cluster determinant expression by reverse transcriptase polymerase chain reaction

We describe a new, rapid, sensitive, and reproducible method for examining gene expression of several cell specific surface cluster determinants, CD2, CD3-gamma, CD4, CD8-beta, CD14, CD19, CD20, CD23, and CD25-alpha, and terminal deoxynucleotidyl transferase which heretofore have been commonly detected by flow cytometry. The method presented uses the reverse transcriptase polymerase chain reaction (RT-PCR) to analyze CD gene expression in stable human cell lines, peripheral blood lymphocytes, bone marrow, and lymph node cells. Polymerase chain reaction products were quantitated by incorporation of radiolabeled nucleotide during PCR and the amount of nucleotide incorporated into DNA was measured by ion exchange filter chromatography. The usefulness of this methodology is demonstrated in an analysis of peripheral blood samples from a patient who presented with B cell deficiency. Results of analyses of peripheral blood samples from this patient by flow cytometry and RT-PCR are similar except that the increased sensitivity of RT-PCR permitted the detection of CD19, CD20, and CD23 in the blood samples of this patient who otherwise appeared to be lacking in all markers of B cell development.

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

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

Sequence analysis of the thyrotropin (TSH) receptor gene in congenital primary hypothyroidism associated with TSH unresponsiveness

Congenital primary hypothyroidism due to thyrotropin (TSH) unresponsiveness is a very rare disorder and only a few cases have been documented previously. To elucidate whether structural abnormalities in the TSH receptor (TSHR) could be a primary underlying mechanism of this disorder, we analyzed nucleotide sequence of the entire coding region of the TSHR gene in three patients diagnosed with congenital primary hypothyroidism associated with TSH unresponsiveness. Diagnosis of TSH unresponsiveness was largely made based on the following criteria: (a) congenital primary hypothyroidism with autosomal recessive inheritance, (b) a nongoitrous thyroid gland in a normal position with low thyroidal radioactive iodine uptake, (c) normal in vitro TSH bioactivity or absent in vivo response to exogenous TSH, and (d) absence of thyroid autoantibodies. The TSHR cDNA was successfully obtained from RNA of peripheral mononuclear leukocytes with reverse transcription and polymerase chain reaction, and was sequenced directly. Comparison of these nucleotide sequences with the normal TSHR sequence revealed no difference in the predicted amino acid sequence with a heterozygous polymorphism in codon 601 in one patient, indicating absence of TSHR structural abnormalities in these patients. Our results indicate that congenital primary hypothyroidism associated with TSH unresponsiveness is unlikely to be due to mutations in the TSHR-structure gene.

Measurement of gut hormone gene expression: mRNA and peptides

During the past decade numerous methods for measurement of mRNA and peptides have been developed. Since the expression cascade from DNA to protein is regulated at all levels, the methods should be carefully designed to accomplish the purpose of the analysis. Regulation of the nuclear processing, the translational activity and the decay of a particular mRNA changes the proportionality between transcriptional activity and production of prepropeptide. Moreover, the post-translational maturation of the pro-hormones may be attenuated. Detection of mRNA is valuable and feasible because it is easy to generate cDNA probes for most hormones, and because mRNA demonstration unequivocally indicates the cellular site of gene expression. The deduction of preprohormone structures has also made it possible to improve the versatility of radioimmunoassays (RIA). Monospecific antibodies and pure tracers have allowed the development of sequence-specific RIA libraries for bioactive peptides and their precursors. Recently we have introduced a simple processing-independent analysis (PIA) for clinical use, since the post-translational maturation of gut peptides may be changed in gastrointestinal diseases. So far PIA has improved the diagnostic sensitivity for gut hormone tumours.

Searching for the 1 in 2,400,000: a review of dystrophin gene point mutations

The past few years have seen a rapid increase in our knowledge of naturally occurring mutations in the dystrophin gene. Although earlier studies were limited to gross rearrangement mutations, we are now in a position to draw lessons on the molecular etiology of the remaining one-third of cases of Duchenne and Becker muscular dystrophy (DMD, BMD) which are associated with small mutations. This paper reviews 70 published and unpublished small mutations in the dystrophin gene and asks what we can learn about their nature, their distribution, and approaches to their characterisation. Strikingly for such a well-conserved gene, missense mutations are extremely rare, and the vast majority of DMD point mutations, like the gross rearrangements, result in premature translational termination. It seems increasingly likely that almost all cases of DMD arise solely as a result of a reduction in the level of dystrophin transcripts, and we argue that > 95% of DMD mutations contribute nothing to the functional dissection of the dystrophin protein. Most of the few BMD point mutations presented here are missense mutations in the N-terminal or C-terminal domains or are splice-site mutations that probably act, like BMD deletions, via the production of in-frame, interstitially deleted transcripts.

Molecular diagnosis of familial adenomatous polyposis

BACKGROUND

Familial adenomatous polyposis is an inherited disease characterized by multiple colorectal tumors. The diagnosis has classically been based on the detection of multiple colorectal adenomas. The recent identification of germline mutations of the APC gene in patients with familial adenomatous polyposis makes presymptomatic molecular diagnosis possible, but the widespread distribution of the many mutations within this very large gene have heretofore made the search for such mutations impractical. We describe a novel approach that allows molecular genetic diagnosis in the majority of patients with the disease.

METHODS

We screened 62 unrelated patients from the Johns Hopkins Familial Adenomatous Polyposis Registry for germline APC mutations. Primary screening was accomplished by analysis of protein synthesized in vitro from surrogate APC genes. In addition, the relative amount of transcript from each APC allele was determined with an allele-specific--expression assay.

RESULTS

The protein assay revealed truncated protein in 51 of the 62 patients (82 percent). In 3 of the 11 remaining patients, the allele-specific--expression assay revealed significantly reduced expression of one allele of the APC gene. The use of these two assays in combination successfully identified germline APC mutations in 87 percent of the 62 patients.

CONCLUSIONS

The protein and allele-specific--expression assays provide a practical and sensitive method for molecular diagnosis of familial adenomatous polyposis. This approach will facilitate care, allowing routine testing of subjects at risk and genetic confirmation of spontaneous mutations.

Detection of Duchenne muscular dystrophy gene products in amniotic fluid and chorionic villus sampling cells

We have examined the expression of several Duchenne muscular dystrophy (DMD) gene products in amniotic fluid (AF) and chorionic villus sampling (CVS) cells. Variable amounts of dystrophin could be detected in most CVS and AF samples by immunoprecipitation followed by Western blot analysis. PCR analysis demonstrated the presence of the muscle type dystrophin mRNA in all AF cell cultures. The brain type dystrophin mRNA was also detected in some of these cultures. These DMD gene transcripts are of fetal origin and are produced by most or all clonable AF cells. The results may facilitate the development of a method for prenatal diagnosis of DMD, based on the expression of the gene in AF and CVS cells.

Differential regulation of natriuretic peptide receptor messenger RNAs during the development of cardiac hypertrophy in the rat

The heart expresses the three natriuretic peptide receptors (NPR), namely NPR-A, NPR-B, and NPR-C. We have examined the temporal relationship between the expression of mRNA transcripts for atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) and their receptors in the heart during the development of cardiac hypertrophy in the aortovenocaval fistula rat. Messenger RNAs were measured by cDNA amplification. Progressive cardiac hypertrophy was accompanied by increased ANP mRNA prevalence throughout the heart and increased BNP mRNA in the left atrium. The most striking observation was the gradual disappearance of NPR-C transcripts (the putative "clearance" receptor) in all chambers; this was in marked contrast to the increase in mRNA levels for NPR-A and NPR-B (the guanylyl cyclase-linked receptors). Our observations have important therapeutic implications if the transcript changes are mirrored at the receptor protein level because (a) the apparent down-regulation of NPR-C may enhance the local action of natriuretic peptides on the heart, and (b) the loss of NPR-C, particularly if it is widespread, may reduce the rate of elimination of the natriuretic peptides, restricting the therapeutic potential of specific NPR-C ligands designed to reduce peptide clearance.

Differential splicing of COL4A5 mRNA in kidney and white blood cells: a complex mutation in the COL4A5 gene of an Alport patient deletes the NC1 domain

PCR conditions were optimized to amplify the COL4A5 cDNA from lymphoblasts and kidney tissue. Sequencing of the COL4A5 mRNA isolated from the kidney of an Alport syndrome patient revealed two differences with the published sequence. One divergence, the insertion of an 18 bp sequence between exon 11 and 10 of the COL4A5 mRNA added two Gly-X-Y triplets to the COL4A5 sequence and was subsequently found in the mRNA of four normal kidney mRNA samples. This sequence was absent in all white blood cell RNA samples sequenced by us, indicating tissue specific splicing with the presence of an additional exon in kidney COL4A5 mRNA. This finding of differential splicing of COL4A5 mRNA in kidney and white blood cells might affect the use of white blood cell mRNA for the analysis of Alport mutations. Second, a complex mutation was detected in the mRNA from the AS patient introducing a premature stop codon in the message, deleting part of the triple helical domain and the complete NC domain. The mother of the patient was shown to be heterozygous for this mutation.

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

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

Nucleotide sequence of cDNA encoding the group II allergen of cocksfoot/orchard grass (Dactylis glomerata), Dac g II

Cocksfoot/orchard grass (Dactylis glomerata) anther cDNA clones encoding the group II allergen Dac g II were previously isolated on the basis of immunoreactivity of human, rabbit, and murine antibodies with a 24-kDa protein expressed as a fusion protein with beta-galactosidase. Nucleotide sequencing reveals an open reading frame predicting expression of a 98-amino-acid (11-kDa) polypeptide exhibiting > 90% homology with the group II allergen of Lolium perenne, Lol p II. In vitro translation of different sized clone fragments generated by polymerase chain amplification confirms eukaryotic expression of a 10-12-kDa polypeptide by SDS-PAGE and the position of a translational stop apparently unrecognized during expression of lambda gt11 in E. coli. The unusual characteristics of the prokaryote-expressed fusion proteins may be exerting conformational alterations in Dac g II, as reflected by previous demonstrations of differences in human IgE immunoreactivity. Northern blot analysis using PCR-generated partial and full-length probes suggests that group II allergens may be encoded by a different family or families of temporally expressed genes from those encoding group I major allergens, although a group I gene may have been the progenitor.

Heterogeneous isoactin gene expression in the adult rat gastrointestinal tract

BACKGROUND

Normal gastrointestinal development is a complex process involving the precise integration of multiple cell types. To gain a better understanding of these processes, the present study examined isoactin gene expression in the adult rat gastrointestinal tract.

METHODS

Northern blot analysis was performed on specified segments of the adult rat esophagus, stomach, small intestine, cecum, colon, rectum, and anus using actin isoform-specific complementary DNAs for all six vertebrate isoactins.

RESULTS

Smooth muscle and cytoplasmic isoactins were heterogeneously coexpressed in a segment-specific manner throughout the gastrointestinal tract. In addition, striated muscle isoactin expression was also detected in segments of the adult rat esophagus, stomach, colon, cecum, rectum, and anus. Histological analysis indicated that the adult rat esophagus, stomach, and anus contained significant quantities of skeletal muscle, providing a source for the striated muscle isoactins detected in these gut segments. A similar source of striated muscle isoactin expression in the cecum, colon, and rectum was not identified. Both coordinate and independent regulation of isoactin gene expression was observed in the gastrointestinal tract, although distinct patterns of autoregulation were absent.

CONCLUSIONS

This study represents the first complete analysis of isoactin gene expression in the adult rat gastrointestinal tract and provides the basis for future studies designed to investigate the factors responsible for these processes.

Dopamine D4 receptor variants in unrelated schizophrenic cases and controls

The D4 dopamine receptor (D4DR) exists in multiple allelic forms (Van Tol et al.: Nature 358:149-152, 1992) which involve different numbers of a 48 basepair repeat sequence in the putative third cytoplasmic loop. Different binding properties have been reported for at least three of the alleles in cDNA binding assays with clozapine, an atypical neuroleptic, and spiperone (Van Tol et al., 1992). We have examined 115 unrelated schizophrenic cases defined by DSM-III-R criteria and 115 controls of similar ethnicity to determine the frequency of seven different D4 alleles in these groups. No statistically significant difference in the distribution of the alleles existed between cases and controls, although a trend towards a greater prevalence of homozygotes for the 4-repeat allele was observed in schizophrenics.

Detecting single-base mutations

The ability to detect single-base changes is of fundamental importance in molecular genetics. This is particularly true in human genetics, where interest in linking mutations of identified genes to particular disease phenotypes is most intense, and where a demand exists for clinical diagnosis of defined mutations. In the following article, techniques are described for screening unknown mutations, as well as diagnosing those that have been identified previously. The underlying methods are explained briefly and guidelines are offered for choosing one technique in preference to another.

Restriction-site PCR: a direct method of unknown sequence retrieval adjacent to a known locus by using universal primers

Fast acquisition of unknown nucleotide sequences around a known sequence has important implication in molecular biology, especially in genome mapping. We have developed a method, termed restriction site polymerase chain reaction (RS-PCR), that utilizes specially designed primers that recognize, anneal, and sustain PCR. These primers, termed restriction site oligonucleotides (oligonucleotide primers specific for a given restriction enzyme recognition sequence or RSOs), could be generated corresponding to any restriction enzyme irrespective of the length of the recognition site and used as PCR primers corresponding to the unknown region of a DNA segment. In this method a first round of PCR is carried out in different tubes with a set of RSOs and a primer specific to the known region. A second round of PCR is then performed on the products of the first PCR with the same RSOs and another specific primer internal to the first one. Subsequently, the products of the last round of PCR are transcribed with an appropriate RNA polymerase and sequenced with a reverse transcriptase with an end-labeled specific primer internal to the second specific PCR primer. To demonstrate the applicability of RS-PCR in retrieving unknown sequences around a known sequence, we have used a set of four RSOs and three specific primers representing the known sequence and have successfully obtained hitherto unknown factor IX sequences (12 of 12 times) from three species starting from genomic DNA. The sequences obtained indicate the presence of a conserved stretch of 20 nucleotides in the 3' noncoding region of the factor IX gene.(ABSTRACT TRUNCATED AT 250 WORDS)

Deletions of the carboxy terminus of herpes simplex virus type 1 UL42 define a conserved amino-terminal functional domain

The herpes simplex virus type 1 UL42 protein was synthesized in reticulocyte lysates and assayed for activity in vitro. Three functional assays were used to examine the properties of in vitro-synthesized UL42: (i) coimmunoprecipitation to detect stable complex formation with purified herpes simplex virus type 1 DNA polymerase (Pol), (ii) a simple gel-based assay for DNA binding, and (iii) a sensitive assay for the stimulation of Pol activity. UL42 synthesized in reticulocyte lysates formed a stable coimmunoprecipitable complex with Pol, bound to double-stranded DNA, and stimulated the activity of Pol in vitro. Carboxy-terminal truncations of the UL42 protein were synthesized from restriction enzyme-digested UL42 gene templates and gene templates made by polymerase chain reaction and assayed for in vitro activity. Truncations of the 488-amino-acid (aa) UL42 protein to aa 315 did not abolish its ability to bind to Pol and DNA or to stimulate Pol activity. Proteins terminating at aas 314 and 313 showed reduced levels of binding to Pol, but these and shorter proteins were unable to bind to DNA or to stimulate Pol activity. These results suggest that all three of the biochemical functions of UL42 colocalize entirely within the N-terminal 315 aas of the UL42 protein. Amino acid sequence alignment of alpha herpesvirus UL42 homologs revealed that the N-terminal functional domain corresponds to the most highly conserved region of the protein, while the dispensable C terminus is not conserved. Conservative aa changes at the C terminus of the 315-aa truncated protein were used to show that conserved residues were important for activity. These results suggest that 173 aa of UL42 can be deleted without a loss of activity and that DNA-binding and Pol-binding activities are correlated with the ability of UL42 to stimulate Pol activity.

Molecular monitoring of the immunosuppressive effects of cyclosporine in renal transplant patients by using a quantitative polymerase chain reaction

We have developed a rapid (24 hours) quantitative PCR assay to measure the direct effect of cyclosporine on IL-2 mRNA production by activated PBMC cultures from renal transplant patients. The PBMCs were purified from normal laboratory volunteers (group A, n = 26), CsA-treated renal transplant patients with good renal function, tested between 3 and 8 weeks (group B, n = 14) or between 2 and 8 years (group C, n = 15) after surgery, and stimulated with PHA in media supplemented with either patient serum or pooled commercially obtained AB serum. The mRNA was then isolated and, using semiquantitative PCR or quantitative PCR with a competitive inhibitor, the relative levels or exact levels of IL-2 mRNA (in attomoles) could be measured. A 3-day confirmatory lymphoproliferation assay of [3H]thymidine incorporation was also performed on the samples. Kinetic analysis of the data from group A showed that the peak level of IL-2 transcription into mRNA occurred at 6 hours after mitogen stimulation. Increasing in vitro concentrations of CsA in this group resulted in lower IL-2 mRNA levels and a shift in the peak time to 12-24 hours. In the transplant recipients, there was no correlation between individual CsA blood levels and proliferation responses. However, some correlation was found between CsA blood levels and IL-2 mRNA levels.(ABSTRACT TRUNCATED AT 250 WORDS)

Amplification and cloning of sugarcane sucrose synthase cDNA by anchored PCR

We have used a strategy based on the polymerase chain reaction (PCR) to amplify and construct full-length sucrose synthase (SS) cDNA of sugarcane. Two SS-specific internal primers were synthesized based on their complementarity to published consensus sequences of the SS gene of maize and wheat. Amplification of full-length cDNA was achieved by an anchored PCR method utilizing primers which extend to 5' and 3' ends of specific cDNA. In the first step, a homopolymeric oligo(dC) tail was added to the 3' end of single-stranded cDNAs. The two SS cDNAs were amplified, one with a 5' end (SSp1) and the other with a 3' end (SSp2) using one internal SS primer and the other anchored end primer. Finally, overlapping fragments were identified by restriction mapping, and the non-overlapping fragments were excised and religated to reconstruct full-length cDNA. Partial sequences of the reconstructed cDNAs (SS-5' and SS-3') were compared with the published SS sequences to confirm that the amplified DNA was a copy of the SS transcript.

COL4A5 splice site mutation and alpha 5(IV) collagen mRNA in Alport syndrome

Mutations affecting the COL4A5 gene encoding the alpha 5 chain of type IV collagen, are involved in the pathogenesis of X-linked Alport syndrome. We used denaturing gradient gel electrophoresis (DGGE) to screen PCR amplified exons of COL4A5 for point mutations in a set of 18 Alport patients previously characterized by Southern blotting. One sequence variant was identified in the exon 38 region of a male Alport patient. Sequence analysis revealed a G to C transversion in the 5' intron splice donor site downstream from exon 38 (GT to CT). To determine the effect of the mutation on mRNA splicing, alpha 5(IV) cDNA was generated from total RNA of peripheral blood lymphocytes. Subsequent cDNA PCR yielded a product 81 base pairs shorter in the affected Alport patient, compared to normal controls. The absence of exon 38 from the alpha 5(IV) cDNA was confirmed by sequence analysis. The results demonstrated that the mutation leads to skipping of exon 38 in the processing of alpha 5(IV) pre-mRNA. The shortened transcript lacked 27 codons encoding a Gly-X-Y-repeat sequence with a preserved reading frame, enabling the translation of codons further downstream. Clinically, the patient presented with juvenile onset Alport syndrome, end-stage renal failure, and deafness. He had no ocular lesions. Typical ultrastructural changes of the glomerular basement membrane (GBM) were shown on electron microscopy. The patient developed anti-GBM antibodies after renal transplantation, however, renal function deteriorated only moderately.

Current methods of mutation detection

Mutation detection is important in all areas of biology. Detection of unknown mutations can involve sequencing of kilobases of DNA, often in many patients. This has lead to the development of methods to screen DNA for mutations as well as methods to detect previously described mutations. This review discusses current methods used for such purposes with special emphasis on genetic diseases of humans. However, savings can be made by similar means in other areas of biology where repetitive or extensive sequencing for comparative purposes needs to be done. This review covers the methods used for detection of unknown mutations, namely the ribonuclease, denaturing gradient-gel electrophoresis, carbodiimide, chemical cleavage, single-strand conformation polymorphism, heteroduplex and sequencing methods. Once mutations have been defined they can be searched for repeatedly by methods referred to as diagnostic methods. Such methods include allele-specific oligonucleotide hybridization, allele-specific amplification, ligation, primer extension and the artificial introduction of restriction sites. We can now choose from a range of excellent methods, but the choice will usually depend on the background of the laboratory and/or the application in hand. Screening methods are evolving to more satisfactory forms, and the diagnostic methods can be automated to screen whole populations inexpensively.

Infidelity in the structure of ectopic transcripts: a novel exon in lymphocyte dystrophin transcripts

Ectopic (or "illegitimate") transcripts have recently become popular as a means of facilitating the study of transcripts normally considered to have a pattern of expression restricted to one or a few tissues. It has been generally assumed that the structure of an ectopic transcript faithfully represents that of its tissue-specific counterpart. We describe here the inclusion of a novel exon in 50% of ectopic dystrophin transcripts from human peripheral blood lymphocytes. The novel sequence resembles a conserved region in the 3' untranslated region of members of the carcinoembryonic antigen gene family and lies within the first intron of the human dystrophin gene. This constitutes a significant departure from the expected in vivo splicing behaviour in an ectopic transcript and suggests that there may be exceptions to the assumption that ectopic transcripts are processed in a similar way to their tissue-specific counterparts.

A quantitative reverse transcriptase-polymerase chain reaction for HIV-1-specific RNA species

The ability to evaluate the patterns and levels of human immunodeficiency virus type I (HIV-1)-specific RNA in latently and productively-infected cell lines, and primary human cells, is critical to the understanding of HIV-1 expression in cell cultures and possibly in vivo. We have developed a quantitative reverse transcriptase-polymerase chain reaction (RT-PCR), utilizing in vitro transcribed RNA standards, to evaluate the copy number per cell and per microgram of total cellular RNA of multiply-spliced, unspliced and total HIV-1-specific RNA species. The latently-infected monocytic and T-lymphocyte cell lines, U1 and ACH-2 respectively, are shown to express between 10(4) to 10(6) copies of total HIV-1-specific RNA per cell, based on the state of cellular stimulation. A dramatic increase of unspliced HIV-1-specific RNA in both the U1 cell line and the ACH-2 cell line is demonstrated by this quantitative RT-PCR, 24 h after stimulation with phorbol esters. These data suggest that a single integrated HIV-1 provirus can rapidly express large quantities of HIV-1-specific RNA. Quantitative RT-PCR, for HIV-1-specific transcripts, should prove extremely useful in evaluating retroviral load and pathogenesis in cell cultures and in vivo.

Widespread co-localization of mRNAs encoding the guanylate cyclase-coupled natriuretic peptide receptors in rat tissues

Natriuretic peptides modulate vasorelaxation, diuresis, and natriuresis through the stimulation of cGMP production by the guanylate cyclase-coupled natriuretic peptide receptors, GC-A and GC-B. We used reverse transcription-polymerase chain reaction to determine the distribution of mRNA encoding both receptors in rat tissues. GC-A and GC-B transcripts were detected in all peripheral and neural tissues examined. Since the atrial natriuretic peptide gene is expressed in all these tissues, our widespread detection of GC-A and GC-B mRNAs now suggests that natriuretic peptides may act as endocrine and paracrine hormones as well as neurotransmitters via both GC-A and GC-B receptors.

Amplification of protein expression in a cell free system

Large quantities of a catalytically active protein have been produced in a cell free system. More than 10(9) copies of protein were produced from each DNA plasmid containing DNAfol, the bacterial gene encoding dihydrofolate reductase (DHFR). The strategy employed, denoted gene amplification with transcription/translation (GATT), involves sequential coupling of (i) DNA amplification by the polymerase chain reaction (PCR) and (ii) in vitro RNA transcription by T7 RNA polymerase, followed by (iii) translation of the run-off transcripts in a rabbit reticulocyte system. The protein product had the expected size (18 kDa) and catalyzed the NADPH-dependent reduction of 7,8-dihydrofolic acid to 5,6,7,8-tetrahydrofolic acid as efficiently as authentic DHFR. Potential applications of the strategy include large scale production of enzymes containing synthetic amino acids and facilitation of the characterization of the function of genes encountered in genomic mapping studies.

In vitro translation of proteins with terminal deletions by SP6 RNA polymerase-mediated transcription of PCR products

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Selection of T cell receptor V beta elements by HLA-DR determinants predisposing to rheumatoid arthritis

OBJECTIVE

Rheumatoid arthritis (RA) is genetically linked to a sequence motif encoding for the middle portion of the alpha-helical loop, which is adjacent to the antigen-binding groove of the HLA-DR molecule. The disease-associated element might be involved in binding the antigen or in interacting with the T cell receptor (TCR). To investigate the contribution of the disease-associated element in T cell recognition events, we studied structural requirements in the interaction of T cell clones with HLA-DR determinants.

METHODS

T cell clones restricted to disease-associated HLA-DR determinants were established by allogeneic stimulation of HLA-DRB1*0401+ or *0401- responders with HLA-DRB1*0404/8+ stimulators. Allele specific primer sets were used to identify the V beta gene segment expressed by individual clones. Sequence analysis was applied to study the diversity of the TCR beta-chain junctional regions.

RESULTS

The repertoire of TCR V beta elements was strongly biased toward the usage of V beta 6. HLA-DRB1*0401+ and *0401- donors preferentially recruited V beta 6+ T cells to recognize the disease-associated HLA-DR determinant. Sequence data revealed that the V beta 6.6/7 and V beta 6.8/9 subtypes of the V beta 6 multigene family were overrepresented. The TCR beta chains were characterized by a high degree of junctional diversity, supporting the view that a multitude of peptide-DR complexes were recognized and that the preferential use of V beta 6 was dictated by the TCR beta chain-DR beta 1 chain contact.

CONCLUSION

T cells reactive with the disease-associated HLA-DR structure are nonrandomly selected. The HLA-DR component predisposing to RA might define molecular requirements that restrict the TCR-HLA interaction. Thus, the phenomenon of HLA association in RA might reflect a genetic control of T cell recognition, through the selection of the TCR repertoire.

Identification of a new DMD gene deletion by ectopic transcript analysis

The detailed genetic analysis of the Duchenne/Becker muscular dystrophy gene is hindered by the large number of exons involved and their separation by huge introns. These problems can be overcome by the analysis of mRNA rather than genomic DNA and ectopic transcripts derived from peripheral blood lymphocytes provide a convenient source of material. Using reverse transcription and nested PCR, we show here a comprehensive strategy for the rapid and complete analysis of the coding sequences from complex genes and illustrate its potential by the identification of a hitherto undescribed single exon deletion.

De novo splice site mutation in the antithrombin III (AT3) gene causing recurrent venous thrombosis: demonstration of exon skipping by ectopic transcript analysis

A single basepair substitution at conserved position -1 in the exon 3a donor splice site of the liver-expressed antithrombin III (AT3) gene was detected by PCR/direct sequencing in a patient with sporadic type 1 ATIII deficiency and recurrent venous thrombosis. The lesion, a heterozygous silent AAG----AAA transition at Lys 176 occurred de novo in the proposita. Ectopic transcript analysis of lymphocyte mRNA demonstrated the presence of an abnormally sized mRNA specific to the patient which was shown by cDNA sequencing to lack exon 3a. Oligonucleotide discriminant hybridization demonstrated the absence of any detectable transcript of normal length derived from the disease allele. These findings demonstrate the utility of ectopic transcript analysis in the characterization of defects of mRNA splicing.

cDNA sequence and alternative mRNA splicing of surfactant-associated protein C (SP-C) in rabbit lung

An 784 base pair (bp) copy DNA (cDNA) for the low molecular weight hydrophobic surfactant-associated protein C (SP-C) has been isolated from a lambda gt11 cDNA library constructed from fetal rabbit lung mRNA. The cDNA, which coded for a 193 amino-acid proprotein with 6 bp 5' and 193 bp 3' untranslated segments, possesses considerable nucleic acid and predicted amino-acid homology with previously reported SP-C cDNAs. The predicted amino-acid sequence of the 35 amino-acid mature polypeptide shares 94-97% identity with human, rat and mouse SP-C and is 88-91% homologous to the mature proteins from bovine, porcine and canine lung. The last 12 amino acids of mature SP-C are highly hydrophobic and invariant. Alignment of the rabbit and human nucleic acid sequences required introduction of a 27 bp gap in the rabbit sequence at a site corresponding to the exon-intron junction of the 5th exon of the human genomic sequence. Since previous studies have identified differential splicing at the 5' and 3' ends of the human 5th exon, we investigated the potential existence of alternative splicing of rabbit SP-C mRNA. Reverse transcription (RT) of total RNA followed by polymerase chain reaction (PCR) was used to establish the relative abundance of alternative splicing products from fetal and adult lung and from rabbit kidney, placenta and liver. The relative abundance of the 250, 280 and 350 bp bands observed was the same in lung and other tissues. PCR amplification of genomic rabbit DNA indicated that the 350 bp fragment corresponds to the unspliced nascent transcript. The lack of developmental or tissue-specific abundance patterns implies the absence of secondary influences on SP-C mRNA polymorphism. Indeed, free energy of formation calculations predicted the presence of hairpin structures favouring formation of the more abundant 250 bp form. These observations plus the absence of any effect of alternative splicing on SP-C protein structure led us to conclude a physiological role is unlikely.

Homozygosity for the HLA-DRB1 allele selects for extraarticular manifestations in rheumatoid arthritis

Seropositive rheumatoid arthritis is genetically linked to a group of HLA-DRB1 alleles sharing a sequence motif within the third hypervariable region. Controversy exists over the role of the distinct allelic variants in affecting not only the risk to develop disease, but also in modifying the expression of the disease. We have stratified 81 patients according to their patterns of disease manifestations and identified the HLA-DRB1 alleles by polymerase chain reaction amplification and subsequent oligonucleotide hybridization. To identify precisely the allelic combinations at the HLA-DRB1 locus, homozygosity was confirmed by locus-specific cDNA amplification and subsequent sequencing. Our study demonstrated a high correlation of allelic combinations of disease-associated HLA-DRB1 alleles with the clinical manifestations. Characteristic genotypes were identified for patients who had progressed toward nodular disease and patients who had developed major organ involvement. Rheumatoid nodules were highly associated with a heterozygosity for two disease associated HLA-DRB1 alleles. Homozygosity for the HLA-DRB1*0401 allele was a characteristic finding for RA patients with major organ involvement. Our data suggest a role of the disease-associated sequence motif in determining severity of the disease. The finding of a codominant function of HLA-DRB1 alleles suggests that the biological function of HLA-DR molecules in thymic selection might be important in the pathogenesis of RA.

A donor splice site mutation in the parathyroid hormone gene is associated with autosomal recessive hypoparathyroidism

Investigation of one kindred with autosomal recessive isolated hypoparathyroidism, which had resulted from a consanguineous marriage, has identified a g to c substitution in the first nucleotide of intron 2 of the parathyroid hormone (PTH) gene. This donor splice mutation could be detected by restriction enzyme cleavage with Ddel, and this revealed that the patients were homozygous for the mutant alleles, the unaffected relatives were heterozygous, and unrelated normals were homozygous for the wild type alleles. Defects in messenger RNA splicing were investigated by the detection of illegitimate transcription of the PTH gene in lymphoblastoid cells. The mutation resulted in exon skipping with a loss of exon 2, which encodes the initiation codon and the signal peptide, thereby causing parathyroid hormone deficiency.

Screening for mutations by RNA single-strand conformation polymorphism (rSSCP): comparison with DNA-SSCP

Single-strand conformation polymorphism (SSCP) is a simple method for detecting the presence of mutations in a segment of DNA, but the fraction of all mutations detected is unclear. We have evaluated SSCP for the detection of single-base mutations in the factor IX gene. Multiple conditions were examined including electrophoresis temperature, electrophoresis buffer concentration, acrylamide to bis-acrylamide ratio, and water-cooled versus fan-cooled gel apparatuses. Depending on conditions, 10-11 of 12 known mutations were detected in a 183 bp segment whereas only 11-14 of 22 known mutations were detected in a 307 bp segment. We hypothesized that single stranded RNA should have a larger repertoire of secondary structure because shorter hairpins form stable duplexes and the 2' hydroxyl group is available for sugar-base and sugar-sugar hydrogen bonds. By incorporating phage promoter sequences into PCR primers, RNA-SSCP (rSSCP) could be compared directly with standard DNA SSCP. rSSCP was generally superior to SSCP, especially for the 307 bp segment. In addition, the abundance of transcript produced as a result of rSSCP allows the rapid, nonradioactive detection of mutations by staining the gel with ethidium bromide. To gauge the utility of the method in a prospective manner, a blinded study was performed in which SSCP, rSSCP, and direct genomic sequencing were compared in 28 patients with hemophilia B. A total of 2.6 kb of factor IX genomic sequence was examined in nine regions ranging from 180 to 497 nucleotides of factor IX sequence. Sequence changes at 20 different sites were detected by direct genomic sequencing; 70% of these were detected by rSSCP while only 35% were detected by SSCP.