Analysis of altered gene expression by differential display

Isolation and characterization of novel pituitary tumor related genes: a cDNA representational difference approach

Recently, progress has been made in understanding human pituitary tumor pathogenesis by the investigation of differences in gene expression between normal pituitary tissue and pituitary tumors. A number of approaches, including differential display (DD), representational difference analysis (RDA), and microarray analysis have been used and several molecular targets potentially associated with pituitary tumor development and invasion have been identified. We have used RDA to compare gene expression patterns between normal human pituitary and clinically non-functioning pituitary adenomas, and identified genes with growth suppression function which are expressed in the normal pituitary but not in pituitary tumors. In particular, we have focused on an imprinted gene, Maternally Expressed Gene 3 (MEG3), which is specifically associated with clinically non-functioning pituitary adenomas of a gonadotroph lineage. MEG3 functions to suppress tumor cell growth, increase protein expression of the tumor suppressor p53, and selectively activate p53 target genes. Interestingly, MEG3 does not encode a protein but a non-coding RNA. Therefore, these studies have revealed novel mechanisms for the function of a non-coding RNA in pituitary physiology and tumorigenesis.

Automated fluorescent differential display for cancer gene profiling

Since its invention in 1992, differential display (DD) has become the most commonly used technique for identifying differentially expressed genes because of its many advantages over competing technologies such as DNA microarray, serial analysis of gene expression (SAGE), and subtractive hybridization. A large number of these publications have been in the field of cancer, specifically on p53 target genes. Despite the great impact of the method on biomedical research, there had been a lack of automation of DD technology to increase its throughput and accuracy for systematic gene expression analysis. Many previous DD work has taken a "shotgun" approach of identifying one gene at a time, with a limited number of polymerase chain reactions (PCRs) set up manually, giving DD a low-tech and low-throughput image. We have optimized the DD process with a platform that incorporates fluorescent digital readout, automated liquid handling, and large-format gels capable of running entire 96-well plates. The resulting streamlined fluorescent DD (FDD) technology offers an unprecedented accuracy, sensitivity, and throughput in comprehensive and quantitative analysis of gene expression. These major improvements will allow researchers to find differentially expressed genes of interest, both known and novel, quickly and easily.

Reciprocal subtraction differential RNA display (RSDD): an efficient technology for cloning differentially expressed genes

Identification of differentially expressed genes is an essential step in comprehending the molecular basis of complex physiological and pathological processes. Subtraction hybridization and differential RNA display (DDRT-PCR) are two methods that are widely and successfully employed to clone differentially expressed genes. Unfortunately, both methods have inherent problems and limitations requiring improvements in the technique. A combination of these two methods termed reciprocal subtraction differential RNA display is described here that considerably reduces the complexity of DDRT-PCR and facilitates the rapid and efficient identification and cloning of both abundant and rare differentially expressed genes.

Cloning differentially expressed genes using rapid subtraction hybridization (RaSH)

Differential gene expression represents the entry point for comprehending complex biological processes. In this context, identification and cloning of differentially expressed genes represent critical elements in this process. Many techniques have been developed to facilitate achieving these objectives. Although effective in many situations, most currently described approaches are not trouble-free and have limitations, including complexity of performance, redundancy of gene identification (reflecting cloning biases) and false-positive gene identification. A detailed methodology to perform a rapid and efficient cloning approach, called rapid subtraction hybridization is described in this chapter. This strategy has been applied successfully to a number of cell culture systems and biological processes, including terminal differentiation and cancer progression in human melanoma cells, resistance or sensitivity to HIV-1 in human T cells and gene expression changes following infection of normal human fetal astrocytes with HIV-1 or treatment with neutrotoxic agents. Based on its simplicity of performance and high frequency of genuine differential gene identification, the rapid subtraction hybridization (RaSH) approach will allow wide applications in diverse systems and biological contexts.

A protocol for differential display of mRNA expression using either fluorescent or radioactive labeling

Since its invention in the early 1990s, differential display (DD) has become one of the most commonly used techniques for identifying differentially expressed genes at the mRNA level. Unlike other genomic approaches, such as DNA microarrays, DD systematically detects changes in mRNA profiles among multiple samples being compared without the need of any prior knowledge of genomic information of the living organism being studied. Here, we present an optimized DD protocol with a fluorescent digital readout as well as traditional radioactive labeling. The resulting streamlined fluorescent DD process offers an unprecedented accuracy, sensitivity and throughput in comprehensive and quantitative analysis of eukaryotic gene expression. Results usually can be obtained within days using a limited number of primer combinations, but a comprehensive DD screen may take weeks or months to accomplish, depending on gene coverage required and the number of differentially expressed genes present within a biological system being compared.

From differential display to DNA microarrays--a personal account

This article is a tribute to Dr. Arthur Pardee, one of the most innovative and brilliant scientists of our time, on the occasion of his 85th birthday. In this partially perspective and partially review piece, I look back how fate, by twist and turn, has led me eventually to his lab at Harvard where we worked out the Differential Display technology from scratch, how the method has revolutionized the field of gene expression analysis and where DD is taking us in the "era" of DNA microarrays.

Gene expression in the adapting small bowel after massive small bowel resection

BACKGROUND

Intestinal adaptation occurs in the residual bowel following the loss or resection of a proportion of the small bowel. The purpose of the adaptive response is to return absorptive and digestive properties to near normal levels. This study employed a rat model of massive small bowel resection (MSBR) to study the adaptive response in the residual terminal ileum and the jejunum. The time points were chosen to reflect changes in gene expression early on in the response, because these are the genes that alter to initiate and maximize the response observed during adaptation.

METHODS

Sprague Dawley rats underwent an 80% resection. Differential display polymerase chain reaction (DD-PCR) analysis was performed on mRNA extracted from the remnant ileum and jejunum 0, 1, 2, 4, and 7 days post-MSBR.

RESULTS

DD-PCR identified 11 genes that were possibly regulated following MSBR. Genes confirmed to be regulated were 16S ribosomal RNA, lymphocyte antigen 6 (LY6)-like molecule, Krüppel-like factor-3 (KLF-3), G-protein-binding protein (CRFG), system A transporter 2 (SAT2), and an intestine-specific gene (similar to mKIAA0493).

CONCLUSIONS

DD-PCR analysis showed regulation of a number of genes not previously known to be involved in adaptation after MSBR or previously characterized in the intestine. These genes may be important in bringing about the complement of changes seen during the adaptive response.

Identification of differentially expressed genes in scarless wound healing utilizing polymerase chain reaction- suppression subtractive hybridization

Wound healing in fetal skin is well known to proceed without scarring, whereas adult (postnatal) skin wound healing is accompanied by scar formation. To identify differentially expressed genes during fetal wound (FW) healing, we have used polymerase chain reaction-suppression subtractive hybridization. This technique allows for a comparative analysis across the entire transcriptome of FW vs. unwounded fetal control tissue, including even potentially novel sequences. Our subtractive hybridization protocol identified 15 clones that are overexpressed in healing FWs, and 20 clones that are underexpressed. These include genes with both known and unknown functions. We have confirmed the differential pattern of expression for four of these candidate genes: elongation factor 1 alpha, elongation initiation factor 4e, and two transcripts thus far known only as an expressed sequence tags. With this approach, we have also identified novel genes potentially involved in scarless wound healing.

DARFA: a novel technique for studying differential gene expression and bacterial comparative genomics

We have developed a powerful method, named differential analysis of restriction fragments amplification (DARFA), which enables researchers to perform comprehensive transcriptome analysis as well as bacterial DNA fingerprinting. The key feature of this novel technique lies within the usage of a type IIS enzyme, Hpy188III, which cleaves cDNA or genomic DNA at a TC/NNGA recognition sequence. Cleavage at this particular site results in the production of a pool of restriction fragments which can be divided into 120 subsets based on the 2-nt 5'-overhang sequence. Each subset of restriction fragments is then selectively amplified by PCR after ligation with a pair of hairpin adaptors containing 2-nt overhangs which are complementary to those in the subset of fragments that are to be analyzed. The results obtained from the analysis of strain-specific and tissue-specific differences using DARFA and further confirmation by DNA sequencing and Northern analysis have demonstrated that the DARFA technique provides a novel tool for expression profiling, as well as bacterial DNA fingerprinting.

Differentiation of chromaffin cells elicited by ELF MF modifies gene expression pattern

Chromaffin cells exposed to extremely low frequency magnetic fields (ELF MF, 60 Hz, 0.7 mT) differentiate into sympathetic neuron-like cells. This complex process must involve both qualitative and quantitative variations in gene expression. This study looks at whether ELF MF treatment provokes changes in the global transcription profile of chromaffin cells, using the RT-Differential Display method. When the gene expression patterns of experimental groups (nerve growth factor (NGF) and ELF MF) were compared to those receiving no treatment, at least 53 transcripts showing differential expression were detected. Eight RT-PCR products, corresponding to six genes, were re-amplified, sequenced and compared with the rat gene bank. Sequence analysis showed that these genes most likely encode: phosphoglucomutase-1, neurofibromatosis-2 interacting protein, microtubule associated protein-2, thiamine pyrophosphokinase, and two unidentified hypothetical proteins (RNOR02022103 and ROR01044577), and that the presumed regulatory regions of these genes contained CTCT-clusters, which are thought to be required for electromagnetic field-dependent gene expression.

Reproducibility, bioinformatic analysis and power of the SAGE method to evaluate changes in transcriptome

The serial analysis of gene expression (SAGE) method is used to study global gene expression in cells or tissues in various experimental conditions. However, its reproducibility has not yet been definitively assessed. In this study, we have evaluated the reproducibility of the SAGE method and identified the factors that affect it. The determination coefficient (R²) for the reproducibility of SAGE is 0.96. However, there are some factors that can affect the reproducibility of SAGE, such as the replication of concatemers and ditags, the number of sequenced tags and double PCR amplification of ditags. Thus, corrections for these factors must be made to ensure the reproducibility and accuracy of SAGE results. A bioinformatic analysis of SAGE data is also presented in order to eliminate these artifacts. Finally, the current study shows that increasing the number of sequenced tags improves the power of the method to detect transcripts and their regulation by experimental conditions.

Molecular biology of nickel carcinogenesis: identification of differentially expressed genes in morphologically transformed C3H10T1/2 Cl 8 mouse embryo fibroblast cell lines induced by specific insoluble nickel compounds

Inhalation of mixtures of insoluble and soluble nickel compounds by humans during nickel refining has been associated with excess lung and nasal sinus cancers. Insoluble nickel subsulfide (Ni3S2) and nickel oxide (NiO) are carcinogenic to rodents by inhalation. We previously showed that insoluble Ni3S2, crystalline nickel monosulfide (NiS), and green (high temperature, HT) and black (low temperature, LT) NiO, induced morphological transformation in cultured C3H/10T1/2 Cl 8 (10T1/2) mouse embryo cells. To understand molecular mechanisms of carcinogenesis by insoluble nickel compounds, we used random, arbitrarily primed-polymerase chain reaction (RAP-PCR) mRNA differential display and identified nine cDNA fragments that were differentially expressed between nontransformed and nickel-transformed cell lines in approximately 10.0% of the total mRNA. Expression of the calnexin gene (encoding a type I membrane protein/molecular chaperone), the ect-2 proto-oncogene, and the stress-inducible gene, Wdr1, was upregulated. Expression of six genes--the vitamin D interacting protein/thyroid hormone activating protein 80 (DRIP/TRAP-80) gene, the insulin-like growth factor receptor 1 (IGFR1) gene, the small nuclear activating protein (SNAP C3) gene, and three unknown genes, was down-regulated, in nickel-transformed cell lines. We hypothesize that these resulting aberrations in gene expression could contribute to the induction and/or maintenance of morphological transformation induced by specific insoluble nickel compounds.

Reduced KIAA0471 mRNA expression in Alzheimer's patients: a new candidate gene product linked to the disease?

Alzheimer's disease (AD) phenotype complexity raises the question whether genetic features remain unknown. Although a few percentage of patients are familial cases linked to mutations in amyloid precursor protein, presenilin 1 or presenilin 2 genes, the remainder are considered mainly sporadic late-onset cases with a complex etiology. However, changes in gene expression or other genetic features of the individual can clearly contribute to develop the illness. Consequently, in this paper we have focused on the identification of new genes, the expression of which is altered in AD. We used the technique of differential display reverse transcriptase-polymerase chain reaction (DDRT-PCR) in order to study the gene expression differences in brain tissue from patients in an advanced stage of AD. After studying medial septum and hippocampus brain areas, we found an inhibition of the KIAA0471 gene expression in three out of six AD patients, including one with a presenilin 1 gene mutation. This gene encodes for a large protein that presents, in its predicted form, 95% homology with IDN4-GGTR sequences. These results may provide significant clues for understanding the molecular mechanisms underlying septohippocampal neurodegeneration. In addition, they may open a new area of research for diagnostic and therapeutic tools, the relevance of which is also considered.

Molecular targets of lithium action

Lithium is an effective drug for both the treatment and prophylaxis of bipolar disorder. However, the precise mechanism of lithium action is not yet well understood. Extensive research aiming to elucidate the molecular mechanisms underlying the therapeutic effects of lithium has revealed several possible targets. The behavioral and physiological manifestations of the illness are complex and are mediated by a network of interconnected neurotransmitter pathways. Thus, lithium's ability to modulate the release of serotonin at presynaptic sites and modulate receptor-mediated supersensitivity in the brain remains a relevant line of investigation. However, it is at the molecular level that some of the most exciting advances in the understanding of the long-term therapeutic action of lithium will continue in the coming years. The lithium cation possesses the selective ability, at clinically relevant concentrations, to alter the PI second-messenger system, potentially altering the activity and dynamic regulation of receptors that are coupled to this intracellular response. Subtypes of muscarinic receptors in the limbic system may represent particularly sensitive targets in this regard. Likewise, preclinical data have shown that lithium regulates arachidonic acid and the protein kinase C signaling cascades. It also indirectly regulates a number of factors involved in cell survival pathways, including cAMP response element binding protein, brain-derived neurotrophic factor, bcl-2 and mitogen-activated protein kinases, and may thus bring about delayed long-term beneficial effects via under-appreciated neurotrophic effects. Identification of the molecular targets for lithium in the brain could lead to the elucidation of the pathophysiology of bipolar disorder and the discovery of a new generation of mood stabilizers, which in turn may lead to improvements in the long-term outcome of this devastating illness (1).

Serial analysis of gene expression in the skeletal muscle of endurance athletes compared to sedentary men

Physical exercise produces several adaptive changes in skeletal muscle. However, the molecular mechanisms of these effects are poorly understood. We performed serial analysis of gene expression (SAGE) to quantify the global gene expression profile in sedentary and endurance-trained muscle. A total of 10869 SAGE tags was sequenced and represented 4727 genes. The genes most expressed in muscle are mainly involved in contraction and energy metabolism. Thirty-three genes were differentially expressed between endurance athletes and sedentary individuals. Four genes such as myosin binding protein C fast-type, glycogen phosphorylase, and pyruvate kinase were expressed less in endurance athletes, whereas eight genes coding for expressed sequence tag similar to (EST) crystallin alpha B, EST myosin light chain 2, EST surfactant pulmonary-associated protein A1, EST thrombospondin, EST fructose-bisphosphate aldolase A, EST cytochrome oxidase 1, NADH dehydrogenase 3, and G8 protein were up-regulated. Most of the up-regulated tags corresponded to novel genes. On the other hand, different isoforms of fructose-bisphosphate aldolase A were also differentially expressed. The current study underlying the most highly expressed genes allows a better understanding of global muscle characteristics in normal and endurance-trained individuals. Moreover, the current data suggest novel candidate genes that may be responsible for enhanced endurance performance.

Identification of cellular mRNA targets for RNA-binding protein Sam68

Sam68 (Src-associated in mitosis, 68 kDa), a nuclear RNA-binding protein, has been postulated to play a role in cell-growth control as a modulator of signal transduction and activation of RNA metabolism. Although Sam68 was demonstrated to bind to the UAAA sequences in synthetic oligoribonucleotides and poly(U) homopolymers in vitro, the legitimate cellular mRNA target remained unclear. By using the differential display and cDNA-representational difference analysis techniques, followed by reverse transcription polymerase chain reaction of RNAs co-immunoprecipitated with Sam68 from a HeLa cell lysate, we identified 10 mRNA species that bind in vivo to Sam68 in an RNA-binding domain-dependent manner. Among them, the mRNA species for hnRNP A2/B1 and beta-actin were found to bind prominently in vivo as well as in vitro, suggesting the possible involvement of Sam68 in the post- transcriptional regulation of these genes. Mapping of the Sam68-binding sequence revealed that Sam68 associates with these mRNAs through different nucleotide motifs, UAAA for hnRNP A2/B1 mRNA and UUUUUU for beta-actin mRNA, and that both binding sequences must reside in a loop structure for recognition by Sam68. The results indicated that Sam68 recognizes both the UAAA motif and poly(U) sequences in vivo for binding to cellular target mRNAs.

Hepatic cytochrome p450-2A and phosphoribosylpyrophosphate synthetase-associated protein mRNA are induced in gerbils after consumption of isoflavone-containing protein

Soy intake reduces cholesterol levels, but neither the exact component in soy causing this reduction nor the mechanism by which cholesterol is reduced is known with certainty. In this study, a genetic screen was performed to identify hepatic mRNA in gerbils regulated by soy or soy isoflavones. Gerbils were fed casein, an alcohol-washed soy-based diet (containing low levels of isoflavones), and the soy-based diet supplemented with an isoflavone-containing soy extract. After feeding for 28 d, gerbils were killed, hepatic RNA was isolated, and genes that were differentially expressed in any of the three dietary conditions were identified. Fifteen different mRNA were originally selected, including two mRNA that were studied further and shown to be highly regulated. Messenger RNA levels for both cytochrome P450-2A and phosphoribosylpyrophosphate synthetase-associated protein were up-regulated in a dose-dependent manner when soy replaced casein in the diet at 0, 33, 67 and 100% of original casein levels. A subsequent experiment used purified amino acid mixtures resembling the percentage amino acid composition of soy and casein to ensure that isoflavone-free protein sources could be tested. Using these mixtures, a 2 x 2 x 2 design tested: natural vs. synthetic protein sources, casein- vs. soy-based diets, and isoflavone extract-supplemented or supplement-free diets. This design demonstrated that these two mRNA were again significantly up-regulated more than twofold (P < 0.05) in gerbils fed all diets containing isoflavones. Induction of these two mRNA by soy may be due to the aryl hydrocarbon receptor element in the promoter region of both genes.

Identification of a disulfide isomerase protein of Leishmania major as a putative virulence factor

Several approaches have been previously used to elucidate the genetic basis of Leishmania virulence. In general, they were based on laboratory Leishmania clones genetically modified or grown in the presence of selecting agents. In a previous study, we demonstrated that Leishmania major freshly isolated from human cutaneous lesions showed significant differences in the severity of the experimental disease induced in BALB/c mice. Here, using the mRNA differential display technique, we analyzed gene expression in L. major promastigotes showing different levels of virulence. We have identified a novel Leishmania gene encoding a 477-amino-acid protein exhibiting two distinct regions that are identical to the putative active-site sequence (CGHC) of the eukaryotic protein disulfide isomerase (PDI). The recombinant protein displayed a specific PDI enzymatic activity. This L. major disulfide isomerase protein (LmPDI) is predominantly expressed, at both the mRNA and protein levels, in highly virulent strains. Specific PDI inhibitors abolished the enzymatic activity of the recombinant protein and profoundly affected parasite growth. These findings suggest that LmPDI may play an important role in Leishmania natural pathogenicity and may constitute a new target for anti-Leishmania chemotherapy.

Overexpression of sorcin, a calcium-binding protein, induces a low level of paclitaxel resistance in human ovarian and breast cancer cells

Paclitaxel, an antimitotic, anticancer agent, induces cell cycle arrest in the mitotic phase by binding to the beta-tubulin subunit and forming highly stable microtubule polymers that resist depolymerization. The overexpression of the P-glycoprotein (P-gp) and/or alteration in the cellular microtubules is associated with the development of paclitaxel resistance. However, we have established a paclitaxel-resistant human ovarian carcinoma subline (2008/13/4) wherein the degree of resistance could not be correlated with overexpression of P-gp, alterations in the alpha- and beta-tubulin isotypes, or changes in the drug-binding affinity of the microtubules. mRNA differential display analysis revealed the overexpression of sorcin, a calcium-binding protein in the 2008/13/4 cells. However, no detectable changes in the intracellular calcium levels were detected in the parental and the paclitaxel-resistant variant. Furthermore, co-treatment with A23187, a calcium ionophore, did not alter the cytotoxicity of paclitaxel against the parental and the paclitaxel-resistant cells. Transfection of the parental 2008 cells with full-length sorcin cDNA induced a low level (3-5-fold) of paclitaxel resistance. In addition, transfection of human breast cancer cells with the full-length sorcin cDNA also led to the induction of a low level of paclitaxel resistance in the transfectants. Although the overexpression of sorcin did not produce high levels of paclitaxel resistance, the results obtained present compelling evidence of the involvement of sorcin in developing low-level paclitaxel resistance in a variety of tumor cells. The precise biochemical mechanism(s) by which sorcin overexpression induces low-level paclitaxel resistance is currently under investigation.

B cell activation leads to upregulated expression of the murine Sik-similar protein gene

B cells stimulated by the combination of CD40L plus anti-Ig were screened for upregulated gene expression in an unbiased fashion through differential display. An inducible transcript was obtained that corresponds to a sequence previously isolated from pre-B cells and termed murine Sik-similar protein (mSSP). The mSSP gene is predominantly expressed in lymphoid tissues, including spleen and thymus, as well as testis, with lesser amounts in kidney and ovary. Among lymphocyte cell lines, mSSP expression varies widely. The mSSP protein is localized to the nucleus in NIH3T3 cells, and its expression in BAL-17 B cells varies with cell cycle progression. Expression of mSSP increased significantly within the first hours of B cell treatment with either CD40L, anti-IgM, or phorbol myristate acetate (PMA) with or without ionomycin. The predicted amino acid sequence of mSSP bears some homology to proteins involved in ribosomal RNA synthesis and processing. mSSP is a previously identified pre-B cell gene now shown for the first time to be an activation-responsive transcript in mature, primary B cells.

Genetic dissection of corticosterone receptor function in the rat hippocampus

The hippocampus, a brain structure with a crucial role in learning and memory and an involvement in stress-related neurological or psychiatric disorders, is extremely sensitive to aberrant levels of corticosteroid stress hormones (CORT). We hypothesized that CORT-affected brain disorders are the result of aberrant expression of specific CORT-responsive genes. In order to identify such genes, we have applied several gene expression profiling techniques such as differential display, DNA micro-arrays and in particular the highly sensitive serial analysis of gene expression (SAGE). Using SAGE, a total of 76,790 hippocampal tags were generated which together represent 28,748 unique mRNAs of which 4626 gave a hit with rat sequences in Genbank. By comparing SAGE profiles derived from rat hippocampi treated with different concentrations of corticosteroids, we have identified over 200 CORT-responsive genes with significant differential expression in hippocampus. The identified products include genes that are important for the plasticity of hippocampal neurones such as neural cell adhesion molecules, growth-promoting proteins, genes involved in axogenesis, synaptogenesis and signal-transduction. One novel corticosteroid-responsive gene, classified as Ca2+/calmodulin-dependent protein kinase (CaMK)-VI, exhibited structural resemblance with the family of CaMKs, in particular with that of CaMK-IV. We also identified an alternatively spliced mRNA of this gene encoding a peptide (CaMK-kinase related peptide or CARP) which may function in an autoregulatory feedback loop. These findings suggest a novel mode of operation of the CaMK pathway in control of Ca2+ homeostasis relevant for CORT-related brain disorders.

Searching for excystment-regulated genes in Sterkiella histriomuscorum (Ciliophora, Oxytrichidae): a mRNA differential display analysis of gene expression in excysting cells

In the absence of food, the oxytrichid Sterkiella histriomuscorum transforms like many ciliates into resting cysts. When transferred back into feeding medium, the cyst re-transforms into a vegetative cell. The entry into and exit from the dormant cyst stage are complex developmental processes still poorly investigated at the molecular level. Assuming that these changes in state could involve changes in gene expression, we have used the technique of mRNA differential display to detect differentially expressed genes in cysts and two different stages of excysting cell. Variation in the temporal expression pattern of transcripts could be detected and, in using an inverse-PCR strategy on circularized macronuclear DNA, we have sequenced the macronuclear genes of three of the isolated cDNAs. which correspond to 1) a nucleotide-binding domain-encoding gene, 2) a DHHC-domain-carrying gene, and 3) a phosphatase type 2C-encoding gene. For the first two genes, Northern blot analyses supported an excystment-associated regulated gene expression. We discuss their possible role during excystment and we show that the combination of differential display and inverse PCR constitutes a powerful approach to isolate excystment-regulated genes in hypotrichs.

Identification of rat enamel organ RNA transcripts using differential-display

Enamel formation is a complex process which involves the expression of a number of genes, the most obvious being those related to the mineralized extracellular matrix. In this study the differential-display technique, first described by Liang and Pardee, has been used to identify genes specifically expressed in enamel organ cells. By comparing results obtained from RNA derived from rat enamel organ with RNA derived from other cellular sources, a number of differentially expressed transcripts have been identified. The nucleotide sequences of two of these have been analyzed and shown to have no homology with any previously published sequences. Further analysis will provide information on the type of protein that they may encode, their tissue distribution and their potential role in enamel formation.

Modulations in gene expression and mapping of genes associated with cyst nematode infection of soybean

Infection of the soybean root by the soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) induces a well-documented, yet poorly understood, response by the host plant. The plant response, involving the differentiation of a feeding structure, or "syncytium," facilitates the feeding and reproduction of the nematode to the detriment of the host. We used a genetic system involving a single dominant soybean gene conferring susceptibility to an inbred nematode strain, VL1, to characterize the nematode-host interaction in susceptible line PI 89008. The restriction fragment length polymorphism marker pB053, shown to map to a major SCN resistance locus, cosegregates with resistance among F2 progeny from the PI 89008 x PI 88287 cross. Cytological examination of the infection process confirmed that syncytium development in this genetic system is similar to that reported by others who used noninbred nematode lines. Our study of infected root tissue in the susceptible line PI 89008 revealed a number of genes enhanced in expression. Among these are catalase, cyclin, elongation factor 1alpha, beta-1,3-endoglucanase, hydroxy-methylglutaryl coenzyme A reductase, heat shock protein 70, late embryonic abundant protein 14, and formylglycinamidine ribonucleotide synthase, all of which we have genetically positioned on the public linkage map of soybean. Formylglycinamidine ribonucleotide synthase was found to be tightly linked with a major quantitative trait locus for SCN resistance. Our observations are consistent with the hypothesis proposed by others that feeding site development involves the dramatic modulation of gene expression relative to surrounding root cells.

Partial transcriptome of the developing pituitary gland

The anterior lobe of the pituitary gland is composed of five hormone-producing cell types and develops from Rathke's pouch, an invagination of oral ectoderm. In mice, rapid cell proliferation occurs in the pouch from embryonic day 12.5 (e12.5) to e14.5, preceding the appearance of most hormone transcripts. Cell-type-specific commitment probably occurs prior to e14.5, but cell differentiation can be demonstrated only by detection of hormone transcripts. Although several transcription factors critical for pouch expansion are known, few of their target genes have been identified. To identify putative transcription factor target genes and cell-type-specific markers, we used differential display PCR analysis of RNA prepared from e12.5 and e14.5 Rathke's pouches. We present an expression profile of the developing pituitary gland including 83 transcripts, 40% of which are novel. The tissue distribution, cell specificity, and developmental regulation were determined for a subset of the transcripts.

Clinical and preclinical evidence for the neurotrophic effects of mood stabilizers: implications for the pathophysiology and treatment of manic-depressive illness

Recent neuroimaging studies have demonstrated regional central nervous system volume reductions in mood disorders, findings that are complemented by postmortem observations of cell atrophy and loss. It is thus noteworthy that lithium and valproate have recently been demonstrated to robustly increase the expression of the cytoprotective protein bcl-2 in the central nervous system. Chronic lithium not only exerts neuroprotective effects in several preclinical paradigms but also enhances hippocampal neurogenesis. Valproate robustly promotes neurite outgrowth and activates the ERK mitogen-activated protein kinase pathway, a signaling pathway utilized by many endogenous neurotrophic factors. Consistent with its preclinical neurotrophic/neuroprotective effects, chronic lithium treatment of patients with manic-depressive illness increases brain N-acetylaspartate (a putative marker of neuronal viability and function) levels, an effect that is localized almost exclusively to gray matter. To determine if lithium was producing neuropil increases, quantitative three-dimensional magnetic resonance imaging studies were undertaken, which revealed that chronic lithium significantly increases total gray matter volume in the human brain of patients with manic-depressive illness. Together, these results suggest that a reconceptualization about the optimal long-term treatment of recurrent mood disorders is warranted. Optimal long-term treatment for these severe illnesses may only be achieved by the early use of agents with neurotrophic/neuroprotective effects, irrespective of the primary, symptomatic treatment.

Identification of a novel ligand-receptor pair constitutively activated by ras oncogenes

The Ras signaling pathway is thought to control the expression of a subset of yet to be defined genes that are crucial for cell growth and differentiation. Here we have identified by differential display a novel oncogenic Ras target, mob-5, encoding a 23-kDa cytokine-like secreted protein. Mob-5 expression could be induced by oncogenic Ha-ras and Ki-ras, but not by normal ras activation. Inhibitors of both Ha-Ras and mitogen-activated protein kinase kinase completely abolished the mob-5 expression in ras transformed cells, with concomitant loss of the transformation phenotype. Using an alkaline phosphatase-tagged Mob-5 as ligand, a putative Mob-5 receptor was identified on the cell surface of oncogenic ras transformed cells. Thus, the Mob-5/Mob-5 receptor may represent a novel putative autocrine loop coordinately activated by ras oncogenes.

Identification of ragAB as a temperature-regulated operon of Porphyromonas gingivalis W50 using differential display of randomly primed RNA

Porphyromonas gingivalis is a gram-negative, black-pigmented anaerobe that has been associated with advanced periodontal disease. The genome of P. gingivalis has the potential to produce a number of virulence determinants including proteases, hemagglutinins, hemolysin, invasion-associated proteins, and products of the pathogenicity island ragAB; however, little is known about how their expression is controlled. Periodontal pockets experience a higher temperature during inflammation, and this elevated temperature may influence the pathogenicity of P. gingivalis by changing its patterns of gene expression. In this study, RNA has been isolated from cells of P. gingivalis grown to steady state at temperatures of 37, 39, and 41 degrees C under hemin excess conditions (pH 7.0) in a chemostat. The RNA was subjected to PCR amplification following reverse transcription, using various combinations of randomly selected oligonucleotide primers. Reproducible RNA fingerprints have been obtained; however, differences were demonstrated in the RNA profiles of cells grown at the three temperatures, indicating differences in gene expression. Several PCR fragments were isolated that appeared to represent temperature-regulated genes. The nucleotide sequence of one of these has been identified as part of the ragAB locus, which codes for both a 55-kDa immunodominant antigen (RagB) and a homologue of the family of TonB-linked outer membrane receptors (RagA). These data indicate that expression of ragAB may be modulated in response to changes in temperature and that this may suggest a mechanism of evading the host response in the inflamed periodontal pocket.

Placental transforming growth factor-beta is a downstream mediator of the growth arrest and apoptotic response of tumor cells to DNA damage and p53 overexpression

The p53 tumor suppressor gene and members of the transforming growth factor-beta (TGF-beta) superfamily play central roles in signaling cell cycle arrest and apoptosis (programmed cell death) in normal development and differentiation, as well as in carcinogenesis. Here we describe a distantly related member of the TGF-beta superfamily, designated placental TGF-beta (PTGF-beta), that is up-regulated in response to both p53-dependent and -independent apoptotic signaling events arising from DNA damage in human breast cancer cells. PTGF-beta is normally expressed in placenta and at lower levels in kidney, lung, pancreas, and muscle but could not be detected in any tumor cell line studied. The PTGF-beta promoter is activated by p53 and contains two p53 binding site motifs. Functional studies demonstrated that one of these p53 binding sites is essential for p53-mediated PTGF-beta promoter induction and specifically binds recombinant p53 in gel mobility shift assays. PTGF-beta overexpression from a recombinant adenoviral vector (AdPTGF-beta) led to an 80% reduction in MDA-MB-468 breast cancer cell viability and a 50-60% reduction in other human breast cancer cell lines studied, including MCF-7 cells, which are resistant to growth inhibition by recombinant wild-type p53. Like p53, PTGF-beta overexpression was seen to induce both G(1) cell cycle arrest and apoptosis in breast tumor cells. These results provide the first evidence for a direct functional link between p53 and the TGF-beta superfamily and implicate PTGF-beta as an important intercellular mediator of p53 function and the cytostatic effects of radiation and chemotherapeutic cancer agents.

Fluorescent differential display identifies circadian clock-regulated genes in Arabidopsis thaliana

Circadian rhythms in gene expression were first observed in plants more than 13 years ago, but the underlying mechanism controlling rhythmic gene expression is still not understood. The isolation of novel circadian clock-controlled genes (ccgs) is likely to provide new tools for studying circadian rhythms. Fluorescent differential display (FDD) was used to screen Arabidopsis thaliana mRNAs for cycling transcripts. Seventy PCR primer pairs were screened, and 17 different cycling bands were observed out of an estimated 10,500 bands screened. The identities of 10 bands were determined, and the rhythmic gene expression was confirmed using northern blot analysis. The 10 cycling bands represent 7 different genes, 6 of which are present in the databases and 1 that does not match anything in current databases. The rhythmic expression of the 7 genes is composed of four distinct phases of clock regulation. The results demonstrate that FDD can be used to isolate ccgs. The genes identified in this screen range from known A. thaliana ccgs, as well as genes shown to be clock controlled in other plant species, to a novel gene that may encode a pioneer protein. Further study of these ccgs is likely to increase our understanding of circadian-regulated gene expression.

Signalling pathways in the brain: cellular transduction of mood stabilisation in the treatment of manic-depressive illness

The long-term treatment of manic-depressive illness (MDI) likely involves the strategic regulation of signalling pathways and gene expression in critical neuronal circuits. Accumulated evidence has identified signalling pathways, in particular the family of protein kinase C (PKC) isozymes, as targets for the long-term action of lithium. Chronic lithium administration produces a reduction in the expression of PKC alpha and epsilon, as well as a major PKC substrate, MARCKS, which has been implicated in long-term neuroplastic events in the developing and adult brain. More recently, studies have demonstrated robust effects of lithium on another kinase system, GSK-3beta, and on neuroprotective/neurotrophic proteins in the brain. Given the key roles of these signalling cascades in the amplification and integration of signals in the central nervous system, these findings have clear implications not only for research into the neurobiology of MDI, but also for the future development of novel and innovative treatment strategies.

Cloning of DLM-1, a novel gene that is up-regulated in activated macrophages, using RNA differential display

Tumors interact with their environment, reprogramming host cells to induce responses such as angiogenesis, inflammation, immunity and immune suppression. To understand these processes, it is important to identify and isolate new genes whose expression is induced in host tissues in response to tumors. Ascites tumors offer an attractive model for isolating such genes, because responding host peritoneal lining tissues can be cleanly separated from tumor cells growing in suspension within the peritoneal cavity. We here report the cloning by differential display of a novel gene, DLM-1, that is highly up-regulated in the peritoneal lining tissue of mice bearing MOT ascites tumors. Mouse peritoneal macrophages, stimulated by IFN-gamma or LPS, also expressed significant amounts of DLM-1. Up-regulation of DLM-1 became evident by 4h after stimulation with IFN-gamma and was not blocked by cycloheximide, suggesting the presence of IFN responding elements in its transcription regulation region. DLM-1 RNA was detected at significant levels in normal mouse lung, intestinal epithelium, liver and thymus by Northern blot analysis. In situ hybridization of MOT and HT-29 mouse subcutaneous transplanted solid tumors revealed strong DLM-1 expression in the host reactive stromal cells, but not the tumor cells. Sequence analysis of the full-length cDNA clone revealed that it encodes a protein of approx. M(r) 44330 with multiple potential protein kinase C and casein kinase II phosphorylation sites. Our data suggest that DLM-1 plays a role in such important processes as host response in neoplasia.

Lithium at 50: have the neuroprotective effects of this unique cation been overlooked?

Recent advances in cellular and molecular biology have resulted in the identification of two novel, hitherto completely unexpected targets of lithium's actions, discoveries that may have a major impact on the future use of this unique cation in biology and medicine. Chronic lithium treatment has been demonstrated to markedly increase the levels of the major neuroprotective protein, bcl-2 in rat frontal cortex, hippocampus, and striatum. Similar lithium-induced increases in bcl-2 are also observed in cells of human neuronal origin, and are observed in rat frontal cortex at lithium levels as low as approximately 0.3 mmol/L. Bcl-2 is widely regarded as a major neuroprotective protein, and genetic strategies that increase bcl-2 levels have demonstrated not only robust protection of neurons against diverse insults, but have also demonstrated an increase the regeneration of mammalian CNS axons. Lithium has also been demonstrated to inhibit glycogen synthase kinase 3 beta (GSK-3 beta), an enzyme known to regulate the levels of phosphorylated tau and beta-catenin (both of which may play a role in the neurodegeneration observed in Alzheimer's disease). Consistent with the increases in bcl-2 levels and inhibition of GSK-3 beta, lithium has been demonstrated to exert robust protective effects against diverse insults both in vitro and in vivo. These findings suggest that lithium may exert some of its long term beneficial effects in the treatment of mood disorders via underappreciated neuroprotective effects. To date, lithium remains the only medication demonstrated to markedly increase bcl-2 levels in several brain areas; in the absence of other adequate treatments, the potential efficacy of lithium in the long term treatment of certain neurodegenerative disorders may be warranted.

Differential gene expression in drug metabolism and toxicology: practicalities, problems and potential

1. An important feature of the work of many molecular biologists is identifying which genes are switched on and off in a cell under different environmental conditions or subsequent to xenobiotic challenge. Such information has many uses, including the deciphering of molecular pathways and facilitating the development of new experimental and diagnostic procedures. However, the student of gene hunting should be forgiven for perhaps becoming confused by the mountain of information available as there appears to be almost as many methods of discovering differentially expressed genes as there are research groups using the technique. 2. The aim of this review was to clarify the main methods of differential gene expression analysis and the mechanistic principles underlying them. Also included is a discussion on some of the practical aspects of using this technique. Emphasis is placed on the so-called 'open' systems, which require no prior knowledge of the genes contained within the study model. Whilst these will eventually be replaced by 'closed' systems in the study of human, mouse and other commonly studied laboratory animals, they will remain a powerful tool for those examining less fashionable models. 3. The use of suppression-PCR subtractive hybridization is exemplified in the identification of up- and down-regulated genes in rat liver following exposure to phenobarbital, a well-known inducer of the drug metabolizing enzymes. 4. Differential gene display provides a coherent platform for building libraries and microchip arrays of 'gene fingerprints' characteristic of known enzyme inducers and xenobiotic toxicants, which may be interrogated subsequently for the identification and characterization of xenobiotics of unknown biological properties.

Long RNA hairpins that contain inosine are present in Caenorhabditis elegans poly(A)+ RNA

Adenosine deaminases that act on RNA (ADARs) are RNA-editing enzymes that convert adenosine to inosine within double-stranded RNA. In the 12 years since the discovery of ADARs only a few natural substrates have been identified. These substrates were found by chance, when genomically encoded adenosines were identified as guanosines in cDNAs. To advance our understanding of the biological roles of ADARs, we developed a method for systematically identifying ADAR substrates. In our first application of the method, we identified five additional substrates in Caenorhabditis elegans. Four of those substrates are mRNAs edited in untranslated regions, and one is a noncoding RNA edited throughout its length. The edited regions are predicted to form long hairpin structures, and one of the RNAs encodes POP-1, a protein involved in cell fate decisions.

Characterization of differentially expressed genes in purified Drosophila follicle cells: toward a general strategy for cell type-specific developmental analysis

Axis formation in Drosophila depends on correct patterning of the follicular epithelium and on signaling between the germ line and soma during oogenesis. We describe a method for identifying genes expressed in the follicle cells with potential roles in axis formation. Follicle cells are purified from whole ovaries by enzymatic digestion, filtration, and fluorescence-activated cell sorting (FACS). Two strategies are used to obtain complementary cell groups. In the first strategy, spatially restricted subpopulations are marked for FACS selection using a green fluorescent protein (GFP) reporter. In the second, cells are purified from animals mutant for the epidermal growth factor receptor ligand gurken (grk) and from their wild-type siblings. cDNA from these samples of spatially restricted or genetically mutant follicle cells is used in differential expression screens employing PCR-based differential display or hybridization to a cDNA microarray. Positives are confirmed by in situ hybridization to whole mounts. These methods are found to be capable of identifying both spatially restricted and grk-dependent transcripts. Results from our pilot screens include (i) the identification of a homologue of the immunophilin FKBP-12 with dorsal anterior expression in egg chambers, (ii) the discovery that the ecdysone-inducible nuclear hormone receptor gene E78 is regulated by grk during oogenesis and is required for proper dorsal appendage formation, and (iii) the identification of a Drosophila homologue of the human SET-binding factor gene SBF1 with elevated transcription in grk mutant egg chambers.

Differential display identification of plunc, a novel gene expressed in embryonic palate, nasal epithelium, and adult lung

We have identified a novel gene transcript of approximately 1.1 kilobases in length that is expressed in the presumptive nasal epithelium of the mouse embryo. In situ hybridization analysis shows discrete regions of expression associated with the palate, nasal septum, and nasal conchae. This transcript is also expressed strongly in the trachea and bronchi of the adult lung. Screening of a mouse heart cDNA library yielded several overlapping clones to give a continuous sequence of 1113 bases, containing an open reading frame of 278 codons comprising the complete mRNA. No significant homologies with known genes were observed at the nucleotide level; limited amino acid homology with two salivary gland-specific proteins was noted. A search for functionally significant protein motifs revealed consensus sequences for N-glycosylation, protein kinase C and casein kinase phosphorylation, and a leucine zipper. Additionally, we observed a unique amino acid sequence pattern, consisting of the residues Gly-(Leu/Pro/Gln)-(Pro/Leu)-Leu-Pro-Leu, repeated four times near the amino-terminal portion of the protein with two amino acid residues separating the repeats. Based on these observations, we propose that we have identified a new gene, which we call plunc (for palate, lung, and nasal epithelium clone; GenBankTM accession number U69172).

Isolation of 10 differentially expressed cDNAs in differentiated Neuro2a cells induced through controlled expression of the GD3 synthase gene

Recently, we showed that transfection of GD3 synthase cDNA into Neuro2a cells, a mouse neuroblastoma cell line, causes cell differentiation with neurite sprouting. In a search for the genes involved in this ganglioside-induced Neuro2a differentiation, we used a tetracycline-regulated GD3 synthase cDNA expression system combined with differential display PCRs to identify mRNAs that were differentially expressed at four representative time points during the process. We report here the identification of 10 mRNAs that are expressed highly at the Neuro2a differentiated stage. These cDNAs were named GDAP1-GDAP10 for (ganglioside-induced differentiation-associated protein) cDNAs. It is interesting that in retinoic acid-induced neural differentiated mouse embryonic carcinoma P19 cells, GDAP mRNA expression levels were also up-regulated (except that of GDAP3), ranging from three to >10 times compared with nondifferentiated P19 cells. All the GDAP genes (except that of GDAP3) were developmentally regulated. The GDAP1, 2, 6, 8, and 10 mRNAs were expressed highly in the adult mouse brain, whereas all the other GDAP mRNAs were expressed in most tissues. Our results suggested that these GDAP genes might be involved in the signal transduction pathway that is triggered through the expression of a single sialyltransferase gene to induce neurite-like differentiation of Neuro2a cells.

Heme initiates changes in the expression of a wide array of genes during the early erythroid differentiation stage

Heme is central to oxygen sensing and utilization in all living organisms. It directly regulates numerous molecular and cellular processes for systems that sense or use oxygen. In mammals, heme plays an indispensable role in erythroid cell differentiation. To investigate heme regulatory functions, we identified, by differential display, and confirmed, by quantitative RT-PCR and Northern blotting analysis, the genes whose expression is altered by heme during the early stage of K562 cell differentiation. These include genes encoding a GAP-associated p62 protein, histone H2A.Z, a subunit of the small nuclear ribonucleoprotein complex, and the chaperonin Tcp20, and a cellular immediate-early-response gene. The results suggest that heme initiates changes in key factors that control a wide array of processes ranging from cell cycle and Ras signaling to chromatin structure, splicing and protein folding. These key factors might act together to mediate heme action, which is critical for erythroid cell differentiation.

A potential role for protease nexin 1 overexpression in the pathogenesis of scleroderma

Scleroderma currently affects approximately 75,000-100,000 individuals in the United States. Fibroblasts isolated from lesional skin of scleroderma patients overexpress collagens and other matrix components, and this abnormality is maintained for multiple passages in culture. To understand the molecular basis for matrix gene overexpression, we performed a differential display comparison of fibroblasts from clinically lesional and nonlesional scleroderma skin. The results suggested that protease nexin 1 (PN1), a protease inhibitor, is overexpressed in scleroderma fibroblasts. Northern blot verification showed that lesional and nonlesional scleroderma fibroblasts had three- to five-fold increased levels of PN1 mRNA compared with healthy fibroblasts. Western analysis showed that scleroderma fibroblasts also secreted more PN1. In situ hybridization of skin biopsy specimens demonstrated PN1 expression in the dermis of four out of six scleroderma patients but no PN1 expression in the dermis of six healthy volunteers. Transient or stable overexpression of PN1 in mouse 3T3 fibroblasts increased collagen promoter activity or endogenous collagen transcript levels, respectively. PN1 mutagenized at its active site and antisense PN1 both failed to increase collagen promoter activity. These results suggest that overexpression of enzymatically active PN1 may play a pathogenic role in the development of the scleroderma phenotype.

The mood-stabilizing agents lithium and valproate robustly increase the levels of the neuroprotective protein bcl-2 in the CNS

Differential display of mRNA was used to identify concordant changes in gene expression induced by two mood-stabilizing agents, lithium and valproate (VPA). Both treatments, on chronic administration, increased mRNA levels of the transcription factor polyomavirus enhancer-binding protein (PEBP) 2beta in frontal cortex (FCx). Both treatments also increased the DNA binding activity of PEBP2 alphabeta and robustly increased the levels of bcl-2 (known to be transcriptionally regulated by PEBP2) in FCx. Immunohistochemical studies revealed a marked increase in the number of bcl-2-immunoreactive cells in layers 2 and 3 of FCx. These novel findings represent the first report of medication-induced increases in CNS bcl-2 levels and may have implications not only for mood disorders, but also for long-term treatment of various neurodegenerative disorders.

SEMP1, a senescence-associated cDNA isolated from human mammary epithelial cells, is a member of an epithelial membrane protein superfamily

We have cloned a human cDNA, SEMP1 (senescence-associated epithelial membrane protein 1), using differential display (DD) of mRNA. We compared mRNA expression profiles between cultured normal senescent human mammary epithelial cells (HMECs) and proliferating, early passage HMECs. From the amino acid sequence of the open reading frame (ORF) of the cDNA, we infer that the protein belongs to a family of membrane-associated, epithelial cell-specific proteins. The translation product has 91% identity to a mouse protein, claudin-1, a tight junction (TJ)-associated protein. SEMP1 mRNA is expressed in human tissues, including adult and fetal liver, pancreas, placenta, adrenals, prostate and ovary but at low or undetectable levels in a number of human breast cancer cell lines. SEMP1 is a member of a superfamily of epithelial membrane proteins (EMPs), which may have multiple potential functions, including maintenance and regulation of cell polarity and permeability, perhaps through mechanisms involving tight junctions.

Differentiation in an olfactory cell line. Analysis via differential display

The olfactory epithelium is a unique system, in which new neurons are continually generated throughout adult life. Olfactory neurons are derived from stem cells that lie adjacent to the basal lamina of the olfactory epithelium; these stem cells divide several times and their progeny differentiate into mature sensory neurons. In our laboratory immortalized cell lines have been derived from these dividing cells. The morphology of these cell lines and their expression of neuronal markers varies with culture conditions. When grown in low serum medium one of these cells lines, OLF 442, differentiates by extending long neurites and increasing its expression of neurofilament and B50/GAP43 proteins at the same time reducing expression of glial fibrillary acidic protein (GFAP). Identification of differentially expressed mRNA in cell lines has previously relied on both screening for known markers, and the use of subtractive techniques for identification of unique mRNA species. The differential display technique allows simultaneous detection of differentially expressed mRNA at different time periods and growth conditions. A modified Liang and Pardee differential display technique was used to screen OLF 442 over a number of time intervals in serum-depleted media, and compared with OLF 442 grown in complete media. The differentially displayed fragments were cloned and sequenced, leading to the identification of a number of sequences, both known and unknown. The known sequences include SPARC (encoding a Ca2+ binding secreted Protein which is Acidic and Rich in Cysteine), which is reported to function as a modulator of the cell matrix, and RHAMM, the receptor for hyaluronan-mediated motility. Both the known and the unknown sequences are being studied further to provide insight into the differentiation of olfactory neurons.

Reciprocal subtraction differential RNA display: an efficient and rapid procedure for isolating differentially expressed gene sequences

A reciprocal subtraction differential RNA display (RSDD) approach has been developed that permits the rapid and efficient identification and cloning of both abundant and rare differentially expressed genes. RSDD comprises reciprocal subtraction of cDNA libraries followed by differential RNA display. The RSDD strategy was applied to analyze the gene expression alterations resulting during cancer progression as adenovirus-transformed rodent cells developed an aggressive transformed state, as documented by elevated anchorage-independence and enhanced in vivo oncogenesis in nude mice. This approach resulted in the identification and cloning of both known and a high proportion (>65%) of unknown sequences, including cDNAs displaying elevated expression as a function of progression (progression-elevated gene) and cDNAs displaying suppressed expression as a function of progression (progression-suppressed gene). Sixteen differentially expressed genes, including five unknown progression-elevated genes and six unknown progression-suppressed genes, have been characterized. The RSDD scheme should find wide application for the effective detection and isolation of differentially expressed genes.

Induction of mitogen-inducible nuclear orphan receptor by interleukin 1 in human synovial and gingival fibroblasts

High levels of interleukin 1 (IL-1) found in inflammatory diseases such as rheumatoid arthritis and periodontitis act on the local fibroblasts, resulting in an altered phenotype characterized by hyperplasia and the production of inflammatory mediators and destructive enzymes. The goal of this study was to identify genes induced as an early response to IL-1 in synovial and gingival fibroblasts which might play a regulatory role in the cascade of events leading to their activation. Using the technique of mRNA differential display, we have identified the mitogen-inducible nuclear orphan receptor (MINOR) as a gene up-regulated by IL-1 in human synovial and gingival fibroblasts. The rapid induction of both mRNA and DNA binding activity suggests that MINOR may play an important early role in regulating the response of fibroblasts to inflammation.

Identification of rCop-1, a new member of the CCN protein family, as a negative regulator for cell transformation

By using a model system for cell transformation mediated by the cooperation of the activated H-ras oncogene and the inactivated p53 tumor suppressor gene, rCop-1 was identified by mRNA differential display as a gene whose expression became lost after cell transformation. Homology analysis indicates that rCop-1 belongs to an emerging cysteine-rich growth regulator family called CCN, which includes connective-tissue growth factor, CYR61, CEF10 (v-src inducible), and the product of the nov proto-oncogene. Unlike the other members of the CCN gene family, rCop-1 is not an immediate-early gene, it lacks the conserved C-terminal domain which was shown to confer both growth-stimulating and heparin-binding activities, and its expression is lost in cells transformed by a variety of mechanisms. Ectopic expression of rCop-1 by retroviral gene transfers led to cell death in a transformation-specific manner. These results suggest that rCop-1 represents a new class of CCN family proteins that have functions opposing those of the previously identified members.