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

RIG-E, a human homolog of the murine Ly-6 family, is induced by retinoic acid during the differentiation of acute promyelocytic leukemia cell

In vivo all-trans-retinoic acid (ATRA), a differentiation inducer, is capable of causing clinical remission in about 90% of patients with acute promyelocytic leukemia (APL). The molecular basis for the differentiation of APL cells after treatment with ATRA remains obscure and may involve genes other than the known retinoid nuclear transcription factors. We report here the ATRA-induced gene expression in a cell line (NB4) derived from a patient with APL. By differential display-PCR, we isolated and characterized a novel gene (RIG-E) whose expression is up-regulated by ATRA. The gene is 4.0 kb long, consisting of four exons and three introns, and is localized on human chromosome region 8q24. The deduced amino acid sequence predicts a cell surface protein containing 20 amino acids at the N-terminal end corresponding to a signal peptide and an extracellular sequence containing 111 amino acids. The RIG-E coded protein shares some homology with CD59 and with a number of growth factor receptors. It shares high sequence homology with the murine LY-6 multigene family, whose members are small cysteine-rich proteins differentially expressed in several hematopoietic cell lines and appear to function in signal transduction. It seems that so far RIG-E is the closest human homolog of the LY-6 family. Expression of RIG-E is not restricted to myeloid differentiation, because it is also present in thymocytes and in a number of other tissues at different levels.

Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries

A new and highly effective method, termed suppression subtractive hybridization (SSH), has been developed for the generation of subtracted cDNA libraries. It is based primarily on a recently described technique called suppression PCR and combines normalization and subtraction in a single procedure. The normalization step equalizes the abundance of cDNAs within the target population and the subtraction step excludes the common sequences between the target and driver populations. In a model system, the SSH technique enriched for rare sequences over 1,000-fold in one round of subtractive hybridization. We demonstrate its usefulness by generating a testis-specific cDNA library and by using the subtracted cDNA mixture as a hybridization probe to identify homologous sequences in a human Y chromosome cosmid library. The human DNA inserts in the isolated cosmids were further confirmed to be expressed in a testis-specific manner. These results suggest that the SSH technique is applicable to many molecular genetic and positional cloning studies for the identification of disease, developmental, tissue-specific, or other differentially expressed genes.

Molecular genetic approaches to nociceptor development and function

The activation of peripheral nociceptors is the subject of intense scrutiny, because of its significance in pain regulation. Genetic approaches, including homology cloning, difference cloning and transgenic manipulation of mice are providing useful insights into nociceptor function. Recent work suggests that transcriptional regulators (for example, islet-I), which are expressed relatively selectively in sensory neurones, play a crucial role in defining cellular phenotype. Difference cloning has identified genes which encode both ligand-gated and voltage-gated ion channels expressed by small-diameter sensory neurones. The role of inflammatory mediators such as NGF in regulating nociceptor function has been clarified in mis-expression and deletion studies. An understanding of the mechanisms that regulate gene expression in nociceptors should provide new ways to manipulate nociceptor sensitivity, with potential significance for pain therapy.

Differential display-mediated rapid identification of different members of a multigene family, HSP 16.9 in wheat

Isolation of cDNAs encoding individual members of a gene family is essential for assessing their role in a biological phenomenon. However, this process is often laborious and slow due to highly conserved protein-coding region that interferes with the isolation of the individual members. Identification of gene-specific probes from 3' non-coding regions of different members can assist in the fast retrieval and characterization of individual members of a multigene family. We used the recent technique of differential display for the same purpose. As an example of a multigene family in plants, we selected a heat shock protein gene family, HSP16.9 from wheat, with estimated 12 members. We modified the original differential display technique for selective amplification of the 3' non-coding regions of different wheat HSP16.9 genes by replacing the random 10-mer in the original method with a conserved HSP16.9 gene family-specific primer. Sixteen cDNA fragments from these experiments were sequenced and they represent 8 different members of a 12 member gene family. Our success can be attributed to shorter 3' non-coding regions that are typical of higher-plant genes and use of highly conserved gene family-specific primer in these experiments. This modified differential display technique can be of general application to other plant systems where cloning of the different members of a gene family is desired.

DNA rehybridization during PCR: the 'Cot effect' and its consequences

The rate of amplification of abundant PCR products generally declines faster than that of less abundant products in the same tube in the later cycles of PCR. As a consequence, differences in product abundance diminish as the number of PCR cycles increases. Rehybridization of PCR products which may interfere with primer binding or extension can explain this significant feature in late cycles. Rehybridization occurs with a half-time dependent on the reciprocal of the DNA concentration. Thus, if multiple PCR products are amplified in the same tube, reannealing occurs faster for the more abundant PCR products. In RT-PCR using an internal control, this results in a systematic bias against the more abundant of the two PCR products. In RNA fingerprinting by arbitrarily primed PCR (or differentially display of cDNAs), very large or absolute differences in the expression of a transcript between samples are preserved but smaller real differences may be gradually erased as the PCR reaction proceeds. Thus, this 'Cot effect' may systematically cause an underestimate of the true difference in starting template concentrations. However, differences in starting template concentrations will be better preserved in the less abundant PCR products. Furthermore, the slow down in amplification of abundant products will allow these rarer products to become more visible in the fingerprint which may, in turn, allow rarer cDNAs to be sampled more efficiently. In some applications, where the object is to stochiometrically amplify a mixture of nucleic acids, the bias against abundant PCR products can be partly overcome by limiting the number of PCR cycles and, thus, the concentration of the products. In other cases, abundance normalization at later cycles may be useful, such as in the production of normalized libraries.

Transcriptional responses to tubule challenges

Adaptation to physiological stimuli often involves changes in gene transcription. Studies of hyperosmolar stress in renal epithelial cells have provided an ideal paradigm for understanding regulation of gene expression. Renal epithelial cells respond very differently to hyperosmolar NaCl and urea and several strategies including cloning based on known biological function, candidate gene analysis, and differential display analysis have successfully identified many genes induced by these hyperosmolar challenges. Hyperosmolar NaCl produces adverse effects on cellular biosynthetic processes and compensatory increases are observed in transcription of transporters, stress proteins, and metabolic enzymes. In contrast, hyperosmolar urea fails to inhibit biosynthetic processes but, nonetheless, initiates a very specific program of gene expression in renal epithelial cells. This program appears to involve a urea sensor/receptor system which activates transcription and translation of the zinc-finger transcription factor Egr-1. This work highlights the concept that rapid analysis of differential gene expression will enable one to define cellular programs of gene expression involving up- and down-regulation of functionally-related gene families.

Molecular dissection of corticosteroid action in the rat hippocampus. Application of the differential display techniques

Both adrenal steroids and glutamate are crucial for hippocampal cell viability. In order to identify adrenal steroid- and glutamate-responsive genes controlling hippocampal cell viability, we have used the PCR-based differential display method. We have described the characteristics of this technique and how it can be automated. Using differential display, we have identified a number of rat hippocampal genes of which the expression is affected by a combination of the glutamate analog kainic acid and adrenalectomy. Administration of kainic acid or removal of the adrenals alone gave a limited number of differentially displayed genes. Therefore, our results indicate that the main mode of corticosteroid receptor-controlled gene expression in the hippocampus is interaction with other transcription factors (e.g., CREB, AP-1) and not by binding to hormone-responsive elements of corticosterone-specific genes. Characterization by multiplex PCR experiments of a differentially displayed fragment of which the expression is increased by the combination of kainic acid and adrenalectomy confirmed our differential display results. Further characterization by DNA sequence analysis of the corresponding full-length cDNA clone revealed a gene product with 91.4% sequence identity with the mouse transcription factor KROX-20, suggesting that we have cloned the rat homolog. This finding suggests a role of KROX-20 in corticosteroid- and kainic acid-controlled hippocampal plasticity.

Oestrogen receptors and cardiovascular disease

1. Animal and human studies indicate that female sex hormones are protective against the development of coronary atherosclerosis. 2. Experiments on vascular smooth muscle cells suggest a direct effect of oestrogen on vascular tissue. Although oestrogen receptors (ER) in vascular tissues and an association between ER stimulation and physiological effects have been demonstrated, the cellular mechanisms underlying the effects of oestrogen on the arterial wall remain to be defined. 3. Elucidation of the cellular mechanism underlying the effects of oestrogen on vascular smooth muscle will provide insights into coronary atherosclerosis and will provide an opportunity to apply the protective effects of oestrogen to women in older age groups and to the male population.

Osmotic stress protein 94 (Osp94). A new member of the Hsp110/SSE gene subfamily

Preservation of cell viability and function in the hyperosmolar environment of the renal medulla is a complex process that requires selective gene expression. We have identified a new member of the heat shock protein (hsp) 70 superfamily that is up-regulated in renal inner medullary collecting duct cells (mIMCD3 cells) during exposure to hyperosmotic NaCl stress. Known as osmotic stress protein 94, or Osp94, this 2935-base pair cDNA encodes an 838-amino acid protein that shows greatest homology to the recently discovered hsp110/SSE gene subfamily. Like the hsps, Osp94 has a putative amino-terminal ATP-binding domain and a putative carboxyl-terminal peptide-binding domain. The in vitro translated Osp94 product migrated as a 105-110-kDa protein on SDS-polyacrylamide gel electrophoresis. In mIMCD3 cells, Osp94 mRNA expression was greatly up-regulated by hyperosmotic NaCl or heat stress. In mouse kidney, Osp94 mRNA expression paralleled the known corticomedullary osmolality gradient showing highest expression in the inner medulla. Moreover, inner medullary Osp94 expression was increased during water restriction when osmolality is known to increase. Thus, Osp94 is a new member of the hsp110/SSE stress protein subfamily and likely acts as a molecular chaperone.

Differential display PCR reveals increased expression of 2',3'-cyclic nucleotide 3'-phosphodiesterase by lithium

Differential display PCR was used to study the effects of lithium on gene expression. Four candidate genes were isolated and verified by Northern hybridization after 1 week treatment of C6 glioma cells with therapeutically relevant concentrations of LiCl (1 mM). Sequencing analysis revealed three previously unidentified cDNA fragments in addition to a sequence with 99% homology with the cDNA for 2',3'-cyclic nucleotide 3'-phosphodiesterase type II (CNPaseII). Since CNPaseII is important in myelinogenesis and possibly neuronal growth and repair, the present findings suggest that lithium treatment may regulate these processes.

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

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

AdipoQ is a novel adipose-specific gene dysregulated in obesity

Adipose differentiation is accompanied by changes in cellular morphology, a dramatic accumulation of intracellular lipid and activation of a specific program of gene expression. Using an mRNA differential display technique, we have isolated a novel adipose cDNA, termed adipoQ. The adipoQ cDNA encodes a polypeptide of 247 amino acids with a secretory signal sequence at the amino terminus, a collagenous region (Gly-X-Y repeats), and a globular domain. The globular domain of adipoQ shares significant homology with subunits of complement factor C1q, collagen alpha 1(X), and the brain-specific factor cerebellin. The expression of adipoQ is highly specific to adipose tissue in both mouse and rat. Expression of adipoQ is observed exclusively in mature fat cells as the stromal-vascular fraction of fat tissue does not contain adipoQ mRNA. In cultured 3T3-F442A and 3T3-L1 preadipocytes, hormone-induced differentiation dramatically increases the level of expression for adipoQ. Furthermore, the expression of adipoQ mRNA is significantly reduced in the adipose tissues from obese mice and humans. Whereas the biological function of this polypeptide is presently unknown, the tissue-specific expression of a putative secreted protein suggests that this factor may function as a novel signaling molecule for adipose tissue.

Differential display RT PCR of total RNA from human foreskin fibroblasts for investigation of androgen-dependent gene expression

Male sexual differentiation is a process that involves androgen action via the androgen receptor. Defects in the androgen receptor, many resulting from point mutations in the androgen receptor gene, lead to varying degrees of impaired masculinization in chromosomally male individuals. To date no specific androgen regulated morphogens involved in this process have been identified and no marker genes are known that would help to predict further virilization in infants with partial androgen insensitivity. In the present study we first show data on androgen regulated gene expression investigated by differential display reverse transcription PCR (dd RT PCR) on total RNA from human neonatal genital skin fibroblasts cultured in the presence or absence of 100 nM testosterone. Using three different primer combinations, 54 cDNAs appeared to be regulated by androgens. Most of these sequences show the characteristics of expressed mRNAs but showed no homology to sequences in the database. However 15 clones with significant homology to previously cloned sequences were identified. Seven cDNAs appear to be induced by androgen withdrawal. Of these, five are similar to ETS (expression tagged sequences) from unknown genes; the other two show significant homology to the cDNAs of ubiquitin and human guanylate binding protein 2 (GBP-2). In addition, we have identified 8 cDNA clones which show homologies to other sequences in the database and appear to be upregulated in the presence of testosterone. Four of these clones again are similar to ETS from unknown genes. Three differential expressed sequences that appear to be upregulated in the presence of testosterone show significant homology to the cDNAs of L-plastin and one to the cDNA of testican. This latter gene codes for a proteoglycan involved in cell social behavior and therefore of special interest in this context. The results of this study are of interest in further investigation of normal and disturbed androgen-dependent gene expression.

Isolation, characterization, and mapping to human chromosome 11q24-25 of a cDNA encoding a highly conserved putative transmembrane protein, TMC

We report the isolation of a novel human cDNA encoding a putative transmembrane protein, TMC. The predicted protein sequence is highly conserved evolutionarily. The cDNA clone was mapped to human chromosome 11q24-25 by fluorescence in situ hybridization. mRNA expression was observed in all tissues tested with the highest levels in testes and ovary.

Induction of inositol 1,4,5 trisphosphate receptor genes by ionizing radiation

We used differential display, a method designed to amplify partial cDNA sequences from subsets of mRNAs, to identify mRNAs induced by ionizing radiation in human Epstein Barr Virus (EBV)-transformed lymphoblastoid cells. Increased expression of a cDNA corresponding to the inositol 1,4,5 trisphosphate receptor (InsP3R) type 1 was observed after exposure of cells to 3Gy gamma-rays. This was confirmed by Northern blot analysis. The increase in mRNA for InsP3R type 1 was accompanied by a corresponding increase in the level of InsP3R type 1 protein as determined by Western blotting. Exposure of cells from patients with the human genetic disorder ataxia-telangiectasia (A-T), characterized by hypersensitivity to ionizing radiation, failed to change the levels of InsP3R type 1 mRNA and, as expected, there was no increase in InsP3R type 1 protein in A-T cells in response to radiation exposure. Protein levels for two other InsP3Rs, types 2 and 3, were observed to increase in control and A-T cells after exposure to ionizing radiation. The induction of the InsP3R type 1, which is primarily located in the endoplasmic reticulum, may play an important role in radiation signal transduction.

Differential replication and DNA elimination in the polytene chromosomes of Euplotes crassus

The transposon-like Tec elements of Euplotes crassus are precisely excised during formation of polytene chromosomes in the developing macronucleus. To determine whether all Tec elements exhibit identical developmental timing of excision, we used polymerase chain reaction to visualize amplification and diminution at numerous randomly selected Tec insertion sites. Two classes of sites are evident. Early replicating sites show one or more rounds of amplification and diminution (corresponding to excision) and frequently occur within macronuclear-destined sequences. Late replicating sites do not undergo diminution until chromosome fragmentation and are predominantly associated with eliminated sequences. We conclude that the previously described clustering of macro-nuclear-destined sequences in the micronuclear genome allows for their differential replication at the polytene stage and results in targeting of these sequences for transcriptional activation and highly specific deletion and chromosome fragmentation processes.

Light, immediate-early genes, and circadian rhythms

Many diverse behaviors exhibit clear circadian rhythms in their expression. In mammals, these rhythms originate from a neural circadian clock located in the suprachiasmatic nuclei (SCN). Recently, signaling pathways activated by light in the SCN have begun to be identified. A specific set of immediate-early genes is induced by light in the SCN, and their expression is correlated with the resetting of circadian behavioral rhythms. These light-regulated immediate-early genes offer multiple inroads into the biology of the SCN: first, they are functional markers for the activation of SCN neurons by light; second, they can direct us to the upstream light-activated (and clock-regulated) signal transduction pathways which mediate their induction; and finally, they encode transcription factor proteins which may play a role in the molecular mechanism of resetting the circadian clock.

PCR-mediated differential display and cloning of a melanocyte gene decreased in malignant melanoma and up-regulated with sensitization to DNA damage

Characterization of genes expressed in normal cells and decreased in their malignant counterparts is important for detecting candidate tumor suppressor genes. We have now used comparative differential display of MRNAs from B16 melanoma and matched syngeneic normal melanocytes to detect a G0A gene expressed preferentially in resting G0 melanocytes compared to proliferating cells. Cloning and sequencing revealed no homology of G0A in the GenBank Database, suggesting that this is a new gene. Northern blot analysis with the cloned probe, confirmed about a five-fold higher expression in normal melanocytes compared to melanoma. Up-regulation of this gene was not detected by L-tyrosine induction of B16 melanoma terminal differentiation, but was seen in these cells, when exposed to the radiation sensitizer bromodeoxyuridine and subsequent UV radiation. Our differential expression data suggest that the G0A gene is important for melanocytic growth control and for the response of melanoma cells to radiation sensitizers.

Isolation of 10 differentially expressed cDNAs in p53-induced apoptosis: activation of the vertebrate homologue of the drosophila seven in absentia gene

We report the isolation of 10 differentially expressed cDNAs in the process of apoptosis induced by the p53 tamor suppressor. As a global analytical method, we performed a differential display of mRNA between mouse M1 myeloid leukemia cells and derived clone LTR6 cells, which contain a stably transfected temperature-sensitive mutant of p53. At 32 degrees C wild-type p53 function is activated in LTR6 cells, resulting in programmed cell death. Eight genes are activated (TSAP; tumor suppressor activated pathway), and two are inhibited (TSIP, tumor suppressor inhibited pathway) in their expression. None of the 10 sequences has hitherto been recognized as part of the p53 signaling pathway. Three TSAPs are homologous to known genes. TSAP1 corresponds to phospholipase C beta 4. TSAP2 has a conserved domain homologous to a multiple endocrine neoplasia I (ZFM1) candidate gene. TSAP3 is the mouse homologue of the Drosophila seven in absentia gene. These data provide novel molecules involved in the pathway of wild-type p53 activation. They establish a functional link between a homologue of a conserved developmental Drosophila gene and signal transduction in tumor suppression leading to programmed cell death.

Analysis of lipopolysaccharide-response genes in B-lineage cells demonstrates that they can have differentiation stage-restricted expression and contain SH2 domains

Bacterial lipopolysaccharide (LPS) is a potent stimulator of B-cell activation, proliferation, and differentiation. We examined the genetic response of B-lineage cells to LPS via trapping of expressed genes with a gene-trap retrovirus. This analysis showed that expression of only a small fraction of genes is altered during LPS stimulation of B-lineage cells. Isolation of the cellular portion of the trapped LPS-response genes via 5' RACE (rapid amplification of cDNA ends) cloning identified novel genes for all the cloned loci. These novel LPS-response genes were also found to have differentiation stage-restricted expression within the B-lymphoid lineage. That LPS-response genes in B cells also have differentiation stage-restricted expression suggests that these genes may be involved in the control of B-cell function and differentiation, since the known members of this class of genes have frequently been found to play a role in the function and differentiation of B-lineage cells. The isolation of novel members of this class of genes, including a gene that contains a putative SH2 domain, will further increase our understanding of the molecular events involved in the control of B-cell differentiation and function.

DUB-1, a deubiquitinating enzyme with growth-suppressing activity

Cytokines regulate cell growth by inducing the expression of specific target genes. Using the differential display method, we have cloned a cytokine-inducible immediate early gene, DUB-1 (for deubiquitinating enzyme). DUB-1 is related to members of the UBP superfamily of deubiquitinating enzymes, which includes the oncoprotein Tre-2. A glutathione S-transferase-DUB-1 fusion protein cleaved ubiquitin from a ubiquitin-beta-galactosidase protein. When a conserved cysteine residue of DUB-1, required for ubiquitin-specific thiol protease activity, was mutated to serine (C60S), deubiquitinating activity was abolished. Continuous expression of DUB-1 from a steroid-inducible promoter induced growth arrest in the G1 phase of the cell cycle. Cells arrested by DUB-1 expression remained viable and resumed proliferation upon steroid withdrawal. Our results suggest that DUB-1 regulates cellular growth by modulating either the ubiquitin-dependent proteolysis or the ubiquitination state of an unknown growth regulatory factor(s).

Screening of differentially amplified cDNA products from RNA arbitrarily primed PCR fingerprints using single strand conformation polymorphism (SSCP) gels

Arbitrarily primed PCR fingerprinting of RNA and differential display resolved on an acrylamide gel has been extensively used to detect differentially expressed RNAs. However, after a differentially amplified product is detected the next steps are labor-intensive: a small portion of the fingerprinting gel that contains the differentially amplified product is cut out, reamplified and the correct product is determined, typically by cloning and sequencing what is often a mixture of products of similar size. Here we use a native acrylamide gel to separate DNAs in the reamplified mixture based on single-stranded conformation polymorphisms. Reamplifications are performed for the region carrying the differentially amplified product and a corresponding region from an adjacent lane where the product is less prominent or not visible. Denaturation of the reamplified DNA followed by side-by-side comparison on an SSCP gel allows the classification of reamplified material into (i) those that can be directly cloned because the differentially amplified product is relatively pure, (ii) those that need to be reamplified from the SSCP gel before cloning and (iii) those that are too complex for further study. This screen should save considerable effort now wasted on directly cloning unsuitable products from RNA fingerprinting experiments. An example is presented of cloning a gene differentially expressed in Trypanosoma brucei life cycle.

Multiplex messenger assay: simultaneous, quantitative measurement of expression of many genes in the context of T cell activation

The hybridization signature approach, using colony filters and labeled complex probes, can provide high throughput measurement of gene activity. We describe here the implementation of this method to follow the expression levels of 47 genes in resting and activated T cells, as well as in epithelial cells. Using 4-fold spotting of colonies, imaging plate detection and various correction and normalization procedures, the technique is sensitive enough to quantify expression levels for sequences present at 0.005% abundance in the probe. Comparison with Northern blotting shows good consistency between the two methods. Upon activation of a T cell clone by an anti-CD3 antibody variations ranging from 2- to 20-fold are measured, some of which had not been reported previously. This 'multiplex messenger assay' method, performed using available commercial apparatus, can be used in many cases where simultaneous assessment of mRNA levels for many genes is of interest.

Interleukin 8 is induced by cholesterol loading of macrophages and expressed by macrophage foam cells in human atheroma

In order to identify novel genes expressed in macrophage-derived foam cells, we used a multigene assay to examine the expression of genes in control versus cholesterol-loaded macrophages. We compared THP-1 macrophages incubated with or without acetylated LDL (acLDL) +/- acyl-CoA:cholesterol O-acyltransferase (ACAT) inhibitor (compound 58035) for 20 h and assessed changes in mRNA of chemokines, growth factors, interleukins, and adhesion molecules. Among 49 genes examined, an increase in mRNA was observed only for interleukin 8 (IL-8) in THP-1 macrophages. Northern analysis confirmed a 3- to 4-fold increase of IL-8 mRNA and an enzyme-linked immunosorbent assay (ELISA) revealed a corresponding increase in IL-8 in conditioned medium. Oxidized LDL (oxLDL) also induced IL-8 mRNA, but native LDL had no effect. 58035 had a moderate effect on IL-8 induction by acLDL. AcLDL-induced IL-8 expression was concentration- and time-dependent. The time course of IL-8 induction paralleled that of cholesterol loading. MCP-1, a chemokine implicated in recruiting monocytes in atherogenesis, was also induced by acLDL. The induction of MCP-1, however, peaked at 1 h after addition of acLDL and returned to basal level by 20 h while IL-8 induction peaked at 8 h and was still 2-fold higher than basal level at 20 h. IL-8 induction was also observed in fresh human monocyte-derived macrophage cells treated with acLDL. Finally, immunohistochemistry and in situ hybridization studies using specimens of human coronary atheromas showed expression of IL-8 mRNA in a macrophage-rich area. We conclude that IL-8 is induced in macrophage foam cells as a response to cholesterol loading. The chemoattractant and/or mitogenic effects of IL-8 on neutrophils, T cells, smooth muscle, or vascular endothelial cells may contribute to the progression and complications of atherosclerosis.

Isolation of up- and down-regulated cDNAs associated with hepatocellular carcinoma by a subtraction-enhanced display technique

Identification of gene products exclusively or abundantly expressed in hepatocellular carcinoma (HCC) and in normal liver may yield novel tumor markers. We have isolated 36 up- and down-regulated cDNAs from diethylnitrosamine-induced rat hepatocellular carcinoma and normal liver tissue by using the subtraction-enhanced display technique. Nucleotide sequence analysis revealed that the majority of 20 subtraction-enriched cDNA fragments were well-characterized oncogenes and tumor-associated genes, like c-myc, alpha-prothymosin, p21, glutathione-S transferase (G-ST) and alpha 1-acid glycoprotein (AGP). As demonstrated by Northern blot detection, all of them were preferentially expressed either in HCC or in normal liver (2- to 7-fold). As paradigm, G-ST and AGP were shown to be exclusively overexpressed in tumor nodules by in situ hybridization. In addition, 14 of the remaining 16 novel genes were analysed on Northern blot, 10 of which were differentially expressed in HCC.

Cloning of a novel human RNA polymerase II subunit downregulated by doxorubicin: new potential mechanisms of drug related toxicity

Using the differential display PCR method, we have isolated an mRNA downregulated in doxorubicin resistant human cell lines. The full length cDNA clone was identified as the human homologue of yeast RPB11 subunit of RNA polymerase II. Northern blot analysis of normal tissues detected a particularly high expression of RPB11 mRNA in heart and skeletal muscle. Reduction of this mRNA expression was observed in all the cell lines tested after drug treatment and was paralleled by a similar decrease of the protein levels. These findings suggest that doxorubicin may exert in vivo specific inhibitory effects on a major component of the transcription machinery.

The vitamin D(3) receptor in the context of the nuclear receptor superfamily : The central role of the retinoid X receptor

The nuclear hormone 1 α,25-dihydroxyvitamin D(3) (VD) is an important regulator of calcium homeostasis and is also a modulator of the cell cycle. The genomic actions of the hormone are mediated by a single transcription factor, the vitamin D(3) receptor (VDR). On the majority of the known VD response elements, VDR binds as heterodimeric complex with the retinoid X receptor (RXR), which is a member of the nuclear receptor superfamily like VDR. RXR supports not only the DNA binding affinity and specificity of VDR, but allosterically also its transactivation properties. Moreover RXR is a partner in other hormone response systems, which supports the idea that the different nuclear hormone signaling pathways are functionally linked.

Use of a high stringency differential display screen for identification of retinal mRNAs that are regulated by a circadian clock

We report here the initiation of a systematic screen to identify clock-controlled mRNAs from the retina of Xenopus laevis using mRNA differential display. Xenopus retina contains an endogenous circadian clock located within the photoreceptor layer. The retinal block controls many aspects of physiology, including gene transcription. This screen uses differential display, a PCR based procedure, to compare retinal mRNA populations at different times of day in constant darkness, for identification of messages that exhibit rhythmic expression. Out of approx. 2000 mRNAs that we have screened to date, we have identified four candidates for clock-controlled mRNAs. Initial characterization of one of these PCR products shows that it recognizes a pair of mRNA bands on Northern blots that exhibit high amplitude rhythms. This pair of messages is called RM1 and shows peak levels of expression in the subjective night. In situ hybridization shows that this clock-controlled message is specifically localized to the clock containing photoreceptor cell layer within the retina. Identification of new messages that are under the control of the circadian clock has broad relevance in retinal physiology and provides an opportunity to gain insight into the molecular mechanism of vertebrate circadian control.

A novel MAP kinase phosphatase is localised in the branchial arch region and tail tip of Xenopus embryos and is inducible by retinoic acid

Using a differential display strategy, we have isolated a cDNA corresponding to a mRNA which is induced by retinoic acid treatment of late gastrula Xenopus embryos, and much more strongly induced by retinoic acid and cycloheximide. The cDNA, designated X17C, encodes a novel mitogen-activated protein (MAP) kinase phosphatase of 378 amino acid residues which is only distantly related to other known MAP kinase phosphatases. In normal embryogenesis, the X17C mRNA is expressed after the midblastula transition and accumulates during gastrulation. In neurula and tailbud stage embryos the mRNA is localised in two domains, one in the anterior region of the embryo, and one at the tail tip. When expressed from synthetic mRNA injected into oocytes, the X17C protein is found within the cytosolic fraction and not in the nucleus. The X17C protein dephosphorylates and inactivates Xenopus MAP kinase in oocytes stimulated to undergo maturation by progesterone. We indicate the application of X17C as a tool for interfering with MAP kinase signaling in somatic cells of embryos, using FGF receptor-mediated MAP kinase activation in animal cap explants.

Induction of a novel cytochrome P450 (CYP93 family) by methyl jasmonate in soybean suspension-cultured cells

We isolated a cDNA encoding a novel cytochrome P450 (CYP93A1) from soybean suspension-cultured cells that had been treated with methyl jasmonate (MeJA). The amino acid sequence of the gene product had 30-40% identity with those of other plant P450s. The protein contained the heme-binding domain which is highly conserved among plant P450s. Transcription of the cytochrome P450 gene in soybean cells was induced by 30 microM MeJA even in the presence of cycloheximide, and reached maximum level 6 h after MeJA treatment. This is the first report of a plant cytochrome P450 gene whose transcription is induced by MeJA even without protein synthesis.

A role for melanin-concentrating hormone in the central regulation of feeding behaviour

The hypothalamus plays a central role in the integrated regulation of energy homeostasis and body weight, and a number of hypothalamic neuropeptides, such as neuropeptide Y (ref. 1), galanin, CRH (ref. 3) and GLP-1 (ref. 4), have been implicated in the mediation of these effects. To discover new hypothalmic peptides involved in the regulation of body weight, we used differential display polymerase chain reaction to identify messenger RNAs that are differentially expressed in the hypothalamus of ob/+ compared with ob/ob C57B1/6J mice. We show here that one mRNA that is overexpressed in the hypothalamus of ob/ob mice encodes the neuropeptide melanin-concentrating hormone (MCH). Fasting further increased expression of MCH mRNA in both normal and obese animals. Neurons containing MCH are located in the zona incerta and in the lateral hypothalamus. These areas are involved in regulation of ingestive behaviour, but the role of MCH in mammalian physiology is unknown. To determine whether MCH is involved in the regulation of feeding, we injected MCH into the lateral ventricles of rats and found that their food consumption increased. These findings suggest that MCH participates in the hypothalamic regulation of body weight.

Colonization of human lung grafts in SCID-hu mice by human colon carcinoma cells

Human colon carcinoma cell lines were examined in a colonization assay using SCID-hu mice engrafted with human fetal lung (HFL) tissues. Cell lines SW620 and COLO 320DM, derived from metastatic tumors, colonized HFL grafts after i.v. injection into SCID-hu mice. Cell lines SW480 and T34 initiated from primary colon tumors were unable to colonize HFL grafts. The ability to colonize HFL grafts but not mouse lungs of SCID-hu-L mice correctly reflects the clinical origin of these human colon carcinoma cell lines. Expression of a number of cell adhesion molecules was examined on SW480, SW620 and in vivo selected highly aggressive variants of SW620. NCAM and integrin alpha 3 expressed on the surface of SW480 cells were lost from metastatic cells, while carbohydrate ligands sialyl Lewis x and a, previously shown to be upregulated in metastatic colorectal tumors, were expressed at higher levels on colonizing cells. Unlike SW480, SW620 and its in vivo selected variants expressed RNA for calcium binding protein calbindin-D28K, a neuroendocrine marker. Acquisition of neuroendocrine features might be of potential importance in the development of the metastatic phenotype.

Increase in activin beta A mRNA in rat hippocampus during long-term potentiation

We have used mRNA differential display to isolate genes that are induced by neural activity in rat hippocampus. One of these encodes activin beta A subunit. Convulsive seizure caused by kainate significantly induced the expression of activin beta A mRNA. Furthermore high frequency stimulation (HFS) of perforant pathway, which produced a persistent long-term potentiation (LTP) (>10 h), caused a marked increase at 3 h in the level of activin beta A mRNA at the dentate gyrus of urethane-anesthetized rat. The increase was NMDA receptor-dependent. By contrast the level of inhibin alpha mRNA was not changed following the induction of LTP. THe results suggest a role for activin in maintenance of neural plasticity in the adult brain.

Isolation of differentially expressed genes in carcinoma of the esophagus

BACKGROUND

The genetic alterations that occur in the transformation of normal esophageal mucosa (NEM) to carcinoma of the esophagus (CAE) are not well understood. Differential display of mRNA is a recently described technique that uses reverse transcription and PCR to compare cDNA from paired normal and malignant tissue to determine whether there is either genetic loss (putative tumor suppressor gene) or overexpression (putative oncogene) in malignant cells. Our goal was to identify some of these genes from patients with CAE.

METHODS

Specimens of NEM and corresponding CAE were obtained from patients at endoscopy or surgical resection and immediately snap frozen. Total RNA was isolated, reverse transcribed to cDNA, and PCR amplified with a predefined 10-mer oligonucleotide. The products were displayed on a polyacrylamide gel. Differential bands were isolated and sequenced and/or used as probes for Northern analysis.

RESULTS

Application of the differential display method resulted in the isolation of 49 cDNA clones from three patients with CAE. Sequencing of the clones has revealed five unique sequences not previously reported and one that has been identified as histone H3.3. Northern analysis of histone H3.3 has revealed overexpression in four of six CAEs but not the paired NEM. In addition, whereas only 5 of 13 normal human cell lines of various origins overexpressed this gene, 11 of 12 human cancer cell lines (9 of 9 adenocarcinomas) overexpressed it.

CONCLUSIONS

Differential display can be used to isolate potential oncogenes and tumor suppressor genes. We have identified five unique sequences and one known gene that may contribute to the development of CAE.

HMG-CoA reductase mediates the biological effects of retinoic acid on human neuroblastoma cells: lovastatin specifically targets P-glycoprotein-expressing cells

The enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase, involved in de novo cholesterol synthesis and cell-cycle progression, was identified as a potential mediator of the growth inhibitory effects of retinoic acid on human neuroblastoma. Lovastatin, a nonreversible inhibitor of HMG-CoA reductase, induced extensive cytotoxicity that was restricted to drug-resistant P-glycoprotein-expressing neuroblastoma cell lines. This response was potentiated by dibutyryl cyclic AMP but not retinoic acid. Patients with advanced-stage metastatic neuroblastoma often display an acquired chemoresistant phenotype, which may in part be mediated by P-glycoprotein. Our studies support the application or use of HMG-CoA reductase inhibitors as potential therapeutic agents in the treatment of these patients who are refractory to chemotherapy.

Constitutive in vivo mRNA expression by osteocytes of beta-actin, osteocalcin, connexin-43, IGF-I, c-fos and c-jun, but not TNF-alpha nor tartrate-resistant acid phosphatase

Osteocytes have been proposed to be the cells primarily responsible for sensing the effects of mechanical loading in bone. Osteocytes respond to loading in vivo, and have been shown to express osteotropic agents and their receptors, and cell/matrix adhesion molecules in vitro, but the functional significance of such findings is not clear. One obstacle to increased understanding of the role of osteocytes in the regulation of bone mass is that the cells are not easily accessible for study. In situ studies are difficult, and although it is possible to extract and culture osteocytes from neonatal bones, the responses of such cells might be very different from those in older bones in situ. We have developed a technique to investigate osteocyte gene expression in vivo, using the reverse transcriptase linked polymerase chain reaction (PCR), and have shown that they express mRNA for beta-actin (beta-ACT), osteocalcin (OC), connexin-43 (Cx43), insulin-like growth factor I (IGF-I), c-fos and c-jun, but not tumor necrosis factor alpha (TNF-alpha) or tartrate-resistant acid phosphatase (TRAP). The principle behind the method is that after removal of the periosteum, tangential cryostat sections of a tubular bone contain RNA only from osteocytes and a very small number of endothelial cells as long as the marrow cavity is not broached. Using this method, we have investigated gene expression in cells from rat ulnar cortical bone under forming and resorbing bone surfaces. In addition, we have investigated the effect on gene expression of mechanical loading which, if repeated daily, initiates new bone formation on quiescent or resorbing surfaces. Although the expression of the genes we have studied in osteocytes is different from those expressed by the periosteal surfaces overlying the cortex, we have not detected loading-related changes in osteocyte gene expression in any cortical bones. This may be because of the extreme sensitivity of the PCR technique which can only resolve large differences in expression. The use of quantitative methods in the future may allow demonstration of regulated gene expression in osteocytes.

Identifying changes in gene expression in the nervous system: mRNA differential display

The majority of cellular and developmental processes are characterized by changes in gene expression. Recently, several polymerase chain reaction-based methods have been introduced for detecting genes whose expressions differ between cells or tissues. It is now possible to investigate whether novel gene expression occurs within many systems as a response to extracellular signals, and to identify systematically those genes. The characterization of cell-, tissue- or stage-specific gene expression will broaden our understanding of many complex biological processes.

Nerve growth factor treatment of sensory neuron primary cultures causes elevated levels of the mRNA encoding the ATP synthase beta-subunit as detected by a novel PCR-based differential cloning method

The mRNA encoding the rat ATP synthase beta-subunit was rapidly induced by nerve growth factor, within 60 min, in cultured adult rat dorsal root ganglion neurons. ATP synthase beta-subunit cDNA clones were isolated from a lambda library. The library was constructed using rat dorsal root ganglion mRNA that was differentially screened with cDNA-derived probes from untreated and nerve-growth-factor-treated primary cultures of adult rat dorsal root ganglion sensory neurons. Radiolabelled probes were made from submicrogram quantities of RNA, by a novel PCR-based technique, which allows small amounts of primary tissue to be used for library screening. The use of this technique in isolating novel differentially expressed mRNAs is discussed.

Differential-display polymerase chain reaction identifies nucleophosmin as an estrogen-regulated gene in human vascular smooth muscle cells

PURPOSE

Atheroprotective effects of estrogen (E2) are well documented and are due in part to direct effects of E2 on vascular cells. We recently demonstrated that human vascular smooth muscle cells (VSMCs) express a functional E2 receptor capable of activatine gene expression. This study was designed to identify E2-regulated genes in human VSMCs.

METHODS

VSMC mRNA was screened by differential-display polymerase chain reaction (ddPCR) to identify E2-regulated genes. Quiescent human VSMCs were stimulated with 10% fetal bovine serum in the absence or presence of 10(-8) mol/L E2, and total cellular RNA was harvested. ddPCR was performed in triplicate on each RNA sample and differentially expressed candidate genes were isolated. Differential expression of candidate genes were confirmed by dot blotting and positive bands were identified by sequence analysis. E2-mediated regulation at the protein level was investigated by immunoblotting.

RESULTS

ddPCR of RNA harvested from aortic VSMCs identified a 462 bp gene product, EAo8, as a candidate E2- regulated gene. Dot blotting with probes derived from four independent VSMC cultures demonstrated a 5.8 +/- 3.9-fold increase in EAo8 expression in response to E2 treatment (p < 0.05 vs control). Sequence analysis identified EAo8 as nucleophosmin, a nucleolar phosphprotein implicated in the regulation of cell growth and protein synthesis. E2-induced expression of nucleophosmin protein was demonstrated by immunoblotting in both saphenous vein and mammary artery VSMCs.

CONCLUSIONS

E2 induces nucleophosmin expression in human VSMCs, and ddPCR is a useful approach for studying estrogen-regulated gene expression in VSMCs.

Somatic mutagenesis and antimutagenesis in aging research

Somatic mutagenesis and antimutagenesis are reviewed from the point of view of a gerontologist. Aging can be defined as a set of phenotypes that have escaped the force of natural selection. In mammalian species, aberrations in proliferative homeostasis, including a variety of cancers, are conspicuous examples. The author argues that there is a strong coupling between intrinsic biological aging and the biology of neoplasia. Genomic instability is likely to be a dominant mechanism underlying such coupling. Ongoing experiments from his laboratory and those of collaborators are briefly reviewed. The approaches include: (1) the characterization of a striking progeroid mutation of man, the Werner syndrome, which exhibits a deletor mutator phenotype; (2) the comparative analysis of intragenic and chromosomal mutations in mammalian species of contrasting life span potentials; (3) attempts to synthesize antimutator strains of mice. An emerging generalization is that there is a significant degree of species specificity in the patterns of somatic mutation in aging mammals.