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

Role of allograft inflammatory factor-1 in bleomycin-induced lung fibrosis

Allograft inflammatory factor-1 (AIF-1) is a protein expressed by macrophages infiltrating the area around the coronary arteries in a rat ectopic cardiac allograft model. We previously reported that AIF-1 is associated with the pathogenesis of rheumatoid arthritis and skin fibrosis in sclerodermatous graft-versus-host disease mice. Here, we used an animal model of bleomycin-induced lung fibrosis to analyze the expression of AIF-1 and examine its function in lung fibrosis. The results showed that AIF-1 was expressed on lung tissues, specifically macrophages, from mice with bleomycin-induced lung fibrosis. Recombinant AIF-1 increased the production of TGF-β which plays crucial roles in the mechanism of fibrosis by mouse macrophage cell line RAW264.7. Recombinant AIF-1 also increased both the proliferation and migration of lung fibroblasts compared with control group. These results suggest that AIF-1 plays an important role in the mechanism underlying lung fibrosis, and may provide an attractive new therapeutic target.

Allograft inflammatory factor-1 in the pathogenesis of bleomycin-induced acute lung injury

Allograft inflammatory factor-1 (AIF-1) is a protein expressed by macrophages infiltrating the area around the coronary arteries of rats with an ectopic cardiac allograft. Some studies have shown that expression of AIF-1 increased in a mouse model of trinitrobenzene sulfonic acid-induced acute colitis and in acute cellular rejection of human cardiac allografts. These results suggest that AIF-1 is related to acute inflammation. The current study used bleomycin-induced acute lung injury to analyze the expression of AIF-1 and to examine its function in acute lung injury. Results showed that AIF-1 was significantly expressed in lung macrophages and increased in bronchoalveolar lavage fluid from mice with bleomycin-induced acute lung injury in comparison to control mice. Recombinant AIF-1 increased the production of IL-6 and TNF-α from RAW264.7 (a mouse macrophage cell line) and primary lung fibroblasts, and it also increased the production of KC (CXCL1) from lung fibroblasts. These results suggest that AIF-1 plays an important role in the mechanism underlying acute lung injury.

A Critical Role for Allograft Inflammatory Factor-1 in the Pathogenesis of Rheumatoid Arthritis

Rheumatoid arthritis (RA) is characterized by massive synovial proliferation, angiogenesis, subintimal infiltration of inflammatory cells and the production of cytokines such as TNF-alpha and IL-6. Allograft inflammatory factor-1 (AIF-1) has been identified in chronic rejection of rat cardiac allografts as well as tissue inflammation in various autoimmune diseases. AIF-1 is thought to play an important role in chronic immune inflammatory processes, especially those involving macrophages. In the current work, we examined the expression of AIF-1 in synovial tissues and measured AIF-1 in synovial fluid (SF) derived from patients with either RA or osteoarthritis (OA). We also examined the proliferation of synovial cells and induction of IL-6 following AIF-1 stimulation. Immunohistochemical staining showed that AIF-1 was strongly expressed in infiltrating mononuclear cells and synovial fibroblasts in RA compared with OA. Western blot analysis and semiquantitative RT-PCR analysis demonstrated that synovial expression of AIF-1 in RA was significantly greater than the expression in OA. AIF-1 induced the proliferation of cultured synovial cells in a dose-dependent manner and increased the IL-6 production of synovial fibroblasts and PBMC. The levels of AIF-1 protein were higher in synovial fluid from patients with RA compared with patients with OA (p < 0.05). Furthermore, the concentration of AIF-1 significantly correlated with the IL-6 concentration (r = 0.618, p < 0.01). These findings suggest that AIF-1 is closely associated with the pathogenesis of RA and is a novel member of the cytokine network involved in the immunological processes underlying RA.

Redistributions of macrophages expressing the macrophage galactose-type C-type lectin (MGL) during antigen-induced chronic granulation tissue formation

Cell surface lectins are known to regulate trafficking of cells in the immune system, yet the role of macrophage galactose-type C-type lectin 1 and 2 (MGL1/2) is poorly understood. In this study, antigen-specific chronic inflammation was induced in a subcutaneous air pouch model in mice, and distribution of cells expressing MGL1/2 was investigated. Azobenzenearsonate-conjugated acetylated BSA, used as an antigen, was introduced into an air pouch of immunized mice, and tissue formation and distribution of MGL1/2-positive cells in the sub-dermal regions was examined. Thickness of the inflammatory tissue and number of MGL1/2-positive cells simultaneously reached the maximum at day 4 and returned to the control level at day 6 or 8. When additional antigenic challenges were given, a chronic granulation tissue, which had two distinct layers, was generated. In the chronic tissue, CD11b-positive/MGL1/2-negative cells were abundant in the area close to the antigenic stimulus, while the area far from the antigenic stimulus was dominated by MGL1/2-positive/CD11b-negative or -low cells. Flow cytometric analyses of isolated cells from the granulation tissue revealed that MGL1/2-positive cells expressed MHC class II at high levels, CD11b at low levels but no CD11c. MGL1/2-positive and -negative fractions were separated from cells in the granulation tissue and a higher level of IL-1alpha messenger RNA than negative populations was detected in the MGL1/2-positive fraction by the semi-quantitative reverse transcription-PCR method. IL-1alpha production by MGL1/2-positive cells was also immunohistochemically detected. Results suggest that MGL1/2-positive cells represent a distinct sub-population of macrophages, having unique functions in the generation and maintenance of granulation tissue induced by antigenic stimuli.

Inflammatory bowel disease-associated gene expression in intestinal epithelial cells by differential cDNA screening and mRNA display

Intestinal epithelial cells are actively involved in the pathogenesis of inflammatory bowel disease resulting in an altered functional phenotype. The modulation of epithelial gene expression may occur as a consequence of proliferative, metabolic, immune, inflammatory, or genetic abnormalities. Differential screening of epithelial-cell-derived cDNA libraries (from control, ulcerative colitis, and Crohn's disease epithelial cells) and differential display of mRNA were used for investigation of disease-associated gene expression and modulation. Intestinal epithelial gene expression was successfully analyzed by both approaches. Using differential screening with clones encoding mitochondrial genes, quantitative overexpression was observed in both ulcerative colitis and Crohn's disease, while a unique expression of small RNA was noticed in Crohn's disease cells using Alu-homologous clones. Differential display demonstrated that several genes were differentially displayed among control, ulcerative colitis, and Crohn's disease epithelial cells. This was confirmed by immunohistochemical staining of pleckstrin, desmoglein 2 and voltage-dependent anion channel in control and inflammatory bowel disease mucosal samples. In summary, several inflammatory bowel disease-related associations were found. Since both differential screening and display have advantages and limitations, the combination of both techniques can generate complementary information, facilitate search for novel genes, and potentially identify genes uniquely associated with inflammatory bowel disease.

Differentially abundant mRNAs in rat liver in response to diets containing soy protein isolate

Soy diets influence cell growth, regulate lipid metabolism to lower blood cholesterol, and prevent bone losses. These biological effects are most likely due to effects of soy phytochemicals on the expression of genes. In this study, we fed 12 female obese Zucker rats (fa/fa) with a low- or a high-isoflavone soy protein diet and compared the gene expression with animals on a casein diet. Rat livers were compared by differential display of mRNA, and 62 unique sequences were identified. The change in mRNA abundance of these sequences was quantified by cDNA macroarray analysis. Thirty-three mRNAs showed more than twofold increase in abundance on soy diets compared with the control. The corresponding genes include carnitine palmitoyltransferase I, stromal cell-derived factor 1, a protein associated with MYC mRNA, basic transcription element binding protein, and expressed sequence tags (ESTs) of unknown function. Twenty-nine mRNAs showed a less than twofold change in abundance in the two diet treatments. For majority of the genes identified, there was not significant difference between the low- and high-isoflavone diet treatments. Therefore, the contrast between soy protein and casein caused the changes observed in mRNA abundance.

Macrophage-restricted and interferon gamma-inducible expression of the allograft inflammatory factor-1 gene requires Pu.1

Expression of allograft inflammatory factor-1 (Aif-1), a 17-kDa protein bearing an EF-hand Ca(2+) binding motif, increases markedly in monocytes and macrophages participating in allo- and autoimmune reactions, including the perivascular inflammation in transplanted hearts, microglial infiltrates in experimental autoimmune neuritis, and the inflamed pancreas of prediabetic BB rats. To investigate the mechanism of this regulation, we isolated the mouse aif-1 gene and determined its genomic organization. The gene has six exons distributed over 1.6 kilobases, an interferon gamma-inducible DNase I-hypersensitive site near -900, and flanking sequences on either side predicted to associate with nuclear matrix. Reporter gene analyses identified sequences between -902 and -789, including consensus Ets and interferon regulatory factor elements, required for macrophage-specific and interferon gamma-inducible transcriptional activity. Pu.1 bound to the Ets site in electromobility shift assay and forced expression of Pu.1 activated the aif-1 promoter in 3T3 fibroblasts, in which it is normally inactive. However, the transcriptional activity of a concatamer of the Ets site alone did not increase with interferon gamma treatment. Cooperation between Pu.1 and proteins binding to the interferon regulatory factor element appears to be necessary for both macrophage-specific and interferon gamma-inducible expression of the aif-1 gene.

Regulation of ER stress proteins by valproate: therapeutic implications

OBJECTIVES

This paper reviews results of our studies examining the regulation of endoplasmic reticulum (ER) stress proteins by valproate (VPA). and discusses the possible implications in bipolar disorder.

METHODS

Our previous studies in the field are reviewed along with relevant literature.

RESULTS

Using differential display PCR, we identified GRP78 as a VPA-regulated gene in rat cerebral cortex. We also showed that other members of the ER stress proteins family, GRP94 and calreticulin, are also upregulated by VPA. Immunohistochemistry identified that ER stress proteins are increased in frontal and parietal cortex, as well as regions of the hippocampus in rat brain following chronic treatment with VPA.

CONCLUSIONS

Regulation of ER stress proteins by VPA may prove to be important to the mechanism of action of the drug. The neuroprotective role of these proteins may also prove to be involved in the pathophysiology of bipolar disorder.

New intra-renal graft genes associated with tolerance or rejection

BACKGROUND

Recipient type mononuclear cells infiltrating kidney allografts have different phenotypes and functions according to the fate of the graft. We hypothesized that different genetic programs were involved in rejected or accepted tissues and thus, transcripts that correlated with the clinical status could be identified by a differential expression strategy. This strategy was applied to miniature swine class II matched, class I disparate kidney grafts, which are accepted in recipient animals treated for 12 days with Cyclosporin A (CsA).

METHODS

The mRNA differential display RT-PCR technique (DDRT-PCR) was used to detect clinical status-specific transcripts. cDNA templates for this analysis were derived from biopsies of accepted (CsA treated) and rejected (untreated) kidney grafts 8 days post-transplantation.

RESULTS

A first screening procedure identified 23 PCR products differentially amplified in either tolerant or rejector samples. Nucleotide sequence of these partial transcripts showed that 11 out of 23 (48%) sequences had unknown open reading frames while 12 had substantial homology to known sequences. To validate the approach, rejection-associated (RA) cDNA 1 (RA-1) was characterized further. The results indicated that RA-1 is the porcine equivalent of secreted protein acidic and rich in cysteine (SPARC). Expression studies demonstrated that upregulation of SPARC gene transcription preceded other indicators of kidney dysfunction and correlated with the extent of graft infiltration.

CONCLUSION

DDRT-PCR appears to be a powerful technique to identify genes differentially expressed in grafted tissues that correlate with tolerance or rejection. One of the gene transcripts identified through this method, SPARC, may be a reliable marker of tissue injury consequent to cellular infiltration and rejection.

Heart transplantation changes the expression of distinct gene families

We took advantage of the combination of a rat heart transplantation model with a modified differential display RT-PCR method to identify transcriptome changes in the right atria from transplanted compared with native hearts. Based on sequence homology search, the 37 cDNAs differentially displayed both 2 and 7 days posttransplantation were categorized into 7 unknown transcripts, 16 expressed sequence tags (ESTs), and 14 partially or completely characterized genes. The last group cDNAs, validated by relative RT-PCR, belonged to diverse gene families involved in specific metabolisms, protein synthesis, cell signaling, and transcription. Furthermore, we identified differential transcripts corresponding to denervation and fetal gene reexpression. We found coordinate downregulation of genes involved in energy metabolism and protein synthesis regulation, similar to that reported for senescent skeletal muscle. From these transcriptome changes, we propose that heart transplants and senescent muscles share common molecular mechanisms.

Allograft inflammatory factor-1 augments production of interleukin-6, -10 and -12 by a mouse macrophage line

Mouse allograft inflammatory factor-1 (AIF-1) cDNA was cloned and the AIF-1-specific monoclonal antibodies were established to examine its tissue distribution. The mouse AIF-1 was highly conserved among all reported AIF-1 from a variety of species, from invertebrates to mammals, and the cloned cDNA was in good accordance with putative expressed regions of genomic sequences in the mouse major histocompatibility complex (MHC) class III region. The messages of mouse AIF-1 were abundantly expressed in the testis, moderately in the spleen and lymph nodes and slightly in the liver and thymus of normal BALB/c mice. Immunohistological examination revealed that differentiating germ cells in the testis and presumably macrophages in the red pulp of the spleen were positive for AIF-1. To analyse the function of the AIF-1, a macrophage cell line, RAW 264.7, was transfected with mouse AIF-1 cDNA. Upon stimulation with bacterial lipopolysaccharide, the transfectants that overexpressed AIF-1 showed marked morphological changes and produced significantly large amounts of interleukin (IL)-6, IL-10 and IL-12p40 but not IL-12p70 compared with control cells. No difference was noted in production of tumour necrosis factor-alpha, transforming growth factor-beta1 and IL-1alpha. These results suggest that AIF-1 plays an important role in cells of a monocyte/macrophage lineage upon stimulation with inflammatory stimuli by augmenting particular cytokine production.

AIF-1 expression defines a proliferating and alert microglial/macrophage phenotype following spinal cord injury in rats

Microglial cells are among the first and dominant cell types to respond to CNS injury. Following calcium influx, microglial activation leads to a variety of cellular responses, such as proliferation and release of cytotoxic and neurotrophic mediators. Allograft inflammatory factor-1, AIF-1 is a highly conserved EF-handed, putative calcium binding peptide, associated with microglia activation in the brain. Here, we have analyzed the expression of AIF-1 following spinal cord injury at the lesion site and at remote brain regions. Following spinal cord injury, AIF-1+ cells accumulated in parenchymal pan-necrotic areas and perivascular Virchow-Robin spaces. Subsequent to culmination at day 3--a situation characterized by infiltrating blood borne macrophages and microglia activation--AIF-1+ cell numbers decreased until day 7. In remote areas of Wallerian degeneration and delayed neuronal death, a more discrete and delayed activation pattern of AIF-1+ microglia/macrophages reaching maximum levels at day 14 was observed. There was a considerable match between AIF-1+ cells and PCNA (proliferating cell nuclear antigen) or Ki-67+ labeled cells. AIF-1 expression preceded the expression of ED1, thus indicating a pre-phagocytic role. It appears that AIF-1+ microglia/macrophages are among the earliest cells to respond to spinal cord injury. Our results suggest a role of AIF-1 in the initiation of the early microglial response leading to activation and proliferation essential for the acute response to CNS injury. AIF-1 might modulate microgliosis influencing the efficacy of tissue debris removal, myelin degradation, recruitment of oligodendrocytes and re-organisation of the CNS architecture.

Messenger ribonucleic acid encoding interferon-inducible guanylate binding protein 1 is induced in human endometrium within the putative window of implantation

The putative window of embryo implantation in the human opens between days 19--24 of the menstrual cycle. During this period, the endometrium undergoes distinctive structural and functional changes orchestrated by steroid hormones, growth factors, and cytokines to attain a receptive phase in which it acquires the ability to implant the developing embryo. A major challenge in the study of human reproduction is to identify the molecular signals that participate in the establishment of this critical receptive phase in the context of the natural cycle. Toward this goal, we analyzed human endometrial biopsies at various days of the menstrual cycle by employing messenger RNA (mRNA) differential display technique. We isolated several complementary DNAs representing genes that are either up- or down-regulated within the putative window of implantation. We identified one of these genes as that encoding interferon (IFN)-inducible guanylate-binding protein 1 (or GBP1), which possesses GTPase activity. Analysis of endometrial biopsies by Northern blotting and RT-PCR demonstrated that GBP1 mRNA is specifically induced at the midsecretory phase of the menstrual cycle. In situ hybridization analysis revealed that GBP1 mRNA expression is localized in the glandular epithelial cells as well as in the stroma in the immediate vicinity of the glands. We observed that treatment of human endometrial adenocarcinoma cell, Ishikawa, with IFN-gamma or IFN-alpha markedly induced the expression of GBP1 mRNA. IFN-gamma was, however, a more potent inducer of GBP1 than IFN-alpha. Consistent with this finding, the temporal profile of GBP1 expression during the menstrual cycle resembled that of IFN-gamma mRNA more closely than that of IFN-alpha, predicting a regulatory role of IFN-gamma in GBP1 expression in midsecretory human endometrium. Although the precise function of GBP1 in the receptive human uterus remains unclear, its unique expression overlapping the putative window of implantation suggests that it might serve as a useful marker of uterine receptivity in the human.

Genes highly expressed in the early phase of murine graft-versus-host reaction

Graft-versus-host reaction (GVHR) is a complex process initiated upon allorecognition. For detection of early molecular events in GVHR, we first assessed time courses with respect to symptoms and serum interferon (IFN)-gamma levels and then used the differential display method to compare gene transcript patterns during the early phase between acute lethal GVHR mice and syngeneic controls. In the GVHR mice, high expression levels of seven genes encoding the following molecules were detected: TGTP/Mg21 (an IFN-gamma-related signaling molecule), vitronectin, Nedd5 (a mammalian septin), manganese superoxide dismutase, activin betaC subunit, PRCC (a papillary renal cell carcinoma-associated molecule), and an uncharacterized gene corresponding to a mouse expressed sequence tag (EST). The expression levels of most genes peaked before the symptomatological onset and the peak of IFN-gamma levels. Thus, gene expression monitoring may characterize the inductive process of GVHR and aid in the development of gene-based diagnostics and therapies.

Differential expression of aquaporin 8 in human colonic epithelial cells and colorectal tumors

BACKGROUND

The gene expression pattern in tumor cells differs from that in corresponding normal cells. In order to identify differentially expressed genes in colorectal tumors and normal colorectal epithelium, a differential display experiment was used to compare RNA expression in normal and tumor tissue samples.

RESULTS

One gene fragment was expressed only in normal tissue and not, or to a much lesser extent, in the adenomas, carcinomas and cancer cell lines. The isolated gene fragment was identical to Aquaporin 8 (AQP8), a water channel protein. In situ hybridization demonstrated that AQP8 was expressed in the cells facing the lumen in the normal colonic epithelium.

CONCLUSION

Our result suggests that the expression of AQP8 is a marker of normal proliferating colonic epithelial cells and suggest these cells to be involved in fluid transport in the colon.

Comparison of RAP-PCR analysis of gene expression in fresh and immortalised rat hepatocyte cell lines

Primary rat hepatocytes dedifferentiate rapidly losing theactivities of the drug metabolising enzymes involved in thedetoxification of xenobiotics in the liver. An alternativeapproach to using primary hepatocytes for toxicity testing isthe development of immortalised hepatocyte cell lines via thetransfection of primary hepatocytes with SV40 DNA. In order toassess the suitability of immortalised lines as an alternativeto primary cell cultures we have used RNA arbitrarily primedpolymerase chain reaction to compare gene expression inimmortalised rat hepatocyte cell lines with that in primary rathepatocytes. We have found that differences exist in the RNAtranscripts between fresh and immortalised hepatocyteshighlighting RNA arbitrarily primed polymerase chain reaction asa useful screening method for identifying immortalised lineswhich retain the most ;normal' phenotype in relation to theprimary cells from which they originated.

Identification of genes involved in mucosal defense and inflammation associated with normal enteric bacteria

Normal luminal bacteria and their products play a role in experimental colitis and inflammatory bowel disease. However, what molecules from what cells are responsible for mounting and maintaining the mucosal defense against luminal flora is still uncertain. The aim of this study was to identify epithelial gene products involved in mucosal defense and inflammation associated with ubiquitous enteric bacteria. Germ-free ICR mice were given an oral bacterial suspension prepared from conventional components (bacterial reconstitution). Small intestinal and colonic epithelial cells were isolated from bacteria-reconstituted, germ-free, and specific pathogen-free mice. Differential gene expression was investigated by differential display, Northern blot, and sequence analysis. Bacterial reconstitution resulted in acute but self-limited colitis. In epithelial cells, we observed the induction of small intestine-specific genes of the cryptdin family and colon-specific expression of serum amyloid A1 gene. This novel approach allows the identification of known and novel gene products involved in mucosal defense against luminal microorganisms and the associated inflammatory response.

mRNA differential display of acute-phase proteins in experimental Escherichia coli infection

We present a modification of mRNA differential display in which increased throughput results from the use of an automated fluorescent sequencer. The sequence analysis is performed directly on purified fragments without further cloning. The amplified fragments carry a T7 RNA polymerase promoter sequence tag for in vitro transcription of riboprobes for nonradioactive in situ hybridization. We compared changes in gene expression in the liver and colon of group II phospholipase A2 transgenic and group II phospholipase A2 deficient mice during the course of experimental Escherichia coli infection. Fluorescent mRNA differential display comprising a 7 x 24 set of primers was used to study a total of 31,257 amplified cDNA fragments. Sequence analysis of the displayed fragments associated with infection identified classical acute-phase proteins in the liver and host defense proteins in the colon. The displayed mRNAs associated to transgenicity were the transgene itself, i.e., human group II phospholipase A2, and glutathione-S-transferase in the liver. In the colon, the displayed mRNAs associated with transgenicity were the pancreatitis-associated protein and mucin. The results show that fluorescent mRNA differential display is a reliable method to identify differences in the expression of the genes of acute-phase proteins.

A putative resistant DNA marker for wool yellowing susceptibility in sheep

An Australian Merino flock was screened for low (resistant) and high (susceptible) yellow predictive colour (YPC) breeding values in order to compare extreme individuals using the differential display of mRNA technique. One differentially expressed cDNA band was visualised only in the resistant group. This band showed no identity with the DNA sequences of public databases; however, they showed short homologies with three database sequences related to transmembrane signalling functions. The use of these candidate genes as DNA markers needs to be confirmed against sheep with a wide range of susceptibility to wool yellowing to verify the results.

Identification and characterization of three differentially expressed genes, encoding S-adenosylhomocysteine hydrolase, methionine aminopeptidase, and a histone-like protein, in the toxic dinoflagellate Alexandrium fundyense

Genes showing differential expression related to the early G(1) phase of the cell cycle during synchronized circadian growth of the toxic dinoflagellate Alexandrium fundyense were identified and characterized by differential display (DD). The determination in our previous work that toxin production in Alexandrium is relegated to a narrow time frame in early G(1) led to the hypothesis that transcriptionally up- or downregulated genes during this subphase of the cell cycle might be related to toxin biosynthesis. Three genes, encoding S-adenosylhomocysteine hydrolase (Sahh), methionine aminopeptidase (Map), and a histone-like protein (HAf), were isolated. Sahh was downregulated, while Map and HAf were upregulated, during the early G(1) phase of the cell cycle. Sahh and Map encoded amino acid sequences with about 90 and 70% similarity to those encoded by several eukaryotic and prokaryotic Sahh and Map genes, respectively. The partial Map sequence also contained three cobalt binding motifs characteristic of all Map genes. HAf encoded an amino acid sequence with 60% similarity to those of two histone-like proteins from the dinoflagellate Crypthecodinium cohnii Biecheler. This study documents the potential of applying DD to the identification of genes that are related to physiological processes or cell cycle events in phytoplankton under conditions where small sample volumes represent an experimental constraint. The identification of an additional 21 genes with various cell cycle-related DD patterns also provides evidence for the importance of pretranslational or transcriptional regulation in dinoflagellates, contrary to previous reports suggesting the possibility that translational mechanisms are the primary means of circadian regulation in this group of organisms.

Increased expression of the gene for alpha-interferon-inducible protein in cardiomyopathic hamster heart

Cardiomyopathic (CM) hamsters have a disruption in the delta-sarcoglycan gene which leads to progressive cardiac necrosis by 30 to 40 days of age, hypertrophy by 120 days, and heart failure by 250 days. We used differential display to detect other changes in mRNA levels in 30-, 60-, and 90-day-old wild-type and CM hamsters. We identified a 400-bp cDNA with sequence similarity to the human alpha-interferon-inducible protein (p27). This cDNA annealed with a 570-base mRNA whose steady-state levels were increased in 30-, 60-, and 90-day-old CM compared to wild-type heart. Increased expression of this hamster homolog of p27 (p27-h) was detected in CM hamster cardiac and skeletal muscle at 60 days of age but not in liver, kidney, or brain. Thus, an inherited defect in CM hamsters leads to increased expression of p27-h in advance of the development of hypertrophy and heart failure.

Structural changes of atrial myocardium during chronic atrial fibrillation

Of all known arrhythmia's, atrial fibrillation (AF) is the most often met in the clinical setting and it is associated with an increase in mortality risk. Several risk factors for AF have been described and several mechanisms of induction and maintenance have been proposed. Studies in patients with AF have shown that structural changes occur in the atria, but the relationship between the structural remodelling and the chronicity of the arrhythmia are not well understood. The changes mainly concern adaptive (dedifferentiation of cardiomyocytes) and maladaptive (degeneration of cells with replacement fibrosis) features. In order to characterise the time course of the structural remodelling the need for animal models which adequately mimic chronic atrial fibrillation in humans is felt essential. In this review, the structural changes that are observed during prolonged sustained AF in patients and animal models, are described. Furthermore, the time course and potential mechanisms of structural remodelling are discussed and methods for elucidation of the underlying molecular mechanisms are presented.

Identification and characterization of genes whose expressions are altered in rat 6 fibroblasts transformed by mutant p53(val135)

The wild-type tumor suppressor gene p53 is known as a transcription factor in activating or suppressing target genes that encode proteins in regulating genome stability, DNA damage, cell arrest, and apoptosis. However, the role of mutant p53 in the process of cell transformation is still unclear. Our recent work indicated that overexpression of mutant p53(val135) induced high incidence of spontaneous transformation in prolonged cultures of Rat 6 fibroblasts. In order to identify genes related to neoplastic transformation induced by the mutant p53, the p53(val135)-overexpressor R6#13-8 and its derived spontaneously transformed cell line T2 were analyzed by mRNA differential display. In a systematic screening with 80 primer sets of RT-PCR reactions, three genes were found to be differentially expressed between R6#13-8 and T2 cells. Two genes, identified as homologues of the growth factor inducible immediate-early gene Cyr61 and the human nonmuscle myosin heavy chain-B, were down-regulated in T2 cells. Interestingly, both genes were also suppressed in Rat 6 cells transformed by c-H-ras and v-myc, but not by v-src genes. The third gene is a homologue of the frizzled related protein, a gene family that acts, in some cases, as an antagonist to the Wnt signaling pathway. It is intriguing that the rat homologue of the frizzled related protein was only expressed in p53(val135)-overexpressing cells, but not in the parental Rat 6 cells. However, the same gene was also highly expressed in ras-transformed Rat 6 cells, and moderately expressed in v-src-transformed Rat 6 cells. This is the first study in which the association of mutant p53 to these three genes is revealed. Our current report may provide new clues to the role of mutant p53 in the process of cell transformation.

Cloning and uterus/oviduct-specific expression of a novel estrogen-regulated gene (ERG1)

The steroid hormone estrogen profoundly influences growth and differentiation programs in the reproductive tract of cycling and pregnant mamals. It is thought that estrogen exerts its cellular effects by regulating the expression of specific target genes. We utilized a messenger RNA differential display method to identify the genes whose expression is modulated by estrogen in the preimplantation rat uterus. Here we report the cloning of a novel gene (ERG1) that is tightly regulated by estrogen in two key reproductive tissues, the uterus and oviduct. Spatio-temporal analyses reveal that ERG1 mRNA is expressed in a highly stage-specific manner in the uterus and oviduct, and its expression is restricted to the surface epithelium of both of these tissues. Nucleotide sequence analysis of the full-length ERG1 cDNA indicates that it has an open reading frame of 1821 nuceotides encoding a putative protein of 607 amino acids with a single transmembrane domain and a short cytoplasmic tail. The extracellular part of the protein contains several distinct structural motifs. These include a zona pellucida binding domain, which is present in a number of proteins such as the zona pellucida sperm binding proteins, and uromodulin, In addition, there is a repeat of a motif called CUB domain, which exists in a number of genes involved in development and differentiation such as bone morphogenetic protein 1 (BMP1). Although the precise function of ERG1 eludes us presently, its unique pattern of expression in the uterus and oviduct and its regulation by estrogen, a principal reproductive hormone, lead us to speculate that this novel gene plays an important role in events during the reproductive cycle and early pregnancy.

Differential display analysis can reveal patterns of gene expression in immortalised hepatoma cells which are similar to those observed in young adult but not old adult liver cells

We used the differential display technique to examine whether there were any patterns of gene expression which were characteristic of both young adult rat liver and of immortalised rat hepatoma cell lines, but not of old adult rat liver. No genes were detected which appeared to be clearly expressed in young liver and immortalised cell lines, but not in old liver. However, 14 genes were detected in old liver which were down-regulated in young liver and the hepatoma cell lines. This observation lends support to the idea that immortalisation of malignant cells may involve, at least in some aspects, a reversal of the ageing process in these cells and that the genes involved have a recessive action.

Potential regulation of membrane trafficking by estrogen receptor alpha via induction of rab11 in uterine glands during implantation

The steroid hormone estrogen profoundly influences the early events in the uterus leading to embryo implantation. It is thought that estrogen triggers the expression of a unique set of genes in the preimplantation endometrium that in turn control implantation. To identify these estrogen-induced genes, we used a delayed implantation model system in which embryo attachment to endometrium is dependent on estrogen administration. Using a mRNA differential display (DD) method, we isolated a number of cDNAs representing mRNAs whose expression is either turned on or turned off in response to an implantation-inducing dose of estrogen. We identified one of these cDNAs as that encoding rab11, a p21ras-like GTP-binding protein (G protein), which functions in the targeting of transport vesicles to the plasma membrane. In normal pregnant rats, rab11 mRNA was expressed at low levels on days 1-2 of pregnancy, but its expression was markedly enhanced (approximately 6- to 8-fold) between days 3-5 immediately before implantation. In situ hybridization and immunocytochemistry revealed that rab11 expression in the uterus was predominantly in the glandular epithelium. In ovariectomized rats, the expression of rab11 mRNA was induced in the endometrium in response to estrogen. To determine whether this effect of estrogen was mediated through its nuclear receptors, we examined rab11 expression in a transformed endometrial cell line, Ishikawa. In transient transfection experiments, we observed that overexpression of estrogen receptor (ER) alpha or beta induced endogenous rab11 mRNA in a hormone-dependent manner. ER bound to an antagonist, ICI 182,780, failed to activate this gene expression. These findings, together with the observation that ER alpha but not ER beta is detected in the glands of the preimplantation uterus, indicate that rab11 is one of the proteins that are specifically induced by estrogen-complexed ER alpha in rat endometrium at the onset of implantation. Our results imply that estrogen, which induces the synthesis of many growth factors and their receptors and other secretory proteins that are thought to be critical for implantation, may also facilitate their transport to the membrane and/or secretion by stimulating the expression of rab11, a component of the membrane-trafficking pathway. This study therefore provides novel insights into the diverse cellular mechanisms by which estrogen, acting via its nuclear receptors, may influence blastocyst implantation.

Viral myocarditis: identification of five differentially expressed genes in coxsackievirus B3-infected mouse heart

Differences in host susceptibility to viral myocarditis caused by a given strain of coxsackievirus B3 (CVB3) are known to be largely related to host genetic factors. Little is known, however, about the key genes that encode determinants (mediators) of myocarditis development or the nature of injury. To identify these genes and further understand the molecular mechanisms of the disease process, we have used a murine model and the differential display technique to fingerprint mRNAs from CVB3-infected mouse hearts. Total RNA was extracted from hearts of 4- and 10-week-old A/J(H-2(a)) mice at day 4 after CVB3 infection, and mRNAs were detected by reverse transcriptase-polymerase chain reaction and subsequently analyzed on polyacrylamide DNA sequencing gels. The differentially displayed bands were confirmed by Northern hybridization using the bands as cDNA probes. Twenty-eight upregulated or downregulated bands were selected from the sequencing gels; among these, 2 upregulated and 3 downregulated cDNA fragments were confirmed by Northern hybridization. DNA sequence analysis and GenBank searching have determined that 4 of the 5 candidate genes are homologous to genes encoding Mus musculus inducible GTPase, mouse mitochondrial hydrophobic peptide (a subunit of NADH dehydrogenase), mouse beta-globin, and Homo sapiens cAMP-regulated response element binding protein (CREB) binding protein (CBP), respectively. The remaining candidate gene matches an unpublished cDNA clone, M musculus Nip21 mRNA (GenBank accession number, AF035207), which is homologous to human Nip2, a Bcl-2 binding protein. Our data suggest preliminarily that both structural and nonstructural genes are involved in myocarditis development. For the structural gene, beta-globin, we further confirmed its downregulation at the protein level by measuring the mean cell volume of red blood cells and found it was marginally reduced in the CVB3-infected group (P<0.06), with no change in hemoglobin concentration. Cardiac myoglobin concentration was also measured and found to be decreased (P<0.005), with a parallel decrease in total soluble protein in the CVB3-infected mouse myocardium (P<0.01). We also noted that the ratio of myoglobin to total protein was not significantly changed; this may be due to the downregulation of additional genes in the host heart, a number being observed on the differential display gels. The significant downregulation of beta-globin major gene expression in the heart may be relevant to impaired cardiac function in both the early and late postinfection period. The other identified nonstructural genes are known to be involved in regulation of gene expression, signal transduction pathways, and apoptotic cell death. The altered expression of structural and nonstructural genes may play important roles in the mediation of myocarditis development and perhaps other pathological processes in the heart.

Identification of different gene expression patterns in low and high grade non-Hodgkin's lymphomas by differential display

We have compared the patterns of gene expression in non-Hodgkin's lymphoma (NHL) biopsy samples from patients with either low grade or high grade disease, by the polymerase chain reaction (PCR) based technique of differential display. By using a combination of 30 primer pairs we estimate that we were able to survey over 3,000 genes expressed in these tissues. In this study we compared a group of three low grade follicular centre lymphomas with a group of two high grade diffuse large cell lymphomas and scored only those PCR products that were represented in all samples of each group. In doing so we were able to avoid many of the problems associated with the occurence of false PCR-positives. 139 differences were then scored as representing genes which may be differentially expressed during the transformation from low to high grade disease. However, as many of these might simply reflect changing populations of cells, we focused on only those genes which appeared to be expressed exclusively in either low grade or high grade disease. We have identified 14 such genes, of which 10 were low grade specific and 4 were high grade specific. This approach therefore appears to offer a systematic method for the identification and characterisation of differentially expressed genes, which are characteristic of different NHL sub-types.

Identification of true differentially expressed mRNAs in a pair of human bladder transitional cell carcinomas using an improved differential display procedure

Differential display in combination with arbitrarily primed polymerase chain reaction (PCR) fingerprinting has become one of the most powerful techniques to identify and isolate mRNAs that are differentially expressed in pairs of biological samples. However, in many cases the cDNA band corresponding to the differentially amplified product contains several cDNA species that comigrate with the cDNA of interest due to the poor resolution of the fingerprinting gels, thus hampering further analysis and identification of the desirable cDNA. To improve the electrophoretic resolution of differentially amplified cDNAs, we have utilized Resolver Gold agarose gel electrophoresis (Ingenius) as an additional step to overcome downstream problems encountered during RNA fingerprinting experiments. To illustrate the power of the modified differential display procedure we present a detailed analysis of the cDNA products differentially displayed in tumor biopsies obtained from a noninvasive (grade II, Ta) and an invasive (grade III, T2-T4) human bladder transitional cell carcinoma (TCC). Several genes that were differentially expressed in this tumor pair were identified. These included: tropomyosin 4, the protein disulfide isomerase precursor (PDI), MRP14, signal transducer CD24, keratins 8 and 13, cytochrome oxidase subunit IV (COXIV), putative transcription factor HOX-1.3, as well as two novel genes of yet unknown function. All of the identified cDNAs were shown to be truly differentially expressed by Northern blotting, reverse transcriptase-PCR (RT-PCR), and two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) analysis of the corresponding lesions.

Identification of differentially expressed mRNAs in human fetal liver across gestation

Differential gene expression, with its precise start and stop times, is believed to be critical for the programmed development of new cells and tissues. Within the developing fetus, one tissue of particular interest is fetal liver. This organ undergoes rapid changes in the pathway toward liver development in utero since it is also the major site of hematopoiesis, until bone marrow hematopoiesis predominates. Believing that patterns would emerge from the bi-weekly large-scale inspection of expressed genes in the fetal liver, we employed differential display reverse transcription-polymerase chain reaction (DDRT-PCR) as ourprimary inspection tool. Using DDRT-PCR, we isolated cDNAs differentially expressed throughout fetal liver development and in adult liver. We displayed approximately 25 000 cDNAs from 10 and 24 week fetal liver and adult liver. From this initial screen, we determined that approximately 0.1-1% of the mRNA population undergoes expression changes. We extracted, purified and sequenced 25 differentially displayed cDNA bands. Fourteen cDNAs had similarities to known genes, while 11 cDNAs were not similar to any characterized gene. The differentially expressed cDNAs from known genes present in fetal liver include alpha-fetoprotein, stem cell factor, erythroid alpha-spectrin, 2,3-bisphosphoglycerate mutase, insulin-like growth factor-2, porphobilinogen deaminase and Mac30. The differentially expressed cDNAs present in adult liver but not in 10 week fetal liver were nicotinamide deaminase, human fibrinogen-related protein and alpha-acid glycoprotein. The majority of differentially expressed genes found during this effort appear to be turned on during organogenesis, however, some genes were found that are apparently turned off completely.

A novel rat CC chemokine, identified by targeted differential display, is upregulated in brain inflammation

A novel rat chemokine, termed ST38, was identified through its upregulation in ischemic brain tissue using a biased differential display technique targeting mRNAs with regulatory AUUUA-motifs typically found in transcripts of cytokine and immediate early genes. ST38 transcripts were transiently induced in ischemic cortex between 4 and 24 h after middle cerebral artery occlusion. ST38 is a member of the CC chemokine family, closely related to human Exodus-1. The gene of the mouse ST38 homologue was mapped to the central region of chromosome 1. In experimental autoimmune panencephalomyelitis ST38 expression correlated with the onset of inflammation and was significantly reduced by TNF-neutralization in vivo. Inflammatory stimuli induce ST38 transcription in astrocyte, microglia and macrophage cultures. These findings suggest a role of ST38 in the control of neuroinflammatory tissue responses.

Modulation of mitochondrial gene expression in pulmonary epithelial cells exposed to oxidants

Oxidants are important in the regulation of signal transduction and gene expression. Multiple classes of genes are transcriptionally activated by oxidants and are implicated in different phenotypic responses. In the present study, we performed differential mRNA display to elucidate genes that are induced or repressed after exposure of rat lung epithelial (RLE) cells to H2O2 or crocidolite asbestos, a pathogenic mineral that generates oxidants. After 8 or 24 hr of exposure, RNA was extracted, reverse transcribed, and amplified by polymerase chain reaction with degenerate primers to visualize alterations in gene expression. The seven clones obtained were sequenced and encoded the mitochondrial genes, NADH dehydrogenase subunits ND5 and ND6, and 16S ribosomal RNA. Evaluation of their expression by Northern blot analysis revealed increased expression of 16S rRNA after 1 or 2 hr of exposure to H2O2. At later time periods (4 and 24 hr), mRNA levels of 16S rRNA and NADH dehydrogenase were decreased in H2O2-treated RLE cells when compared to sham controls. Crocidolite asbestos caused increases in 16S rRNA levels after 8 hr of exposure, whereas after 24 hr of exposure to asbestos, 16S rRNA levels were decreased in comparison to sham controls. In addition to these oxidants, the nitric oxide generator spermine NONOate caused similar decreases in NADH dehydrogenase mRNA levels after 4 hr of exposure. The present data and previous studies demonstrated that all oxidants examined resulted in apoptosis in RLE cells during the time frame where alterations of mitochondrial gene expression were observed. As the mitochondrion is a major organelle that controls apoptosis, alterations in expression of mitochondrial genes may be involved in the regulation of apoptosis.

Control of expression of a gene encoding an extensin by phytochrome and a blue light receptor in spores of Adiantum capillus-veneris L

In the present study, using a newly developed fluorescent differential display technique, we have carried out large-scale screening for genes whose expression was regulated by phytochrome and antagonistically by a blue light receptor in the spores of the fern Adiantum capillus-veneris L. Spores after imbibition were briefly irradiated with red, red/blue or blue light and collected 8 h after the irradiation. Total RNA was isolated from each sample and used to make cDNA with an oligo-dT primer. The cDNA was then used as a template for PCR with the oligo-dT primer and 80 arbitrary primers. The resulting PCR products were analyzed by an automated fluorescent DNA sequencer. Among 8000 displayed bands, we identified 15 up-regulated and four down-regulated bands by red light, and this red light effect was irreversibly reversed by blue light. We cloned one of the up-regulated cDNA fragments and used it to screen a cDNA library prepared from the spores. The isolated insert is predicted to encode Ser-(Pro)n repeats and showed homology with cell wall-associated extensins. The expression of this cDNA was induced 8 h after a red light treatment and the red light induction was photoreversibly prevented by far-red light and photoirreversibly by blue light. The mRNA of this gene was detectable 4 h after red light irradiation and gradually increased in germinating spores.

Identification of immediate early genes during TPA-induced human myeloblastic leukemia ML-1 cell differentiation

Human myeloblastic ML-1 can be induced to differentiate into monocytes/macrophages by 12-0-tetradecanoylphorbol-13-acetate (TPA). In order to understand the molecular mechanism regulating ML-1 cell differentiation, we focused on the characterization of immediate early genes activated by TPA using the mRNA differentiation display polymerase chain reaction (DD-PCR) and Northern analyses. A modified procedure, the reverse dot slot, was developed to confirm upregulated genes during the early stages of TPA-induced ML-1 cell differentiation. DNA sequencing analyses of 10 subcloned cDNA fragments, selected on the basis of the outcome of the reverse dot slot procedure, revealed that eight were derived from distinct genes. Among these clones, one was a novel gene (G07-5), another (A02-1) was highly homologous to the sequence of a fetal brain cDNA fragment, and the remaining six corresponded to jun-D, rantes, ssat, CD 14, ferritin heavy chain (fhc) and transposons Tn10-like transcript, respectively. Although these genes were all upregulated by TPA, the peak time of mRNA expression varied. jun-D, ssat and A02-1 expressions were superinduced in the presence of cycloheximide, which indicates that they belong to the immediate early gene family. On the other hand, TPA-induced rantes expression was not superinduced by cycloheximide, suggesting a protein synthesis-dependent process. As there are no previous reports of expression of these genes in TPA-induced ML-1 cells, little or no information is available concerning their function in mediating myeloblastic cell differentiation. Thus, this study illuminates new avenues of research for elucidating the function of genes regulating terminal differentiation of myeloid progenitors. 1998 Elsevier Science B.V.

AML1-like transcription factor induces serine elastase activity in ovine pulmonary artery smooth muscle cells

In previous studies, we showed that induction of pulmonary artery (PA) smooth muscle cell (SMC) elastase activity by serum-treated elastin (STE) requires DNA transcription. We therefore used differential mRNA display to identify transcripts expressed coincident with elastase induction. Twenty-four individual transcripts were differentially expressed from a screen of approximately 2000 mRNA sequences. An mRNA with sequence homology to the human transcription factor AML1 was identified and subsequently cloned from ovine PA SMCs. Since AML1 binds to a consensus sequence in the promoter of neutrophil elastase, we pursued the possibility that AML1 is a candidate transcription factor for SMC elastase. We documented by immunohistochemistry that serum stimulation induces increased expression of AML1 in the nucleus of PA SMCs. We also showed that STE induction of elastase activity is associated with early expression of AML1 mRNA and protein and that AML1 consensus sequence DNA binding activity is increased in nuclear extracts of STE-treated cells. In addition, AML1 antisense oligonucleotides reduced serum induction of elastase activity. Our study thus provides the first functional evidence of AML1 transcriptional activity related to elastase genes and offers novel insights into the broader biological significance of AML1 in nonmyeloid cells.

Identification of a novel gene--SSK1--in human endothelial cells exposed to shear stress

To identify transcriptionally regulated genes potentially involved in the effect of shear stress on endothelial gene expression, we performed a differential display analysis of mRNAs from human umbilical vein endothelial cell (HUVEC) exposed to laminar shear stress (12 dynes/cm2) in comparison to HUVEC maintained in static condition. We identified a cDNA fragment overexpressed by laminar shear stress. The full-length, SSK1, was 3653 long and encoded for a novel protein of 1050 amino acids. Northern blot demonstrates that SSK1 mRNA is expressed at high levels also in placenta, a weak transcript was present in heart, skeletal muscle, kidney and pancreas. Homology searches of the protein databases showed that SSK1 is related to numerous serine-threonine kinases. The highest homology was found with a very recently described gene, BUBR1, an analogue of BUB1, which is a kinase involved in the regulation of cell cycle. The most conserved residues in catalytic domains II, III, VIb, VII, VIII and IX of serine-threonine protein kinases were found in the C terminal region of SSK1 which further supports the kinase nature of the new protein. The putative serine-threonine kinase SSK1 may represent a tool by which mechanical forces regulates phosphorylation events within endothelial cells.

Application of mRNA differential display to investigate gene expression in thermotolerant cells of Saccharomyces cerevisiae

We have described the use of differential display of PCR-amplified reverse transcribed mRNA (DDRT-PCR) to survey changes in gene expression profiles induced by heat shock and carbon catabolite derepression in Saccharomyces cerevisiae. It is well established that either of these states elicits thermotolerant phenotypes. An initial analysis conducted on cells of an inherently thermosensitive strain (Ysen) indicated that approximately 10% of the total number of cDNAs detected were either up or down regulated following heat shock at 37 degrees C (30 min) in comparison to control cells (25 degrees C). In addition, whereas 7% of all PCR products were preferentially expressed during derepressive growth, approximately 2% were found to be common to both heat-shocked and derepressed cells. A repeat analysis, performed on all three cell types of Ysen as well as cells of a relatively thermoresistant strain (Yres) yielded 30 differentially displayed cDNA fragments common to heat-shocked and derepressed cells of both strains. Eighteen of these generated signals on Northern blots, of which three were confirmed as regulated. Five amplicons, including one not detected by Northern analysis and another from the derepressed state, were cloned and sequenced. Three of these exhibited homology to S. cerevisiae genes with well-characterized protein products: HSP 90, HXK1 and STA1. The remaining two applicons showed nucleotide identity to YTIS11, a homolog of the mammalian TIS11 and putative transcriptional activator, and an orphan gene encoding a hypothetical transmembrane protein belonging to the multi-drug resistance translocase family. Our novel application of DDRT-PCR has identified new and known genes that may be further evaluated as factors involved in stress regulation and has demonstrated the potential of the technique to systematically analyse gene expression in yeast.

Differential display analysis of gene expression indicates that age-related changes are restricted to a small cohort of genes

It is clear that there is a genetic component associated with the ageing process. Although evolutionary theory has suggested that the activity of certain genes may facilitate ageing by favouring resource utilisation by the germ cells at the expense of somatic cells, there is reason to believe that the senescent phenotype, which is the endpoint of the ageing process, may be due to alterations in the levels of expression of other genes. To investigate this situation we have used the differential display technique to survey gene expression during ageing of the rat brain, heart and liver. By optimising this technique it is possible to identify up to 10000-14000 PCR products, which represent genes expressed in the tissue under study. Interestingly, only a relatively small cohort (approximately 2%) of these genes appear to show significant changes in their levels of expression during ageing. Characterisation of the latter has so far revealed certain genes, such as glial fibrillary acidic protein, which are associated with the senescent phenotype. It has also revealed that the level of fos, a component of the AP-1 transcription factor, decreases with age, which has implications for AP-1 regulated genes. The differential display technique has also revealed an increase in mitochondrial RNA during ageing of the heart, which may be due to a gene dosage effect caused by the presence of increased numbers of mitochondrial genomes in myocytes in old age. The differential display technique therefore appears to offer a powerful tool for identifying genes which contribute to the emergence of a senescent phenotype.

Immunobiology of renal transplantation

The clinical application of our knowledge of the immune barriers to transplantation has advanced allo-organ replacement therapy to the level of routine practice, while simultaneously engendering a critical shortage in available donors. Recent work in xenotransplantation addresses this need. The current understanding of the immune barriers to transplantation has evolved to consider alternate responses to alloantigen, namely acceptance. The delineation and application of recent discoveries in T cell costimulatory events, antigen presentation, and differential T lymphocyte responses are opening pathways towards the development of tolerogenic protocols for use in clinical transplantation. This article presents a review of transplant immunobiology with special attention to antigen presentation and T-cell activation as phases of the immune response relevant to the discussion of transplant tolerance.

Interaction and effect of annealing temperature on primers used in differential display RT-PCR

Differential display of mRNA is a simple, sensitive and powerful method to identify differentially expressed gene fragments. The main drawback of differential display is the lack of reproducibility and the inability to read and compare complex gels. This issue results from employing unoptimized primer combinations and non-specific amplification, most likely due to unavoidable low annealing temperatures. In order to display most of the expressed transcripts (80-120 bands/lane), 26 different 5' primers were used in conjunction with nine different 3' poly (dT) primers. These primer combinations, used with the optimized annealing temperature for each set of primers, produced highly reproducible bands. BSA has a direct effect on the number of bands resolved. Variations in ramping time (9-40 s) had little or no effect on the resolution and reproducibility of differential display.

IL-1 beta alters the expression of the receptor tyrosine kinase gene r-EphA3 in neonatal rat cardiomyocytes

To identify proinflammatory cytokine responsive genes in the myocardium, we used differential display to study RNA isolated from neonatal rat cardiac myocytes treated with tumor necrosis factor-alpha (TNF-alpha) and interleukin-1 beta (IL-1 beta). Sequence analysis of differential display products confirmed by reverse Northern blots revealed one clone as the partial sequence of an Eph-related receptor tyrosine kinase (r-EphA3). In cardiac myocytes, 36-h exposure to TNF-alpha and IL-1 beta reduced r-EphA3 transcripts to 59.9% (P < 0.01) of control levels; this effect was largely dependent on IL-1 beta. Western blot analysis showed that changes in r-EphA3 protein levels reflect that seen for transcripts. Cardiac nonmyocytes expressed substantially lower levels of r-EphA3. Full-length r-EphA3 cDNA clone (3,077 base pair) yielded an amino acid sequence with 90-98% homology to the Eph receptor human EphA3, chick EphA3, and mouse EphA3. In the adult rat, r-EphA3 transcripts were most abundant in the heart, brain, and lung. These results suggest that IL-1 beta may exert its effect on cardiac myocytes at least in part by altering r-EphA3 expression.

In search of differentially expressed genes and proteins

A great challenge for modern cell biology is the successful examination of the co-expression of thousands of genes under physiological or pathological conditions and how the expression patterns define the different states of a single cell, tissue or a microorganism. Gene expression can be analyzed today on a large scale by advanced technical approaches for differential screening of proteins and mRNAs. The identification of differentially expressed mRNAs has been successfully applied to understand gene function and the underlying molecular mechanism(-s) of differentiation, development and disease state. Analysis of gene expression by the systematic mapping of thousands of proteins present in a cell or tissue can be achieved by the use of two-dimensional (2D) gel electrophoresis, quantitative computer image analysis, and protein identification techniques. In this article, we comment on some of these techniques and try to stress their advantages and drawbacks. We show how data from RNA/DNA mapping, sequence information from genome projects and protein pattern profiling can be linked with each other and annotated. These comprehensive approaches permit the study of differential gene and protein expressions in cells or tissues.