Use Of cDNA Probes Research Articles

Regulation of HLA class II expression and its role in autoimmune disease.

Excessive HLA class II expression is found on the target tissues of the majority of human autoimmune diseases, together with activated (interleukin 2 receptor-expressing) T lymphocytes, suggesting that the target tissues act as antigen-presenting cells for infiltrating autoreactive cells, which in turn produce molecules that maintain class II expression. This vicious cycle has been shown to operate in Graves' thyroiditis, because interferon-gamma (IFN-gamma) induces class II expression on thyrocytes, and thyrocytes expressing class II antigens present their autoantigens to T cells cloned from thyroid tissue of Graves' disease patients. These results led us to consider whether the same mechanisms operate in other autoimmune diseases. In investigations into class II induction in other cell types we found that IFN-gamma is not the only regulator of HLA class II expression and that synergy exists among mediators regulating class II differentially on different cell types. This concept makes it possible to envisage selective diminution of class II antigens on target tissues without loss of class II on antigen-presenting cells. The study of mediators regulating class II expression on cells in vitro led us to ask whether the appropriate regulator molecules are important in disease states. To investigate this question we have developed the use of cDNA probes to analyse the expression of lymphokines, other cytokines, and receptors in small local biopsy samples of tissue from patients with autoimmune diseases. Results obtained so far indicate that mRNAs for many lymphokines are present in synovial fluid cell samples from patients with rheumatoid arthritis.

Alternatives to whole animal testing: Use of cDNA probes for studies of phase I and II enzyme induction in isolated plaice hepatocytes

Studies of xenobiotic metabolism and the regulation of enzyme systems for their metabolism (Phase I and II enzyme systems) require large numbers of animals, intensive use of experimental aquarium systems and in some instances can pose major problems when the compounds are scarce, expensive or too toxic to be disposed of easily. Previous studies have demonstrated the usefulness of isolated primary hepatocytes of fish for metabolic and enzyme induction studies. Functionally and structurally competent hepatocytes were isolated from juvenile plaice and after overnight acclimation to culture conditions, were exposed to a variety of PAHs for 24h. The levels of CYP1A1, phenol UDPGT and GST-A mRNAs were then estimated by slot blotting and hybridisation to their cDNA probes. The method enabled rapid and easy determination of the structure/activity relationships of these compounds as inducers of these key Phase I and II enzymes, and is potentially useful for screening large numbers of compounds both as an invitro toxicity test and for mechanistic studies.

Loss of glucose transporters is an early event in differentiation of HD3 cells.

The HD3 cell, a chicken erythroblast cell line infected with a temperature-sensitive avian erythroblastosis virus, becomes committed to differentiate to an erythrocyte upon temperature shift in presence of inducers. Before induction, the HD3 cell transports glucose and 2-deoxyglucose (2-DG). 3-O-methylglucose is poorly taken up. Upon induction of differentiation, glucose and 2-DG transport activity fall. Twenty-four hours postinduction, up to 75% of the glucose transport activity may disappear. By use of cDNA probes for chicken glucose transporters, two species of mRNA of 3.1 and 1.7 kb (equivalent to mammalian GLUT1 and GLUT3 mRNA, respectively) are detected. Both messages virtually disappear within 48 h after induction. Run-on assays show the cessation of synthesis of the corresponding RNAs parallel to the loss of glucose transport. In contrast to the glucose transporters, the nucleoside transporter level increases after induction of hematopoiesis. This developmental pattern is consistent with earlier studies showing that mature chicken erythrocytes have little glucose transport activity but retain appreciable levels of the nucleoside transporter and that nucleosides and glutamine provide major sources of oxidizable carbon compounds to sustain metabolism in circulating chicken erythrocytes.

Use of cDNA Probes for Typing Cells of B Lymphoid Lineage: Application of Early Response Genes to the Analysis of Mature B Cell Malignancies.

In vitro phorbol ester-induced plasmacytoid differentiation of primary B chronic lymphocytic leukaemia (BCLL) cells is accompanied by the rapid, transient increased expression of a large number of early response genes (ERGs) whose expression is highly cell type specific. We have examined phorbol ester-responsive expression of a panel of 13 ERGs in a series of B cell lines representing different stages of differentiation and in primary malignant cells from patients with hairy cell leukaemia and with centroblastic-centrocytic non-Hodgkin's lymphoma. The results revealed a spectrum of ERG expression which appeared to be correlated with stage of differentiation relative to BCLL cells, where no two cell types gave an identical ERG response. These results, while preliminary, suggest that panels of ERG probes provide a useful approach for analysis of cell type which may help in mapping stages of differentiation arrest and defining cell lineage relationships amongst mature B cell malignancies.

Duchenne and Becker Muscular Dystrophies: Genetics, Prenatal Diagnosis, and Future Prospects

DMD and BMD are now understood at the genetic, biochemical, and molecular levels. At the genetic level, both disorders result from mutations of the X-linked gene encoding dystrophin. At the biochemical level, DMD results from the deficiency of a large protein called dystrophin, whereas BMD results when dystrophin is present, though abnormal in either amount or molecular structure. To date, thousands of patients have been analyzed for mutations of the dystrophin gene in peripheral blood DNA or alterations of the dystrophin protein in muscle tissue. The severity of the clinical phenotype of these patients has been compared with their dystrophin gene mutations and corresponding dystrophin protein alterations, revealing an unexpectedly high degree of correlation. Thus, information derived from the molecular analysis (DNA or protein) of a particular patient provides a "molecular diagnosis," which is highly predictive of the clinical course that patient can be expected to follow. Because molecular diagnoses are independent of the patient's age, they provide a prognosis for the large majority of muscular dystrophy patients even before clinical symptoms of their disease become apparent. Such prognostic molecular diagnoses have proven particularly valuable when the patient is an isolated case, with no family history for the disorder. Prenatal genetic diagnosis of DMD or BMD may involve use of Southern blot or PCR techniques to search for a deletion in the DNA of at-risk fetuses or more complicated family linkage studies using intragenic and flanking RFLPs. More recently, assay of dystrophin content in fetal skeletal or cardiac muscle from at-risk abortuses has been accomplished, allowing definitive discrimination of affected and normal fetuses in cases in which deletion analyses and family DNA studies were equivocal. In utero fetal skeletal muscle biopsy for dystrophin protein assay has actually been accomplished in at least one at-risk pregnancy in which family DNA studies were uninformative. Dystrophin was present in skeletal muscle from this 20-week-old male fetus, and the pregnancy continued, resulting in the term birth of a healthy male infant. The future holds exciting opportunities for neonatal screening and treatment of these devastating neuromuscular diseases.

Comparison of the Dot Blot Hybridization Assay with Antigen Detection Assays for the Diagnosis of Infectious Bursal Disease Virus Infections

The use of cDNA probes as diagnostic tools for detecting infectious bursal disease virus (IBDV) antigens was compared with the agar-gel precipitin (AGP) and immunofluorescence (IF) assays. Specific-pathogen-free chickens were inoculated with the STC or IN strains of IBDV in three separate experiments. Tissue samples were collected at various intervals postinoculation (PI) and examined for viral antigens using the IF assay, the AGP assay, and the hybridization assay. Viral antigen was detected by the AGP assay for a period of approximately 3 days beginning 2 days PI and by the IF assay for approximately 4 days beginning 2 days PI. Virus was detected by the hybridization assay through the length of all the experiments (longest experiment was 24 days) beginning 1 day PI. These results suggested that the hybridization assay is more sensitive than the IF assay and the AGP assay.

Expression of fibrillar types I and III and basement membrane collagen type IV genes in myocardium of tight skin mouse

The aim was to study the expression of fibrillar collagen types I and III and basement membrane type IV collagen in the heart of the tight skin mouse, a genetic mutant with collagen overproduction in various organs. Collagen gene expression was measured in the ventricular tissues of the heart of the tight skin mouse and the age matched homozygous (+/+) litter mates by the use of cDNA probes to alpha 2 (I), alpha 1 (III) and alpha 2 (IV) procollagen and northern and dot blot analysis. Collagen deposition was examined by immunofluorescent light microscopy using monospecific antibodies to types I, III and IV collagens. Heterozygous male (TSK/+) and normal (+/+) mice, 1.5-2 months old of the C57BL/6 strain were used. The animals were anaesthetised and the hearts were rapidly excised and processed for RNA extraction and antibody staining. The results of northern and dot blot analyses showed a 41% increase in mRNA level for collagen type I, a 63% increase in mRNA level for type III and a 33% increase in type IV collagen in the ventricular myocardium (right and left ventricles) of the tight skin mouse compared to its counterpart in age matched homozygous (+/+) litter mates. mRNA levels for beta actin showed no significant increase. Immunofluorescent light microscopy and monospecific antibodies to types I, III and IV collagens were used to examine collagen deposition. The results showed that collagen type I fibres are thicker and denser in perivascular areas of the tight skin mouse heart compared to normal heart. No abnormal accumulation of type III fibres was observed. The heart of the tight skin mouse may be an appropriate model for studying the up regulation of cardiac collagen gene expression and its potential contribution to myocardial diseases.

Production of tumor necrosis factor (TNF-alpha) and lymphotoxin (TNF-beta) by murine pre-B and B cell lymphomas.

Media from murine pre-B and B lymphoma cell cultures, but not from myeloma cell cultures, was cytotoxic to WEHI 164 cells, causing these TNF-sensitive targets to release 51Cr. The cytotoxic activity in the culture medium reached maximum levels approximately 4 days after the cell culture was initiated. The constitutive production of the factors was not influenced by depletion of serum from the medium or by the addition of either phorbol ester or bacterial endotoxin. The factor has a Mr greater than 10 kDa, and its cytotoxicity was abolished by anti-serum against murine TNF. Northern blot analysis with the use of cDNA probes to murine tumor necrosis factor (TNF-alpha) and lymphotoxin (LT, TNF-beta) showed high levels of TNF-mRNA in the pre-B cell lines, lower levels in the mature B cell lines and no TNF-mRNA in the myeloma cell lines. LT mRNA was present in pre-B cell lines, at a much lower concentration in only one of the B cell lines, and was not present in three other B lymphomas or in the myelomas tested. The results show a positive correlation between the presence of TNF and/or LT mRNA and the 51Cr-releasing activity present in the cell culture medium. Our data indicate that TNF and LT can be produced by murine B cells and that the synthesis of these cytokines may be restricted to certain differentiation stages of the B cell lineage.

Molecular probe protocol for determining carrier status in Duchenne and Becker muscular dystrophies

By use of cDNA probes, molecular deletions were identified in 66.6% of 42 patients with Duchenne muscular dystrophy (DMD) or Becker muscular dystrophy (BMD). Owing to this high deletion rate, a new strategy for detecting DMD/BMD carriers is feasible in which the polymerase chain reaction is used as an initial screen for detecting the deletions occurring in specific deletion-prone exons. Because the deletions do not occur randomly, specific cDNA probes are utilized first with Southern blot analysis. Identification of a deletion permits direct analysis for DMD carrier status and removes the inherent limitations of the conventional restriction fragment length polymorphism technique. Carrier status is determined by scanning the autoradiographs with a densitometric spectrophotometer or by detection of a junction fragment.

Restriction fragment length variations and chromosome mapping of two mouse metallothionein genes, Mt-1 and Mt-2.

Restriction endonuclease fragment length variations (RFLVs) were found through the use of cDNA probes for metallothionein genes 1 (Mt-1) and 2 (Mt-2) in the mouse. RFLVs were detected in restriction patterns generated by BglII and XbaI in the Mt-1 gene and by PvuII in the Mt-2 gene. All laboratory strains carry the Mt-1a and Mt-2a alleles. Among strains of wild origin, some Western European subspecies (Mus mus domesticus and M. m. brevirostris) also carry the Mt-1a and Mt-2a alleles. In contrast, a European subspecies (M. m. musculus) and the great majority of subspecies from East Asian countries (M. m. molossinus, Chinese mice of wild origin, and M. m. yamashinai) carry the Mt-1b and Mt-2b alleles. A domesticus strain from Bulgaria and two castaneus strains from Thailand and Philippines carry the intermediate combination of Mt-1b and Mt-2a alleles. Using the RFLVs, we mapped the Mt-1 and Mt-2 genes on chromosome 8, and they appear to be very closely linked since no recombination was observed between them in any of the mice examined. Data from three-point cross tests showed that the recombination frequencies are 4.31% between Os and Mt, 15.52% between Mt and Prt-2, and 19.83% between Os and Prt-2. The gene order of Os-Mt-1,Mt-2-Prt-2 has been confirmed.

Prenatal diagnosis of Duchenne muscular dystrophy: A three‐year experience in a rapidly evolving field

Application of molecular genetic techniques has greatly increased diagnostic possibilities of hereditary disorders. In 1983 the first linkage of Duchenne muscular dystrophy with flanking DNA probes was described, which made carrier detection possible in a limited number of cases. The first published prenatal diagnosis for Duchenne muscular dystrophy dates from 1985. DNA-analysis for Duchenne muscular dystrophy and Becker muscular dystrophy has become increasingly informative, firstly by the development of more flanking markers, followed by intragenic probes detecting deletions and, more recently, by the use of cDNA probes detecting a deletion or duplication mutation in over 60% of the Duchenne and Becker muscular dystrophy patients. Although these developments allow a highly reliable (greater than 99%) carrier detection and prenatal diagnosis in over 90% of cases, the continuing introduction of new probes and/or technologies has necessitated constant reappraisal of many families to derive maximum information. During the past 3 years we applied prenatal diagnosis for Duchenne and Becker muscular dystrophies with DNA-analysis on 53 male fetuses in 47 families. Twenty-two healthy male babies were born, after being diagnosed to have a low Duchenne muscular dystrophy risk. Two pregnancies also diagnosed as low risk have not yet come to term. In the other cases a high risk for Duchenne muscular dystrophy was found and the parents chose abortion. Our studies also revealed a number of important diagnostic pitfalls, such as non-paternity, karyotypic anomalies and gonadal mosaicism.

Possibilities and limitation of prenatal diagnosis and carrier determination for Duchenne and Becker muscular dystrophy using cDNA probes.

Two cDNA probes, cf23a and cf56a, identify deletions of selected exons in about 50% of our DMD/BMD patients. We have estimated the most likely order of the 11 exons detectable with both probes with respect to the different extensions of the deletions. In one of our BMD pedigrees, the observed deletion could be traced in the affected males through three generations. This result shows that with the use of cDNA probes detecting deletions, the only risk of error in genomic prenatal diagnosis is the general high frequency of new mutations for DMD/BMD. This is important progress in diagnosis compared to the 2 to 5% risk of misdiagnosis because of crossing over events using conventional linkage analysis with bridging or intragenic probes. The first prenatal diagnosis of an unaffected fetus of a woman who is a DMD carrier according to ultrasound examination is described. In one of our DMD males, the cDNA probe cf56a detects a deletion breakpoint. His sister also shows the altered band and is therefore a DMD carrier, while his mother has a totally normal band pattern. The interpretation of this observation could be either germline mosaicism or two identical new mutations. The identification of deletion breakpoints is a new diagnostic strategy, especially for carrier determination, which excludes misdiagnosis owing to crossing over events and the problems of dosage estimation. It is, however, limited by the low frequency of breakpoints detectable with cDNA probes. Therefore, the generation of new intron probes in this region is an important goal.

Hormonal Regulation of Coliagen Gene Expression in Osteoblastic Cells-Overview and New Findings

Type I collagen synthesis in osteoblasts is regulated by a variety of systemic hormones, growth factors and locally produced factors. With the use of cDNA probes and hybridization analysis, it appears that many of these agents alter collagen synthesis by a pretranslational mechanism.

The nucleocapsid gene of infectious hematopoietic necrosis virus, a fish rhabdovirus

The complete nucleotide sequence of the infectious hematopoietic necrosis virus (IHNV) nucleocapsid gene has been determined using cDNA clones of genomic and messenger RNAs. Genomic clones were generated by using random DNA oligomers to prime cDNA synthesis and were mapped to their respective locations on the genome by the use of cDNA probes derived from viral mRNAs. Interesting features of the IHNV nucleocapsid gene sequence elucidated by the sequencing of these clones include short homologies with N genes of other rhabdoviruses at the 5′ and 3′ nontranslated termini of the mRNA, as well as an exceptionally long 5′ noncoding region of the mRNA, suggesting a leader RNA may be coupled to the N mRNA. A comparison of the IHNV N protein coding sequence with other rhabdoviral N genes shows some homologies at the amino acid level which indicates the possible evolutionary relationship of these N proteins. The determination of the nucleotide sequences of IHNV genes and intergenic regions will be useful for studying the mechanisms of rhabdoviral transcription and replication.

Optimal conditions for the use of cDNA probes to measure the concentration of barley yellow dwarf virus in barley ( Hordeum vulgare)

Experiments which optimise the conditions for the measurement of the relative concentration of BYDV in barley ( Hordeum vulgare) tissues using cDNA probes are described herein. These studies have shown that both the pH of the buffer and the ratio of buffer to tissue used to homogenise plant material greatly affects the amount of cDNA probe which hybridises to leaf extracts immobilised on nitro-cellulose. These studies also showed that the measurement of this virus was greatly facilitated by using a dot-blot apparatus which allows samples contact with a piece of nitrocellulose 10 mm in diameter rather than a 3 mm (approx) diameter piece of nitrocellulose as is the case with most commercial dot-blot apparatuses. Further experiments using this technique showed that there was a large difference in the rate of replication of the PAV, BYDV serotype between BYDV-resistant and BYDV-susceptible cultivars of barley. These data suggest that a BYDV-resistant cultivar can easily be distinguished from a BYDV-susceptible one if the BYDV content of leaves is measured between 7 and 14 days after inoculation.

CDNA probes of individual genes of human rotavirus distinguish viral subgroups and serotypes

The use of cDNA probes for detection of rotaviruses has been investigated using plasmids containing inserts specific for each of the eleven genes of human rotavirus strain Wa. In a dot-blot detection system in which radioactive DNA probes were hybridized to viral RNA extracted from cultivatable rotavirus strains, cDNAs of genes 7, 8, 10 and 11, were found to be the most reliable probes for detecting a range of rotavirus strains. Unexpectedly, rotaviruses could be distinguished with respect to subgroup and subtype specificities when cDNAs of genes 6 and 9, which encode the immunologically relevant proteins VP6 (group-specific antigen) and VP7 (type-specific antigen), were used as probe, even though the nucleic acid sequences of these genes are known to have a high degree of sequence homology.

Chapter 8 Impulse activity differentially regulates co-localized transmitters by altering messenger RNA levels

Publisher Summary This chapter focuses on the role of depolarization in the regulation of transmitter plasticity and reviews experiments employing rat sympathetic neurons and adrenomedullary chromaffin cells as models in vivo and in vitro . The chapter also discusses the mechanisms by which depolarization regulates transmitter metabolism and expression in sympathetic neurons. Evidence indicates that plasticity persists into adulthood. Regulation in the adrenomedullary chromaffin cell is examined as the availability of appropriate complementary DNA (cDNA) probes has helped to identify molecular loci governing plasticity attendant to depolarization. The concepts of the combinatorial potential of neural communication have undergone a revolution with the realization that neurons use multiple transmitters simultaneously. Studies of sympathetic neurons during development as well as maturity indicate that co-localized transmitter molecules are profoundly plastic. Different co-localized transmitter systems are differentially regulated by extraneuronal stimuli, such as trans-synaptic impulse traffic and depolarization. Moreover, the use of cDNA probes in sympathetic neurons and adrenal medulla has revealed that membrane depolarization and sodium ion influx, specifically and differentially, alter the levels of messenger RNA coding for transmitter molecules.

Isolation and characterization of the apolipoprotein genes.

These types of studies lay the foundation for understanding the human apolipoproteins at the genetic level. In addition, through a few specific examples, we have already shown evidence at the DNA level that lesions in apolipoprotein genes can play a role in human atherosclerosis. This work is in its infancy but, in the future, we hope it will have a major impact on our ability to understand genetic susceptibility to atherosclerosis in the general population.

Rat liver glutathione S-transferases. Complete nucleotide sequence of a glutathione S-transferase mRNA and the regulation of the Ya, Yb, and Yc mRNAs by 3-methylcholanthrene and phenobarbital.

With the use of cDNA probes reverse transcribed from purified glutathione S-transferase mRNA templates, four cDNA clones complementary to transferase mRNAs have been identified and characterized. Two clones, pGTB38 and pGTB34, have cDNA inserts of approximately 950 and 900 base pairs, respectively, and hybridize to a mRNA(s) whose size is approximately 980 nucleotides. In hybrid-select translation experiments, pGTB38 and pGTB34 select mRNAs specific for the Ya and Yc subunits of rat liver glutathione S-transferases. Clone pGTB33, which harbors a truncated cDNA insert, hybrid-selects only the Ya mRNA. All of the clones, pGTB38, pGTB34, and pGTB33, hybrid-select another mRNA which is specific for a polypeptide with an electrophoretic mobility slightly greater than the Ya subunit. The entire nucleotide sequence of the full length clone, pGTB38, has been determined and the complete amino acid sequence of the corresponding polypeptide has been deduced. The mRNA codes for a protein comprising 222 amino acids with Mr = 25,547. We have also identified a cDNA clone complementary to a Yb mRNA of the rat liver glutathione S-transferases. This clone, pGTA/C36, hybrid-selects only Yb mRNA(s) and hybridizes to a mRNA(s) whose size is approximately 1200 nucleotides. Although the Ya, Yb, and Yc mRNAs are elevated coordinately by phenobarbital and 3-methylcholanthrene, the Ya-Yc mRNAs are induced to a much greater extent compared to the Yb mRNA(s). These data suggest that the mRNAs for each transferase isozyme are regulated independently.