Differential display. A general protocol

Identification of genes involved in the drought adaptation and recovery in Portulaca oleracea by differential display

Portulaca oleracea is one of the richest plant sources of ω-3 and ω-6 fatty acids and other compounds potentially valuable for nutrition. It is broadly established in arid, semiarid and well-watered fields, thus making it a promising candidate for research on abiotic stress resistance mechanisms. It is capable of withstanding severe drought and then of recovering upon rehydration. Here, the adaptation to drought and the posterior recovery was evaluated at transcriptomic level by differential display validated by qRT-PCR. Of the 2279 transcript-derived fragments amplified, 202 presented differential expression. Ninety of them were successfully isolated and sequenced. Selected genes were tested against different abiotic stresses in P. oleracea and the behavior of their orthologous genes in Arabidopsis thaliana was also explored to seek for conserved response mechanisms. In drought adapted and in recovered plants changes in expression of many protein metabolism-, lipid metabolism- and stress-related genes were observed. Many genes with unknown function were detected, which also respond to other abiotic stresses. Some of them are also involved in the seed desiccation/imbibition process and thus would be of great interest for further research. The potential use of candidate genes to engineer drought tolerance improvement and recovery is discussed.

What have we learned about non-involved psoriatic skin from large-scale gene expression studies?

Psoriasis is a chronic inflammatory skin disorder; its genetic background has been widely studied in recent decades. Recognition of novel factors contributing to the pathogenesis of this disorder was facilitated by potent molecular biology tools developed during the 1990s. Large-scale gene expression studies, including differential display and microarray, have been used in experimental dermatology to a great extent; moreover, skin was one of the first organs analyzed using these methods. We performed our first comprehensive gene expression analysis in 2000. With the help of differential display and microarray, we have discovered several novel factors contributing to the inherited susceptibility for psoriasis, including the EDA+ fibronectin splice variant and PRINS. The long non-coding PRINS RNA is expressed at higher levels in non-involved skin compared to healthy and involved psoriatic epidermis and might be a factor contributing cellular stress responses and, specifically, to the development of psoriatic symptoms. This review summarizes the most important results of our large-scale gene expression studies.

Identification of differentially expressed genes in gauze-exposed omentum of dogs using differential display RT-PCR

Molecular mechanisms governing peritonitis caused by the presence of aseptic gauze have remained unclear. To identify the genes involved, sterile gauze-exposed omentum was collected at 0, 6, 12, 24, and 48 h intervals, and analyzed by differential display RT(reverse transcription)-PCR. Among over 1,200 bands, 230 bands were found differentially expressed. These bands represented the fragment sizes of approximately 200 to 1,500 bp. The eight fragments were expressed differentially in the treatment group but not in the control. The sequences of two bands were similar to those of genes associated with the inflammatory process and a band was related to repair and regeneration process. Another one was related with spermatogonia and the rest four were unknown. Additionally, amplicons corresponding to the full-length sequences of two inflammatory gene fragments were synthesized by rapid amplification of cDNA end PCR. One showed 99% similarity to the major histocompatibility complex class II dog leukocyte antigen-DR beta chain and the other was canis familiaris proteasome beta type 3. Results of the present study suggested that sterile gauze induced the differential expression of genes in the omentum involved in inflammation and healing process.

Transcriptomic profiling during the post-harvest of heat-treated Dixiland Prunus persica fruits: common and distinct response to heat and cold

Cold storage is extensively used to slow the rapid deterioration of peach (Prunus persica L. Batsch) fruit after harvest. However, peach fruit subjected to long periods of cold storage develop chilling injury (CI) symptoms. Post-harvest heat treatment (HT) of peach fruit prior to cold storage is effective in reducing some CI symptoms, maintaining fruit quality, preventing softening and controlling post-harvest diseases. To identify the molecular changes induced by HT, which may be associated to CI protection, the differential transcriptome of peach fruit subjected to HT was characterized by the differential display technique. A total of 127 differentially expressed unigenes (DEUs), with a presence-absence pattern, were identified comparing peach fruit ripening at 20°C with those exposed to a 39°C-HT for 3 days. The 127 DEUs were divided into four expression profile clusters, among which the heat-induced (47%) and heat-repressed (36%) groups resulted the most represented, including genes with unknown function, or involved in protein modification, transcription or RNA metabolism. Considering the CI-protection induced by HT, 23-heat-responsive genes were selected and analyzed during and after short-term cold storage of peach fruit. More than 90% of the genes selected resulted modified by cold, from which nearly 60% followed the same and nearly 40% opposite response to heat and cold. Moreover, by using available Arabidopsis microarray data, it was found that nearly 70% of the peach-heat responsive genes also respond to cold in Arabidopsis, either following the same trend or showing an opposite response. Overall, the high number of common responsive genes to heat and cold identified in the present work indicates that HT of peach fruit after harvest induces a cold response involving complex cellular processes; identifying genes that are involved in the better preparation of peach fruit for cold-storage and unraveling the basis for the CI protection induced by HT.

SUZ12 is a candidate target of the non-canonical WNT pathway in the progression of chronic myeloid leukemia

Polycomb proteins form multiprotein complexes that repress target genes by chromatin remodeling. In this work, we report that the SUZ12 polycomb gene is over-expressed in bone marrow samples of patients at the blastic phase of chronic myeloid leukemia. We also found a direct interaction between polycomb group genes and the WNT signaling pathway in chronic myeloid leukemia transformation. Electrophoretic mobility shift assay (EMSA), Chromatin immunoprecipitation assay (ChIP), and mass spectrometry assays identified noncanonical WNT pathway members, such as WNT5A and WNT11, bound to the SUZ12 promoter. Immunohistochemistry and immunofluorescence with WNT5A and WNT11 antibodies confirmed nuclear localization. Knockdown of WNTs 1, 5A, and 11 with RNAi approaches showed that WNT members are capable of activating SUZ12 transcription with varying promoter affinities. Finally, we suggest that SUZ12 is blocking cellular differentiation, as SUZ12 knockdown release differentiation programs in chronic myeloid blastic phase (CML-BP) transformed cell line.

Analysis of molecular markers in three different tomato cultivars exposed to ozone stress

Three differentially expressed cDNAs have been isolated from ozone treated tomato seedlings. Their level of expression after ozone exposure has been analysed in three tomato cultivars with different sensitivity to ozone (Nikita, Alisa Craig and Valenciano). These comparative analyses have been extended to a number of genes involved in antioxidative, wounding or pathogenesis responses, showing several differences among cultivars that could be related with their different sensitivity to ozone. Gene response to ozone was affected not only by the period and dose of ozone exposure (short time or chronic), but also by growth conditions (controlled growth chamber or field). Comparison of gene expression patterns puts on evidence the needing of validation in field of experiments performed with plants grown under controlled conditions. Our results suggest that changes in genes expression, observed after ozone treatment in field, are affected by additional factors related to environmental clues.

Identification of prostate cancer mRNA markers by averaged differential expression and their detection in biopsies, blood, and urine

The advent of serum prostate-specific antigen (PSA) as a biomarker has enabled early detection of prostate cancer and, hence, improved clinical outcome. However, a low PSA is not a guarantee of disease-free status, and an elevated PSA is frequently associated with a negative biopsy. Therefore, our goal is to identify molecular markers that can detect prostate cancer with greater specificity in body fluids such as urine or blood. We used the RT-PCR differential display method to first identify mRNA transcripts differentially expressed in tumor vs. patient-matched nontumor prostate tissue. This analysis led to the identification of 44 mRNA transcripts that were expressed differentially in some but not all tumor specimens examined. To identify mRNA transcripts that are differentially expressed in most tumor specimens, we turned to differential display of pooled tissue samples, a technique we name averaged differential expression (ADE). We performed differential display of mRNA from patient-matched nontumor vs. tumor tissue, each pooled from 10 patients with various Gleason scores. Differentially expressed mRNA transcripts identified by ADE were fewer in number, but were expressed in a greater percentage of tumors (>75%) than those identified by differential display of mRNA from individual patient samples. Differential expression of these mRNA transcripts was also detected by RT-PCR in mRNA isolated from urine and blood samples of prostate cancer patients. Our findings demonstrate the principle that specific cDNA probes of frequently differentially expressed mRNA transcripts identified by ADE can be used for the detection of prostate cancer in urine and blood samples.

Marqueurs biologiques du cancer de la prostate

Screening for prostate cancer is currently based on the assessment of blood prostate specific antigen (PSA). Although PSA was shown to be an adequate tool in prostate cancer screening, beginning from 4.0 ng/mL, its specificity is less significant. In men with a PSA between 4.0 and 10 ng/mL its predictive value is low. Therefore, there is a need for new instruments likely to improve the specificity of blood PSA levels between 4.0 and 10 ng/mL and the screening for prostate cancer in subjects with low PSA. Recent data are reviewed.

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.

The cyclin–like uracil DNA glycosylase (UDG) of murine oocytes and its relationship to human and chimpanzee homologues

Examination of electrophoretically resolved randomly generated PCR amplicons from mature murine oocytes revealed the presence of a short sequence with partial homology to a cyclin-like human uracil DNA glycosylase (UDG2), a member of an important group of base-excision enzymes that remove misincorporated or cytosine-derived uracil from nascent DNA. A combination of 3' R.A.C.E. and in silico 'cloning' of the 5' region of the original EST uncovered a predicted murine mRNA sequence with limited homology to human UDG2 at both nucleotide and amino acid levels. An alternative contig for human UDG2 showed stronger similarity with the homologous murine and chimp genomic and protein sequences and contained both N and C terminal cyclin box elements. This contig is also an Ensembl annotated alternative splice-site variant of the UDG2 gene (Udg2v2). We suggest that uracil-excision repair in oocytes is likely to be mediated by Udg2v2, or alternatively that Udg2v2 is involved in a process related to oocyte-specific maturation by virtue of its cyclin-like domains.

Upregulation of a tonoplast-localized cytochrome P450 during petal senescence in Petunia inflata

BACKGROUND

Gene expression in Petunia inflata petals undergoes major changes following compatible pollination. Severe flower wilting occurs reproducibly within 36 hours, providing an excellent model for investigation of petal senescence and programmed cell death. Expression of a number of genes and various enzyme activities involved in the degradation and remobilization of macromolecules have been found to be upregulated during the early stages of petal senescence.

RESULTS

By performing differential display of cDNAs during Petunia inflata petal senescence, a highly upregulated gene encoding a cytochrome P450 was identified. Analysis of the complete cDNA sequence revealed that the predicted protein is a member of the CYP74C family (CYP74C9) and is highly similar to a tomato CYP74C allene oxide synthase (AOS) that is known to be active on 9-hydroperoxides. Cloning of the petunia genomic DNA revealed an intronless gene with a promoter region that carries signals found in stress-responsive genes and potential binding sites for Myb transcription factors. Transcripts were present at detectable levels in root and stem, but were 40 times more abundant in flowers 36 hours after pollination. Ethylene and jasmonate treatment resulted in transitory increases in expression in detached flowers. A protein fusion of the CYP74C coding region to a C-terminal GFP was found to be located in the tonoplast.

CONCLUSION

Though oxylipins, particularly jasmonates, are known to be involved in stress responses, the role of other products of CYP74 enzymes is less well understood. The identification of a CYP74C family member as a highly upregulated gene during petal senescence suggests that additional products of fatty acid metabolism may play important roles during programmed cell death. In contrast to the chloroplast localization of AOS proteins in the CYP74A subfamily, GFP fusion data indicates that the petunia CYP74C9 enzyme is in the tonoplast. This result suggests that the highly similar CYP74C enzymes that have been identified in two other Solanaceous plants may also be associated with the vacuole, an organelle known to have a prominent role in programmed cell death.

Identification of a mouse synaptic glycoprotein gene in cultured neurons

Neuronal differentiation and aging are known to involve many genes, which may also be differentially expressed during these developmental processes. From primary cultured cerebral cortical neurons, we have previously identified various differentially expressed gene transcripts from cultured cortical neurons using the technique of arbitrarily primed PCR (RAP-PCR). Among these transcripts, clone 0-2 was found to have high homology to rat and human synaptic glycoprotein. By in silico analysis using an EST database and the FACTURA software, the full-length sequence of 0-2 was assembled and the clone was named as mouse synaptic glycoprotein homolog 2 (mSC2). DNA sequencing revealed transcript size of mSC2 being smaller than the human and rat homologs. RT-PCR indicated that mSC2 was expressed differentially at various culture days. The mSC2 gene was located in various tissues with higher expression in brain, lung, and liver. Functions of mSC2 in neurons and other tissues remain elusive and will require more investigation.

Effect of the Chinese traditional medicine "Bushen Yinao Pian" on the cerebral gene expression of the senescence-accelerated mouse prone 8/ta

The effect of Chinese traditional medicine "Bushen Yinao Pian," a complex prescription used for anti-aging, on the cerebral gene expression of the senescence-accelerated mouse prone 8/Ta (SAMP8/Ta) had been studied with messenger ribonuclear acids reverse transcription differential display polymerase chain reaction (mRNA DDRT-PCR). Eight differential displayed bands had been discerned and sequenced. The sequences of those fragments are matched to adipocyte-specific protein-5; low density lipoprotein receptor-related protein associated protein-1; reticulon-3; cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein-1; cytochrome c oxidase subunit-2 (Cox-2); cytochrome c gene, MC1; DNA sequence from clone RP23-72M11 on chromosome X, respectively and a novel sequence fragment. Most of these genes are aging-related. It can be proved that the "Bushen Yinao Pian" truly has anti-aging function.

Molecular cloning and expression pattern of the Fkbp25 gene during cerebral cortical neurogenesis

Neocortical neurons are generated predominantly from the cells that proliferate in the ventricular zone of the telencephalon. In order to understand the nature of these expanding cortical neuronal progenitor cells, we selected by differential display some transcripts that were enriched in the telencephalon as compared to the more caudal regions (diencephalon/mesencephalon). This systematic screening revealed one of the differentially expressed transcripts, namely the Fkbp25 mRNA that encodes a member of the FK506 binding proteins (FKBPs). Northern blot analysis showed that the expression of the single 1.4kb Fkbp25 transcript reached a maximum level on embryonic day 11.5 at the start of cortical neurogenesis in the mouse and was followed by a weak basal expression in the adult brain. In the embryo, Fkbp25 gene was strongly expressed in the telencephalon ventricular zone but also in areas active in myogenesis (walls of the ventricle and the atrium) and chondrogenesis (the cartilage of the rib and the hindlimb). An increase in the transcript levels of the Fkbp25 gene was also observed during the two successive proliferation waves of the cerebellum development. Immunostaining on primary cultures of embryonic day 10.5 telencephalon stem cells showed that the Fkbp25 protein was present in the cytoplasm and nuclei of cells cultured for 6h but exclusively in the nuclei of the Tuj-1 immunoreactive neurons obtained after 3 days of culture (The sequence data reported here have been submitted to GenBank under accession no. AF135595.).

In silico analysis of angiogenesis associated gene expression identifies angiogenic stage related profiles

In vitro models have been extensively used to map gene expression in ECs but few studies have used cells from in vivo sources directly. Here, we compare different gene expression surveys on both cultured and fresh tissue derived ECs, and it emerges that gene expression profiles can be paralleled with the angiogenic stage of the cells. ECs stimulated with different growth factors in monolayer cultures exhibit gene expression profiles indicative of an active proliferative state, whereas gene expression in tube forming cells in vitro involves genes implicated in cell adhesion processes. Genes overexpressed in tumor ECs are biased towards extracellular matrix remodeling, a late event in angiogenesis. The elucidation of gene expression profiles under these different conditions will contribute to a better understanding of the molecular mechanisms during angiogenesis in both pathological and physiological circumstances and will have implications for the development of angiogenesis interfering treatment strategies.

Adhesion properties of adhesion-regulating molecule 1 protein on endothelial cells

Numerous adhesion molecules have been described, and the molecular mechanisms of lymphocyte trafficking across the endothelium is starting to be elucidated. Identification of the molecules involved in the organoselectivity of this process would help in the targeting of drug therapy to specific tissues. Adhesion-regulating molecule-1 (ARM-1) is an adhesion-regulating molecule previously identified on T cells. It does not belong to any known families of adhesion molecules. In this study, we show the presence of ARM-1 in endothelial cells, the adhesion partners of lymphocytes. ARM-1 mRNA was found to be differentially expressed in endothelial cell lines of various tissue origin and lymphocyte cell lines. Interestingly, ARM-1 is absent from skin endothelial cells. In our assay, skin endothelial cells display a distinct capacity to mediate adhesion of activated T lymphocytes. Overexpression of ARM-1 in skin endothelial cells increased adhesion of CEMT4 and NK lymphocytes, confirming that ARM-1 also regulates adhesion in endothelial cells. We also show that ARM-1 is a cytosolic protein associated with the plasma membrane. However, no cell surface expression of the protein was observed. These results suggest an indirect role of ARM-1 in adhesion rather than a direct role as an adhesion molecule itself.

Identification of differentially expressed genes of primary spermatocyte against round spermatid isolated from human testis using the laser capture microdissection technique

The method of laser capture microdissection (LCM) combined with suppressive subtractive hybridization (SSH) was developed to isolate specific germ cells from human testis sections and to identify the genes expressed during differentiation and development. In the present study, over 10,000 primary spermatocytes and round spermatid cells were successfully isolated by LCM. Using the cDNAs from primary spermatocytes and round spermatids, SSH cDNAs library of primary spermatocyte-specific was constructed. The average insert size of the cDNA isolated from 75 randomly picked white clones was 500 bp, ranging from 250 bp to 1.7 kb. Using the dot-blot method, a total of 421 clones were examined, resulting in the identification of 390 positive clones emitting strong signals. Partial sequence of cDNAs prepared from each clone was determined with an overall success rate of 84.4%. Genes encoding cytochrome c oxidase II and the rescue factor-humanin were most frequently expressed in primary spermatocytes, suggesting their roles involved in meiosis.

Identification and characterization of a novel, psoriasis susceptibility-related noncoding RNA gene, PRINS

To identify genetic factors contributing to psoriasis susceptibility, gene expression profiles of uninvolved epidermis from psoriatic patients and epidermis from healthy individuals were compared. Besides already characterized genes, we identified a cDNA with yet unknown functions, which we further characterized and named PRINS (Psoriasis susceptibility-related RNA Gene Induced by Stress). In silico structural and homology studies suggested that PRINS may function as a noncoding RNA. PRINS harbors two Alu elements, it is transcribed by RNA polymerase II, and it is expressed at different levels in various human tissues. Real time reverse transcription-PCR analysis showed that PRINS was expressed higher in the uninvolved epidermis of psoriatic patients compared with both psoriatic lesional and healthy epidermis, suggesting a role for PRINS in psoriasis susceptibility. PRINS is regulated by the proliferation and differentiation state of keratinocytes. Treatment with T-lymphokines, known to precipitate psoriatic symptoms, decreased PRINS expression in the uninvolved psoriatic but not in healthy epidermis. Real time reverse transcription-PCR analysis showed that stress signals such as ultraviolet-B irradiation, viral infection (herpes simplex virus), and translational inhibition increased the RNA level of PRINS. Gene-specific silencing of PRINS by RNA interference revealed that down-regulation of PRINS impairs cell viability after serum starvation but not under normal serum conditions. Our findings suggest that PRINS functions as a noncoding regulatory RNA, playing a protective role in cells exposed to stress. Furthermore, elevated PRINS expression in the epidermis may contribute to psoriasis susceptibility.

The Chinese traditional medicine 'Bushen Yinao Pian' increased the level of ageing-related gene LRPAP-1 expression in the cerebral tissue of accelerated senescence-prone mouse 8/Ta

The molecular mechanism of the Chinese traditional medicine 'Bushen Yinao Pian' (a complex prescription used for clinical anti-ageing in China for over 20 years) is elusive. In this study, the cDNA of low-density lipoprotein related-receptor associated protein-1 (LRPAP-1), an ageing-related gene, which functions as a chaperon or escort protein in the intracellular transport of low-density lipoprotein related-receptor, a transporter of amyloid beta protein (AbetaP), had been cloned by screening cDNA library based on analyzing the gene expression in cerebral tissue between the test and the control accelerated senescence-prone mouse 8/Ta (SAMP8/Ta). The result shows that this complex prescription increased the expression level of LRPAP-1. It indicated that the Chinese traditional medicine 'Bushen Yinao Pian' plays an important role in anti-ageing by increasing LRPAP-1 expression level.

Stress induces the expression of AtNADK-1, a gene encoding a NAD(H) kinase in Arabidopsis thaliana

A novel Arabidopsis thaliana gene (AtNADK-1) was identified based on its response to radiation and oxidative stress. Levels of AtNADK-1 mRNA increase eight-fold following exposure to ionising radiation and are enhanced three-fold by treatment with hydrogen peroxide. The gene also appears to be differentially regulated during compatible and incompatible plant-pathogen interactions in response to Pseudomonas syringae pv. tomato. The full-length AtNADK-1 cDNA encodes a 58-kDa protein that shows high sequence homology to the recently defined family of NAD(H) kinases. Recombinant AtNADK-1 utilises ATP to phosphorylate both NAD and NADH, showing a two-fold preference for NADH. Using reverse genetics, we demonstrate that AtNADK-1 deficient plants display enhanced sensitivity to gamma irradiation and to paraquat-induced oxidative stress. Our results indicate that this novel NAD(H) kinase may contribute to the maintenance of redox status in Arabidopsis thaliana.

Stromal cell-derived factor-1 (SDF-1) signalling regulates human placental trophoblast cell survival

Stromal cell-derived factor-1 (SDF-1 or CXCL12) is the physiologic ligand for the chemokine receptor CXCR4. CXCR4-mediated signalling regulates cell migration and apoptosis in certain haematopoietic and neuronal cells. Using gene profiling, we determined that CXCR4 is the only chemokine receptor for which mRNA expression is regulated during trophoblast differentiation in vitro. Based on the known effects of CXCR4 ligation, we hypothesized that CXCR4 activation may regulate placental trophoblast cell survival (i.e. protection from apoptosis), an important mechanism for the establishment and maintenance of the uteroplacental barrier. Human cytotrophoblasts (CTBs) were cultured in defined media and treated with graded doses of SDF-1 (10-100 ng/ml) or with an anti-CXCR4 neutralizing antibody. Exposure to anti-CXCR4 antibody reduced CTB cell numbers by 25-40%. Treatment with SDF-1 decreased the proportions of apoptotic terminal deoxynucleotidyl transferase-mediated dUTP-FITC nick-end labelling(+) cells (apoptotic index [AI] of 2.79+/-0.61% [control] versus 1.88+/-0.56% [SDF-1]; P<0.05) and caspase-activated cells (AI of 7.95+/-2.49% [control] versus 3.81+/-1.49% [SDF-1]; P<0.05). We determined that SDF-1 also activated the triple MAP Kinase isoforms ERK1/2 and p38 in trophoblasts. Immunocytochemistry confirmed SDF-1-induced nuclear translocation of phosphorylated ERK1/2. Blocking of ERK1/2 signalling with the specific inhibitor PD98059 reversed SDF-1-mediated inhibition of apoptosis (AI of 1.65+/-0.34 [SDF-1] versus 3.50+/-0.5 [SDF-1 + PD98059]; P<0.05), suggesting that SDF-1 acts through this pathway as a trophoblast survival factor. These results indicate that SDF-1/CXCR4 signalling stimulates anti-apoptotic pathways in cultured trophoblasts. This chemotactic ligand/receptor system may promote trophoblast survival during pregnancy. Alterations in SDF-1 and/or CXCR4 expression or function may be associated with specific pregnancy disorders.

DNA microarray analysis of pancreatic malignancies

Pancreatic ductal adenocarcinoma (PDAC) has an extremely poor prognosis. To improve the prognosis, novel molecular markers and targets for earlier diagnosis and adjuvant and/or neoadjuvant treatment are needed. Recent advances in human genome research and high-throughput molecular technologies make it possible to cope with the molecular complexity of malignant tumors. With DNA array technology, mRNA expression levels of thousand of genes can be measured simultaneously in a single assay. As several studies using microarrays in PDAC have already been published, this review attempts to compare the published data and therefore to validate the results. In addition, the applied techniques are discussed in the context of pancreatic malignancies.

FOXO1 and c-jun transcription factors mRNA are modulated in endometriosis

Endometriosis is a polygenic gynaecological condition affecting 5-15% of women of childbearing age. Major symptoms of the disease are pelvic pain and infertility. No clear link has been established between symptoms and the stage of the disease. Although some aspects have begun to be clarified, clinical understanding of endometriosis remains partial at the molecular level. In this perspective, we targeted isolation of differentially expressed genes in the eutopic endometrial tissue. Our assumption was that the endometrial cells of patients presented an unusual gene expression profile, allowing their implantation and survival in an ectopic site, leading to endometriotic lesions. Here, we report that mRNA steady-state levels of two key transcription factors are modulated in endometriosis. FOXO1 (also known as FKHR) levels were 1.6-fold lower in endometriosis compared to the control group at the onset of the secretory phase (day 15-21), while c-jun mRNA was present at higher amounts in endometriosis (1.5-fold) at the proliferative phase of the menstrual cycle. These results were derived from a large sample composed of 157 control subjects and 209 patients with endometriosis. Gene profiling was conducted by real-time quantitative PCR, and data were quality controlled before statistical analysis. Whether protein levels are affected as well remains to be investigated.

Identification of a novel brain-specific and reelin-regulated gene that encodes a protein colocalized with synapsin

We carried out a screening of genes that are differentially expressed in normal mice and reeler mutants and are characterized by abnormal neuronal migration and neurite deployment due to defective Reelin signalling. A novel gene, provisionally named C61, was overexpressed in Reelin-deficient embryonic mouse brain RNA. C61 encodes a 3.7 kb mRNA that is brain specific and developmentally regulated, with predominant expression in differentiating neurons. The predicted protein is 664 amino acids long, and contains LAG1 and Ezrin/Radixin/Moesin-Myosin-Filament motifs, suggesting that it may function as an intracellular adaptor. From E14.5 to birth, C61 was highly expressed in all neuronal differentiation fields, with the highest signal in the telencephalic cortical plate and mitral cells in the olfactory bulb. When expressed as a GFP fusion protein in transfected non-neuronal cells and primary neurons, this protein localizes, respectively, to the nuclear membrane or axonal outgrowths, indicating a function in axonal traffic or signalling.

Changes in gene expression at the precursor --> stem cell transition in leech

The glossiphoniid leech, Theromyzon trizonare, displays particularly large and accessible embryonic precursor/stem cells during its early embryonic cleavages. We dissected populations of both cell types from staged embryos and examined gene expression profiles by differential display polymerase chain reaction methodology. Among the approximately 10,000 displayed cDNA fragments, 56 (approximately 0.5%) were differentially expressed at the precursor --> stem cell transition; 29 were turned off (degraded, precursor-specific); and 27 were turned on (transcribed, stem cell-specific). Several putative differentially expressed cDNAs from each category were confirmed by Northern blot analysis on staged embryos. DNA sequencing revealed that 19 of the cDNAs were related to a spectrum of genes including the CCR4 antiproliferation gene, Rad family members, and several transcriptional regulators, while the remainder encoded hypothetical (10) or novel (27) sequences. Collectively, these results identify dynamic changes in gene expression during stem cell formation in leech and provide a platform for examining the molecular aspects of stem cell genesis in a simple invertebrate organism.

Toxicogenomics in drug development

Toxicogenomics represents the merging of toxicology with technologies that have been developed, together with bioinformatics, to identify and quantify global gene expression changes. It represents a new paradigm in drug development and risk assessment, which promises to generate a wealth of information towards an increased understanding of the molecular mechanisms that lead to drug toxicity and efficacy, and of DNA polymorphisms responsible for individual susceptibility to toxicity. Gene expression profiling, through the use of DNA microarray and proteomic technologies will aid in establishing links between expression profiles, mode of action and traditional toxic endpoints. Such patterns of gene expression, or 'molecular fingerprints' could be used as diagnostic or predictive markers of exposure, that is characteristic of a specific mechanism of induction of that toxic or efficacious effect. It is anticipated that toxicogenomics will be increasingly integrated into all phases of the drug development process particularly in mechanistic and predictive toxicology, and biomarker discovery. This review provides an overview of the expression profiling technologies applied in toxicogenomics. and discusses the promises as well as the future challenges of applying this discipline to the drug development process.

Genes induced by a high-oxygen environment in Entamoeba histolytica

Entamoeba histolytica, although a microaerophilic protozoan parasite, encounters a high-oxygen environment, during invasive amoebiasis. The parasite requires specific regulation of certain proteins to maintain its physiological functions to survive in the more oxygenated condition. Our endeavor was to know how does amoeba adapt itself in a high-oxygen environment. Reactive oxygen species (ROS) was found to accumulate in an increasing concentration within the stressed trophozoites in a time-dependent manner. Increased cytopathic activity was detected at 2h in high-oxygen-exposed E. histolytica lysate compared to lysate of normal E. histolytica trophozoites by Ussing chamber assay. The differential display and semi-quantitative polymerase chain reaction showed overexpression in the mRNA levels of thiol-dependent peroxidase (Eh29), superoxide dismutase (SOD), EhCP5, G protein, HSP70, and peptidylprolyl isomerase at different time periods of oxidative stressed trophozoites compared to normally cultured E. histolytica. Analyses of the up-regulated genes that are associated with stress response, viz., signal transduction, tissue destruction, and oxidative stress management, including enhanced expression of a 29-kDa Eh29, suggest that this organism has several protective mechanisms to deal with oxidative stress during invasion.

Differentially expressed genes in hypertensive rats developing cerebral ischemia

The molecular events occurring after cerebral ischemia in hypertension may include de novo expression of numerous genes. Receptor genes are predominantly involved in the process of cell death, neuroprotection and reconstruction after ischemic injury. Ischemic stroke was observed in the non-genetic, non-surgical model of hypertension, the cold-induced hypertensive rat. In hypertensive rats suppression subtractive hybridization analysis was used to identify differentially expressed receptor genes in stroke-tissue compared to normal rat brain. We found 76 genes predominantly expressed in hypertensive rat stroke-tissue. These predominantly expressed genes included genes involved in energy metabolism, signal transduction/cell regulation, and replication/transcription/translation. For example, the T3 receptor alpha was predominantly expressed in stroke-tissue, indicating that regeneration of nerves in stroke tissue may be facilitated by increased T3 receptor alpha expression.

Novel human, mouse and xenopus genes encoding a member of the RAS superfamily of low-molecular-weight GTP-binding proteins and its downregulation in W/WV mouse jejunum

BACKGROUND AND AIM

Interstitial cells of Cajal (ICC) are pacemakers and mediators of neurotransmission in gastroenteric smooth muscles. Interstitial cells of Cajal require cellular signaling via KIT, a receptor tyrosine kinase, for development and maintenance of cellular phenotype. Much of the evidence demonstrating the functions of ICC comes from studies of W/W V mutant mice, which have reduced KIT function. The aim of the present study was to differentially examine gene expression in the small intestines of wild-type and W/W V mice.

METHODS

RNA from the jejunum of wild-type and W/W V mice was analyzed using a differential gene display method.

RESULTS

One candidate gene, encoding a novel small GTPase of the RAS superfamily, was significantly suppressed both in fed and starved W/WV mice. The full-length clone of the murine gene and its human and xenopus counterparts were designated GTP-binding protein, 28 kDa (G28K). Human G28K cDNA encodes a protein of 258 amino acids with homology to the human cell division cycle 42/G25K protein. This gene is located at 1q42.11-q42.3. G28K was abundantly expressed in the human stomach and the small intestine. Semi-quantitative reverse transcription-polymerase chain reaction analysis revealed expression of G28K mRNA within single isolated ICC.

CONCLUSIONS

Gene analysis showed that G28K was differentially expressed in the small intestines of wild-type and W/W V mice. Interstitial cells of Cajal within the small intestine expressed mRNA for G28K. The specific downregulation of G28K in the jejunum of W/W V mice, and high expression in human intestinal tissue suggest that the G28K gene might be associated with ICC function in mice and in humans.

Differences between retinal and choroidal microvascular endothelial cells (MVECs) under normal and hypoxic conditions

The morphological and functional differences between the retinal and choroidal vascular bed raise the question of whether the smallest functional unit, the microvascular endothelial cell (MVEC), also differs in its basal characteristics. Here, we examined bovine retinal and choroidal MVECs (rMVECs, cMVECs) for the presence and regulation of angiogenic mediators and their receptors, and cytokines at the mRNA level using quantitative RT-PCR and differential display. Vascular endothelial growth factor (VEGF) mRNA was expressed in both rMVECs and cMVECs. The basal and hypoxia-increased VEGF mRNA levels were significantly higher in cMVECs, which may indicate a higher capacity for autocrine stimulation in these cells. The mRNA for two VEGF receptors, Flt-1 and Flk-1, was present in rMVECs and cMVECs. Interestingly, rMVECs expressed higher Flt-1 but lower Flk-1 mRNA levels compared to cMVECs. Examining the angiopoietin (Ang)/Tie-2 system, we only detected Ang-1 mRNA at very low levels. While Ang-2 mRNA levels were high in both rMVECs and cMVECs, rMVECs expressed 2-3 times the basal and hypoxia-upregulated Ang-2 mRNA levels than did cMVECs. No difference was found in basal Tie-2 mRNA levels. rMVECs are the more potent producers of macrophage colony-stimulating factor (M-CSF) and granulocyte-macrophage CSF (GM-CSF), whereas cMVECs expressed higher RANTES mRNA levels. In our second approach - screening rMVECs and cMVECs for differentially expressed genes - we found liprin-beta1, calnexin, and sushi-repeat-containing protein, x chromosome (SRPX) mRNA in both MVEC types at varying levels. In summary, MVECs from the retinal and choroidal vascular beds showed quantitative differences in angiogenic regulator expression and in their capability to produce cytokines.

New targets for therapy in prostate cancer: differential display code 3 (DD3PCA3), a highly prostate cancer–specific gene

Identification of new markers for diagnosis and new targets for therapy would represent a considerable advance in the treatment of prostate cancer. Differential display code 3 (DD3(PCA3)) is a novel gene with characteristics that indicate its potentially valuable role in early identification of malignancy and in the construction of interventions directed specifically toward malignantly transformed cells. DD3(PCA3) has a messenger RNA product that is highly overexpressed in tumors. Compared with other genetic markers that are associated with prostate tissue, DD3(PCA3) is the most specific marker for malignant disease. Indeed, it is not expressed in any other normal human tissue, including breast, bladder, testis, gastrointestinal organ, and musculoskeletal tissue. This specific relation of DD3(PCA3) to prostate tissue has been confirmed by reverse transcription-polymerase chain reaction analysis. Clonal investigation of the DD3(PCA3) transcription unit indicates that the gene has 4 distinct exons, which can give rise to a number of differently sized transcripts. Open reading frame analysis has also confirmed that the DD3(PCA3) exons are populated by an unusual number of stop codons. The dramatic prostate-specific expression and pronounced upregulation of DD3(PCA3) in prostate cancer suggest a unique transcriptional regulation. A quantitative assay for DD3(PCA3) would be a potentially valuable tool for the detection of malignant cells in blood, urine, or other clinical specimens, and it could have important implications for the earlier diagnosis and molecular staging of prostate cancer. Although further studies are needed, gene therapies based on identification to delineate the range of transcription factors that interact with the DD3(PCA3) promoter represent a promising area for preclinical investigation.

Novel putative nonprotein-coding RNA gene from 11q14 displays decreased expression in brains of patients with schizophrenia

A modified method of differential display was employed to identify a novel gene (named PSZA11q14), the expression of which was reduced in brains from patients with schizophrenia. Decreased expression of PSZA11q14 was identified initially in Brodmann's area (BA) 21 from a small group of patients with schizophrenia (n = 4) and normal controls (n = 6) and was confirmed subsequently using independent RT-PCR assay in BA 21, 22, and 9, and in hippocampus from a larger group of patients with schizophrenia (n = 36) and controls (n = 35). PSZA11q14 is located on chromosome 11q14, an area shown previously to co-segregate with schizophrenia and related disorders in several families. Decreased expression of PSZA11q14 in patients with schizophrenia and its location on 11q14 provide converging lines of evidence indicating that PSZA11q14 may be involved in at least some cases of schizophrenia. PSZA11q14 shows no significant homology with any known gene. It has no introns and produces two RNA transcripts of approximately 4.5 and approximately 7.0 kb. The largest open reading frame (ORF) in the PSZA11q14 transcripts may potentially encode for a short polypeptide of 71 amino acids. High frequency of rare codons, the short size of this ORF, and low homology with mouse sequences, however, indicate that PSZA11q14 may instead represent a novel member of a family of nonprotein-coding RNA genes that are not translated and that function at the RNA level. PSZA11q14 is located within the first intron of the DLG-2 gene and transcribed in the opposite direction to DLG-2. These results suggest that PSZA11q14 may be considered a candidate gene for schizophrenia acting as an antisense regulator of DLG-2, which controls assembling functional N-methyl-D-aspartate (NMDA) receptors.

Differential gene expression profile in the small intestines of mice lacking pacemaker interstitial cells of Cajal

BACKGROUND

We previously identified eight known and novel genes differentially expressed in the small intestines of wild type and W/WV mice, which have greatly reduced populations of the interstitial cells of Cajal, that are responsible for the generation of electrical slow waves, by using a differential gene display method.

METHODS

By using the same method we isolated additional candidate genes that were specifically down- or up-regulated in W/WV mice. Novel transcripts were designated as DDWMEST.

RESULTS

We isolated seven candidates that were specifically down- or up-regulated in W/WV mice. Two novel transcripts, DDWMEST 1 and -91 were increased in both fed and fasted W/WV mice. Expression of another five genes was suppressed in W/WV mice: ARG2 (Arginase II), ONZIN (encoding leukemia inhibitory factor regulated protein), and three novel transcripts: DDWMEST62, -84, and -100. Together with the previous report, we identified fifteen differentially expressed genes in total in the small intestines of W/WV mice. Eight of these genes were reduced in the jejunums of W/WV mice compared to age matched wild type mice, whereas the other seven genes showed an increase in expression. Differential expression was the same in fasted and fed animals, suggesting that the differences were independent of the dietetic state of the animal.

CONCLUSIONS

Several known and novel genes are differentially expressed in the small intestines of W/WV mice. Differential gene comparison might contribute to our understanding of motility disorders associated with the loss of the interstitial cells of Cajal.

Understanding the molecular responses to hypoxia using Drosophila as a genetic model

We have previously discovered that Drosophila melanogaster could recover from extended periods of anoxia (0% oxygen) with no apparent consequential injuries. We have since employed forward and reverse genetic approaches to decipher the molecular basis for anoxia tolerance. In so doing, we have identified several independent mutant lines that demonstrated increased sensitivity to anoxia. Characterization of one of these mutants resulted in the identification of a dADAR gene that plays a role in the sensitivity to low levels of oxygen. We have also used microarrays to study all known Drosophila genes, the expression of which may be altered by hyoxia. Microarrays experiments have generated a large body of information that is being currently analyzed. We believe that these undertakings will provide insight into the genetic mechanisms of hypoxia tolerance and ischemic injuries.

Attenuation of cell adhesion in lymphocytes is regulated by CYTIP, a protein which mediates signal complex sequestration

An important theme in molecular cell biology is the regulation of protein recruitment to the plasma membrane. Fundamental biological processes such as proliferation, differentiation or leukocyte functions are initiated and controlled through the reversible binding of signaling proteins to phosphorylated membrane components. This is mediated by specialized interaction modules, such as SH2 and PH domains. Cytohesin-1 is an intracellular guanine nucleotide exchange factor, which regulates leukocyte adhesion. The activity of cytohesin-1 is controlled by phospho inositide-dependent membrane recruitment. An interacting protein was identified, the expression of which is upregulated by cytokines in hematopoietic cells. This molecule, CYTIP, is also recruited to the cell cortex by integrin signaling via its PDZ domain. However, stimulation of Jurkat cells with phorbol ester results in re-localization of CYTIP to the cytoplasm, and membrane detachment of cytohesin-1 strictly requires co-expression of CYTIP. Consequently, stimulated adhesion of Jurkat cells to intracellular adhesion molecule-1 is repressed by CYTIP. These findings outline a novel mechanism of signal chain abrogation through sequestration of a limiting component by specific protein-protein interactions.

The identification of novel wound-healing genes through differential display

Effective methods to identify novel genes in complicated dynamic tissue processes are needed in molecular biology research. Traditional techniques primarily target known genes and are inefficient in the pursuit of unknown genes. Here we describe the use of a modified differential display polymerase chain reaction (DD-PCR) protocol for the identification of genes differentially expressed in wound healing. Full-thickness dorsal wounds were made on 35 adult rats, followed by wound harvest at 12 hours, 24 hours, 3 days, 5 days, 7 days, 10 days, and 14 days after injury. Modified DD-PCR was performed and gene fragments displaying definite changes during wound healing were cloned and sequenced. Gene fragments from DD-PCR were compared with available gene bank database sequences. Specific primer PCR was used to confirm DD-PCR expression patterns. As a result, over 1000 gene fragments were amplified by DD-PCR, 35 of which demonstrated distinct differences during repair. Cloning and sequencing of 13 of these gene fragments revealed that some were homologous to several characterized genes with previously unsuspected roles in repair, whereas others were completely novel genes with no known function. Specific primer PCR further confirmed expression of six of these 13 gene fragments. Only one of the 13 cloned fragments, later identified as interleukin-1beta, had well-recognized associations with tissue injury. Other fragments corresponded to various genes involved in cellular processes such as differentiation, proliferation, exocytosis, and myofibril assembly. No prior studies have linked them to wound healing. We have demonstrated that modified DD-PCR can be used to effectively identify novel genes differentially expressed during repair. Because DD-PCR allows for the simultaneous amplification of multiple arbitrary transcripts, it is a powerful genetic screening tool for complicated dynamic tissue processes, particularly when multiple, limited-sized samples are involved.

New class of cargo protein in Tetrahymena thermophila dense core secretory granules

Regulated exocytosis of dense core secretory granules releases biologically active proteins in a stimulus-dependent fashion. The packaging of the cargo within newly forming granules involves a transition: soluble polypeptides condense to form water-insoluble aggregates that constitute the granule cores. Following exocytosis, the cores generally disassemble to diffuse in the cell environment. The ciliates Tetrahymena thermophila and Paramecium tetraurelia have been advanced as genetically manipulatable systems for studying exocytosis via dense core granules. However, all of the known granule proteins in these organisms condense to form the architectural units of lattices that are insoluble both before and after exocytosis. Using an approach designed to detect new granule proteins, we have now identified Igr1p (induced during granule regeneration). By structural criteria, it is unrelated to the previously characterized lattice-forming proteins. It is distinct in that it is capable of dissociating from the insoluble lattice following secretion and therefore represents the first diffusible protein identified in ciliate granules.

Differential gene expression in breast cancer cell lines and stroma-tumor differences in microdissected breast cancer biopsies revealed by display array analysis

To examine gene-expression patterning in late-stage breast cancer biopsies, we used a microdissection technique to separate tumor from the surrounding breast tissue or stroma. A DD-PCR protocol was then used to amplify expressed products, which were resolved using PAGE and used as probe to hybridize with representative human arrays and cDNA libraries. The probe derived from the tumor-stroma comparison was hybridized with a gene array and an arrayed cDNA library derived from a GCT of bone; 21 known genes or expressed sequence tags were detected, of which 17 showed differential expression. These included factors associated with epithelial to mesenchymal transition (vimentin), the cargo selection protein (TIP47) and the signal transducer and activator of transcription (STAT3). Northern blot analysis was used to confirm those genes also expressed by representative breast cancer cell lines. Notably, 6 genes of unknown function were restricted to tumor while the majority of stroma-associated genes were known. When applied to transformed breast cancer cell lines (MDA-MB-435 and T47D) that are known to have different metastatic potential, DD array analysis revealed a further 20 genes; 17 of these genes showed differential expression. Use of microdissection and the DD-PCR array protocol allowed us to identify factors whose localized expression within the breast may play a role in abnormal breast development or breast carcinogenesis.

Differential display: analysis of gene expression during plant cell separation processes

An essential component in the study of cell growth and development in any organism is the analysis of differential gene expression. There are numerous techniques available for comparison of two or more systems at the molecular level, including subtractive hybridization, reverse transcriptase (RT), polymerase chain reaction (PCR), differential screening of cDNA libraries, and, more recently, cDNA microarrays. Differential display has advantages in that it is relatively less time-consuming and can result in the identification of rare cDNA, which may be missed by conventional cDNA library screening. In addition, cDNA microarrays are a valuable asset to the analysis of regulated gene expression but the technique is expensive to employ. Although we successfully applied differential display to isolate novel mRNAs that are up- and downregulated during cell separation processes in plants, the technique can be applied to any system where two or more mRNA sets are to be compared.

Perspective: micoarrays and differential display PCR-tools for studying transcript levels of genes in neuroendocrine systems

A central goal of neuroendocrinology is the understanding of how hormones modulate a variety of neurobiological functions including releasing factors for anterior pituitary secretions and behavior. We know that mechanisms of hormone actions clearly include the activation and repression of genes either directly through nuclear hormone receptors or indirectly, through a series of transduced signals originating from membrane receptors. Until recently, identification of the differentially expressed genes has been a "gene-at-a-time" proposition. With the advent of the completion of sequencing of several genomes including those of the human and mouse, new methods for the simultaneous assessment of many genes' expression are proving especially timely. Two such methods, differential display PCR and gene microarrays, are based on the well-established principles of DNA amplification and nucleic acid hybridization, respectively. With properly designed and well-executed experiments, these methods are powerful tools in the assessment of differentially expressed genes yielding results both expected and unanticipated.

Approaches to the analysis of gene expression using mRNA: a technical overview

Messenger RNA is the blueprint for all proteins expressed within living systems. Therefore, the study of mRNA expression within normal and diseased tissues is central to our understanding of biological systems. However, blueprints, in themselves, perform no function unless they are used to produce the material for which they code. Spurious results may frequently result from poorly designed or inappropriate studies. This review seeks to highlight both the pitfalls and the promise of various approaches to the analysis of mRNA in different systems and to place these studies in the wider context of research approaches aimed at understanding the function of living systems. The various techniques for the analysis of mRNA are discussed, with particular reference to their potential uses and problems and relevant examples are cited from the literature. It is hoped that this overview of the uses of analytical approaches will allow both the novice researcher and the more experienced scientist to better structure research approaches.

Characterizing gene expression during lens formation in Xenopus laevis: evaluating the model for embryonic lens induction

Few directed searches have been undertaken to identify the genes involved in vertebrate lens formation. In the frog Xenopus, the larval cornea can undergo a process of transdifferentiation to form a new lens once the original lens is removed. Based on preliminary evidence, we have shown that this process shares many elements of a common molecular/genetic pathway to that involved in embryonic lens development. A subtracted cDNA library, enriched for genes expressed during cornea-lens transdifferentiation, was prepared. The similarities/identities of specific clones isolated from the subtracted cDNA library define an expression profile of cells undergoing cornea-lens transdifferentiation ("lens regeneration") and corneal wound healing (the latter representing a consequence of the surgery required to trigger transdifferentiation). Screens were undertaken to search for genes expressed during both transdifferentiation and embryonic lens development. Significantly, new genes were recovered that are also expressed during embryonic lens development. The expression of these genes, as well as others known to be expressed during embryonic development in Xenopus, can be correlated with different periods of embryonic lens induction and development, in an attempt to define these events in a molecular context. This information is considered in light of our current working model of embryonic lens induction, in which specific tissue properties and phases of induction have been previously defined in an experimental context. Expression data reveal the existence of further levels of complexity in this process and suggests that individual phases of lens induction and specific tissue properties are not strictly characterized or defined by expression of individual genes.

Selective alteration of gene expression in response to natural and synthetic retinoids

BACKGROUND

Retinoids are very potent inducers of cellular differentiation and apoptosis, and are efficient anti-tumoral agents. Synthetic retinoids are designed to restrict their toxicity and side effects, mostly by increasing their selectivity toward each isotype of retinoic acids receptors (RARalpha,beta, gamma and RXRalpha, beta, gamma). We however previously showed that retinoids displayed very different abilities to activate retinoid-inducible reporter genes, and that these differential properties were correlated to the ability of a given ligand to promote SRC-1 recruitment by DNA-bound RXR:RAR heterodimers. This suggested that gene-selective modulation could be achieved by structurally distinct retinoids.

RESULTS

Using the differential display mRNA technique, we identified several genes on the basis of their differential induction by natural or synthetic retinoids in human cervix adenocarcinoma cells. Furthermore, this differential ability to regulate promoter activities was also observed in murine P19 cells for the RARbeta2 and CRABPII gene, showing conclusively that retinoid structure has a dramatic impact on the regulation of endogenous genes.

CONCLUSIONS

Our findings therefore show that some degree of selective induction or repression of gene expression may be achieved when using appropriately designed ligands for retinoic acid receptors, extending the concept of selective modulators from estrogen and peroxisome proliferator activated receptors to the class of retinoid receptors.

Discordant protein and mRNA expression in lung adenocarcinomas

The relationship between gene expression measured at the mRNA level and the corresponding protein level is not well characterized in human cancer. In this study, we compared mRNA and protein expression for a cohort of genes in the same lung adenocarcinomas. The abundance of 165 protein spots representing 98 individual genes was analyzed in 76 lung adenocarcinomas and nine non-neoplastic lung tissues using two-dimensional polyacrylamide gel electrophoresis. Specific polypeptides were identified using matrix-assisted laser desorption/ionization mass spectrometry. For the same 85 samples, mRNA levels were determined using oligonucleotide microarrays, allowing a comparative analysis of mRNA and protein expression among the 165 protein spots. Twenty-eight of the 165 protein spots (17%) or 21 of 98 genes (21.4%) had a statistically significant correlation between protein and mRNA expression (r > 0.2445; p < 0.05); however, among all 165 proteins the correlation coefficient values (r) ranged from -0.467 to 0.442. Correlation coefficient values were not related to protein abundance. Further, no significant correlation between mRNA and protein expression was found (r = -0.025) if the average levels of mRNA or protein among all samples were applied across the 165 protein spots (98 genes). The mRNA/protein correlation coefficient also varied among proteins with multiple isoforms, indicating potentially separate isoform-specific mechanisms for the regulation of protein abundance. Among the 21 genes with a significant correlation between mRNA and protein, five genes differed significantly between stage I and stage III lung adenocarcinomas. Using a quantitative analysis of mRNA and protein expression within the same lung adenocarcinomas, we showed that only a subset of the proteins exhibited a significant correlation with mRNA abundance.

Identification and characterization of transcription factor target genes using gene-targeted mice

Critical to understanding biological roles for transcription factors is an appreciation of the target genes regulated by the transcription factor. The identification of target genes can often expand the understanding of known biological roles for a transcription factor and may reveal unappreciated and unexpected functions. This article focuses on the identification and characterization of transcription factor target genes using mouse molecular genetics. The use of genetically engineered (knockout) mice and global gene expression analysis to identify transcription factor target genes is reviewed, with emphasis on important technical considerations. Detailed protocols for the application of real-time reverse transcription polymerase chain reaction and immunohistochemistry in target gene expression analysis are described. The article closes with a discussion of the use of mouse molecular genetics for the characterization of target genes as downstream effectors of transcription factors.

Identification of tooth-specific downstream targets of Runx2

Odontogenesis or tooth development is a highly regulated process that involves complex epithelial-mesenchymal signaling interactions that lead to cuspal morphogenesis, cell differentiation and the subsequent formation of the specialized matrices of enamel, dentin, cementum and bone. Although studies on tooth epithelial-mesenchymal signaling interactions have greatly increased our understanding of molecules that regulate tooth initiation and early morphogenesis (review: Jernvall and Thesleff, Mech. Dev. 92 (2000) 19), the precise nature of the molecular events controlling late morphogenesis and terminal cytodifferentiation is not known. We have recently reported a unique phenotype involving dentition in mice lacking a functional Runx2 gene (D'Souza et al., Development 126 (1999) 2911). The markedly hypoplastic tooth organs as well as defects in the maturation of ameloblasts and odontoblasts point to an important and non-redundant role for Runx2 in tooth morphogenesis and cytodifferentiation. In order to identify genes that are affected by the absence of Runx2, a cDNA library was generated from Runx2(-/-) and Runx2(+/+) first molar organs. Thus far, our analysis has revealed several tooth-specific downstream target genes of Runx2 that include extracellular matrix proteins, kinases, receptors, growth factors, mitochondrial proteins and transcription molecules. Sequence analysis of 61 differentially expressed genes revealed that 96.03% of the clones matched previously described genes in the GenBank/EBML database and 3.96% did not match any entries in the database. Our preliminary expression analysis of one of the differentially expressed clones which encodes for a zinc finger transcription factor termed Zfp reveals that the gene is temporally regulated during tooth development. In conclusion, we have successfully generated a library enriched in genes expressed in Runx2(+/+) molar tooth organs and performed preliminary studies to assess the role of Zfp in tooth development.