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

Ras activation of genes: Mob-1 as a model

The ras oncogenes function by indirectly controlling expression of a subset of yet-undefined genes that are crucial for cell growth and differentiation. In a differential display strategy, numerous genes were identified on the basis of their differential expression in rat embryo fibroblasts transformed by the cooperation of mutant Ha-ras and p53 genes. We demonstrate here that one such gene, designated mob-1, is a downstream target of the Ras signaling pathway. The 417-bp mob-1 promoter, which contains dual NF-kappa B and AP-1 binding sites, confers the Ras inducibility. Oncogenic Ras as well as serum growth factors that activate endogenous Ras can induce mob-1 expression, but with a fundamental difference in that the oncogenic induction is constitutive whereas the serum induction is transient. mob-1 encodes a small secretory protein with a high degree of homology to IP-10, a member of a proinflammatory cytokine family. These findings link chronic inflammatory response to constitutive ras activation and tumorigenesis. Mob-1 may serve as a secreted marker for oncogenic Ha-ras mutations.

Analysis of gene expression by tissue and developmental stage

High-throughput sequencing of cDNAs from multiple tissue- and stage-specific libraries is an efficient method for characterizing gene expression by tissue and developmental stage. When combined with functional information derived from the systematic study of transcription factors, signal transducers, and other regulatory molecules in model systems, data from expressed sequence tag projects provide an increasingly detailed picture of gene expression and its regulation. Understanding this picture will require the development of highly sophisticated databases to organize and correlate these data.

Genetic basis of susceptibility to melanoma

The search for candidate genes involved in the genesis of common cancers has traditionally been hampered by ambiguities in the process of determining by reliable, clinical criteria which persons harbor the genetic lesion that confers malignant susceptibility. In the case of cutaneous melanoma, the existence of genetic susceptibility has long been evident from its tendency to cluster in families, but it has been unclear until recently whether the genetic basis of familial melanoma derives from the concerted interaction of multiple genes or from a major locus with properties of a tumor suppressor gene. The original strategy used to circumvent difficulties in identifying those who harbor the genetic defect exploited a proposed melanoma precursor lesion, the dysplastic nevus, as the phenotypic marker from which the presence of the melanoma-associated genotype was inferred. That strategy in genetic linkage studies provided the first indication of a major gene for melanoma and assigned the locus to the short arm of chromosome 1. In part because the criteria for the dysplastic nevus have been neither well-defined nor generally agreed upon, multiple independent attempts to confirm the assignment of a gene to that location have failed. The probable map position of a major gene became clear when the most frequently deleted region of the human genome in melanoma tumors was localized to chromosome 9p. The significance of this assignment was established when genetic linkage studies of multiple melanoma kindreds subsequently evaluated the correlated inheritance between melanoma gene carriers, as assigned by a history of melanoma, and molecular markers for DNA polymorphisms near the 9p candidate region; this analysis provided strong statistical evidence of linkage to a melanoma susceptibility locus. Once this candidate tumor suppressor gene) as well as other relevant suppressor loci that may exist is actually cloned and characterized, rapid advances can be expected in our understanding of the pathophysiologic basis for development of melanoma. This will provide opportunities for exploring the mechanisms underlying defects in the gene and the molecular consequences of its loss of function. It will then be possible to identify precisely those persons with a genetic risk for melanoma; as a result, surveillance efforts can be more appropriately focused than has heretofore been possible.

cDNA sequencing: a means of understanding cellular physiology

High-throughput automated sequencing has enabled researchers to examine large numbers of clones from a cDNA library as a measure of the steady-state levels of mRNA species. The past year has witnessed many new applications of this technique to allow the qualitative and quantitative comparison of the changes in transcript levels from multiple genes.

On the nature and differential distribution of mRNAs in hippocampal neurites: implications for neuronal functioning

Neurons are highly polarized cells with a mosaic of cytoplasmic and membrane proteins differentially distributed in axons, dendrites, and somata. In Drosophila and Xenopus, mRNA localization coupled with local translation is a powerful mechanism by which regionalized domains of surface or cytoplasmic proteins are generated. In neurons, there is substantial ultrastructural evidence positing the presence of protein synthetic machinery in neuronal processes, especially at or near postsynaptic sites. There are, however, remarkably few reports of mRNAs localized to these regions. We now present direct evidence that an unexpectedly large number of mRNAs, including members of the glutamate receptor family, second messenger system, and components of the translational control apparatus, are present in individual processes of hippocampal cells in culture.

A new class of retinoids with selective inhibition of AP-1 inhibits proliferation

Retinoids regulate many biological processes, including differentiation, morphogenesis and cell proliferation. They are also important therapeutic agents, but their clinical usefulness is limited because of side effects. Retinoid activities are mediated by specific nuclear receptors, the RARs and RXRs, which can induce transcriptional activation through specific DNA sites or by inhibiting the transcription factor AP-1 (refs 12-15), which usually mediates cell proliferation signals. Because the two types of receptor actions are mechanistically distinct, we investigated whether conformationally restricted retinoids, selective for each type of receptor action, could be identified. Here we describe a new class of retinoids that selectively inhibits AP-1 activity but does not activate transcription. These retinoids do not induce differentiation in F9 cells but inhibit effectively the proliferation of several tumour cell lines, and could thus serve as candidates for new retinoid therapeutic agents with reduced side effects.

Retinoic acid prevents downregulation of ras recision gene/lysyl oxidase early in adipocyte differentiation

Adipocyte differentiation of 3T3-L1 cells is a complex process which is inhibited by retinoic acid (RA). Since RA acts by nuclear receptors which directly regulate gene expression, we postulate that the primary targets of RA action in this system are genes which are regulated early in adipose conversion. In this study, we demonstrate the use of the differential display technique to search for early events in adipose commitment which are sensitive to RA. A mRNA was identified on the basis of its RA-dependent gene expression 24 h after initiation of a standard differentiation protocol. Molecular cloning of the cDNA revealed it to be identical to the ras recision gene (rrg), for lysyl oxidase. Indeed, two mRNAs identical to those recognized by lysyl oxidase probes were expressed in preadipocytes and tandemly repressed with 24 h of exposure to differentiation conditions. Lysyl oxidase activity was similarly reduced in the media of differentiated cells. RA completely blocked the differ-entiation-related reduction in rrg/lysyl oxidase gene expression, although RA had no independent stimulatory effect on rrg/lysyl oxidase expression in cells not exposed to differentiating conditions. Thus, differential display has been successfully used to identify rrg/lysyl oxidase as an early marker for adipose conversion that is responsive to RA.

Identification of differentially transcribed RNA and DNA helicase-related genes of Plasmodium falciparum

Chloroquine antimalarial action was assessed by the analysis of changes in gene expression. With this aim, Plasmodium falciparum cultures were submitted to chloroquine and to other stresses to determine which transcripts were specifically induced. P. falciparum in vitro control culture was compared to cultures where chloroquine was added and to cultures where serum was omitted, or where higher partial oxygen pressure was used, and, finally, at a temperature of 40 degrees C instead of 37 degrees C. Poly (A)+RNAs were reverse-transcribed and detected by the differential display technique. Two specific cDNAs were obtained and cloned, and a part of the genes was sequenced. The deduced protein, referred to as Pfhel-1, was related to a RNA helicase and was thought to be involved in protein translation control. The second deduced protein, called Pfhel-2, possessed consensus sequences of ATP-dependent helicase domains. Pfhel-2 may be involved either in mitotic control or in DNA repair. The possible roles of both helicase-related genes in chloroquine therapeutic activity are discussed.

Interactions among regulators of RNA abundance characterized using RNA fingerprinting by arbitrarily primed PCR

Using RNA fingerprinting by arbitrarily primed PCR it is possible to infer convergent transcript regulatory pathways from the coordinate behavior of subsets of anonymous transcripts without cloning any genes. The number of transcripts in each response category can be estimated. The same may be true for differential display. We demonstrate these claims by treating a cell line with two known modulators of RNA abundance, transforming growth factor-beta (TGF beta) and cycloheximide (CX), used together and alone. The responses of over 1700 anonymous transcripts were monitored under these three conditions and in an untreated control. Eight of the twenty-seven [3(3)] possible transcript response categories were observed among 86 differentially expressed transcripts. For example, CX stabilizes or induces as many as 2.7% of transcripts of which about one third do not accumulate when TGF beta is also present. This intersection may reflect CX stabilization or induction of an important class of RNAs that otherwise usually have short half-lives. We predict that RNAs in this class constitute the majority of transcripts targeted for rapid down regulation in response to TGF beta and perhaps most other natural transcriptional modulators.

Cholinotoxic effects on acetylcholinesterase gene expression are associated with brain-region specific alterations in G,C-rich transcripts

To study the mechanisms underlying cholinotoxic brain damage, we examined ethylcholine aziridinium (AF64A) effects on cholinesterase genes. In vitro, AF64A hardly affected cholinesterase activities yet inhibited transcription of the G,C-rich AChE DNA encoding acetylcholinesterase (AChE) more than the A,T-rich butyrylcholinesterase (BChE) DNA. In vivo, intracerebroventricular injection of 2 nmol of AF64A decreased AChE mRNA in striatum and septum by 3- and 25-fold by day 7, with no change in BChE mRNA or AChE activity. In contrast, hippocampal AChE mRNA increased 10-fold by day 7 and BChE mRNA and AChE activity decreased 2-fold. By day 60 post-treatment, both AChE mRNA and AChE levels returned to normal in all regions except hippocampus, where AChE activity and BChE mRNA were decreased by 2-fold. Moreover, differential PCR displays revealed persistent induction, specific to the hippocampus of treated rats, of several unidentified G,C-rich transcripts, suggesting particular responsiveness of hippocampal G,C-rich genes to cholinotoxicity.

Cyclin G is a transcriptional target of the p53 tumor suppressor protein

Through a PCR-based differential screening method, cyclin G was identified as a novel transcriptional target of the p53 tumor suppressor gene product. In both a mouse p53 temperature-sensitive leukemic cell line and mouse embryonic fibroblasts (MEF) after gamma-irradiation, cyclin G mRNA was rapidly induced. MEF from a p53-deficient mouse expressed cyclin G at a level > 10-fold lower than that from a wild-type mouse. Using a DNA binding assay, a specific p53 binding site was identified upstream from the cyclin G gene, which functioned as a p53-dependent cis-acting element in a transient transfection assay. These results suggest that cyclin G might participate in a p53-mediated pathway to prevent tumorigenesis.

Isolation of genomic DNA fragments corresponding to genes modulated in vivo by a transcription factor

A new methodology for the identification of genes modulated by transcription factors in vivo is described. Mouse genomic DNA fragments bound by the thyroid hormone receptor (T3R) were selected and amplified in vitro. Subsequent hybridisation with biotinylated cDNA allowed the selection of those DNA fragments containing binding sites for T3R that corresponded to transcribed DNA. Expression analysis of the corresponding genes showed that more than 80% are indeed modulated by thyroid hormones in vivo in the liver. Together with the presence of consensus binding sites for T3R this result suggests that the selected DNA fragments may contain T3R transcriptional regulatory elements. This method, extensive to other ligand-modulated transcription factors, might be useful to all transcription factors with slight modifications.

Calcium regulation of immediate-early response genes

A rise in intracellular Ca2+ concentration induces the transcription of a number of eukaryotic genes through transcription factors interacting with calcium response elements. Immediate-early response genes encode proteins that couple extracellular signals to phenotypic alterations by modulating the transcription rates of target genes. Since the activation of early response genes occurs within minutes, this class of genes has served as a paradigm for the understanding of the molecular mechanisms by which external signals are conveyed to the nucleus to induce changes in genetic programs. In this review, we outline the recent information which has been gained specifically on how the Ca2+ messenger system modulates early response gene expression. We also discuss some lines of research with the intent of linking closer Ca2+ homeostasis and gene expression studies which in the past have followed their own separate routes.

Differential expression of sgk mRNA, a member of the Ser/Thr protein kinase gene family, in rat brain after CNS injury

We cloned genes the expression of which were induced 3 days after cortical injury of rat brain by a differential display technique, and four novel and known sequences were isolated. Among these sequences, the sgk gene which was recently identified as a novel member of the serine/threonine protein kinase gene family, was selected for analysis of its expression patterns in rat brain by northern blotting and in situ hybridization, because hybridization signals were strong at the lesion sites. Expression of sgk mRNA was induced within 3 days after injury, and was maintained at a high level for at least 14 days. The cells which strongly expressed the sgk gene were in the deep layers of the cortex and in the corpus callosum. In situ hybridization analysis for sgk and myelin proteolipid protein mRNA using serial sections showed that the distribution of both signals was very similar at the damaged regions. Therefore, it is likely that the sgk transcript is expressed by oligodendrocytes after brain injury. Investigation of the developmental expression of the sgk gene showed that neurons in layers I and II of the cortex, lateroposterior and laterodorsal thalamic nucleus, and ventral posterolateral and posteromedial thalamic nucleus strongly expressed sgk mRNA at postnatal day 1 and day 7, but these neurons showed no expression in fetal or adult brain. These results suggest that the induction of sgk gene may be associated with a series of axonal regenerations after brain injury, and in addition, the sgk gene may also play important roles in the development of particular groups of neurons in the postnatal brain.

Characterization of three cloned cell lines from a N-nitrosobis(2-hydroxypropyl)amine-induced transplantable hamster pancreatic ductal adenocarcinoma

To investigate characteristics of pancreatic carcinoma growth behavior, the cloned cell lines, HPD1NR, HPD2NR, and HPD3NR, were established from a transplantable hamster ductal adenocarcinoma induced by N-nitrosobis(2-hydroxypropyl)amine (BHP). All three clones showed similar epithelial cell morphology and grew as sheets in culture with no differences in doubling times, ranging from 23-28 h. Mutation in the c-Ki-ras exon 1 was detected in common. The modal chromosome numbers were also found to be similar at 60, 62, and 60-62 in the less than tetraploid cells in the three clones. In contrast, a clear difference in frequencies of tetraploid or polyploid cells at 24.7, 22.5, and 75.5% in HPD1NR, HPD2NR, and HPD3NR, respectively, was evident. Tumorigenic potency evaluated by transplanting individual clones revealed HPD3NR to display pronouncedly less growth in syngeneic hamsters. The results suggest that increase in frequency of tetraploid or polyploid cells might be associated with a decreased in vivo growth potential of hamster pancreatic ductal adenocarcinomas, and suggest that these clones might become a valuable tool for understanding in vivo growth mechanisms of cancer cells.

Identification of genes expressed in premalignant breast disease by microscopy-directed cloning

Histopathologic study of human breast biopsy samples has identified specific lesions which are associated with a high risk of development of invasive breast cancer. Presumably, these lesions (collectively termed premalignant breast disease) represent the earliest recognizable morphologic expression of fundamental molecular events that lead to the development of invasive breast cancer. To study molecular events underlying premalignant breast disease, we have developed a method for isolating RNA from histologically identified lesions from frozen human breast tissue. This method specifically obtains mRNA from breast epithelial cells and has identified three genes which are differentially expressed in premalignant breast epithelial lesions. One gene identified by this method is overexpressed in four of five noncomedo ductal carcinoma in situ lesions and appears to be the human homologue of the gene encoding the M2 subunit of ribonucleotide reductase, an enzyme involved in DNA synthesis.

A rapid and simple PCR-based method for isolation of cDNAs from differentially expressed genes

Recently two techniques have been reported which use arbitrarily primed RT-PCR amplification of cDNA fragments from subsets of mRNAs to detect cDNA fragments from differentially expressed mRNAs. Here we report a simple and rapid PCR-based protocol to both detect and isolate cDNA fragments of up to 3000 base pairs from differentially expressed genes in two easy steps. To generate cDNAs from most mRNAs, the first step consisted of reverse transcription using a fully degenerated 6-mer oligonucleotide as primer. The second step consisted of PCR amplification of internal regions of the cDNAs with two or three longer primers with arbitrary but defined sequences. DNA fragments were easily displayed by agarose gel electrophoresis and then excised for direct use in cloning, sequencing, and Northern blot analysis. By repeating the PCR amplification (second step) on the same cDNA templates (first step) ten times with different sets of primers, over 170 discrete cDNA fragments were obtained from a single tissue. By combining the two-step procedure with 3'-RNA-anchored cDNA extension, additional DNA fragments can be generated from the same mRNA. The new procedure was used here to define 3600 bp of a new brain-specific mRNA.

Transgenic engineering of neuromuscular junctions in Xenopus laevis embryos transiently overexpressing key cholinergic proteins

To examine the role of key cholinergic proteins in the formation of neuromuscular junctions (NMJs), we expressed DNAs encoding the mouse muscle nicotinic acetylcholine receptor (nAChR) or human brain and muscle acetylcholinesterase (hAChE) in developing Xenopus laevis embryos. Acetylthiocholine hydrolysis and alpha-bungarotoxin binding in homogenates of transgenic embryos revealed transient overexpression of the respective proteins for at least 4 days postfertilization. Moreover, hAChE injection induced an approximately 2-fold increase in endogenous Xenopus nAChR. Electron microscopy coupled with cytochemical staining for AChE activity revealed that AChE-stained areas, which reached 0.17 microns2 in NMJs of control embryos raised at 21 degrees C, increased up to 0.53 and 0.60 microns2 in nAChR and hAChE transgenics, respectively. These increases coincided with the appearance of a class of large NMJs with average postsynaptic lengths up to 1.8-fold greater than controls. As much as 57% and 34% of the NMJs in animals transgenic for nAChR and hAChE, respectively, displayed AChE activity in nerve terminals in addition to muscle labeling, as compared with 10% nerve-labeled NMJs in control animals. Moreover, area, but not length values, were > 2-fold larger in hAChE-expressing NMJs labeled in their nerve terminals than in those labeled in muscle alone, reflecting a hAChE-induced increase in synaptic cleft width. These findings indicate that modulation of cholinergic neurotransmission in NMJs modifies the features of nerve-muscle connections.

Fluorescent differential display: arbitrarily primed RT-PCR fingerprinting on an automated DNA sequencer

We established robust, reliable protocols for 'Differential Display (DD),' an RNA fingerprinting method originally developed by Liang and Pardee [(1992) Science 257, 967-971] using RT-PCR with arbitrary primers. Our protocols are optimized so that reliable DD analysis can be performed on a fluorescent DNA sequencer to ensure high throughput as well as improved operational safety, compared with the original one using radioactive compounds. Such 'Fluorescent Differential Display (FDD)' techniques will accelerate the identification of differentially expressed as well as polymorphic transcripts to address various biological questions.

Identification and characterization of transcribed sequences on human chromosome 9q32-34

The gene responsible for the neuromuscular disease idiopathic torsion dystonia (DYT1) has recently been mapped to human chromosome 9q32-34. Our goal is to identify candidate genes for torsion dystonia as well as other neurologically important genes in this region. To accomplish this we have characterized the expression patterns of transcribed sequences identified within a collection of 3000 human 9q32-34-specific clones. Screening of this clone collection with cDNA probes from various brain and peripheral tissues resulted in the identification of 143 clones corresponding to 9q32-34-specific transcripts. Thirty three of these corresponded to transcripts expressed in a brain-specific manner and thus represent preferred candidates for the dystonia gene. None of these candidates were expressed specifically in the putative dystonia target tissue, basal ganglia. The 9q32-34 collection was screened with a subtracted probe enriched in striatal sequences using a directional tag PCR subtraction method. This resulted in the identification of several genes exhibiting preferential expression in the striatum as compared to cerebellum.

MAAP: a versatile and universal tool for genome analysis

Multiple arbitrary amplicon profiling (MAAP) uses one or more oligonucleotide primers (> or = 5 nt) of arbitrary sequence to initiate DNA amplification and generate characteristic fingerprints from anonymous genomes or DNA templates. MAAP markers can be used in general fingerprinting as well as in mapping applications, either directly or as sequence-characterized amplified regions (SCARs). MAAP profiles can be tailored in the number of monomorphic and/or polymorphic products. For example, multiple endonuclease digestion of template DNA or the use of mini-hairpin primers can enhance detection of polymorphic DNA. Comparison of the expected and actual number of amplification products produced with primers differing in length, sequence and GC content from templates of varying complexity reveal severe departures from theoretical formulations with interesting implications in primer-template interaction. Extensive primer-template mismatching can occur when using templates of low complexity or long primers. Primer annealing and extension appears directed by an 8 nt 3'-terminal primer domain, requires sites with perfect homology to the first 5-6 nt fom the 3' terminus, and involves direct physical interaction between amplicon annealing sites.

Antisense oligonucleotide inhibition of acetylcholinesterase gene expression induces progenitor cell expansion and suppresses hematopoietic apoptosis ex vivo

To examine the role of acetylcholinesterase (EC 3.1.1.7) in hematopoietic cell proliferation and differentiation, we administered a 15-mer phosphorothioate oligonucleotide, antisense to the corresponding ACHE gene (AS-ACHE), to primary mouse bone marrow cultures. Within 2 hr of AS-ACHE addition to the culture, ACHE mRNA levels dropped by approximately 90%, as compared with those in cells treated with the "sense" oligomer, S-ACHE. Four days after AS-ACHE treatment, ACHE mRNA increased to levels 10-fold higher than in S-ACHE cultures or in fresh bone marrow. At this later time point, differential PCR display revealed significant differences between cellular mRNA transcripts in bone marrow and those in AS-ACHE- or S-ACHE-treated cultures. These oligonucleotide-triggered effects underlay considerable alterations at the cellular level: AS-ACHE but not S-ACHE increased cell counts, reflecting enhanced proliferation. In the presence of erythropoietin it also enhanced colony counts, reflecting expansion of progenitors. AS-ACHE further suppressed apoptosis-related fragmentation of cellular DNA in the progeny cells, and it diverted hematopoiesis toward production of primitive blasts and macrophages in a dose-dependent manner promoted by erythropoietin. These findings suggest that the hematopoietic role of acetylcholinesterase, anticipated to be inverse to the observed antisense effects, is to reduce proliferation of the multipotent stem cells committed to erythropoiesis and megakaryocytopoiesis and macrophage production and to promote apoptosis in their progeny. Moreover, these findings may explain the tumorigenic association of perturbations in ACHE gene expression with leukemia.

Human serum-sensitive Trypanosoma brucei rhodesiense: a comparison with serologically identical human serum-resistant clones

Trypanosoma brucei rhodesiense clones, which are susceptible to lysis by normal human serum, were isolated from 3 different human serum-resistant clones originally derived from strain ETat 1.10. Serologically, these pairs of serum-sensitive and serum-resistant clones displayed the same variant surface glycoprotein (VSG) on their surface. Acquisition of human serum sensitivity correlated with susceptibility to lysis by human high density lipoprotein, a trypanocidal factor in normal human serum. Analysis of these paired populations by two-dimensional gel electrophoresis of whole trypanosomes and various subcellular fractions failed to reveal any differences in mobility of VSG and other proteins. Northern blot analysis of mRNAs from serum-sensitive and serum-resistant clones showed no differences when probed with a previously described resistance-specific probe. In addition, the ethanolamine membrane transport system and the overall membrane lipid fluidity did not reveal any detectable biochemical or biophysical differences in membrane properties. If resistance to lysis is indeed mediated by membrane changes at the enzymatic or structural level, the data presented suggest that the gene product(s) responsible for this change in human serum sensitivity may be present in very small quantities.

Identification and upregulation of galactose/N-acetylgalactosamine macrophage lectin in rat cardiac allografts with arteriosclerosis

Using differential mRNA display to uncover potential mediators associated with chronic rejection, we identified a cDNA fragment induced in Lewis to F344 rat cardiac allografts with arteriosclerosis but not Lewis syngrafts. The full-length cDNA (1.4 kb) isolated from a rat cardiac allograft cDNA library was 99% identical to galactose/N-acetylgalactosamine (Gal/GalNAc) macrophage lectin, a cell-surface receptor. This cDNA hybridized in Northern analysis with total RNA from eight cardiac allografts but not with host hearts, syngrafts, or other organs. There was a significant allograft-specific increase in transcript levels measured by reverse transcriptase PCR at days 7, 14, 28, and 75 in comparison with paired F344 host hearts (subject to same circulation but histologically normal), day-0 hearts, and syngrafts (P < 0.008, n = 4 at each time). Transcript levels in cardiac allografts were higher than those in paired host spleens (a major source of inflammatory cells) (P < 0.0001), indicating the localized nature of Gal/GalNAc lectin induction. By in situ hybridization and immunostaining, Gal/GalNAc lectin expression localized to a subset of inflammatory cells in cardiac allografts. These findings link Gal/GalNAc macrophage lectin to the chronic rejection process, as a possible mediator of macrophage infiltration.

Targeted RNA fingerprinting: the cloning of differentially-expressed cDNA fragments enriched for members of the zinc finger gene family

We have developed and applied a modification of an 'RNA Fingerprinting' protocol previously published by Welsh and McClelland (Nucleic Acids Research 19: 5275-5279 1991) such that cDNA fragments which are both differentially-expressed and enriched for members of a specific gene family can readily be identified. cDNA fragments were amplified with an arbitrary primer initially used in the reverse transcription reaction in combination with a member of a primer set which corresponded to a conserved region within a specific gene family. This technique was used to isolate cDNAs encoding a recently described protein kinase as well as an unknown gene that contained a zinc finger. Several other known genes that contained a zinc finger domain and that were differentially-expressed were also isolated.

Chronic cardiac rejection: identification of five upregulated genes in transplanted hearts by differential mRNA display

Transplant arteriosclerosis, the major manifestation of chronic rejection, develops after allogeneic (Lewis to F344) but not syngeneic (Lewis to Lewis) rat cardiac transplantation. To identify transcriptionally regulated mediators associated with chronic cardiac rejection, we adapted the differential mRNA display technique for in vivo transplant specimens. Gene transcript patterns in four allogeneic hearts showing early signs of chronic rejection were compared with those in two syngeneic hearts exposed to the same surgical procedure but histologically normal. Twelve differentially expressed cDNA bands were identified. We improved the probability of isolating one or more allograft-specific cDNAs from a single display band by first using recovered and reamplified PCR products as probes in RNA blot analysis. cDNA fragments cloned from individual bands were then used in a second RNA blot analysis, which allowed for the correlation of specific mRNA transcripts with cDNA clones. Five cDNA clones produced time-dependent, allograft-specific hybridization. Sequence analysis demonstrated that two of these cDNAs corresponded to unknown genes, whereas the other three represented known genes not previously associated with chronic rejection. The latter group included the macrophage lectin specific for galactose/N-acetylgalactosamine (a cell-surface receptor), the nuclear P1 gene (a homologue of a yeast replication protein), and a ubiquitin-like gene. Our application of the differential display technique allowed the direct identification of potential mediators under in vivo conditions that preserve the environment of the disease process--including infiltrating cell populations critical to the inflammatory response.

Identification of multiple genes in bovine retinal pericytes altered by exposure to elevated levels of glucose by using mRNA differential display

Loss of capillary pericytes, a characteristic finding in diabetic retinopathy, is strongly associated with hyperglycemia. The pathologic aberrations associated with diabetic retinopathy are localized primarily in the retinal capillaries and are only poorly reversed by subsequent euglycemic control. Since hyperglycemia significantly inhibits pericyte growth in culture, we investigated the regulation of gene expression in retinal pericytes exposed to physiologic (5.5mM) and pathologic (20 mM) glucose concentrations. By utilizing modifications of the mRNA differential display technique, over 14,000 mRNA species were screened, and 35 candidate clones were obtained. Partial DNA sequence demonstrated that 25 of these were distinct genes, including 7 known, 16 previously unreported, and 2 sequences with known homologues. Northern blot analysis demonstrated altered gene expression in 10 (40%), undetectable signals in 12 (48%), and nonregulation in 3 (12%). Genes with glucose-regulated expression included those encoding fibronectin (51% +/- 15%, P = 0.003; mean percentage of control +/- SD), caldesmon (68% +/- 18%; P = 0.026), two ribosomal proteins (201% +/- 72%, P = 0.011; 136% +/- 16%, P = 0.036), Rieske FeS reductase (66% +/- 17%; P = 0.029), three previously unreported sequences (57%, 167%, 271%), and molecules homologous to autoantigens (213%) and tyrosine kinases (down 16- to 33-fold). Caldesmon protein concentrations in pericytes and smooth muscle cells demonstrated decreases by Western blot analysis concordant with mRNA levels. These studies identify genes whose expression is significantly altered after 7 days of exposure to elevated glucose levels and provide new targets for understanding the adverse effects of hyperglycemia on vascular cells. In addition, this study provides strong support for the use of differential mRNA display as a method to rapidly isolate differentially expressed genes in metabolic systems.

Analysis of gene expression in the preimplantation mouse embryo: use of mRNA differential display

The analysis of differential gene expression during preimplantation embryogenesis has been hindered by the paucity of biological material. We report modifications of the recently described mRNA differential display method (Liang, P. & Pardee, A. B. (1992) Science 257, 967-971) to analyze differential gene expression during mouse preimplantation development. The method detects the appropriate changes in the temporal pattern of expression of an amplicon that by DNA sequence analysis is the cytokeratin endo A, a gene whose temporal pattern of expression has been previously determined by S1 nuclease digestion. In addition, this method identifies amplicons that likely represent genes (i) that encode maternal mRNAs, (ii) that are products of early and late zygotic gene activation, (iii) whose expression is greatest during the eight-cell stage (i.e., expressed in a stage-specific manner), and (iv) whose expression is greatest in the blastocyst. In addition to endo A, sequence analysis of these amplicons reveals that an amplicon that displays a temporal pattern of expression consistent with it being a maternal mRNA is the alpha subunit of the mitochondrial F1 ATP synthase.

Mouse preimplantation embryo development in vitro: effect of sodium concentration in culture media on RNA synthesis and accumulation and gene expression

Results of previous studies indicate that culture of preimplantation mouse embryos in SOM medium containing 85 mM NaCl promotes better development in vitro, as well as supporting higher rates of protein synthesis, when compared to culture in SOM containing 125 mM NaCl (Anbari and Schultz, 1993, Mol Reprod Dev 35:24-28; Biggers et al., 1993, Mol Reprod Dev 34:380-390). In the present study we compare the effect of culturing embryos in these 2 media on several aspects of RNA synthesis and gene expression in order to determine whether the reduced development in SOM containing 125 mM NaCl and lower rates of protein synthesis are correlated with decreases in RNA synthesis and stability and changes in gene expression. Although no apparent differences in the metabolism of [3H]uridine to UMP, UDP, and UTP and its incorporation into total RNA are observed when 2-cell embryos are cultured to the morula stage in either medium, a 20% decrease in the rate of mRNA synthesis is found when embryos are cultured in SOM containing 125 mM NaCl. In addition, pulse-chase experiments reveal that total mRNA is less stable when the embryos are cultured in SOM containing 125 mM NaCl. Using a reverse transcription-polymerase chain reaction to assay for changes in the relative amounts of specific mRNAs, the relative amounts of mRNAs for IGF-I and IGF-II and their cognate receptors are dramatically reduced in embryos cultured in SOM containing 125 mM NaCl, whereas only a mild reduction is observed in the relative amount of actin mRNA. In contrast, when freshly isolated morulae are cultured to the blastocyst stage in either of these 2 media, similar amounts of these mRNAs are observed. Last, high-resolution, 2-dimensional gel electrophoresis reveals significant changes in the pattern of protein synthesis when the embryos are cultured in SOM containing 125 mM NaCl. Results of these experiments suggest that culture of embryos in medium containing lower concentrations of NaCl that are normally present in various culture media results in higher rates of mRNA synthesis and greater mRNA stability. These changes in RNA synthesis may underlie, at least in part, the improved development in vitro that is fostered by SOM containing 85 mM NaCl.

Anterior endoderm is a specific effector of terminal cardiac myocyte differentiation of cells from the embryonic heart forming region

The ability of anterior lateral plate mesoderm cells in the heart-forming region (HFR) of stage 6 chicken embryos to respond to cardiogenic stimuli from cells in adjacent germ layers has been investigated using explants cultured under defined conditions. Two types of explantation were evaluated: those in which two germ layers were explanted in contiguity, and those in which germ layers were isolated and co-cultured. Two parameters--contractility and expression of sarcomeric alpha-actin--were monitored to evaluate the terminal differentiation of cardiac myocytes. Contiguously explanted anterior endoderm/mesoderm became multilayered and underwent terminal differentiation within 2 days. By contrast, although contiguous anterior ectoderm/mesoderm or posterior endoderm/mesoderm co-explants also became multilayered, these explants did not differentiate, up to 5 days. To ascertain the cardiogenic potential of cells from different regions of the embryo, individual germ layers were isolated and co-cultured by placing the explants in separate areas of the culture chamber. These determinations demonstrated that anterior, but not posterior, endoderm effected differentiation of anterior mesoderm. As before, mesoderm in both types of co-culture survived and became multilayered; by contrast, mesoderm did not survive when cultured in isolation. These experiments provide evidence that anterior endoderm regulates the terminal differentiation, as opposed to growth, of presumptive cardiac myocytes in mesoderm cells from the anterior lateral plate. Finally, anterior endoderm was co-cultured with mesoderm from the posterior half of the embryo, which does not contain an HFR. The failure of these co-cultured explants to differentiate infers that pre-cardiac myoblasts in stage 6 anterior mesoderm are previously specified to respond to the terminal cardiogenic effects of endoderm.

Rapid isolation of tissue-specific and developmentally regulated brain cDNAs using RNA arbitrarily primed PCR (RAP-PCR)

RNA arbitrarily primed PCR (RAP-PCR) was used to isolate cDNAs that represent developmentally regulated brain-specific genes. Five clones with a restricted pattern of expression were identified and sequenced. Four cDNAs had no obvious homology to the sequences in GenBank. One clone had over 95% homology to a Ca2+/calmodulin-insensitive adenylyl cyclase, a recently cloned gene that was isolated from rat brain and was shown to be expressed only in adult brain and lung. Two novel cDNAs were investigated further by Northern blot analysis and were found to be expressed differentially during development; their expression was confined to the forebrain in the adult mouse. Further characterization by in situ hybridization showed that the mRNA corresponding to one clone was localized to a limited number of differentiating functional structures in the developing nervous system. In the adult brain, this message is confined to the forebrain with the highest level of expression in the cortex. These data suggest that the product of this gene is involved in the establishment of neuronal networks during brain development and in synaptic plasticity in the mature cortex. This work demonstrates that RAP-PCR is a powerful method for the simultaneous detection of differences between multiple RNA populations and, as such, can be used to study differential gene expression in the brain.

Rapid method for screening and cloning cDNAs generated in differential mRNA display: application of northern blot for affinity capturing of cDNAs

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The use of arbitrary primers and the RADES method for the rapid identification of developmentally regulated genes in trypanosomes

Biological processes, such as the cell-division cycle, differentiation and development, are driven by changes in gene expression. Short oligodeoxyribonucleotide primers (10-mers) of arbitrary sequence are currently used in the polymerase chain reaction (PCR) to generate genomic fingerprints (RAPDs) for the characterisation and differentiation of organisms and for mapping loci of interest. Since the products of such reactions are generally less than 1 kb in size, the use of arbitrary primers on cDNA should generate RAPDs which are characteristic of expressed genes. To assess this possibility, two model systems were employed; one in which actively dividing Trypanosoma brucei brucei bloodstream forms differentiate to non-dividing forms, and the second in which non-dividing metacyclic forms of T. congolense differentiate to actively dividing bloodstream forms. In the technique herein, mRNA from each differentiated form was reverse transcribed into cDNA which was then used as the template in the PCR. The resultant products were examined by agarose-gel electrophoresis. As few as 10(3) trypanosomes were sufficient for the generation of a RAPD print after first amplifying the total cDNA through exploitation of the fixed 3' and 5' ends of trypanosome nuclear mRNAs. Differences in RAPD patterns between the differentiated forms examined were mainly due to differences in gene expression. The technique can rapidly identify genes expressed at very low levels and which are up- or down-regulated in the different forms examined. PCR products of interest are easily purified from the agarose gels for direct cloning and complete sequence determination due to their relatively small size (0.1-1 kb).

Genetic aberrations in human brain tumors

Over the last decade, much has been learned about the genetic changes that occur in human neoplasia and how they contribute to the neoplastic state. Oncogenes and tumor suppressor genes have been identified, and many powerful molecular genetic techniques have emerged. Brain tumors have been intensively studied as part of this process. Specific and recurring genetic alterations have been identified and are associated with specific tumor types. In astrocytomas, for example, losses of genetic material on chromosomes 10 and 17 and amplification of the epidermal growth factor receptor gene seem important in pathogenesis, with the loss of chromosome 10 and the amplification of epidermal growth factor receptor being strongly associated with glioblastoma multiforme. Meningiomas, on the other hand, have usually lost part or all of chromosome 22. Brain tumors also express growth factors and growth factor receptors that may be important in promoting tumor growth and angiogenesis. These include epidermal growth factor, transforming growth factor-alpha, platelet-derived growth factor, the fibroblast growth factors, and vascular endothelial growth factor. In this article, we review the genetic aberrations that occur in the major types of brain tumors, including glial tumors, meningiomas, acoustic neuromas, medulloblastomas, primitive neuroectodermal tumors, and pituitary tumors. Wherever possible, clinical correlations have been made concerning the prognostic and therapeutic implications of specific aberrations. We also provide some background about the cytogenetic and molecular genetic techniques that have contributed to the description and understanding of these alterations and speculate as to some clinical and basic science issues that might be explored in the future.

The DNA binding domain of retinoic acid receptor beta is required for ligand-dependent suppression of proliferation. Application of general purpose mammalian coexpression vectors

We have developed a family of mammalian coexpression vectors that permit identification of living or fixed cells overexpressing a gene of interest by surrogate detection of a coexpressed marker protein. Using these ‘pMARK’ vectors, a fluorescence-based, single cell proliferation assay was developed and used to study the effect of retinoic acid receptor beta (RAR-beta) on cell cycling. We demonstrate that transient overexpression of RAR-beta in the presence, but not absence, of all-trans retinoic acid results in a dramatic suppression of cell proliferation. We further show that this effect requires the DNA binding (C) domain of RAR-beta. It has been previously shown that RAR-beta expression is markedly altered in a variety of neoplasms and cell lines. Our data support the hypothesis that loss of RAR-beta may contribute to tumor progression by removing normal restraints on proliferation. The pMARK vectors should be useful for studying other genes that putatively suppress or enhance proliferation.

Identification of enriched sequences from a cDNA subtraction-hybridization procedure

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Differential expression of protease inhibitor and small proline-rich protein genes between normal human oral tissue and odontogenic keratocysts

The technique of differential hybridization was used to compare gene transcription between normal oral mucosa and odontogenic keratocyst lining. Protease inhibitors, elafin and stefin-B as well as beta-actin and two epithelial-specific small proline-rich (spr) proteins, which we have named SPRC and SPRK and which are distinct from salivary proline-rich proteins, were differentially expressed. Increased abundance of alpha I(I) collagen and elafin transcripts was demonstrated in the keratocyst, with decreased abundance of stefin B, SPRC and cytokeratins 4 and 13 transcripts compared to normal palatal mucosa. The deduced protein sequences of SPRC and SPRK were described and compared, and the relative abundance of their respective cDNAs in palatal and keratocyst libraries determined. Identification of factors controlling transcription of these genes could advance our understanding of the development of odontogenic keratocysts.

Reverse genetics of the mouse central nervous system: targeted genetic analysis of neuropeptide function and reverse genetic screens for genes involved in human neurodegenerative disease

The development of gene targeting technology in mouse embryonic stem cells allows reverse genetics to be used to investigate the function of any cloned gene in the developing and adult brain. Promoter-trap, replacement and insertion vector strategies can be used to generate defined mutations in the chromosomal copy of a cloned gene in embryonic stem cells. These cells can be used to make chimaeric mice, some of which transmit the in vitro mutation via the germline to transgenic offspring. The phenotype of complete loss-of-function mutations (gene knock-outs) can be studied at molecular, cell biological, neurophysiological and behavioural levels, and allows inferences about gene function to be made. Precise small mutations can also be made using integrative vector or two-step replacement vector strategies, allowing specific questions to be asked about regulation and protein structure-function relationships. Reverse genetics can therefore be used as an alternative or additional approach to pharmacology for the study of molecular functions in the central nervous system. Reverse genetic studies of the involvement of particular molecules in neurological disease syndromes may be superior to pharmacological studies to the extent that the syndrome is determined by genetic predisposition. The general ways in which reverse genetics of the mouse can be used to ask questions about molecules in the central nervous system are illustrated by examples from ongoing work of this laboratory. Neuropeptides are an important class of transmitters in the brain, but only in very few cases have specific CNS functions been assigned to a particular neuropeptide. Targeted mutation of neuropeptide precursor and receptor genes offers a rapid way to learn about neuropeptide function. Complete loss-of-function mutations will provide information on any developmental roles of a neuropeptide and on overall behavioural and physiological effects of loss-of-function. More specific targeted mutations allow dissection of the individual roles of multiple neuropeptides that derive from a common precursor protein, and allow in vivo studies of the functional importance of particular amino acids. Experimental progress towards targeted mutation of the neurotensin receptor is described as an example. Recent technological improvements makes targeted mutation of a number of genes possible. This allows reverse genetic screening to be undertaken for genes involved in particular neurobiological phenomena: genes are identified on the basis of molecular criteria (e.g. expression pattern), and gene-targeting used to check their relevance to a phenotype. Neurodegenerative disease is an important aspect of the human phenotype.(ABSTRACT TRUNCATED AT 400 WORDS)

Stress-inducible gene of Salmonella typhimurium identified by arbitrarily primed PCR of RNA

Fingerprinting of RNA by arbitrarily primed PCR (RAP) can be used to identify conditionally expressed genes in prokaryotes. Differential gene expression in Salmonella typhimurium LT2 in response to peroxide treatment was examined as a system in which to demonstrate this strategy. This treatment models the induction of bacterial protective proteins that may occur when mammalian phagocytes use peroxide to fight S. typhimurium infection. To identify genes inducible by hydrogen peroxide stress, total RNA from peroxide-treated and untreated bacterial cultures were RAP fingerprinted with six different arbitrarily selected primers. A 435-base RAP product that was differentially amplified by RAP using the reverse sequencing primer was cloned and sequenced. Northern blot analysis confirmed that the RNA corresponding to this clone, RSP435, was induced when bacteria were treated with hydrogen peroxide. The RNA was not induced in an oxyR1 mutant that constitutively expressed a subset of hydrogen peroxide-inducible genes. Using pulsed-field gel electrophoresis and dot blot hybridization to an array of induced Mud-P22 integrations, the gene corresponding to RSP435 was mapped to two places, one between 19 and 21.5 min and one between 56 and 57 min. Thus, two similar or identical stress-inducible genes were found in different parts of the genome. Identification, cloning, and mapping of the conditionally expressed RSP435 cDNA were performed entirely by physical means, demonstrating that the strategy should complement genetic methods for many prokaryotic or archaebacterial systems and should be applicable to organisms in which genetic methods are difficult to perform or have not yet been developed.

Vitamin D receptors in breast cancer cells

1,25-(OH)2-Vitamin D3, the active metabolite of vitamin D, is a secosteroid hormone with known differentiating activity in leukemic cells. Studies have demonstrated the presence of vitamin D receptors (VDR) in a wide range of tissues and cell types. Antiproliferative activity of 1,25-(OH)2-vitamin D3 has been documented in osteosarcoma, melanoma, colon carcinoma, and breast carcinoma cells. This study was designed to analyze vitamin D receptor level in breast cancer cells as a marker of differentiation and as a predictor of growth inhibition by 1,25-(OH)2-vitamin D3. VDR messenger RNA was found to be present in relatively high levels in well-differentiated cells and in low levels in poorly differentiated cells. All cell lines had detectable VDR mRNA. Radiolabeled ligand binding assay showed a similar pattern. MCF-7 and T47D cells, which express VDR at moderate levels, showed significant growth inhibition by 10(-9) M1,25-(OH)2-vitamin D3 (p < 0.05). MDA-MB-231 cells, which have very low levels of VDR, demonstrated no growth inhibition by 1,25-(OH)2-vitamin D3 at concentrations up to 10(-6) M. Based on these results it can be stated that VDR expression is lost with de-differentiation and that receptor is essential for the antiproliferative response to 1,25-(OH)2-vitamin D3.

Colorectal cancer and the integrin family of cell adhesion receptors: current status and future directions

Tumour progression is thought to be determined, at least in part, by the balance between available cell surface receptors and the nature of the surrounding extracellular matrix. The integrin family of transmembrane adhesion receptors involved in tumour cell-matrix interactions mediates cell adhesion, migration, and differentiation. Certain patterns of integrin receptor expression on normal and malignant colon epithelial cells are emerging, and it is now clear that integrins can also regulate such divergent processes as cell proliferation and programmed cell death in this tumour type. This implies that integrins are involved in signal transduction events within colon carcinoma cells consequent upon their adhesive interaction with matrix molecules. A better understanding of the mechanisms involved in these events may lead to useful therapeutic strategies in the management of this disease.