Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction

Trichoplusia ni attacin A, a differentially displayed insect gene coding for an antibacterial protein

The mRNA differential display method was used to isolate antibacterial defense genes from Trichoplusia ni. The mRNA population in last-instar T. ni larvae injected with bacteria was compared to that of untreated larvae. Using a PCR amplified probe corresponding to an induced mRNA, we were able to clone an attacin homolog from a lambda cDNA library from vaccinated larvae. The corresponding protein showed 63% identity to Hyalophora cecropia acidic attacin. The induction kinetics of T. ni attacin A gave optimal mRNA levels at 20 h post-infection. Genomic analysis showed this to be a single-copy gene with two introns.

An effective elimination of false positives isolated from differential display of mRNAs

A reverse Northern analysis that effectively eliminates the false positives isolated from differential display of mRNAs (DD) is demonstrated. Preparation of probe by one-step labeling in reverse transcription reaction is found to be more effective and specific as compared to the preparation of probe by random priming of reverse transcribed cDNA pool. Reverse Northern assay of DNA fragments isolated from DD prior to their cloning into plasmid, analysis of multiple fragments on single slot blot, and requirement of RNA only in small amounts as compared to conventional Northern makes the protocol quick, effective, and economic.

Analysis of upregulated cellular genes in pseudorabies virus infection: use of mRNA differential display

Virus infection usually alters the host cell and shuts off the synthesis of cellular macromolecules. In order to screen the upregulated cellular transcripts during pseudorabies virus (PRV) infection, we employed the mRNA differential display technique. The screen is based on positive selection at the mRNA level for genes expressed in normal cells but increased in corresponding PRV-infected cells. Over 14000 species of mRNA, isolated from mock-infected and PRV-infected Madin-Darby bovine kidney cell at 1 h post infection, were screened, and 40 candidate clones were recovered. Southern blot analysis revealed that 17 out of 40 candidate clones, were enhanced in PRV-infected cells. Partial DNA sequences demonstrated that 17 clones were distinct cellular genes, including those encoding the modulators of signal transduction (saposin, 14-3-3, adenylate kinase, adenylyl cyclase, protein kinase C-alpha), those encoding the components of translation (fau, ribosomal proteins S11, L31, L36), other cellular genes (peptidase, cyclin E, rch1, oligo-C-rich single-stranded nucleic acid binding protein, rap, arginyl-tRNA synthetase), and two unknown genes. Thus, this study identifies successfully the transcriptionally regulated cellular genes which are associated with PRV infection. Furthermore, this study provides support for the use of mRNA differential display as a method to rapidly isolate differentially expressed genes in virus infection.

Identification of differentially expressed mRNA species during HIV infection by RNA arbitrarily primed PCR

BACKGROUND

A number of strategies, such as subtractive cDNA libraries and high through-put sequencing, have been devised to assess differential gene expression. Most of these approaches, however, are cumbersome and/or require tremendous technological power. In this paper, we describe a method, RNA fingerprinting using arbitrarily primed polymerase chain reaction (RAP-PCR), that is rapid, less cumbersome and can differentiate low levels of mRNA expression.

OBJECTIVES

To identify genes that are differentially expressed following human immunodeficiency virus type 1 (HIV-1) infection in different cell types by RAP-PCR.

STUDY DESIGN

RNA was extracted from both HIV-1-infected and uninfected HUT78 cells and peripheral blood mononuclear cells (PBMCs), reverse transcribed, and RAP-PCR amplified using numerous primer sets.

RESULTS

Three genes, gamma-actin, the HIV-1 nef and an unknown sequence, were identified as being differentially expressed in HUT78 cells. The level of gamma-actin mRNA expression is increased after HIV infection and, as expected, the nef gene was solely expressed in HIV-infected cells. In contrast, the unknown mRNA is down-regulated by HIV. Northern blot analysis and/or specific PCR confirmed the differential expression of these three genes. RNA fingerprinting using phytohemagglutinin (PHA)-activated PBMCs infected by HIV in vitro, revealed that gamma-actin is still up-regulated by HIV, whereas the unknown product no longer shows down-regulation.

CONCLUSIONS

These results illustrate the usefulness of the RAP-PCR method for isolating and identifying differentially expressed genes during HIV-1 infection of primary lymphocytes.

The metastatic phenotype--prognostic implications

Strong efforts are being made in order to better understand the molecular mechanisms underlying cancer dissemination. We have attempted to summarise some of the findings in this area. A large number of differences in gene expression have been described in metastatic and non-metastatic cells. In the mouse B16 melanoma system, more than 50 different markers have been described. It is likely that many of these differences reflect the same genetic alteration (i.e. a mutation in a regulatory gene alters the expression of a set of co-regulated target genes). One could argue that it is more effective to study mutations in regulatory as opposed to expression of down-stream target genes. However, we feel that proto-oncogenes are less suitable as markers compared to target genes, since it is difficult to screen for mutations at multiple levels in regulatory pathways. In contrast, measuring the expression of a small number of target genes (i.e. one of the targets in Fig. 1), the expression of which are stimulated by upstream regulators, is accomplished more easily. It is anticipated that the future of optimised panels of independent markers will sharpen cancer diagnosis and lead to individualised therapy.

Human immunodeficiency virus type 1 infection of H9 cells induces increased glucose transporter expression

A clone obtained from a differential display screen for cellular genes with altered expression during human immunodeficiency virus (HIV) infection matched the sequence for the human GLUT3 facilitative glucose transporter, a high-velocity-high-affinity facilitative transporter commonly expressed in neurons of the central nervous system. Northern (RNA) analysis showed that GLUT3 expression increased during infection. Flow cytometry showed that GLUT3 protein expression increased specifically in the HIV-infected cells; this increase correlated with increased 2-deoxyglucose transport in the HIV-infected culture. HIV infection therefore leads to increased expression of a glucose transporter normally expressed at high levels in other cell types and a corresponding increase in glucose transport activity. If HIV infection places increased metabolic demands on the host cell, changes in the expression of a cellular gene that plays an important role in cellular metabolism might provide a more favorable environment for viral replication.

Cellular targets and molecular responses associated with photodynamic therapy

The positive clinical results associated with photodynamic therapy (PDT) have led to an expanded need to identify the cellular targets and molecular responses associated with this treatment. Increased knowledge regarding the mechanisms of action associated with PDT-mediated cytotoxicity should contribute to the continued advancement of this therapy. This report focuses on recent studies analyzing PDT resistance and examining stress protein and early response gene activation induced by photosensitizer mediated oxidative stress. Recurring observations from these studies indicate that subcellular targets and cellular responses associated with PDT can vary significantly for different photosensitizers.

Use of messenger RNA differential display to identify interleukin-11-responsive genes in human umbilical cord blood mononuclear cells: IL-11 upregulates the expression of the hMAL gene

Human umbilical cord blood (HUCB) mononuclear cells represent a source of hematopoietic stem and progenitor cells, including cells responsive to interleukin-11 (IL-11). To investigate the molecular mechanisms associated with IL-11 action, we have used HUCB mononuclear cells as a model system to identify genes that are transcriptional targets of IL-11. Using the technique of messenger RNA differential display, we have identified 17 candidate cDNA differentially expressed in mononuclear cells incubated without and with IL-11. Fifteen of these cDNA were recovered, and 11 were sequenced. DNA sequence analysis has identified one of these cDNA as being the human MAL gene, originally identified as a marker for intermediate stages of T cell differentiation. Northern analysis using a MAL-specific probe confirms the upregulation of MAL by IL-11 in HUCB cells.

Interferon-inducible protein-10 involves vascular smooth muscle cell migration, proliferation, and inflammatory response

Interferon-inducible protein-10 (IP-10) is a member of the C-X-C chemokine family. Using mRNA differential display, we isolated a rat homologue to murine and human IP-10 from lipopolysaccharide-stimulated carotid arteries. Our studies demonstrated that IP-10 is a potent mitogenic and chemotactic factor for vascular smooth muscle cells, the critical features of smooth muscle cells for their contribution to the pathogenesis of atherosclerosis and restenosis. IP-10 induced a concentration-dependent stimulation of DNA synthesis, cell proliferation, and cell migration of rat aortic smooth muscle cells. A concentration- and time-dependent IP-10 mRNA induction was observed in lipopolysaccharide- or interferon-gamma-stimulated, but not interleukin-1beta- or tumor necrosis factor-alpha-stimulated smooth muscle cells. A marked synergistic effect on IP-10 mRNA expression was observed when smooth muscle cells were challenged with interferon-gamma together with interleukin-1beta or tumor necrosis factor-alpha. Furthermore, IP-10 mRNA expression was induced in the rat carotid artery after balloon angioplasty. The mitogenic and chemotactic features of IP-10 for smooth muscle cells, along with its discrete induction in cultured vascular smooth muscle cells and in carotid arteries after balloon angioplasty (neointima formation) suggest that IP-10 may play an active and distinct role in vascular remodeling processes.

Identification of vascular endothelial genes differentially responsive to fluid mechanical stimuli: cyclooxygenase-2, manganese superoxide dismutase, and endothelial cell nitric oxide synthase are selectively up-regulated by steady laminar shear stress

Early atherosclerotic lesions develop in a topographical pattern that strongly suggests involvement of hemodynamic forces in their pathogenesis. We hypothesized that certain endothelial genes, which exhibit differential responsiveness to distinct fluid mechanical stimuli, may participate in the atherogenic process by modulating, on a local level within the arterial wall, the effects of systemic risk factors. A differential display strategy using cultured human endothelial cells has identified two genes, manganese superoxide dismutase and cyclooxygenase-2, that exhibit selective and sustained up-regulation by steady laminar shear stress (LSS). Turbulent shear stress, a nonlaminar fluid mechanical stimulus, does not induce these genes. The endothelial form of nitric oxide synthase also demonstrates a similar LSS-selective pattern of induction. Thus, three genes with potential atheroprotective (antioxidant, antithrombotic, and antiadhesive) activities manifest a differential response to distinct fluid mechanical stimuli, providing a possible mechanistic link between endothelial gene expression and early events in atherogenesis. The activities of these and other LSS-responsive genes may have important implications for the pathogenesis and prevention of atherosclerosis.

Origins of immunity: Relish, a compound Rel-like gene in the antibacterial defense of Drosophila

NF-kappa B/Rel transcription factors are central regulators of mammalian immunity and are also implicated in the induction of cecropins and other antibacterial peptides in insects. We identified the gene for Relish, a compound Drosophila protein that, like mammalian p105 and p100, contains both a Rel homology domain and an I kappa B-like domain. Relish is strongly induced in infected flies, and it can activate transcription from the Cecropin A1 promoter. A Relish transcript is also detected in early embryos, suggesting that it acts in both immunity and embryogenesis. The presence of a compound Rel protein in Drosophila indicates that similar proteins were likely present in primordial immune systems and may serve unique signaling functions.

Age-related changes in gene expression in the rat brain revealed by differential display

We have used the polymerase chain reaction (PCR)-based technique of differential display to analyse changes in gene expression during ageing of the rat brain. In this approach we have compared three young adult (6 months) with three old adult (20 months) animals. RNA preparations from the homogenised brains were subjected to reverse transcriptase (RT)-PCR using 36 different combinations of primer pairs. Any PCR product which was consistently found to be more prominent in the three young brains compared to the three old brains, and vice versa, was scored as potentially representing a gene which was differentially expressed during the ageing of this tissue. Out of a possible 2000+ PCR products we identified 44 that might represent genes that exhibit differential expression during ageing of the rat brain. An initial screen of these fragments, by Southern-blotting the PCR products and hybridising them with cDNA probes derived from either young or old brain RNA preparations, indicated that 40% of them represented genes that were differentially expressed. This approach is likely to prove invaluable for identifying cohorts of genes that show differential expression during the ageing process.

Rapid identification of differentially expressed RNA transcripts in apoptotic T lymphocytes

The mRNA differential display technique has several advantages over conventional subtractive hybridization due to its simplicity and high sensitivity. However, the relatively high incidence of 'false positive' bands makes it more difficult to identify cDNAs derived from differential display, especially when subsequent large scale screening is required to isolate specific genes of interest. In this paper, we describe a simple, fast and efficient procedure which includes two-cycle PCR based probe labeling and direct sequencing of differential display products using 5' arbitrary and 3' oligo(dT) anchored primers for the rapid identification of differential display products. As demonstrated by identification of up-regulated RNA transcripts in apoptotic T lymphocytes, we showed that this modified technique greatly simplified the original procedure for the identification of differential display products and facilitated the application of differential display technique in the isolation and characterization of differentially expressed genes.

Sequence analysis of PG10.2, a gene expressed in the pineal gland and the outer nuclear layer of the retina

A cDNA (PG10.2) was cloned from rat using RNA fingerprinting by arbitrarily primed PCR (AP-PCR). Initially, a 145-bp DNA fragment was isolated from a pineal-specific band revealed on a sequencing gel. Riboprobes generated from the DNA fragment were used for hybridization histochemical and Northern analyses. Both techniques indicate a gene (8 kb mRNA) expressed only in the pineal gland and the outer nuclear layer of the retina. Two 4-kb cDNA fragments generated by 5'-RACE (rapid amplification of cDNA ends) and 3'-RACE were obtained using a long template PCR-based RACE technique. DNA sequencing revealed a single long open reading frame (ORF) encoding a predicted protein of 1239 amino acids, containing multiple motifs: a typical signal sequence of 20 amino acids at the NH2-terminus, a long extracellular domain with multiple potential glycosylation sites, a 31-amino-acid transmembrane domain near the COOH-terminus and a 109-amino-acid cytoplasmic tail. There are also two domains similar, but not identical, to EGF-like (epidermal growth factor-like) domains located just upstream of the transmembrane domain. These features suggest that this gene may encode a glycoprotein involved in cell adhesion, growth, and differentiation of pineal and retinal photoreceptor cells.

The murine DUB-1 gene is specifically induced by the betac subunit of interleukin-3 receptor

Cytokines regulate cell growth and differentiation by inducing the expression of specific target genes. We have recently isolated a cytokine-inducible, immediate-early cDNA, DUB-1, that encodes a deubiquitinating enzyme. The DUB-1 mRNA was specifically induced by the receptors for interleukin-3, granulocyte-macrophage colony-stimulating factor, and interleukin-5, suggesting a role for the beta common (betac subunit known to be shared by these receptors. In order to identify the mechanism of cytokine induction, we isolated a murine genomic clone for DUB-1 containing a functional promoter region. The DUB-1 gene contains two exons, and the nucleotide sequence of its coding region is identical to the sequence of DUB-1 cDNA. Various regions of the 5' flanking region of the DUB-1 gene were assayed for cytokine-inducible activity. An enhancer region that retains the beta c-specific inducible activity of the DUB-1 gene was identified. Enhancer activity was localized to a 112-bp fragment located 1.4 kb upstream from the ATG start codon. Gel mobility shift assays revealed two specific protein complexes that bound to this minimal enhancer region. One complex was induced by betac signaling, while the other was noninducible. Finally, the membrane-proximal region of human betac was required for DUB-1 induction. In conclusion, DUB-1 is the first example of an immediate-early gene that is induced by a specific subunit of a cytokine receptor. Further analysis of the DUB-1 enhancer element may reveal specific determinants of a betac-specific signaling pathway.

Anti-cancer drug characterisation using a human cell line panel representing defined types of drug resistance

Differential drug response in a human cell line panel representing defined types of cytotoxic drug resistance was measured using the non-clonogenic fluorometric microculture cytotoxicity assay (FMCA). In total 37 drugs were analysed; eight topoisomerase II inhibitors, eight anti-metabolites, eight alkylating agents, eight tubulin-active agents and five compounds with other or unknown mechanisms of action, including one topoisomerase I inhibitor. Correlation analysis of log IC50 values obtained from the panel showed a high degree of similarity among the drugs with a similar mechanism of action. The mean percentage of mechanistically similar drugs included among the ten highest correlations, when each drug was compared with the remaining data set, was 100%, 92%, 88% and 52% for the topoisomerase II inhibitors, alkylators, tubulinactive agents and anti-metabolites respectively. Classification of drugs into the four categories representing different mechanisms of action using a probabilistic neural network (PNN) analysis resulted in 29 (91%) correct predictions. The results indicate the feasibility of using a limited number of cell lines for prediction of mechanism of action of anti-cancer drugs. The present approach may be well suited for initial classification and evaluation of novel anti-cancer drugs and as a potential tool to guide lead compound optimisation.

Differential display PCR: a new age in nutrition investigation

Molecular biology has provided nutrition science with a powerful experimental tool for exploring the molecular basis of essential nutrient deficiencies. Differential display polymerase chain reaction has emerged as an instrument of unlimited potential for assessing the manner by which nutrients regulate cell functions.

Leishmania mexicana amazonensis: differential display analysis and cloning of mRNAs from attenuated and infective forms

The virulence of Leishmania mexicana is determined by the concerted action of several parasite molecules. These cells lose their infectivity to host macrophages after prolonged cultivation in axenic growth media. Both virulent and attenuated variants of the parasite cells were cloned. The differential display reverse transcription-polymerase chain reaction technique was employed to understand whether this natural attenuation of the parasite cells is accompanied by differential expression of selected genes in those cells. Twelve different dinucleotide-anchored oligo(dT) antisense primers were used to make cDNAs from poly(A)+ mRNAs isolated from a clonal population of virulent and avirulent cells following a protocol optimized for Leishmania mRNAs. Those cDNAs were subjected to amplifications using each of the three different arbitrary decanucleotide primers and the corresponding anchored oligo(dT) primer. This procedure revealed four virulent-specific cDNA probes and one avirulent-specific cDNA probe. Differential expressions of these genes were confirmed by northern hybridization using the cloned cDNA probes. These results indicate that differential expression of genes may be the key in determining the molecular basis of leishmanial virulence.

A survey of the goat genome transcribed in the lactating mammary gland

To fulfill its primary function, which is to synthesize milk during the course of lactation, the mammary gland requires efficient transcriptional, translational, and secretory machineries involving multiple genes among which promising candidates underlying the genetic variation of milk production have to be found. With the aim of providing a first transcriptional profile of lactating mammary tissue, a non-normalized cDNA library has been constructed from the udder of a lactating goat. After having discarded cDNA clones encoding the major milk proteins the rapid characterization of genes expressed in this tissue, by automated partial cDNA sequencing, was used to analyze a total of 435 cDNA clones. Examination of the Expressed Sequence Tags (ESTs) for similarities with sequence databases identified 234 cDNAs corresponding to 140 unique genes or proteins. Eighty-three clones, not similar to any current database entries, representing 77 novel sequences unrelated to previously described genes, were thus identified. Tissue specificity and relative abundance of 18 of these 77 unidentified clones were examined by dot blot and RT-PCR experiments. Sequence data were subsequently used to assign six genes of unknown localization in the bovine genome, to synteny groups by use of bovine-hamster cell hybrids and PCR.

Enhanced expression of macrophage migration inhibitory factor in prostatic adenocarcinoma metastases

OBJECTIVES

Determining the genetic changes associated with the development of metastatic prostate cancer is of utmost importance in patient prognosis and therapy. Our goal is to identify genes whose enhanced expression is associated with metastatic prostate cancer.

METHODS

Total ribonucleic acid was isolated from prostatic tissue exhibiting no histologic evidence of carcinoma and from a prostatic adenocarcinoma lymph node metastasis. The differential display polymerase chain reaction (DD-PCR) technique was used to isolate genes that exhibited increased expression in the metastatic tissue sample. Isolated PCR products were cloned, sequenced, and identified by screening complementary deoxyribonucleic acid (cDNA) databases.

RESULTS

Using DD-PCR, we identified three cDNA clones that exhibit enhanced expression in metastatic prostatic tissue. Two of these cDNA clones have not been identified because they show no homology to known database sequences. The third cDNA is 166 base pairs in length and exhibits 93% homology to nucleotides 662 to 828 of human macrophage migration inhibitory factor (MIF). Slot blot analysis using RNA from various prostate-derived sources suggests that increased expression of MIF is associated with metastatic prostate cancer.

CONCLUSIONS

These results show that the DD-PCR technique is applicable for the identification and cloning of human genes that exhibit enhanced expression in prostate cancer metastases. These results indicate the possibility that MIF production by prostate cancer cells plays a role in the development of metastases. The enhanced expression of MIF by prostate cancer cells may be a potential prognostic marker for metastatic prostate cancer.

Induction of gene expression in Escherichia coli after pilus-mediated adherence

The induction of cascades of virulence factors after contact between bacteria and host cells was investigated. P-pili mediate the binding of uropathogenic Escherichia coli to its host cell receptor. After P-pili binding there was transcriptional activation of a sensor-regulator protein that is essential for the bacterial iron-starvation response. An insertion mutation of the sensor-regulator gene eliminated the ability of uropathogenic E. coli to produce siderophores and their iron-regulated membrane receptors, thereby abolishing their ability to grow in urine. These results suggest that P-pilus-mediated attachment may be an important part of the sensor-regulatory process involved in uropathogenic E. coli urinary tract infection.

Activation of the human homologue of the Drosophila sina gene in apoptosis and tumor suppression

Developmentally regulated genes in Drosophila, which are conserved through evolution, are potential candidates for key functions in biological processes such as cell cycle, programmed cell death, and cancer. We report cloning and characterization of the human homologue of the Drosophila seven in absentia gene (HUMSIAH), which codes for a 282 amino acids putative zinc finger protein. HUMSIAH is localized on human chromosome 16q12-q13. This gene is activated during the physiological program of cell death in the intestinal epithelium. Moreover, human cancer-derived cells selected for suppression of their tumorigenic phenotype exhibit constitutively elevated levels of HUMSIAH mRNA. A similar pattern of expression is also displayed by the p21waf1. These results suggest that mammalian seven in absentia gene, which is a target for activation by p53, may play a role in apoptosis and tumor suppression.

The interaction of agouti signal protein and melanocyte stimulating hormone to regulate melanin formation in mammals

Important regulatory controls of melanogenesis that operate at the subcellular level to modulate the structural and/or the functional nature of the melanins and melanin granules produced in melanocytes are reviewed. Melanocyte stimulating hormone and agouti signal protein have antagonistic roles and possibly opposing mechanisms of action in the melanocyte. In the mouse, melanocyte stimulating hormone promotes melanogenic enzyme function and elicits increases in the amount of eumelanins produced, while agouti signal protein reduces total melanin production and elicits the synthesis of pheomelanin rather than eumelanin. We are now beginning to understand the complex controls involved in regulating this switch at the molecular and biochemical levels. The quality and quantity of melanins produced by melanocytes have important physiological consequences for melanocyte function and undoubtedly play important roles in the various functions of the melanins per se, including hair and skin coloration and photoprotection.

2D-PAGE examination of mRNA populations from Penicillium freii mutants deficient in xanthomegnin biosynthesis

Penicillium freii (Lund and Frisvad 1994) mutants deficient in the synthesis of xanthomegnin were isolated. In vitro translated mRNA populations from selected radiation induced mutants and naturally occurring P. freii strains not able to produce xanthomegnin were examined by 2-dimensional polyacrylamide gel electrophoresis (2D-PAGE). Specific translation products were absent in mutants and natural isolates unable to produce xanthomegnin metabolites. One mutant (TSM 73) did not produce several of these translation products, indicating that a mutation in a regulatory gene involved in xanthomegnin production had occurred.

Identification of an immediate-early salicylic acid-inducible tobacco gene and characterization of induction by other compounds

Tobacco genes that are induced in response to salicylic acid (SA) treatment with immediate-early kinetics were identified by differential mRNA display. Detailed analysis of IS10a, one cDNA clone identified by this method, revealed induction within 30 min of treatment, with a peak of expression at 3 h, that decayed rapidly thereafter. Treatment with the protein synthesis inhibitor, cycloheximide (CHX), also caused induction of IS10a mRNA to comparable levels, but the IS10a mRNA continued to accumulate after 3 h of induction. In combination, CHX and SA led to a superinduction of IS10a mRNA levels that was also sustained. Half-maximal induction was evident at ca. 100-150 microM SA. In addition to SA, induction of IS10a occurred to varying degrees upon treatment with acetylsalicylic acid, benzoic acid, 2,4-dichlorophenoxyacetic acid, methyl jasmonate, and hydrogen peroxide, whereas treatment with other compounds had no effect. The proteins encoded by IS10a and a second highly homologous cDNA show sequence similarity to UDP-glucose: flavonoid glucosyltransferases.

The use of differential display-PCR to isolate and characterize a Legionella pneumophila locus induced during the intracellular infection of macrophages

The differential display (DD)-PCR technique has been modified to identify prokaryotic cDNA fragments that are differentially induced by facultative intracellular bacteria in response to the intracellular environment of eukaryotic cells. Several DD-PCR fragments identified from the intracellular bacterium Legionella pneumophila were induced at 4 h post-infection of the U937 macrophage-like cells. From these, a 700 bp fragment was cloned and sequenced. Neither the DNA sequence nor the predicted protein sequence from the open reading frame has similarity to other sequences in genetic databases. Transcription of the chromosomal locus containing the 700 bp fragment (eml, for early stage macrophage-induced locus) was induced by intracellular bacteria during the first few hours post-infection of macrophages but the expression was downregulated by 12 h post-infection. Transcription of eml was not growth phase-related in vitro, and was not affected by in vitro stress stimuli. A 3.7 kb EcoRI genomic fragment containing the 700 bp DD-PCR product was cloned. Six mini-Tn 10 insertions in the 3.7 kb EcoRI fragment were recombined into the L. pneumophila chromosome. Compared to the wild-type strain, five of the eml isogenic mutants had a similar phenotype of reduced cytopathicity to the U937 cells, showed a 100-fold increase in killing by macrophages during the first 5 h of the intracellular infection, and showed a 100-fold increase in killing during the first 24h of infection of the amoeba Hartmanella vermiformis. The 6th mutant had a phenotype indistinguishable from the wild-type strain. The cytopathicity defect of the mutants to the U937 cells was restored to wild-type levels by complementation of the mutants with a plasmid containing the 3.7 kb EcoRI fragment. These data showed that the 3.7 kb fragment containing eml is a novel L. pneumophila locus whose expression is uniquely induced by non-stress stimuli during early stages of the intracellular infection of phagocytic cells. Expression of this locus is required for survival of L. pneumophila within macrophages and within amoebae during early stages of the infection.

Cloning of human pancreatic islet large conductance Ca(2+)-activated K+ channel (hSlo) cDNAs: evidence for high levels of expression in pancreatic islets and identification of a flanking genetic marker

Insulin secretion from pancreatic beta cells is dependent on membrane potential changes that result from the concerted regulation of multiple ion channels. Among the distinct K+ channels known to be expressed in beta cells, large conductance Ca(2+)-activated K+ channels have been suggested to play an important role in stimulus-secretion coupling. In the course of a strategy to identify transcripts that are enriched in human pancreatic islet cells, we isolated a partial cDNA encoding a human large conductance Ca(2+)-activated K+ channel mRNA (hSlo). Northern analysis of mRNA showed that among a panel of human tissues hSlo is expressed at its highest levels in pancreatic islets. Screening of human insulinoma and islet cDNA libraries with the partial cDNA resulted in the isolation of 19 hSlo cDNAs. These comprised three splice variants: one shared the common underlying structure of previously reported Slo cDNAs, another variant encoded a novel 60-amino acid insertion in the putative Ca(2+)-sensing domain of hSlo, while the third group of clones had an alternate exon encoding eight amino acids in the predicted COOH-terminal end. Analysis of somatic-cell hybrids containing different portions of chromosome 10 indicated that hSlo maps to chromosome 10q22.2-q23.1. Furthermore, high resolution localization was obtained by analysis of genome-wide radiation hybrids and the CEPH "B" mega-YAC library, both of which identified for the first time a highly polymorphic genetic marker (D10S195) linked to hSlo. These studies provide tools with which to explore the physiological role of Ca(2+)-activated K+ channel proteins in pancreatic islets, and also to investigate the contribution of this locus to the inherited susceptibility to non-insulin-dependent diabetes mellitus.

Extensive alteration of fungal gene transcript accumulation and elevation of G-protein-regulated cAMP levels by a virulence-attenuating hypovirus

Persistent infection of the chestnut blight fungus Cryphonectria parasitica with the prototypic hypovirus CHVI-713 results in attenuation of fungal virulence (hypo-virulence) and reduced accumulation of the GTP-binding (G) protein a subunit CPG-1. Transgenic cosuppression of CPG-1 accumulation in the absence of virus infection also confers hypovirulence. We now report the use of mRNA differential display to examine the extent to which virus infection alters fungal gene transcript accumulation and to assess the degree to which modification of CPG-1 signal transduction contributes to this alteration. More than 400 PCR products were identified that either increased (296 products) or decreased (127 products) in abundance as a result of virus infection. Significantly, 65% of these products exhibited similar changes as a result of CPG-1 cosuppression in the absence of virus infection. We also report that both virus infection and CPG-1 cosuppression elevate cAMP levels 3- to 5-fold. Additionally, it was possible to mimic the effect of virus infection and CPG-1 cosuppression on transcript accumulation for representative fungal genes by drug-induced elevation of cAMP levels. These results strengthen and extend previous indications that hypovirus infection causes a significant and persistent alteration of fungal gene expression/transcript accumulation. They further show that this alteration is primarily mediated through modification of the CPG-1 signaling pathway and suggest that, similar to mammalian Gi alpha subunits, CPG-1 functions as a negative modulator of adenylyl cyclase. Finally, these results suggest a role for G-protein-regulated cAMP accumulation in hypovirus-mediated alteration of fungal gene expression.

APEG-1, a novel gene preferentially expressed in aortic smooth muscle cells, is down-regulated by vascular injury

Despite the importance of phenotypic alterations in arterial smooth muscle cells (ASMC) during the pathogenesis of arteriosclerosis, little is known about genes that define differentiated ASMC. Using differential mRNA display, we isolated a novel gene preferentially expressed in the rat aorta and termed this gene APEG-1. The cDNA of rat APEG-1 contained an open reading frame encoding 113 amino acids, which would predict a basic protein of 12.7 kDa. The amino acid sequence of rat APEG-1 was highly conserved among human and mouse homologues (97 and 98%, respectively). Using an APEG-1 fusion protein containing an N-terminal c-Myc tag, we identified APEG-1 as a nuclear protein. By in situ hybridization, APEG-1 mRNA was expressed in rat ASMC. Although APEG-1 was expressed highly in differentiated ASMC in vivo, its expression was quickly down-regulated and disappeared in dedifferentiated ASMC in culture. In vivo, APEG-1 mRNA levels decreased by more than 80% in response to vascular injury as ASMC changed from a quiescent to a proliferative phenotype. Taken together, these data indicate that APEG-1 is a novel marker for differentiated ASMC and may have a role in regulating growth and differentiation of this cell type.

Activation of the gene encoding decay accelerating factor following nerve growth factor treatment of sensory neurons is mediated by promoter sequences within 206 bases of the transcriptional start site

Using two independent differential screening procedures designed to identify novel mRNAs induced by nerve growth factor (NGF) treatment of adult dorsal root ganglion (DRG) neurons, we have isolated cDNA clones derived from the gene encoding decay accelerating factor (DAF). Hybridization analysis and semi-quantitative polymerase chain reaction confirmed that the DAF mRNA was indeed induced in NGF-treated adult DRG neurons. Moreover, the DAF gene promoter is NGF inducible (approximately two- to threefold) when transfected into DRG neurons, and this effect is primarily dependent on sequences between -206 and -77 relative to the transcriptional start site. Hence, the DAF gene constitutes a novel NGF-inducible gene whose mRNA is elevated in response to NGF treatment of DRG neurons. The potential significance of this effect is discussed in terms of the role of NGF in modulating the transcriptional activity and function of adult DRG neurons.

Role of prostatic basal cells in the regulation and suppression of human prostate cancer cells

Cytokeratin expression in normal and malignant prostatic tissue indicates a loss of basal epithelial cells in cancer. We investigated the ability of basal-like prostatic epithelial cells to inhibit the growth of prostatic cancer cells. Human prostate LNCaP cells were grown in medium with or without 10 nM dihydrotestosterone (DHT) on plastic culture dishes or on extracellular matrix derived from basal-like epithelial cells (primary cultures derived from normal peripheral zone of the prostate) that were grown with or without 10 nM DHT. Colorimetric 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assays were used to assess the growth of LNCaP cells. On plastic dishes, growth of LNCaP cells was increased 5-10% by the presence of DHT in the medium. On matrix derived from basal-like cells that were grown in the absence of DHT, growth of LNCaP cells with or without DHT was similar to that on plastic. However, on matrix derived from basal-like cells that were grown with DHT, growth of LNCaP cells was suppressed when compared to all other culture conditions (P < 0.01). To determine whether basal-like cells could alter the function of LNCaP cells, we measured prostate-specific antigen (PSA) mRNA expression with the use of comparative RT-PCR. We found a significant decrease in the mature PSA transcript in cells grown on matrix derived from basal-like cells that were grown with DHT. The expression of PSA transcript was not altered in LNCaP cells that were grown on matrix derived from basal-like cells that were grown in the absence of DHT. Furthermore, using differential display of mRNA, we demonstrated that there were induction and suppression of multiple unique transcripts in the LNCaP cells when grown on the various culture conditions. To determine a possible mechanism for these observations. We used a dot blot immunoassay for several known inhibitory factors. We determined that DHT can induce the basal-like cells to secrete transforming growth factor-beta (TGF-beta 1), and that TGF-beta 1 can inhibit the proliferation of LNCaP cells in a dose dependent manner. We conclude that basal-like epithelial cells, in the presence of DHT, secrete an extracellular matrix o matrix associated factor(s), e.g. TGF-beta 1, that suppresses proliferation and function of prostate cancer cells. Our data suggest that the disappearance of the basal cell layer may be a prerequisite for the progression of prostatic neoplasia.

Isolation of genes differentially expressed in human primary myoblasts and embryonal rhabdomyosarcoma

Using a subtractive hybridization method, we have cloned 48 cDNAs which are expressed in human primary myoblasts but down-regulated in the embryonal-rhabdomyosarcoma (RMS) cell line RD. Twenty-nine sequences could be identified as coding for previously known gene products, while 19 encode unknown proteins. Twelve clones coding for known proteins that were highly down-regulated in the RD cells were chosen for further analysis on Northern blots containing additional normal and RMS cells. The expression pattern of TGF-beta-induced gene product-3 (beta(ig)H3), inhibitory G-protein alpha sub-unit (G(alpha)i2), osteoblast-specific factor-2 (OSF-2), 22-kDa smooth-muscle protein (SM22), clone A3351 (homologous to mouse talin), testican, thrombospondin-1 and thrombospondin-2 suggests involvement of these proteins in the genesis of the neoplastic phenotype. Among the clones with unknown sequence, several are identical or homologous to expressed sequence tags or known cDNAs, such as integrins or laminin. These results suggest that several isolated clones might have an important role in the determination or maintenance of the normal phenotype, and thus their loss is possibly involved in the progression of malignancy.

Differential display of intestinal mRNAs regulated by dietary zinc

Regulation of gene expression by zinc is well established, especially through the metal response elements of the metallothionein genes; however, most other aspects of the functions of zinc in gene expression remain unknown. We have looked for intestinal mRNAs that are regulated by dietary zinc status. Using the reverse transcriptase-PCR method of mRNA differential display, we compared intestinal mRNA from rats that were maintained for 18 days in one of three dietary groups: zinc-deficient, zinc-adequate, and pair-fed zinc-adequate. At the end of this period, total RNA was prepared from the intestine and analyzed by mRNA differential display. Under these conditions, only differentially displayed cDNA bands that varied in the zinc-deficient group, relative to the zinc-adequate groups, were selected. Utilizing two anchored oligo-dT3' PCR primers and a total of 27 arbitrary decamers as 5' PCR primers, our results yielded 47 differentially displayed cDNA bands from intestinal RNA. Thirty were increased in zinc deficiency, and 17 were decreased. Nineteen bands were subcloned and sequenced. Eleven of these were detectable on Northern blots, of which four were confirmed as regulated. Three of these have homology to known genes: cholecystokinin, uroguanylin, and ubiquinone oxidoreductase. The fourth is a novel sequence as it has no significant homology in GenBank. The remainder of those cloned included novel sequences, as well as matches to reported expressed sequence tags, and functionally identified genes. Further characterization of the regulated sequences identified here will show whether they are primary or secondary effects of zinc deficiency.

Isolation of differentially expressed cDNAs during ferret tracheal development: application of differential display PCR

The technique of differential display polymerase chain reaction (DD-PCR) was used to identify cDNA sequences, which are temporally expressed during ferret tracheal airway development. Such differentially expressed cDNAs may ultimately prove to be useful markers in elucidating mechanisms of epithelial differentiation and submucosal gland development in the airway. Using two sets of oligonucleotide primers 15 differentially amplified cDNAs were isolated by comparative reverse transcriptase (RT) PCR of 6-h and 3-day postnatal tracheal poly-A mRNA. In situ hybridization was used to assess the reliability of this method and confirm the differential mRNA expression patterns of cloned cDNAs. Results of in situ hybridization analysis demonstrated that 10 of the 15 cDNA sequences gave a temporally regulated pattern of expression, which was concordant with that of the differential display. Furthermore, sequence analysis of the 15 isolated cDNAs revealed that the majority of clones were amplified from two inverted decamer primers. These findings demonstrate the lack of poly-T priming in the differential display reaction, which suggests that this method may yield substantially more information regarding the coding sequence of cloned genes. In support of this observation, 6 of the 15 cDNA sequences contained one complete open reading frame. Although the majority of cDNAs demonstrated no homology to sequence data bases at the DNA or amino acid level, clone FT-4, which demonstrated a differential expression pattern limited to 3-day tracheal time points, was composed of a 10-amino acid repeat domain that was structurally similar to neuropeptide anthoRFamide and barley D hordein seed protein. A second interesting clone, FT-3, demonstrated an infrequent pattern of expression within a subset of epithelial cells limited to early developmental time points (6 h) and was dramatically reduced by 3 days postnatally. Several additional clones with no homologies to previously cloned genes demonstrated expression patterns that were also temporally regulated throughout tracheal development. Although the function of these temporally regulated genes has not been determined, these genes may ultimately prove to be useful markers of cellular differentiation during tracheal development.

Genetic mechanisms of estrogen-independence in breast cancer

Endocrine therapy is effective in the treatment of breast cancer. Adjuvant treatment with tamoxifen reduces tumor recurrence and achieves increased survival. In metastatic disease, tamoxifen treatment accomplishes objective responses in +/- 50% of the patients with estrogen receptor-positive primary tumors. However, the response duration is limited due to the inevitable development of metastases resistant to tamoxifen. The mechanisms leading to tamoxifen resistance are largely unknown. We have set out to identify genetic pathways in the tumor cells causing failure of tamoxifen therapy. We selected an estrogen-dependent human breast cancer cell line (ZR-75-1) and demonstrated that genetic and epigenetic alterations can change the hormone-response phenotype of these cells. Subsequently, we applied insertional mutagenesis with defective retroviruses to these ZR-75-1 breast cancer cells. Integration of a retrovirus in the cellular DNA alters the genome structure and may modify the expression of genes in its surroundings. As a result of the altered gene expression, the biological phenotype of the infected cell may be changed. The infected ZR-75-1 cells were subjected to tamoxifen selection and a panel of tamoxifen-resistant cell lines has been established. Screening for a common integration site for the retrovirus has provided, so far, compelling evidence for the involvement of at least one genetic locus (BCAR 1) in breast cancer antiestrogen resistance in vitro.

Fungal virulence genes as targets for antifungal chemotherapy

Fungal virulence genes have now met the age of molecular pathogenesis. The definition of virulence genes needs to be broad so that it encompasses the focus on molecular antifungal targets and vaccine epitopes. However, in the broad but simple definition of a virulence gene, there will be many complex genetic and host interactions which investigators will need to carefully define. Nevertheless, with the increasing numbers of serious fungal infections produced by old and newly reported organisms, the paucity of present antifungal drugs, and the likelihood of increasing drug resistance, the need for investigations into understanding fungal virulence at the molecular level has never been more important.

Identification of genes expressed after noise exposure in the chick basilar papilla

We used differential display of mRNA, a method based on reverse transcriptase-PCR, to identify genes whose expression increases in response to acoustic trauma in the chick basilar papilla. Identifying these genes would provide insight into processes involved in repair of the damaged epithelium or in hair cell regeneration. We compared mRNA from the basilar papilla of normal chicks, from chicks exposed to an octave band noise (center frequency: 1.5 kHz) presented at 118 dB for 6 h, and from chicks exposed to noise and allowed to recover for 2 days. Thus far, we have identified 70 bands that appear to be differentially displayed on DNA sequencing gels; approximately 40 of these bands have been subcloned and sequenced. DNA sequences were compared with sequences in the GenBank database to identify genes with significant (70-85%) sequence identity to known genes. Chick cDNAs identified included: the parathyroid hormone-related protein, an immediate early gene; the delta-subunit of the neuronal-specific Ca2+/calmodulin-regulated protein kinase II; and the GTP-binding protein CDC42, a member of the ras superfamily of G proteins. A fourth cDNA had 84% sequence identity to an uncharacterized human cDNA (expressed sequence tag), indicating that this is a novel gene. Slot-blot hybridization analysis of these cDNAs probed with labeled DNA generated from mRNA from each experimental group indicated higher levels of mRNA for each of these four genes after noise exposure. These results indicate the potential involvement of both Ca2+/calmodulin-mediated signaling and GTPase cascades in the response to noise damage and during hair cell regeneration in the chick basilar papilla.

Deficient expression in multiple sclerosis of the inhibitory transcription factor Sp3 in mononuclear blood cells

To evaluate differential gene expression in multiple sclerosis (MS) patients and control subjects, we used differential display to screen for messenger RNAs that are differentially expressed in peripheral blood mononuclear cells from monozygotic twins who are discordant for MS. We identified a 232-bp complementary DNA fragment, present only in material from the normal twin, that exhibited 100% identity with the inhibitory transcription factor Sp3. Oligonucleotide primers corresponding to Sp3 messenger RNA sequences amplified complementary DNA of appropriate size from 83% of control subjects but from only 21% of MS patients (p < 0.001). These results suggest that Sp3 gene transcription is suppressed in peripheral blood mononuclear cells from most MS patients and that other genes whose expression is normally suppressed by Sp3 in immune cells may consequently be overexpressed.

Selective amplification of protein-coding regions of large sets of genes using statistically designed primer sets

We describe a novel approach to design a set of primers selective for large groups of genes. This method is based on the distribution frequency of all nucleotide combinations (octa- to decanucleotides), and the combined ability of primer pairs, based on these oligonucleotides, to detect genes. By analyzing 1000 human mRNAs, we found that a surprisingly small subset of octanucleotides is shared by a high proportion of human protein-coding region sense strands. By computer simulation of polymerase chain reactions, a set based on only 30 primers was able to detect approximately 75% of known (and presumably unknown) human protein-coding regions. To validate the method and provide experimental support for the feasibility of the more ambitious goal of targeting human protein-coding regions, we sought to apply the technique to a large protein family: G-protein coupled receptors (GPCRs). Our results indicate that there is sufficient low level homology among human coding regions to allow design of a limited set of primer pairs that can selectively target coding regions in general, as well as genomic subsets (e.g., GPCRs). The approach should be generally applicable to human coding regions, and thus provide an efficient method for analyzing much of the transcriptionally active human genome.

Advanced mRNA differential display: isolation of a new differentially regulated myosin heavy chain-encoding gene in amphibian limb regeneration

In an effort to make mRNA differential display more amenable as a molecular screen, we have optimized the technology for the isotopic and non-isotopic detection of differentially regulated mRNAs. The number of amplification rounds in the displays was significantly reduced, resulting in the semi-quantitative detection of expression patterns of both low- and high-abundance transcripts. Moreover, we extended the method beyond the display of mRNAs by introducing a direct sequencing approach for the fast molecular analysis of isolated cDNAs. Applying this improved technique to the regenerating amphibian limb system, we have identified cDNA PCR products with a temporal difference in expression. This differential regulation was confirmed by Northern analysis, and DNA sequencing uncovered a novel newt differentiation-specific transcript encoding a skeletal myosin heavy chain (MHC).

Evidence for transcriptional modulation but not acid phosphatase expression during programmed cell death in the colonial tunicate Botryllus schlosseri

Botryllus schlosseri is a clonally modular ascidian in which asexually derived adults (zooids) exhibit developmental synchrony. At the conclusion of the blastogenic (asexual) cycle every 5 days at 21 degrees C, all zooids within a colony die simultaneously in 24 hours and are replaced by a new asexual generation of zooids. This cyclical process, called takeover, involves the selective destruction of the zooid's visceral tissues which include the pharynx, esophagus, stomach, intestine, endostyle, neural complex and heart, whereas bud tissues and mesenchymal components (muscle and blood cells) remain unaffected. Ultrastructural analysis indicates that the most prevalent form of cell death occurs by apoptosis, although necrotic changes are also observed in several tissues (i.e., stomach and intestine). Blood-derived macrophages and neighboring cells subsequently engulf visceral tissues, reducing the zooid to the size of a small vesicle. Here, we have tested the possibility that acid phosphatase, a hydrolase whose presence is associated with cell death in several invertebrate systems, could account for some of the regressive changes observed during takeover. Our observations indicate that acid phosphatase (AP) activity was selectively localized in the gut of parent zooids during the growth phase of the cycle, with the stomach exhibiting the most intense histochemical staining on tissue sections. As zooid regression progressed during takeover, stomach AP staining gradually disappeared. Other visceral tissues never became AP-positive. Therefore, this hydrolase appears to play a minimal role in zooid death. In order to characterize genes whose expression pattern was selectively altered during takeover, we have carried out differential mRNA display analysis. We report on two genes, 790.3 and 790.4, that are down- and upregulated, respectively, during this process. Collectively, these findings indicate that the takeover phase of blastogenesis in Botryllus involves modulated gene expression.

Molecular cloning of a novel thyroid hormone-responsive gene, ZAKI-4, in human skin fibroblasts

Utilizing a method called "differential display of mRNAs by means of polymerase chain reaction", the cDNA fragment of a thyroid hormone-responsive gene ZAKI-4 was cloned from cultured human skin fibroblasts. Northern blot analysis revealed that there were two ZAKI-4 mRNA species (3.4 and 1.4 kilobases (kb)), and they were up-regulated by a physiological concentration of triiodothyronine (T3). This T3 effect was abolished by the treatment with cycloheximide, indicating the possibility that gene ZAKI-4 is regulated by T3 in an indirect fashion, through an intermediate product of T3, rather directly by T3 itself. No effect of T3 on ZAKI-4 mRNA stability suggested that T3 induces the mRNA at the transcriptional level. Rapid amplification of cDNA ends confirmed the presence of two mRNA species. ZAKI-4 mRNA was detected in heart, brain, liver, and skeletal muscle but not in placenta, lung, kidney and pancreas. In skin fibroblasts and skeletal muscle, 3.4-kb mRNA was the major species, whereas 1.4-kb mRNA was dominant in heart, brain, and liver. The sequence analysis suggested that the two mRNA species arise from alternative polyadenylation and code a single protein of 192 amino acids. No homologous protein sequence was found in a data base. Elucidation of the function of ZAKI-4 gene product will provide new insights into an important role of T3 in various organs.