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

Messenger RNA fingerprinting analysis using arbitrarily primed PCR (RAP) of genes expressed during rat C6 glioma cell differentiation

To identify differentially expressed genes involved in rat C6 glioma cell differentiation induced by cyclic AMP, we adopted mRNA fingerprinting using arbitrarily primed polymerase chain reaction (PCR) (RAP). Four complementary DNA (cDNA) fragments differentially expressed during differentiation were isolated, and they appeared to contain coding regions of corresponding mRNAs. RAP can be used to efficiently identify cDNA fragments by comparing nucleotide and deduced amino acid sequences with those in databases, and is thus a useful method to search for and identify important genes involved in complex cellular processes such as glioma cell differentiation.

Identification of novel growth-related genes linked to the mitogenic effect of PACAP on the rat pancreatic acinar cell line, AR4-2J

The mRNA differential display technique was employed in order to identify novel growth-related genes linked to the mitogenic effect of PACAP on AR4-2J cells. Hereby, three differentially expressed and PACAP-inducible genes were found, one of these being homologous to a recently discovered putative growth-related early response gene in mice. In AR4-2J cells, mRNA levels of this novel rat gene are increased by PACAP in a rapid and transient fashion. This effect was enhanced by cycloheximide, whereas actinomycin D prevented the stimulatory effect of PACAP.

Requirement for a noncoding RNA in Drosophila polar granules for germ cell establishment

In Drosophila embryos, germ cell formation is induced by specialized cytoplasm at the posterior of the egg, the pole plasm. Pole plasm contains polar granules, organelles in which maternally produced molecules required for germ cell formation are assembled. An untranslatable RNA, called Polar granule component (Pgc), was identified and found to be localized in polar granules. Most pole cells in embryos produced by transgenic females expressing antisense Pgc RNA failed to complete migration and to populate the embryonic gonads, and females that developed from these embryos often had agametic ovaries. These results support an essential role for Pgc RNA in germline development.

Identification of a novel vertebrate circadian clock-regulated gene encoding the protein nocturnin

Photoreceptors of the Xenopus laevis retina are the site of a circadian clock. As part of a differential display screen for rhythmic gene products in this system, we have identified a photoreceptor-specific mRNA expressed in peak abundance at night. cDNA cloning revealed an open reading frame encoding a putative 388 amino acid protein that we have named "nocturnin" (for night-factor). This protein has strong sequence similarity to the C-terminal domain of the yeast transcription factor, CCR4, as well as a leucine zipper-like dimerization motif. Nocturnin mRNA levels exhibit a high amplitude circadian rhythm and nuclear run-on analysis indicates that it is controlled by the retinal circadian clock at the level of transcription. Our observations suggest that nocturnin may function through protein-protein interaction either as a component of the circadian clock or as a downstream effector of clock function.

p53-independent cyclin G expression in a group of mature neurons and its enhanced expression during nerve regeneration

An increase in cyclin G expression after nerve injury was demonstrated by differential display PCR, carried out to compare references in expression of mRNAs between axotomized and normal hypoglossal motoneurons in the rat. The nerve injury dramatically upregulated the expression of cyclin G mRNA in the motoneurons during the early phase of the nerve regeneration process, suggesting an involvement of cyclin G in the early stage of nerve regeneration. In brain, in situ hybridization studies also demonstrated cyclin G expression in a restricted group of matured neurons, particularly in the telencephalon and the thalamus. This constitutive expression in mature neurons suggests that cyclin G may have a function different from other members of the cyclin group. In addition, although cyclin G has been shown to be a transcription target of p53, the upregulation of cyclin G in injured motoneurons, as well as the expression in the adult rat brain, was not affected in the p53-deficient mouse. These data suggest that the expression of cyclin G, at least in the nervous system, is not regulated by p53 predominantly, and that there may be alternative regulatory factors or pathways for cyclin G expression.

Elevated levels of cyclin D1 mRNA in the undifferentiated chick retina

The retina is derived from precursor neuroectodermal cells that differentiate into six classes of neuronal cells and one class of glial cells (Müller). To gain insight into the molecular events underlying retinal differentiation, we used the differential display polymerase chain reaction (DD-PCR) technique to identify transcripts preferentially expressed in precursor retinal cells prior to their differentiation. One of the cDNAs that we selected using this technique encoded cyclin D1, a G1 cyclin shown to bind to the retinoblastoma protein (pRB) and which is involved in the phosphorylation of pRB during mid to late G1. Similar to what has been reported recently in the mouse retina, we found cyclin D1 mRNA to be highly expressed in the undifferentiated chick retina. Tissue maturation was accompanied by a substantial reduction in cyclin D1 mRNA levels. A similar temporal pattern of expression was observed in the developing brain although transcript levels were lower than in the retina. In contrast, cyclin D1 mRNA levels increased with differentiation in the kidney. These results suggest that the proliferating cells of the developing chick retina require exceptionally high levels of cyclin D1 mRNA, perhaps to promote progression through the cell cycle by countering the effect of molecules with a negative role in the cell cycle such as pRB.

Expression monitoring by hybridization to high-density oligonucleotide arrays

The human genome encodes approximately 100,000 different genes, and at least partial sequence information for nearly all will be available soon. Sequence information alone, however, is insufficient for a full understanding of gene function, expression, regulation, and splice-site variation. Because cellular processes are governed by the repertoire of expressed genes, and the levels and timing of expression, it is important to have experimental tools for the direct monitoring of large numbers of mRNAs in parallel. We have developed an approach that is based on hybridization to small, high-density arrays containing tens of thousands of synthetic oligonucleotides. The arrays are designed based on sequence information alone and are synthesized in situ using a combination of photolithography and oligonucleotide chemistry. RNAs present at a frequency of 1:300,000 are unambiguously detected, and detection is quantitative over more than three orders of magnitude. This approach provides a way to use directly the growing body of sequence information for highly parallel experimental investigations. Because of the combinatorial nature of the chemistry and the ability to synthesize small arrays containing hundreds of thousands of specifically chosen oligonucleotides, the method is readily scalable to the simultaneous monitoring of tens of thousands of genes.

Selecting and amplifying one fragment from a DNA fragment mixture by polymerase chain reaction with a pair of selective primers

A new method for selecting and amplifying a single DNA fragment from a mixture is proposed. This method is applicable for the rapid classification of DNA fragments from a mixture and for preparation of sequencing templates. DNAs of several to tens of kilobases (kb) are digested with a four-base recognition restriction enzyme to produce smaller fragments. The complementary strand extension reactions are then carried out to produce fluorophore-labeled DNA fragments from the digestion products. These fragments can be rapidly classified according to their terminal-base sequences and their sizes are analyzed by capillary-array gel electrophoresis (CAGE). Electropherograms are used to characterize the fragments and to select polymerase chain reaction (PCR) primers. Any fragment in a digestion mixture can be amplified by PCR with a pair of primers selected from a primer pool by referring to the electropherograms of the fragments. This method was successfully used to compare the electropherograms of two different DNA strands and to sequence a several-kb DNA fragment without subcloning. Combined with CAGE, this method could be used to dramatically simplify DNA fragment analysis.

The Xenopus T-box gene, Antipodean, encodes a vegetally localised maternal mRNA and can trigger mesoderm formation

We have used differential display to identify genes inducible by activin and isolated a novel member of the T-box gene family that includes the Xenopus genes Xbrachyury and Eomesodermin. Here we show that this novel gene is unique within the T-box family because it is maternally expressed at a high level. Furthermore, it belongs to a rare class of maternal mRNAs in Xenopus that are localised to the vegetal hemisphere of the egg and we have therefore named it Antipodean. We show here that low amounts of Antipodean injected into ectoderm (animal cap cells) strongly induce pan mesodermal genes such as Xbrachyury and ventral mesodermal genes such as Xwnt-8. Overexpression of Antipodean generates mesoderm of ventral character, and induces muscle only weakly. This property is consistent with the observed late zygotic Antipodean mRNA expression in the posterior paraxial mesoderm and ventral blastopore, and its exclusion from the most dorsal mesodermal structure, the notochord. Antipodean is induced by several molecules of the TGF-beta class, but in contrast to Xbrachyury, not by bFGF. This result suggests that the expression of these T-box genes may be under the control of different regulatory pathways. Finally, we demonstrate that Antipodean and Eomesodermin induce each other and both are able to induce Xbrachyury. The early zygotic expression of Antipodean is not induced by Xbrachyury, though later it is to some extent. Considering its maternal content, Antipodean could initiate a cascade of T-box gene activations. The expression of these genes may, in turn, sustain each other's expression to define and maintain the mesoderm identity in Xenopus.

Bone extracellular matrix induces homeobox proteins independent of androgens: possible mechanism for androgen-independent growth in human prostate cancer cells

BACKGROUND

Differences in gene expression in prostate cells are believed to be secondary to epithelial-stromal interactions. We theorized that bone matrix may provide a fertile "soil" for prostate cancer by inducing androgen-dependent genes and allowing for androgen-independent growth.

METHODS

Human prostate cancer cells (LNCaP) were grown under different conditions and analyzed for differential expression of mRNA. LNCaP cells were grown in the presence of 10 nM dihydrotestosterone (DHT), on extracellular matrix (ECM) derived from bone cells (without exogenous DHT), and on plastic culture dishes without exogenous DHT. A differential display of mRNA produced by LNCaP cells grown in the above conditions was then analyzed.

RESULTS

Multiple unique transcripts were present in cells that were grown in the presence of DHT and on bone ECM (without exogenous DHT), but not on plastic culture dishes without exogenous DHT. Nine of these transcripts were then cloned and analyzed. Many (5/9) of these transcripts were found to contain multiple ATTA motifs in their corresponding 3'-untranslated regions. ATTA motifs have been shown to be homeobox protein-binding sites. Homeobox proteins and their target genes are thought to regulate cellular differentiation. Consistent with this, we demonstrated by reverse transcription polymerase chain reaction (PCR) that homeobox genes were differentially expressed in LNCaP cells when the cells were grown in the presence of DHT and on bone ECM (without exogenous DHT), but not on plastic culture dishes without exogenous DHT. Furthermore, we assayed LNCaP/fetal fibroblast chimeric tumors (n = 8) that were grown in male nude mice. Some of these tumors continued to grow in these mice despite treatment with surgical castration. In blinded studies, we were able to determine which tumor samples were androgen independent by their expression of homeobox genes. All samples that were androgen independent (n = 4) expressed the homeobox genes. Finally, gel retardation assay demonstrated that the homeobox proteins were able to bind to our cloned DNA sequences. Furthermore, footprinting analysis showed that the homeobox proteins bound to the ATTA motif in the 3'-region of our target DNA.

CONCLUSIONS

Bone ECM, in the absence of DHT, has the ability to regulate androgen-responsive genes. Furthermore, many of these genes contain homeobox binding sites and the expression of homeobox genes may itself be regulated by bone ECM. If so, this may partially explain the clinical observation that bone provides a fertile "soil" for prostate cancer growth and metastasis.

Directional random oligonucleotide primed (DROP) global amplification of cDNA: its application to subtractive cDNA cloning

We describe a method of global PCR amplification of cDNA such that the strand sense is maintained. The products of this process are random primed fragments ranging in size from 100 to 500 bp which facilitates uniform PCR amplification of total cDNA. Directional incorporation of a T7 RNA polymerase initiator/promoter sequence allows efficient synthesis of total sense RNA from this material and the use of a biotinylated primer permits the separation of single-stranded cDNA. Isolation of these products from different cell types provides a renewable source of target single-stranded cDNA and driver RNA from limited cell numbers and we demonstrate their use for subtractive hybridisation cloning of differentially expressed cDNAs.

Thymosin beta 15: a novel regulator of tumor cell motility upregulated in metastatic prostate cancer

The Dunning rat prostatic carcinoma is a model system where cell motility closely correlates with the metastatic phenotype. We have identified a novel gene, upregulated in the highly motile and metastatic Dunning cancer cell lines, that represents a new member of the thymosin-beta family, thymosin beta 15. Transfection of antisense thymosin beta 15 constructs into rat prostatic carcinoma cells demonstrates that this molecule positively regulates cell motility, a critical component of the metastatic pathway. Thymosin beta 15 levels are elevated in human prostate cancer and correlate positively with the Gleason tumor grade. Thymosin beta 15 may represent a potential new biochemical marker for human prostate cancer progression.

Ensuring recovery of intact RNA from rat pancreas

The isolation of intact RNA from rat pancreas is compromised by autolysis and by the presence of endogenous ribonucleases. In order to ameliorate recovery we systematically investigated available RNA extraction methods and paid particular attention to the influence of frozen storage and ribonuclease inhibition strategies on overall yield and quality of RNA. Modifications to the basic procedure of Chomczynski and Sacchi (1987) are described which allow, reproducibly, to obtain rat pancreatic RNA suitable for Northern blot hybridization, RT-PCR, and differential display analysis.

Regulation of S100P expression by androgen

BACKGROUND

The growth and function the normal prostate is dependent on the presence of androgen. As prostate tumors progress there is a loss of androgen-dependent cell growth. The identification of the genes that are regulated by androgens may be of pathological and clinical significance.

METHODS

In this study the differential display method was used to identify genes regulated by androgen in an androgen-responsive prostate cancer cell line, LNCaP-FGC.

RESULTS

A gene whose expression is down-regulated in LNCaP-FGC cells after 30 hr of androgen deprivation has been identified. This gene is a previously identified member of the S100 gene family of calcium-binding proteins, namely S100P. Here we show that S100P expression is regulated by the synthetic androgen R1881, but not by serum growth factors. It is dysregulated in the androgen-independent prostate cancer cell lines LNCaP-R, DU145, and PC3.

CONCLUSIONS

The data indicate that S100P may play a role in the etiology of prostate cancer.

Wild-type p53 negatively regulates the expression of a microtubule-associated protein

The product of the p53 tumor suppressor gene has a well-documented activity as a transcriptional activator, and several studies indicate that this function is at least in part essential for the ability of p53 to suppress cellular proliferation. However, there is growing evidence that some activities of wild-type p53 may be independent of its trans-activation function; in fact, recent investigations have indicated that the transcriptional repression function of p53, rather than its trans-activation function, may be influential in p53-mediated apoptosis. The focus of this study has been on the identification of genes that exhibit decreased expression during p53-dependent apoptosis, and therefore represent potential p53-repressed genes influential in programmed cell death. This report identifies the gene encoding the microtubule-associated protein MAP4 as one whose mRNA and protein expression decrease in cells following induction of wild-type p53. Importantly, decreased MAP4 expression following p53 induction can be inhibited by molecules that prevent p53-mediated transcriptional repression and apoptosis, such as the adenovirus E1B-19K protein and the Wilms tumor gene product WT1. Additionally, overexpression of MAP4 in cells induced to undergo p53-dependent apoptosis significantly delays this process, indicating that the negative regulation of this gene by p53 may be influential in the rapid progression of apoptosis.

New potential markers of in vitro tomato morphogenesis identified by mRNA differential display

The identification of plant genes involved in early phases of in vitro morphogenesis can not only contribute to our understanding of the processes underlying growth regulator-controlled determination, but also provide novel markers for evaluating the outcome of in vitro regeneration experiments. To search for such genes and to monitor changes in gene expression accompanying in vitro regeneration, we have adapted the mRNA differential display technique to the comparative analysis of a model system of tomato cotyledons that can be driven selectively toward either shoot or callus formation by means of previously determined growth regulator supplementations. Hormone-independent transcriptional modulation (mainly down-regulation) has been found to be the most common event, indicating that a non-specific reprogramming of gene expression quantitatively predominates during the early phases of in vitro culture. However, cDNA fragments representative of genes that are either down-regulated or induced in a programme-specific manner could also be identified, and two of them (G35, G36) were further characterized. One of these cDNA fragments, G35, corresponds to an mRNA that is down-regulated much earlier in callus- (day 2) than in shoot-determined explants (day 6). The other, G36, identifies an mRNA that is transiently expressed in shoot-determined explants only, well before any macroscopic signs of differentiation become apparent, and thus exhibits typical features of a morphogenetic marker.

The future of PCR technology: diversification of technologies and applications

The polymerase chain reaction has had a major impact on research in molecular biology, on the human genome project and on the diagnosis of disease. In the future, this powerful technique will be increasingly applied to the study of individual genomic variation and to assess the genetic consequences of ecological and demographic events on past and contemporary populations of many organisms.

Comparative gene expression in sexual and apomictic ovaries of Pennisetum ciliare (L.) Link

Limited emphasis has been given to the molecular study of apomixis, an asexual method of reproduction where seeds are produced without fertilization. Most buffelgrass (Pennisetum ciliare (L.) Link syn = Cenchrus ciliaris L.) genotypes reproduce by obligate apomixis (apospory); however, rare sexual plants have been recovered. A modified differential display procedure was used to compare gene expression in unpollinated ovaries containing ovules with either sexual or apomictic female gametophytes. The modification incorporated end-labeled poly(A)+ anchored primers as the only isotopic source, and was a reliable and consistent approach for detecting differentially displayed transcripts. Using 20 different decamers and two anchor primers, 2268 cDNA fragments between 200 and 600 bp were displayed. From these, eight reproducible differentially displayed cDNAs were identified and cloned. Based on northern analysis, one cDNA was detected in only the sexual ovaries, two cDNAs in only apomictic ovaries and one cDNA was present in both types of ovaries. Three fragments could not be detected and one fragment was detected in ovaries, stems, and leaves. Comparison of gene expression during sexual and apomictic development in buffelgrass represents a new model system and a strategy for investigating female reproductive development in the angiosperms.

Cloning differentially expressed mRNAs

Differential gene expression occurs in the process of development, maintenance, injury, and death of unicellular as well as complex organisms. Differentially expressed genes are usually identified by comparing steady-state mRNA concentrations. Electronic subtraction (ES), subtractive hybridization (SH), and differential display (DD) are methods commonly used for this purpose. A rigorous examination has been lacking and therefore quantitative aspects of these methods remain speculative. We compare these methods by identifying a total of 58 unique differentially expressed mRNAs within the same experimental system (HeLa cells treated with interferon-gamma). ES yields digital, reusable data that quantitated steady-state mRNA concentrations but only identified abundant mRNAs (seven were identified), which represent a small fraction of the total number of differentially expressed mRNAs. SH and DD identified abundant and rare mRNAs (33 and 23 unique mRNAs respectively) with redundancy. The redundancy is mRNA abundance-dependent for SH and primer-dependent for DD. We conclude that DD is the method of choice because it identifies mRNAs independent of prevalence, uses small amounts of RNA, identifies increases and decreases of mRNA steady-state levels simultaneously, and has rapid output.

Scanning of nucleic acids by in vitro amplification: new developments and applications

Nucleic acids can be characterized using a variety of "fingerprinting" techniques usually based on nucleic acid hybridization or enzymatic amplification. The scanning of nucleic acids by amplification with arbitrary oligonucleotide primers has become popular because it can generate simple-to-complex patterns from anonymous DNA or RNA templates without requiring prior knowledge of nucleic acid sequence or cloned or characterized probes. Discrete loci are amplified within genomic DNA, DNA complementary to mRNA populations (cDNA), cloned DNA fragments, and even PCR products. The potential and limitations of the various genome scanning techniques, novel improvements, and their recent use in comparative and experimental biology applications, including the analysis of plant and bacterial genomes are discussed.

Transcriptional downregulation of a mouse Golgi mannosidase gene following Salmonella typhimurium uptake into murine macrophages

Uptake of Salmonella typhimurium into murine macrophage cells caused transcriptional downregulation of a mRNA population in eukaryotic cells after 2 h of infection. The cloned cDNA that was identified showed extensive homology with a murine alpha 1,2-mannosidase gene involved in N-oligosaccharide processing. These findings suggest a disruption of eukaryotic protein processing after phagocytosis of S. typhimurium by the murine macrophage cells.

Application of differential display RT-PCR to the analysis of gene expression in a plant-fungus interaction

Establishment of a plant-pathogen interaction involves differential gene expression in both organisms. In order to isolate Botrytis cinerea genes whose expression is induced during its interaction with tomato, a comparative analysis of the expression pattern of the fungus in planta with its expression pattern during in vitro culture was performed by differential display of mRNA (DDRT-PCR). Discrimination of fungal genes induced in planta from plant defense genes induced in response to the pathogen was attempted by including in this comparative analysis the expression patterns of healthy tomato leaves and of tomato leaves infected with two different pathogens, either Rhytophthora infestans or tobacco necrosis virus (TNV). Using a limited set of primer combinations, three B. cinerea cDNA fragments, ddB-2, ddB-5 and ddB-47, were isolated representing fungal genes whose expression is enhanced in planta. Northern blot analysis showed that the transcripts detected with the cDNA clones ddB-2 and ddB-5 accumulated at detectable levels only at late time points during the interaction. The cDNA clone ddB-47 detected two different sizes of transcripts displaying distinct, transient expression patterns during the interaction. Sequence analysis and database searches revealed no significant homology to any known sequence. These results show that the differential display procedure possesses enough sensitivity to be applied to the detection of fungal genes induced during a plant-pathogen interaction. Additionally, four cDNA fragments were isolated representing tomato genes induced in response to the infection caused by B. cinerea, but not by P. infestans.

CADp44: a novel regulatory subunit of the 26S proteasome and the mammalian homolog of yeast Sug2p

We have identified a novel protein, CADp44, based on the analysis of cDNAs derived from the brainstem of the 13-lined ground squirrel, Spermophilus tridecemlineatus. CADp44 has an unmodified molecular mass of 44,178 Da and contains multiple functional domains, including a conserved ATPase domain (CAD) and a leucine zipper motif. We show that distinct regions of the CADp44 sequence are identical to a set of peptides prepared from a recently identified bovine protein, referred to as p42, which is found in the PA700 regulatory complex of the 26S proteasome (DeMartino et al., 1996). We also show that CADp44 is the functional homolog of the newly characterized Sug2 protein from the budding yeast, Saccharomyces cerevisiae (Russell et al., 1996). Consistent with its role as a component of the 26S proteasome, CADp44 mRNA is found in all ground squirrel tissues examined. Evolutionary relationships based on sequence analysis show that both CADp44 and yeast Sug2p are distinct from the other five CAD ATPases found in the PA700, and together comprise the sixth and newest CAD subunit of the regulatory complex of the 26S proteasome.

Identification of the retinoic acid-inducible all-trans-retinoic acid 4-hydroxylase

Retinoic acid (RA) metabolites of vitamin A are key regulators of gene expression involved in embryonic development and maintenance of epithelial tissues. The cellular effects of RA are dependent upon the complement of nuclear receptors expressed (RARs and RXRs), which transduce retinoid signals into transcriptional regulation, the presence of cellular retinoid-binding proteins (CRABP and CRBP), which may be involved in RA metabolism, and the activity of RA metabolizing enzymes. We have been using the zebrafish as a model to study these processes. To identify genes regulated by RA during exogenous RA exposure, we utilized mRNA differential display. We describe the isolation and characterization of a cDNA, P450RAI, encoding a novel member of the cytochrome P450 family. mRNA transcripts for P450RAI are expressed normally during gastrulation, and in a defined pattern in epithelial cells of the regenerating caudal fin in response to exogenous RA. In COS-1 cells transfected with the P450RAI cDNA, all-trans-RA is rapidly metabolized to more polar metabolites. We have identified 4-oxo-RA and 4-OH-RA as major metabolic products of this enzyme. P450RAI represents the first enzymatic component of RA metabolism to be isolated and characterized at the molecular level and provides key insight into regulation of retinoid homeostasis.

Homocysteine-respondent genes in vascular endothelial cells identified by differential display analysis. GRP78/BiP and novel genes

An elevated blood level of homocysteine is associated with arteriosclerosis and thrombosis. The mechanisms by which homocysteine may promote vascular diseases have not been elucidated yet. In the present study, we have applied a modified nonradioactive differential display analysis to evaluate changes in gene expression induced by homocysteine treatment of cultured human umbilical vein endothelial cells (HUVEC). We identified six up-regulated and one down-regulated genes. One up-regulated gene was GRP78/BiP, a stress protein, suggesting that misfolded proteins would accumulate in the endoplasmic reticulum because of redox potential changes caused by homocysteine. Another up-regulated gene encoded a bifunctional enzyme with activities of methylenetetrahydrofolate dehydrogenase and methenyltetrahydrofolate cyclohydrolase, which is involved in a homocysteine metabolism. A third up-regulated gene encoded activating transcription factor 4, and a fourth was a gene whose function is not identified yet. The remaining three were novel genes. We isolated a full-length cDNA of one of the up-regulated genes from a HUVEC library. It encoded a novel protein with 394 amino acids, which was termed reducing agents and tunicamycin-responsive protein (RTP). Northern blot analysis revealed that RTP gene expression was induced in HUVEC after 4 h incubation with homocysteine. RTP mRNA was also observed in unstimulated cells and induced by not only homocysteine but also 2-mercaptoethanol and tunicamycin. The mRNA was ubiquitously expressed in human tissues. These observations indicate that homocysteine can alter the expressivity of multiple genes, including a stress protein and several novel genes. These responses may contribute to atherogenesis.

Identifying differential gene expression in monoterpene-treated mammary carcinomas using subtractive display

Monoterpene-induced/repressed genes were identified in regressing rat mammary carcinomas treated with dietary limonene using a newly developed method termed subtractive display. The subtractive display screen identified 42 monoterpene-induced genes comprising 9 known genes and 33 unidentified genes, as well as 58 monoterpene-repressed genes comprising 1 known gene and 57 unidentified genes. Several of the identified differentially expressed genes are involved in the mitoinhibitory transforming growth factor beta signal tranduction pathway, as demonstrated by isolation of the mannose 6-phosphate/insulin-like growth factor II receptor and the transforming growth factor beta type II receptor. The monoterpene-induced/repressed genes indicate that apoptosis and differentiation act in concert to effect carcinoma regression. Apoptosis is suggested by the cloning of a marker of programmed cell death, lipocortin 1. Consistent with a differentiation/remodeling process occurring during tumor regression, subtractive display identified YWK-II and neuroligin 1. Thus far, of the cDNAs putatively identified as differentially expressed in this complex in situ carcinoma model, 5 were tested, and each one has been confirmed to be differentially expressed. Additionally, many of the identified known genes are expressed as rare transcripts and exhibit small but significant changes in abundance. Together, these points demonstrate the unique utility of this new gene expression screen to identify altered gene expression in a complex in vivo environment.

Use of alternative polyadenylation sites in the synthesis of mRNAs encoding the interferon-induced tryptophanyl tRNA synthetase

The interferon-mediated induction of the gene encoding the human tryptophanyl tRNA synthetase (WRS) results in the production of two mRNA species differing in size by approximately 800 base pairs (bp). Two distinctly sized cDNAs differing by approximately 800 bp were isolated from a cDNA library generated from mRNA prepared from IFN-gamma-treated cells. Northern blot analysis using cDNA probes recognizing different regions of the WRS mRNA reveals distinctly sized mRNAs differing in the length of their 3' untranslated regions. Differential display analysis using oligo dT primers demonstrates that the different sized WRS mRNAs result from alternative polyadenylation of this transcript.

Identification and characterization of differentially expressed cDNAs of the vector mosquito, Anopheles gambiae

The isolation and study of Anopheles gambiae genes that are differentially expressed in development, notably in tissues associated with the maturation and transmission of the malaria parasite, is important for the elucidation of basic molecular mechanisms underlying vector-parasite interactions. We have used the differential display technique to screen for mRNAs specifically expressed in adult males, females, and midgut tissues of blood-fed and unfed females. We also screened for mRNAs specifically induced upon bacterial infection of larval stage mosquitoes. We have characterized 19 distinct cDNAs, most of which show developmentally regulated expression specificity during the mosquito life cycle. The most interesting are six new sequences that are midgut-specific in the adult, three of which are also modulated by blood-feeding. The gut-specific sequences encode a maltase, a V-ATPase subunit, a GTP binding protein, two different lectins, and a nontrypsin serine protease. The latter sequence is also induced in larvae subjected to bacterial challenge. With the exception of a mitochondrial DNA fragment, the other 18 sequences constitute expressed genomic sequence tags, 4 of which have been mapped cytogenetically.

Increased expression of T-plastin gene in cisplatin-resistant human cancer cells: identification by mRNA differential display

The cellular resistance to the potent anticancer agent cis-diamminedichloroplatinum(II) (cisplatin) is thought to be mediated by multiple mechanisms. The technique of differential display of mRNAs was applied to various cisplatin-resistant cell lines and the corresponding parental sensitive human bladder, prostatic, and head and neck cancer cells in order to identify genes that underlie cisplatin resistance. Twenty-four clones were confirmed by Northern blot analysis to be expressed differentially between resistant and the corresponding sensitive cells. Partial DNA sequences of the eight clones that showed a threefold or greater increase in expression in either the resistant cells (seven clones) or sensitive cells (one clone) revealed that two were derived from the T-plastin gene and one from the tissue factor gene. The abundance of T-plastin mRNA in cisplatin-resistant T24/DDP10 cell was approximately 12 times that in the parental T24 cells. Transfection of T24/DDP10 cells with a vector encoding full-length T-plastin antisense RNA demonstrated that reduced T-plastin expression was associated with increased sensitivity to cisplatin. These results are consistent with the hypothesis that several mechanisms participate cooperatively in the acquisition of cisplatin resistance in human cancer.

Oxidative signalling and gene expression during lymphocyte activation

We previously have demonstrated an obligatory requirement for intracellular reactive oxygen species (ROS) generation during T lymphocyte activation, and have proposed that ROS may act as signalling agents in the regulation of certain cellular processes, for example, during cell cycle entry. In order to test this hypothesis, we have been interested to determine which, if any, cell cycle entry events are affected by oxidative signalling. Given the requirement for both oxidative signalling and altered gene expression during the G0 to G1 phase transition, we have attempted to establish the extent to which oxidative signalling affects global gene expression patterns during cell cycle entry, and to isolate and characterize mRNAs whose expression patterns are responsive to oxidative signalling during this process. Using differential display in a phenotypic screening approach, we have identified 10 mRNA species whose expression patterns were altered in response to inhibition of oxidative signalling during cell cycle entry. The expression patterns of 4 of these 10 mRNAs were unaffected during cell cycle arrest caused by a different mechanism, cyclosporin A-induced interference with calcineurin-mediated signalling events, implying that the altered expression patterns seen were not simply a consequence of cell cycle arrest. This suggests that the expression of these 4 mRNAs is regulated by a mechanism both necessary for cell cycle entry and sensitive to oxidative signalling. RNAse protection assays confirmed that 2 of these 4 mRNAs were indeed responsive to redox regulation. These observations strongly suggest an involvement for oxidative signalling in the regulation of gene expression during the G0 to G1 phase transition, in peripheral blood mononuclear cells at least.

Aspects of the adaptive response to very low doses of radiation and other agents

When human lymphocytes and other cells are pre-exposed to very low doses of ionizing radiation and subsequently exposed to a high dose, less genetic damage, i.e., fewer chromosome aberrations, is found than is observed in cells that had not been pre-exposed. This has been termed the adaptive response and has been attributed to the induction of a repair mechanism by the low dose exposure. Several experiments have now been carried out on this adaptive response to better characterize the phenomenon. (A) Experiments with differential display of mRNAs indicate that human lymphocytes exposed to 2 cGy of X-rays have somewhat different mRNAs expressed than do unexposed cells. This is providing access to DNA that might be involved in adaptation. (B) Other experiments with embryonic cells from transgenic mice that are deficient in superoxide dismutase (SOD) have shown that the adaptive response is unrelated to the amount of SOD in the cells, and thus is independent of superoxide radicals. (C) Experiments in which very low doses of various restriction enzymes were electroporated into human lymphocytes have shown that low levels of double-strand DNA breaks alone are able to induce the adaptive response. (D) Experiments in which human male lymphocytes (XY chromosome constitution) and human female lymphocytes (XX chromosome constitution) were cocultivated have shown that adaptation is not caused by a change in the rate of cell progression to mitosis after a challenge dose, and is a further indication that cell stage sensitivity is not a factor in the adaptive response.

Cascade of gene expression induced by Ca2+ signals in neurons

To understand the cellular processes involved in learning and memory, the cellular responses of neurons to calcium (Ca2+) signals, which can be evoked via synaptic activity, should be examined. A series of investigations in primary cultures of neurons revealed that the regulation of brain-derived neurotrophic factor (BDNF) mRNA expression is mediated by almost the same Ca2+ signaling pathways as that of c-fos mRNA expression. Such early co-activation of both genes in response to Ca2+ signals further suggests that sets of calcium-responsive genes (CaRGs) are concurrently activated by Ca2+ signals. The products encoded by CaRGs should then evoke a variety of physiological responses in neurons with the expression of another set of genes, the products of which are directly involved in the outcomes of neuronal functions. Thus, a cascade of gene expression can be induced by Ca2+ signals evoked via synaptic activity. It is of particular interest to identify the CaRGs and investigate the regulational mechanisms of their expression. A cellular approach using primary cultures of neurons would therefore lead to a better understanding of the intracellular processes involved in learning and memory.

Differential gene expression of extracellular matrix components in dilated cardiomyopathy

Extracellular matrix metalloproteinases (MMPs) are activated in dilated cardiomyopathic (DCM) hearts [Tyagi et al. (1996): Mol Cell Biochem 155:13-21]. To examine whether the MMP activation is occurring at the gene expression level, we performed differential display mRNA analysis on tissue from six dilated cardiomyopathy (DCM) explanted and five normal human hearts. Specifically, we identified three genes to be induced and several other genes to be repressed following DCM. Southern blot analysis of isolated cDNA using a collagenase cDNA probe indicated that one of the genes induced during DCM was interstitial collagenase (MMP-1). Northern blot analysis using MMP-1 cDNA probe indicated that MMP-1 was induced three- to fourfold in the DCM heart as compared to normal tissue. To analyze posttranslational expression of MMP and tissue inhibitor of matrix metalloproteinase (TIMP) we performed immunoblot, immunoassay, and substrate zymographic assays. TIMP-1 and MMP-1 levels were 37 +/- 8 ng/mg and 9 +/- 2 ng/mg in normal tissue specimens (P < 0.01) and 2 +/- 1 ng/mg and 45 +/- 11 ng/mg in DCM tissue (P < 0.01), respectively. Zymographic analysis demonstrated lytic bands at 66 kDa and 54 kDa in DCM tissue as compared to one band at 66 kDa in normal tissue. Incubation of zymographic gel with metal chelator (phenanthroline) abolished both bands suggesting activation of neutral MMP in DCM heart tissue. TIMP-1 was repressed approximately twentyfold in DCM hearts when compared with normal heart tissue. In situ immunolabeling of MMP-1 indicated phenotypic differences in the fibroblast cells isolated from the DCM heart as compared to normal heart. These results suggest disruption in the balance of myopathic-fibroblast cell ECM-proteinase and antiproteinase in ECM remodeling which is followed by dilated cardiomyopathy.

Molecular cloning of a gene encoding translation initiation factor (TIF) from Candida albicans

The differential display technique was applied to compare mRNAs from two clinical isolates of Candida albicans with different virulence; high (potent strain, 16240) and low (weak strain, 18084) extracellular phospholipase activities. Complementary DNA fragments corresponding to several apparently differentially expressed mRNAs were recovered and sequenced. A complementary DNA fragment seen distinctly in the potent phospholipase producing strain was highly homologous to the yeast translation initiation factor (TIF). The selected DNA fragment was then used as a probe to isolate its corresponding complementary DNA clone from a library of C. albicans genomic DNA. The sequence of isolated gene revealed an open reading frame of 1194 nucleotides with the potential to encode a protein of 397 amino acids with a predicted molecular weight of 43 kDa. Over its entire length, the amino acid sequence showed strong homology (78-89%) to Saccharomyces cerevisiae TIF and (63-80%) to mouse eIF-4A proteins. Therefore, our C. albicans gene was identified to be TIF (Ca TIF). Northern blot analysis in the two strains of C. albicans revealed that Ca TIF expression is 1.5-fold higher in the potent phospholipase producing strain. The restriction endonuclease digestion of genomic DNA from this potent strain revealed at least two hybridized bands in Southern blot analysis, suggesting two or more closely related sequences in the C. albicans genome.

Selection of probes for fluorescence in situ hybridization analysis by differential display polymerase chain reaction of mRNA from rhabdomyosarcoma

Rhabdomyosarcoma (RMS) is a malignancy of skeletal muscle derivation encompassing two major subtypes, embryonal and alveolar, which differ in clinical behavior and genetic markers. Because RMS is a relatively circumscribed tumor system for which the beginnings of a molecular genetic framework are in place, it becomes an ideal model for the application of improved methods of molecular genetic analysis. We have applied the technique known as differential display polymerase chain reaction (DD-PCR) to characterize expression of RNA in rhabdomyosarcoma subtypes. Our studies have shown that DD-PCR generates a characteristic electrophoretic profile that can be used to isolate subtype specific probes for fluorescence in situ hybridization (FISH) analysis. We have isolated two cDNA fragments and obtained clones suitable for FISH mapping to metaphase chromosomes. One probe was mapped to the centromeric region of human chromosome 22 and the other probe to the human chromosome band 6q25-26. This approach demonstrates the utility of DD-PCR as a technique for isolating novel cDNA expressed in tumors and their subsequent use as probes for FISH analysis. As more genes are identified by DD-PCR and their roles in tumorigenesis become defined, they are likely to provide novel targets for future molecular cytogenetic analysis.

Glucose-stimulated expressed sequence tags from rat pancreatic islets

Available evidence suggests that glucose, the most potent physiologic insulin secretagogue, capacitates glucose-induced insulin secretion by stimulating synthesis of various proteins in the beta cell. To obtain more clues about proteins that might be involved in insulin secretion, rat pancreatic cDNA libraries were screened by differential hybridization for non-preproinsulin transcripts that were increased when pancreatic islets were cultured for 1 day at a high (20 mM) versus a low concentration (1 mM) of glucose. More than 100,000 pfu were initially screened. After repeated rescreening, 33 transcripts were 1-3-fold higher in the presence of the high glucose. For comparison, preproinsulin transcripts were 4-8-fold higher at the high concentration of glucose. The sequences of 12 clones were > or = 85% similar to published sequences. These included annexin, calbindin, protein kinase C receptor, the G protein beta subunit, the guanyl cyclase A/atrial natriuretic peptide receptor and the serotonin 5HT-2 receptor. As previously reported, ferritin H chain transcripts were discovered to be 3-6-fold higher in the presence of the high glucose (MacDonald et al., FASEB J. 8, 777-781, 1994). Unidentified glucose responsive clones have been assigned GenBank accession numbers N55606-N55636, N65938 and N65939. The results implicate the proteins encoded by these mRNAs in insulin secretion.

msg1, a novel melanocyte-specific gene, encodes a nuclear protein and is associated with pigmentation

Messenger RNA transcripts of the highly pigmented murine melanoma B16-F1 cells were compared with those from their weakly pigmented derivative B16-F10 cells by differential display. A novel gene called msg1 (melanocyte-specific gene) was found to be expressed at high levels in B16-F1 cells but at low levels in B16-F10 cells. Expression of msg1 was undetectable in the amelanotic K1735 murine melanoma cells. The pigmented murine melanocyte cell line melan-a expressed msg1, as did pigmented primary cultures of murine and human melanocytes; however, seven amelanotic or very weakly pigmented human melanoma cell lines were negative. Transformation of murine melanocytes by transfection with v-Ha-ras or Ela was accompanied by depigmentation and led to complete loss of msg1 expression. The normal tissue distribution of msg1 mRNA transcripts in adult mice was confined to melanocytes and testis. Murine msg1 and human MSG1 genes encode a predicted protein of 27 kDa with 75% overall amino acid identity and 96% identity within the C-terminal acidic domain of 54 amino acids. This C-terminal domain was conserved with 76% amino acid identity in another protein product of a novel human gene, MRG1 (msg1-related gene), isolated from normal human melanocyte cDNA by 5'-rapid amplification of cDNA ends based on the homology to msg1. The msg1 protein was localized to the melanocyte nucleus by immunofluorescence cytochemistry. We conclude that msg1 encodes a nuclear protein, is melanocyte-specific, and appears to be lost in depigmented melanoma cells.

Developmentally regulated transcripts and evidence of differential mRNA processing in Giardia lamblia

Although encystation and excystation are crucial to transmission of Giardia lamblia, little is known about the regulation of these very distinct differentiation processes. Fingerprinting of giardial mRNA populations throughout the time course of differentiation demonstrated complex patterns in mRNA differential display. Certain transcripts appeared or increased, while others decreased or disappeared at specific times, in response to physiologic stimuli that mimic key stages in parasite descent through the host gastrointestinal tract. This approach has allowed the direct identification of critical stages in differentiation, as well as isolation of genes which may be crucial to the development of G. lamblia. One stage-specific single copy gene (ENC6) whose transcript is greatly upregulated during encystation was analyzed further. Partial sequence analysis revealed no correspondence with known genes. 3'-rapid amplification of cDNA ends (3'-RACE) analysis of ENC6 transcripts at various times of encystation revealed two polyadenylation sites. The more proximal site, 10 nucleotides past the single classic AGTAAA sequence, was utilized only during encystation and its transcript increased approximately 16-fold during the first 24 h of encystation. In contrast, a slightly divergent polyadenylation site 288 nucleotides downstream from the open reading frame (ORF) was used during both vegetative growth and encystation, although its transcript was present at low levels. These studies are the first evidence of differential mRNA processing in G. lamblia and suggest a potential role of the 3'-untranslated region (3'-UTR) in modulating gene expression during differentiation of this primitive eukaryote.

Identification of a c-fos-induced gene that is related to the platelet-derived growth factor/vascular endothelial growth factor family

Using a mRNA differential screening of fibroblasts differing for the expression of c-fos we isolated a c-fos-induced growth factor (FIGF). The deduced protein sequence predicts that the cDNA codes for a new member of the platelet-derived growth factor/vascular endothelial growth factor (PDGF/VEGF) family. Northern blot analysis shows that FIGF expression is strongly reduced in c-fos-deficient cells. Transfection of exogenous c-fos driven by a constitutive promoter restores the FIGF expression in these cells. In contrast, both PDGF and VEGF expression is unaffected by c-fos. FIGF is a secreted dimeric protein able to stimulate mitogenic activity in fibroblasts. FIGF overexpression induces morphological alterations in fibroblasts. The cells acquire a spindle-shaped morphology, become more refractive, disorganized, and detach from the plate. These results imply that FIGF is a downstream growth and morphogenic effector of c-fos. These results also suggest that the expression of FIGF in response to c-fos activation induces specific differentiation patterns and its aberrant activation contributes to the malignant phenotype of tumors.

Molecular cloning of the cDNA encoding a murine sialic acid-specific 9-O-acetylesterase and RNA expression in cells of hematopoietic and non-hematopoietic origin

We describe the isolation of a cDNA encoding a murine sialic acid-specific 9-O-acetylesterase as well as its expression pattern in cells of both hematopoietic and non-hematopoietic origin. This enzyme catalyzes the removal of O-acetyl ester groups from position 9 of the parent sialic acid N-acetylneuraminic acid. The cDNA is 2105 nt in length and encodes a protein of 541 amino acids with a predicted molecular weight of 61 kDa, not including oligosaccharides linked to eight potential N-glycosylation sites. The cDNA encoding the acetylesterase displays a widespread distribution in various cell lines and tissues. Expression studies of B lineage cell lines and primary fetal liver cells revealed a developmentally regulated expression pattern in cells of hematopoietic origin. Given the importance of 9-O-acetylation of sialic acids, the cloning of the cDNA encoding a sialic acid-specific 9-O-acetylesterase will be helpful in understanding further the regulation of this post-translational modification and the biological consequences thereof.

Identification of hypoxically inducible mRNAs in HeLa cells using differential-display PCR. Role of hypoxia-inducible factor-1

Oxygen is an important regulator of gene expression in mammalian cells, though the extent of operation and the organization of the inducible mechanisms involved are still largely undetermined. To define better the response to hypoxia, we have used differential display PCR to identify genes whose expression is induced in HeLa cells exposed to 1% oxygen. Among six genes whose induction by hypoxia was newly defined in this way, three were of known function, encoding the glucose transporter isoform 3 (Glut-3), adenylate kinase isoenzyme 3 (AK-3), and tissue factor, two were expressed sequence tags (ESTs), and one corresponded to a new sequence. One regulator of the transcriptional response to hypoxia has recently been identified as a heterodimeric DNA-binding complex termed hypoxia-inducible factor-1 (HIF-1), which is also inducible by the iron chelator, desferrioxamine. Of the six hypoxically regulated genes, at least four were also induced by exposure of the cells to desferrioxamine. To analyse further the mechanisms underlying induction of the genes identified in the differential display, inducible expression was compared in wild-type mouse hepatoma cells (Hepa-1), and mutant derivatives (c4) which fail to generate HIF-1, due to a functional defect in one component, HIF-1 beta. Two types of response were defined. For Glut-3 and AK-3, mutant (c4) cells showed almost complete loss of the inducible response to both hypoxia and desferrioxamine. In contrast, tissue factor mRNA was more inducible by both stimuli in c4 than wild-type cells. These studies demonstrate the critical importance of HIF-1 beta in newly recognized responses to hypoxia, and provide further evidence of the importance of this system of gene regulation in mammalian cells; they also demonstrate responses to both hypoxia and desferrioxamine which are independent of HIF-1 beta and which appear exaggerated in HIF-1 beta-deficient cells.