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PubMed2001

Identification and classification of differentially expressed genes in renal cell carcinoma by expression profiling on a global human 31,500-element cDNA array.

We investigated the changes in gene expression accompanying the development and progression of kidney cancer by use of 31,500-element complementary DNA arrays. We measured expression profiles for paired neoplastic and noncancerous renal epithelium samples from 37 individuals. Using an experimental design optimized for factoring out technological and biological noise, and an adapted statistical test, we found 1738 differentially expressed cDNAs with an expected number of six false positives. Functional annotation of these genes provided views of the changes in the activities of specific biological pathways in renal cancer. Cell adhesion, signal transduction, and nucleotide metabolism were among the biological processes with a large proportion of genes overexpressed in renal cell carcinoma. Down-regulated pathways in the kidney tumor cells included small molecule transport, ion homeostasis, and oxygen and radical metabolism. Our expression profiling data uncovered gene expression changes shared with other epithelial tumors, as well as a unique signature for renal cell carcinoma. [Expression data for the differentially expressed cDNAs are available as a Web supplement at http://www.dkfz-heidelberg.de/abt0840/whuber/rcc.]

Carcinoma, Renal Cell↗
PubMed2005

Pigment epithelium-derived factor is differentially expressed in peripheral neuropathies.

Peripheral neuropathies are characterized by asymmetrical slowly progressive weakness with no upper motor neuron signs, and can occur either with or without pain. Due to poor knowledge of the disease mechanisms, available pain treatment is very limited. Because of the difficulties and invasiveness involved when performing direct analysis on peripheral and CNS, pathological markers can be searched for in the cerebrospinal fluid (CSF) as an alternative. To investigate pain mechanisms in peripheral neuropathy and find diagnostic markers, CSF samples were analyzed by a differential expression proteomic approach. We studied CSF from: neuropathic patients with pain (PN), without pain (NPN) and healthy controls (CN). 2-DE analysis showed ten protein spots differentially expressed, and six of these were identified by MS. In NPN patients we found an expression level decrease of three pigment epithelium-derived factor (PEDF) protein isoforms. Immunoblot with a specific antibody revealed the presence of additional PEDF isoforms not highlighted by differential expression analysis. Fucose residues on the oligosaccharide chain were found only in the isoforms down regulated in NPN patients. Considered as PEDF has important neurobiological effects, it might be considered an interesting pathology marker.

Adult↗
PubMed1999

Differential expression of prostaglandin receptor mRNAs during adipose cell differentiation.

To clarify the molecular basis for the prostaglandin (PG) mediated effects in adipose cells at various stages of their development, expression of mRNAs encoding receptors specific for prostaglandin E2, F2alpha and I2 (i.e. EP, FP, and IP receptors) was investigated in differentiating clonal Ob1771 pre-adipocytes, as well as in mouse primary adipose precursor cells and mature adipocytes. We have further characterized the differential expression of mRNAs encoding three subtypes of the EP receptor, i.e. EP1, EP3, and EP4, and examined the expression of mRNAs encoding the three isoforms (alpha, beta, and gamma) of the EP3 receptor. Altogether the results show that the expression of IP, FP, EP1, and EP4 receptor mRNAs was considerably more pronounced in pre-adipose cells than in adipose cells, mRNAs encoding the alpha, beta, and gamma isoforms of the EP3 receptor were all exclusively expressed in freshly isolated mature adipocytes. These data may indicate that PGI2, PGF2alpha, and PGE2 may interact directly with specific receptors in pre-adipose cells, whose transduction mechanisms are known to affect maturation related changes. In mature adipocytes, however, the equipment of mRNAs encoding the EP3 receptor isoforms is in agreement with the well known effect of PGE2 on adenylate cyclase and lipolysis in mature adipocytes.

Adipocytes↗
PubMed2002

Identification and characterization of SRSP1, a rat gene differentially expressed during spermatogenesis and coding for a serine stretch-containing protein.

By means of mRNA differential display and cDNA library screening we have characterized a novel gene of the rat that is differentially expressed during spermatogenesis. Northern blot analyses showed that its mRNA reaches the highest level during the first meiotic prophase. The transcript appears to be testis-specific as it was not detectable in any of the nine other tissues tested. The full length ORF encodes a putative phosphoprotein containing a serine stretch and a bipartite nuclear localization signal, which we call Srsp1 ("serin-rich spermatogenic protein 1"). Comparison of the cDNA from SRSP1 with genomic sequences in databases allowed us to determine the number of introns; some putative regulatory sequences are proposed. This is the first report of a gene differentially expressed during spermatogenesis that codes for a protein containing a serine stretch.

Amino Acid Sequence↗
PubMed2005

Proteomic identification of differentially expressed proteins in the aging murine olfactory system and transcriptional analysis of the associated genes.

Decline in olfactory ability has been associated with aging as well as neurodegenerative disorders. The aim of this study was to gain fundamental insight into molecular events associated with the aging olfactory system. We report a comparative proteomic analysis of the olfactory epithelium (OE) and olfactory bulb (OB) of old (80-week old) and young (6-week old) mice with further analysis of age-related differences in differentially expressed proteins at the mRNA level using real-time RT-PCR. Nine proteins in the OE and 20 in the OB were differentially expressed in old and young mice; of these, aldolase 1, peptidyl prolyl isomerase A, mitochondrial aconitase 2, mitochondrial aldehyde dehydrogenase 2 and albumin 1 were identified in the OE; and ATP synthase isoform 1, enolase 1, ferritin heavy chain, malate dehydrogenase 1, tropomyosin alpha 3 chain and dynamin 1 were identified in the OB. At the transcriptional level, aconitase 2 in the OE and ferritin heavy chain 1 in the OB were differentially expressed with aging, in concordance with the proteomic data. Our results demonstrate an altered proteomic profile of the aged murine olfactory system. The identified proteins fall into three broadly defined functional categories: (i) metabolism, (ii) transport/motility and (iii) stress response. Our transcriptional analysis provides insight into possible mechanisms by which protein expression may be regulated in the OE and OB. The results are discussed in relation to the decrement in olfactory sensitivity with aging.

Age Factors↗
PubMed1998

Differential expression of inducible nitric oxide synthase messenger RNA along the longitudinal and crypt-villus axes of the intestine in endotoxemic rats.

OBJECTIVES: To characterize the mechanisms leading to excessive production of nitric oxide within the gut as a consequence of endotoxemia. We sought to: a) determine the time course of inducible nitric oxide synthase (iNOS) messenger RNA (mRNA) expression in the intestine after challenging rats with lipopolysaccharide (LPS); and b) investigate whether there is differential expression of iNOS in enterocytes along the longitudinal or crypt-villus axes of the intestine in rats after LPS administration. DESIGN: Prospective, randomized, unblinded study. SETTING: Research laboratories at a large university-affiliated medical center. SUBJECTS: Male Sprague-Dawley rats. INTERVENTIONS: At T = 0 hr, rats were injected with O111:B4 Escherichia coli LPS (5 mg/kg) or a similar volume of the saline vehicle. At various time points thereafter, samples of duodenum, jejunum, ileum, colon, and liver were harvested for subsequent extraction of RNA. In some cases, populations of enterocytes enriched in either crypt or villus cells were harvested from the ileum. In some studies, rats were injected with cycloheximide (25 mg i.p.) 15 mins before being challenged with LPS or dexamethasone (2 mg i.p.) 30 mins before being injected with LPS. MEASUREMENTS AND MAIN RESULTS: iNOS mRNA was undetectable in ileal tissue from rats under basal conditions, but was evident by T = 1 hr and was maximal at T = 2 hrs after injection of LPS. Thereafter, ileal iNOS mRNA concentrations decreased and were undetectable again at T = 24 hrs. At T = 2 hrs after LPS injection, there was marked expression of iNOS mRNA in the ileum, whereas much lower concentrations of iNOS mRNA were detected in the jejunum and colon, and no iNOS mRNA was detected in the duodenum. At T = 3 hrs after LPS injection, expression of iNOS mRNA was up-regulated in both villus and crypt cells, although LPS-induced iNOS mRNA was more prominent in the former than the latter cell type. Pretreatment of rats with dexamethasone virtually abrogated the expression of iNOS mRNA in ileal samples obtained 3 hrs after the injection of LPS. Prior treatment of rats with the protein synthesis inhibitor, cycloheximide, also blunted LPS-induced iNOS mRNA expression. CONCLUSIONS: LPS-induced iNOS expression is differentially regulated along both the longitudinal and crypt villus axes of the intestinal mucosa, being most prominent in the villus cells of the ileum. LPS-induced iNOS expression is blunted by pretreating rats with dexamethasone or cycloheximide. The latter finding suggests that LPS-induced expression of iNOS mRNA in the gut requires new protein synthesis. Differential regulation of nitric oxide production along the longitudinal and crypt-villus axes of the gut may be a determinant of the pattern of sepsis-induced intestinal damage.

Animals↗
PubMed2000

Differential expression of COUP-TFI, CHL1, and two novel genes in developing neocortex identified by differential display PCR.

Genes that control the specification and differentiation of the functionally specialized areas of the mammalian neocortex are likely expressed across the developing neocortex in graded or restricted patterns. To search for such genes we have performed a PCR-based differential display screen using RNAs from rostral neocortex, which included the primary motor area, and caudal neocortex, which included the primary visual area, of embryonic day 16 rats. We identified 82 differentially expressed gene fragments. Secondary screening by in situ hybridization confirmed that five fragments, representing four genes, are differentially expressed across developing rat neocortex. Two of the genes, chick ovalbumin upstream transcription factor I (COUP-TFI) and close homolog of L1 (CHL1), have been cloned previously, but their differential expression in cortex has not been reported. Sequences from the other two fragments suggest that they represent novel genes. The expression patterns include graded, restricted, and discontinuous expression with abrupt borders that might correlate with those of areas. The differential expression patterns of all four genes are established before the arrival of thalamocortical afferents, suggesting that they are independent of thalamic influence, and could direct or reflect arealization. In addition, COUP-TFI and CHL1 exhibit dynamic expression patterns that undergo substantial changes after thalamocortical afferents invade the cortical plate, suggesting that thalamic axons may influence their later expression. Postnatally, COUP-TFI is most prominently expressed in layer 4, in both rats and mice, and CHL1 is expressed in layer 5. COUP-TFI expression in cortex, and in ventral telencephalon and dorsal thalamus, suggests several possible causes for the loss of layer 4 neurons and the reduced thalamocortical projection reported in COUP-TFI knock-out mice.

Animals↗
PubMed2003

Cloning and characterization of leaf cDNAs that are differentially expressed between wheat hybrids and their parents.

Previous studies have shown that heterosis is associated with differential gene expression between hybrids and their parents. In this study, we performed a screen for genes that are differentially expressed between wheat hybrids and their parents in jointing-stage leaves and flag leaves using the differential display technique. Twenty-four differentially expressed cDNA were cloned and sequenced, and their expression patterns were confirmed by reverse-Northern blotting. Sequence analysis and database searches revealed that among the genes that showed differential expression between hybrid and parents were transcription factor genes and genes involved in metabolism, signal transduction, disease resistance, and retrotransposons. These results indicate that hybridization between two parental lines can cause changes in the expression of a variety of genes, and it is concluded that the altered pattern of gene expression in the hybrid may be responsible for the observed heterosis.

Base Sequence↗
PubMed2000

Identification of differentially expressed genes in nasopharyngeal carcinoma by means of the Atlas human cancer cDNA expression array.

PURPOSE: To investigate genes of critical areas, including cell cycle/growth control, apoptosis, oncogene/tumor suppressors and growth factor/cytokines, that are differentially expressed in nasopharyngeal carcinoma. METHODS: The Human Cancer cDNA Atlas, which contains 588 genes relating to tumor biology, was used to screen normal nasopharyngeal tissue, nasopharyngeal cancer (NPC). The reverse transcription/polymerase chain reaction was used to confirm the expression pattern of some genes identified by Atlas hybridization. RESULTS: The differentially expressed cell cycle/growth control regulators in NPC showed a stronger tendency toward cell proliferation with the up-regulation of cyclin D1, cyclin D2 etc. The expression pattern of apoptosis-related genes demonstrated the up-regulation of both anti-apoptotic factors such as the BCL-2-related protein A1, TRAF3, the inhibitor of apoptosis protein A1 (IAPI) and apoptotic pathway elements such as Fas/Apo-1, Apo-2 ligand etc. Among oncogenes/tumor suppressors, MDM2, STAT1 and STAT2 were found to be up-regulated in NPC. The expression profile of growth factors/cytokines showed the up-regulation of many growth-enhancing factors such as EGR1, tumor-derived growth factor 1, platelet-derived growth factor A chain etc. as well as Th1-type cytokines e.g. interleukin-1beta and interferons. A smaller number of genes were down-regulated in nasopharyngeal cancer, such as those encoding ERK1, Raf, secreted apoptosis-related protein 1, CD27BP, transforming growth factor beta2, pre-B-cell-stimulating factor homologue etc. CONCLUSION: The consistent tendency toward cell proliferation, the possibility of a stronger antiapoptotic force that operates on the normal apoptotic pathway, or the autocrine or paracrine growth factors may account for the development of NPC. Some genes are reported for the first time to have changed expression in nasopharyngeal carcinoma. The simple, quick, and high-throughput method of profiling gene expression by cDNA array hybridization provides us with a quick overview of key factors that may be involved in NPC, and may identify genes suitable for further study of carcinogenesis mechanism or targets for possible molecular diagnosis or therapy.

Apoptosis↗
PubMed2000

Construction of an equalized cDNA library from Colletotrichum lagenarium and its application to the isolation of differentially expressed genes.

To establish an efficient screening system for differentially expressed genes of a phytopathogenic fungus Colletotrichum lagenarium, we constructed an equalized (normalized) cDNA library from C. lagenarium and used this library for differential screening. For the isolation of genes involved in infection-related developments of conidia, conidia undergoing appressorium differentiation were selected as the source of materials for construction of the cDNA library. The equalization of cDNA was performed twice using a kinetic method, and the products were cloned into a plasmid vector. Colony hybridization with nine probes of different abundance showed a reduction in abundance variation from at least 276-fold in the original library to 10-fold in the equalized cDNA library, which demonstrated that the cDNA was successfully equalized. By differential hybridization of 1900 cDNA clones in the equalized cDNA library and RNA blot analysis of candidate clones, we identified 11 independent cDNA clones, designated CAD1 through CAD11, that were expressed in appressorium-differentiating conidia, but not in vegetative mycelia. The transcripts of CAD1 and CAD2 hardly accumulated in preincubated conidia, whereas those of CAD3 and CAD4 accumulated highly and slightly, respectively. The amount of the four CAD transcripts increased at the early stage of the appressorium formation process. Sequence analysis of CAD1 revealed that CAD1 would encode for 101 amino acid polypeptides, which showed homology to metallothioneins. Deduced amino acid sequence of CAD2 would encode 278 amino acid polypeptides, and showed high homology to genes in aflatoxin, and sterigmatocystin gene clusters of Aspergillus parasiticus and A. nidulans, respectively.

Amino Acid Sequence↗
PubMed2006

Differential expression changes in K562 cells during the hemin-induced erythroid differentiation and the phorbol myristate acetate (PMA)-induced megakaryocytic differentiation.

K562 cell line has been used as a model of common progenitor of erythroblasts and magakaryocytes and can be differentiated into erythroid and megakaryocytic lineages by hemin and phorbol myristate acetate (PMA) respectively. We analyzed mRNA expression in un-induced, hemin-induced and PMA-induced K562 cells by differential display reverse transcription polymerase chain reaction (DDRT-PCR) method. 314 differential expression sequence tags (ESTs) were obtained. Among them, 201 ESTs displayed up-regulation and 85 ESTs down-regulation after hemin induction, 186 ESTs showed up-regulation and 72 ESTs down-regulation after PMA induction. The differentially expressed genes included those encoding transcription factors, signaling factors, apoptosis-associated factors and others. 45 of these ESTs stand for genes whose open reading frames were found but whose functions remain unknown. 4 ESTs represent possibly new genes. Furthermore we compared differences of gene expression during hemin-induced erythroid differentiation and PMA-induced megakaryocytic differentiation and found that the expressional changes of some transcription factors and metabolism proteins are the common but the expressional changes of some signal pathways in these two differentiation processes are different. These results suggested that erythroid differentiation and megakaryocytic differentiation are associated in activation and repression of different signal pathways.

Blotting, Northern↗
PubMed2002

[Cloning of differentially expressed cDNA sequences involved in malignant transformation induced by benzo(a)pyrene metabolite dihydroxyepoxy benzo pyrene].

OBJECTIVE: To clone differentially expressed cDNA sequences involved in malignant transformation induced by benzo(a)pyrene metabolite dihydroxyepoxy benzo pyrene (BPDE). METHOD: The malignant transformation of human bronchial epithelial cell line 16HBE induced by BPDE in vitro was used as a model for comparing gene expression between the transformed cells and controls. cDNA representational difference analysis (cDNA-RDA) was performed to isolate differentially expressed cDNA fragment in transformed cells. The cDNA fragments were ligated to pGEM-T vector and transformed into JM109 bacteria. The plasmid DNA were sequenced and compared with data in GenBank by BLASTN. RESULTS: Five cDNA sequences were found to be novel ones and were registered in dbest database, which assigned accession numbers in GenBank are BG354691, BG354692, BG354693, BG354694 and BG354695, respectively. Eight of the remaining cDNA sequences showed sequence homology to those previously reported such as ribosomal protein S23, MLN137, ACTN4, transforming growth factor and G protein gene. CONCLUSIONS: These 13 genes may be involved in BPDE-induced malignant transformation, but their biological characteristics and functions are left to further studies.

Benzopyrenes↗
PubMed2006

Differential expression of HOX genes in neoplastic and non-neoplastic human astrocytes.

HOX genes are a large family of regulatory genes implicated in the control of developmental processes. HOX genes are involved in malignant transformation and progression of different types of tumour. Despite intensive efforts to delineate the expression profiles of HOX genes in other cell types, nothing is known regarding the global expression profile of these genes in normal human astrocytes and astrocytomas. The present study has analysed the expression profile of the 39 class I HOX genes in normal human astrocytes (NHA and E6/E7), two well-established glioblastoma cell lines (U-87 MG and U-1242-MG), as well as neoplastic (WHO grades II/III and IV) and non-neoplastic temporal lobe specimens with hippocampal sclerosis and medically intractable epilepsy. RT-PCR, quantitative real-time PCR, immunocytochemistry, and western blot analyses revealed differential expression of nine HOX genes (A6, A7, A9, A13, B13, D4, D9, D10, and D13) in normal human astrocytic cell lines and non-neoplastic temporal lobe specimens. The data show that HOX genes are differentially expressed in neoplastic and non-neoplastic astrocytes and that multiple HOX genes are overexpressed in glioblastoma cell lines, astrocytomas (II/III), and glioblastoma multiforme. The differential expression of HOX genes in normal and neoplastic astrocytes suggests a role for these genes in brain tumourigenesis.

Astrocytes↗
PubMed1997

Differential expression of transcripts encoding retinoid binding proteins and retinoic acid receptors during placentation of the mouse.

We report the distribution of transcripts from genes encoding the retinol binding protein (RBP), the cellular retinol binding proteins (CRBP I, II) and retinoic acid binding proteins (CRABP I, II), the retinaldehyde dehydrogenase type 2 (RALDH-2), the retinoic acid receptors (RARs), and the retinoid X receptors (RXRs) in mouse placental tissues from 6.5 to 19.5 days postcoitum (dpc). During early placentation, RBP and RALDH-2 gene expression are restricted to the endoderm of the visceral yolk sac and the outer uterine epithelium, respectively, whereas CRBP I transcripts are detected in the visceral yolk sac and in the presumptive chorioallantoic placenta. By 15.5 dpc, CRBP I expression is down-regulated in the yolk sac where CRBP II becomes strongly expressed. Expression of CRBP II is also detected in the trophoblastic giant cells. Throughout placentation, the expression patterns of the CRABP I and II genes partly overlap in the decidual tissue and the vacuolar zones of the decidua, suggesting a role for these binding proteins in sequestering free retinoic acid from maternal blood, thus regulating its availability to the embryo. RAR alpha is ubiquitously expressed in all placental tissues, except in trophoblastic giant cells, at all stages studied. During early placentation, RAR beta and RAR gamma are co-expressed in the decidua but differentially expressed in the chorionic region (RAR beta, 10.5 to 12.5 dpc) and the presumptive labyrinth (RAR gamma, 7.5 to 12.5 dpc). During the same stages, RXR alpha is strongly expressed in the presumptive placenta. RAR gamma remains weakly expressed in the labyrinth until 15.5 dpc, whereas RXR alpha exhibits a strong expression in this zone until birth, suggesting a role for these receptors in the development and function of the definitive placenta.

Animals↗
PubMed2004

Differential expression profiles of growth-related genes in the elongation zone of maize primary roots.

Growth in the apical elongation zone of plant roots is central to the development of functional root systems. Rates of root segmental elongation change from accelerating to decelerating as cell development proceeds from newly formed to fully elongated status. One of the primary variables regulating these changes in elongation rates is the extensibility of the elongating cell walls. To help decipher the complex molecular mechanisms involved in spatially variable root growth, we performed a gene identification study along primary root tips of maize (Zea mays) seedlings using suppression subtractive hybridization (SSH) and candidate gene approaches. Using SSH we isolated 150 non-redundant cDNA clones representing root growth-related genes (RGGs) that were preferentially expressed in the elongation zone. Differential expression patterns were revealed by Northern blot analysis for 41 of the identified genes and several candidate genes. Many of the genes have not been previously reported to be involved in root growth processes in maize. Genes were classified into groups based on the predicted function of the encoded proteins: cell wall metabolism, cytoskeleton, general metabolism, signaling and unknown. In-situ hybridization performed for two selected genes, confirmed the spatial distribution of expression shown by Northern blots and revealed subtle differences in tissue localization. Interestingly, spatial profiles of expression for some cell wall related genes appeared to correlate with the profile of accelerating root elongation and changed appropriately under growth-inhibitory water deficit.

DNA, Complementary↗
PubMed1979

Host dependence of RP1-specified resistance to ampicillin: differential expression in Escherichia coli and Rhizobium leguminosarum.

Rhizobium leguminosarum L4 is able to serve as a host for the plasmid RP1. Properties of R. leguminosarum [RP1] plasmid carrier suggest that the expression of RP1-coded Apr gene(s) is inhibited in this host, although the determinants of transfer and resistance to kanamycin and tetracycline are expressed. This system exemplifies a differential expression of plasmid genes in a new host.

Ampicillin↗
PubMed2004

Comparison of differentially expressed genes in T lymphocytes between human autoimmune disease and murine models of autoimmune disease.

A general view is that critical genes involved in biological pathways are highly conserved among species. To understand human autoimmune diseases, a great deal of effort has been devoted to the study of murine models that mirror many pathologic properties observed in the human disease. We have found that lymphocytes from humans with different autoimmune disease all carry a common conserved gene expression profile. Therefore, we wanted to determine if lymphocytes from common murine models of autoimmune disease carried a gene expression profile similar to the human profile and if both mouse models carried a shared gene expression profile. We identified numerous differentially expressed genes (DEGs) in the autoimmune strains compared to non-autoimmune strains. However, we found very little overlap in the gene expression profile between human autoimmune disease and murine models of autoimmune disease and between different murine autoimmune models. Our research further confirms that murine models of autoimmunity do not perfectly match human autoimmune diseases.

Animals↗
PubMed1989

Differential expression of the 4F2 activation antigen on human follicular epithelium in hair cycle.

The expression of the 4F2 activation molecule has been studied on keratinocytes of human skin and hair follicle using immunoperoxidase staining with three different anti-4F2 monoclonal antibodies. Membranes of basal layer keratinocytes of the skin uniformly expressed this antigen, whereas a differential expression of this antigen was located in specific areas of the hair follicle. Follicles in the complete anagen phase displayed a strong 4F2 positive staining at the matrix and the outer root sheath cells. This positive staining gradually decreased along the proliferation zone, and became negative at the migration zone. Positivity was recovered in follicular cells at the duct of the sebaceous gland and was maintained in the upper outer root sheath where those cells fuse with the keratinocyte basal monolayer. Changes were also detected on different phases of the hair cycle. Follicles in the catagen-telogen phase expressed a very low number of positive cells in the matrix. Positive labeling progressively increased when the follicle was at the initial anagen stage, reaching a complete staining pattern in hair at the anagen phase. These results suggest that the expression of this activation antigen on hair keratinocytes may be related to the proliferation, active metabolism, and/or activation states of these cell types.

Adult↗