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Isolation and Identification of cDNA Sequences Differentially Expressed in Laryngeal Carcinoma.

The isolation of the genes related to laryngeal carcinoma(LC) is necessary for revealing mechanisms of carcinogenesis and genetic predisposition to LC. The mRNA differential display method was used to compare and analyze mRNAs prepared from two adult laryngeal carcinoma tissues and paired tumor-adjacent normal tissues. A total of twenty-two differential display experiments was performed and thirty-five cDNA fragments differentially expressed in normal or malignant laryngeal epithelial tissues were identified. Differential expression of six of these thirty-five cDNA fragmens was confirmed by reverse northern dot blot. Subsequent cloning of six differentially expressed cDNA fragments and sequencing and BLASTn analysis resulted in the identification of twelve distinct cDNA sequences. Four of these were shown to be novel gene sequences that have not been reported. Eight of the remaining cDNA sequences showed sequence homology to those previously reported. The differential expression of these twelve cDNA sequences in the carcinoma or normal tissue of the larynx were confirmed by fixing the twelve cDNA sequences on the membrane, followed by the hybridization with the total cDNA probes from laryngeal carcinoma or normal tumor-adjacent tissues and by differential RT-PCR. These results suggest that these cDNA sequences might be involved in carcinogenesis of laryngeal carcinoma.

Journal Article↗

[Determination of differentially expressed proteins and it's significance among chronic sinusitis, nasal polyps and normal nasal mucosa].

OBJECTIVE: To investigate the differentially expressed proteins among chronic sinusitis, nasal polyps and normal nasal mucosa by means of proteomic technology, and select the candidate biomarkers of chronic sinusitis and nasal polyps. METHODS: Proteins extracted from chronic sinusitis, nasal polyps and normal nasal mucosa were separated and the differentially expressed proteins were identified by series of proteomic tools, including immobilized pH4-7 gradient two-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis, modified coomassie brilliant blue staining, images scanning by the Image Scanner apparatus, PDQuest analysis software, peptide mass fingerprinting based on matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) by in-gel digestion extract, and Mascot searching in NCBInr and SWISS-PROT databases. RESULTS: The 2-DE patterns with high resolution and reproducibility were obtained. The protein spots separated and visualized in chronic sinusitis, nasal polyps and normal nasal mucosa gel were 1020 +/- 40, 1112 +/- 10 and 1008 +/- 25, respectively. And the match rates were (93 +/- 2)%, (95 +/- 1)% [see text] (90 +/- 3)% respectively. Thirteen differentially expressed spots were found from chronic sinusitis, nasal polyps and normal nasal mucosa gel. We selected and recommend Keratin 8 and APOA1 proteins as candidate biomarkers of nasal polyps, and PLUNC protein, PACAP protein, NKEF-B and SOD as candidate biomarkers of chronic sinusitis. CONCLUSIONS: The differentially expressed proteins among chronic sinusitis, nasal polyps and normal nasal mucosa can be efficiently and relatively reliably identified via the techniques of proteomics. These techniques will play a very important role in the researches for new objective indicators possibly employed in the future classifying, staging and prognosis.

Adolescent↗

Microarray analysis of differentially expressed genes in mouse bone marrow tissues after ionizing radiation.

PURPOSE: To identify differentially expressed genes in mouse bone marrow involved in radiation-induced injury. MATERIALS AND METHODS: Microarray analysis was used to identify the differentially expressed genes and other techniques, e.g., polymerase chain reaction (PCR), western-blotting and antisense were also used to validate the results. RESULTS: DNA microarray analysis demonstrated that the mRNA of 34 genes increased and 69 genes decreased in mouse bone marrow cells (BMC) from C57BL mice 6 h after a whole body dose of 6.5 Gy. These differentially expressed genes were involved in a number of processes including DNA replication/repair, proliferation/apoptosis, cell cycle control and RNA processing. In these experiments, a decline of the mammalian homolog Sir2a (an acronym for the silent mating type information regulation 2 homolog [SIRT1]) mRNA accompanied by an increase of P53 protein acetylation was observed in irradiated BMC. To determine whether the reduced SIRT1 is related to the higher acetylation status of P53 after irradiation, we designed and synthesized antisense oligonucleotides (AS) targeting human SIRT1 mRNA. Notably, AS transfection increased tumor protein 53 (P53) protein acetylation and bax-luciferase activity in human bone marrow stromal cell line (HS-5) after radiation. Furthermore, the AS transfer stimulated cell apoptosis in post-irradiation HS-5 cells. CONCLUSION: Ionizing radiation (IR) affects the expression of a series of genes including genes involved in G1/S transition and the P53 pathway. Among those, reduction of SIRT1 was seen to be involved in transactivation of P53.

Animals↗

Identification of genes showing differential expression in anorexia mutant mouse.

Differential display (DD) PCR was applied to identify genes regulated by anorexia (anx) in mouse brain. Of the four apparently differentially expressed genes, three (H2-H4) had high homology with known genes such as apoptotic protease activating factor 1 (Apaf 1), adenylate cyclase 6 (Adcy 6), and myelin proteolipid protein (PLP). H1, designated as HIPA1, had a homology with unknown function gene fragments. Northern blot analysis confirmed HIPA1 expression induced by anorexia. A 1579 bp full-length cDNA of HIPA1 was isolated from a mouse brain cDNA library using a probe from the differentially displayed H1 fragment. Sequence analysis showed that HIPA1 had 98.7% homology to mouse hippocampus cDNA. In situ hybridization demonstrated that the HIPA1 mRNA was highly up-regulated in the hippocampus of anx/anx mouse brain.

Amino Acid Sequence↗

Differential expression profile of MAGE family in non-small-cell lung cancer.

The expression of the melanoma-associated antigen (MAGE) genes consists of variables in all tumor types, such as lung cancer, which are relevant to be silent in all normal tissues except germ cells. They are considered as tumor-specific antigens, and are ideal targets for cancer immunotherapy. A complete MAGE genes differential expression profile analysis of lung cancer can provide this study not only various target genes for immunotherapy, but also valuable markers for further diagnosis and prognosis. This research has constructed a membrane array, which was consisted 32 MAGE genes, to detect whether the differential expression profile occurred in 52 pairs of non-small-cell lung cancer (NSCLC) samples. Nearly 32 MAGE genes have been differential expressed in NSCLC except MAGE-B1 and -E2. MAGE-B, -C, -D, and subgroup -B6, -D4 have showed prominences in lung adenocarcinoma. High-frequent expression of MAGE-D, and subgroup -A2, -D2 has also been discovered in non-metastasis group (p<0.05). However, there is no significant difference of MAGE genes differential expression shown among different primary tumor (T), nodal involvement (N) and overall stages. Several MAGE subgroup genes, such as MAGE-A5, -A7, -A8, -A9, -A11, -B3, -B4, -B10, -D2, -D3, -F1, -G1, -H1, and -L2, have been first discovered to show differential expression in NSCLC. Although the small size of the sample may limit the diagnostic and prognostic value of MAGE genes, the function of the membrane array can provide this study a high-throughput method to detect the whole MAGE genes differential expression profile.

Antigens, Neoplasm↗

Differentially expressed cellular genes following HBV: potential targets of anti-HBV drugs?

The aim of the study was to screen for cellular genes that are differentially expressed following hepatitis B virus (HBV) infection, in an attempt to identify potential targets of anti-HBV drugs. An oligonucleotide microarray containing 231 virus-infection-associated genes was prepared. Differential gene expression in HepG2.2.15 cells compared to control with HepG2 cells was analysed by this in-house microarray. The change in gene expression in HepG2.2.15 cells treated by lamivudine on days 4 and 8 after exposure was also studied. Semi-quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) was used to comfirm the differentially expressed genes induced by HBV and lamivudine. There were 31 upregulated and four downregulated genes in HepG2.2.15 cells compared with the HepG2 control cells. Eleven genes were consistently altered by lamivudine at both time points. Of the 31 genes that were upregulated in HepG2.2.15 cells, there were seven genes which were downregulated by lamivudine. Of the four downregulated genes, there was one gene which was upregulated by lamivudine. Of the differentially expressed genes induced by HBV and lamivudine, the expression of five genes was confirmed by semi-quantitative RT-PCR. These results shed new light on the effects of HBV and lamivudine on cellular gene expression. Differentially expressed genes induced by HBV and lamivudine could potentially become new anti-HBV drug targets in novel therapies.

Antiviral Agents↗

[The differential expression profile of polycystic ovary syndrome associated genes].

OBJECTIVE: To explore the gene differential expression pattern of polycystic ovary syndrome. METHODS: We carried out microarray analysis to define the gene networks by the PCOS granulosa cells in order to identify differentially expressed genes in PCOS patients. These granulosa cells of five PCOS cases and five control cases which were derived during oocyte retrieval from women undergoing IVF. RESULTS: As compared with control human ovarian granulosa cells, 46 genes were screened out, 25 genes were up-regulated, and 21 genes were down-regulated in PCOS. These differentially expressed genes were involved in various biologic functions, such as regulation of fatty acid metabolism, cell-cell signal transduction, immune and inflammatory response, reflecting the complexity of clinical manifestations of PCOS. CONCLUSION: Microarray analysis technology is an effective method to identify novel PCOS associated candidate genes.

Adult↗

Identification of genes differentially expressed in association with acquired cisplatin resistance.

The goal of this study was to identify genes whose mRNA levels are differentially expressed in human cells with acquired cisplatin (cDDP) resistance. Using the parental UMSCC10b head and neck carcinoma cell line and the 5.9-fold cDDP-resistant subline, UMSCC10b/Pt-S15, two suppressive subtraction hybridization (SSH) cDNA libraries were prepared. One library represented mRNAs whose levels were increased in the cDDP resistant variant (the UP library), the other one represented mRNAs whose levels were decreased in the resistant cells (the DOWN library). Arrays constructed with inserts recovered from these libraries were hybridized with SSH products to identify truly differentially expressed elements. A total of 51 cDNA fragments present in the UP library and 16 in the DOWN library met the criteria established for differential expression. The sequences of 87% of these cDNA fragments were identified in Genbank. Among the mRNAs in the UP library that were frequently isolated and that showed high levels of differential expression were cytochrome oxidase I, ribosomal protein 28S, elongation factor 1alpha, alpha-enolase, stathmin, and HSP70. The approach taken in this study permitted identification of many genes never before linked to the cDDP-resistant phenotype.

Cisplatin↗

Differential expression of fetal and mature tau isoforms in primary cultures of rat cerebellar granule cells during differentiation in vitro.

The molecular mechanism(s) responsible for the differential expression of various tau protein isoforms as well as their functional role in morphogenesis, neurofibrillary tangle formation and neurodegeneration have not been completely clarified. We found that the expression of tau proteins in primary cultures of cerebellar granule cells from neonatal rat brain is a developmentally regulated process affecting tau synthesis at different levels. Changes in tau RNA splicing are clearly demonstrated by PCR data showing the switching on of the mRNA containing four internal repeats by DIV 6 and the switching off of the mRNA containing three internal repeats after DIV 12. The changes in mRNA levels of the different tau isoforms during development in vitro occur in parallel with changes in tau protein expression, both qualitatively and quantitatively, as shown by Western analysis of protein extracts from granule cells at different DIV with an anti-tau polyclonal antibody. Finally, as indicated by MAP2 and tau immunocytochemistry data, the switch in tau protein expression appears to be contemporary with neurite outgrowth and cell differentiation. Our data suggest that a differential expression of various tau proteins parallels the degree of cell maturation.

Animals↗

Use of within-array replicate spots for assessing differential expression in microarray experiments.

MOTIVATION: Spotted arrays are often printed with probes in duplicate or triplicate, but current methods for assessing differential expression are not able to make full use of the resulting information. The usual practice is to average the duplicate or triplicate results for each probe before assessing differential expression. This results in the loss of valuable information about genewise variability. RESULTS: A method is proposed for extracting more information from within-array replicate spots in microarray experiments by estimating the strength of the correlation between them. The method involves fitting separate linear models to the expression data for each gene but with a common value for the between-replicate correlation. The method greatly improves the precision with which the genewise variances are estimated and thereby improves inference methods designed to identify differentially expressed genes. The method may be combined with empirical Bayes methods for moderating the genewise variances between genes. The method is validated using data from a microarray experiment involving calibration and ratio control spots in conjunction with spiked-in RNA. Comparing results for calibration and ratio control spots shows that the common correlation method results in substantially better discrimination of differentially expressed genes from those which are not. The spike-in experiment also confirms that the results may be further improved by empirical Bayes smoothing of the variances when the sample size is small. AVAILABILITY: The methodology is implemented in the limma software package for R, available from the CRAN repository http://www.r-project.org

Algorithms↗

[Differential expression of immune-associated genes in two subcloned cell lines from a same human bladder cancer].

AIM: To screen and identify differentially expressed genes in subcloned lines from a same human bladder transitional cell carcinoma (TCC). METHODS: Two bladder TCC cell lines (BLX and BLS-211) with different phenotypes but same origin were used to screen for differentially expressed genes by suppression subtractive hybridization (SSH). RESULTS: 9 over-expressed genes in BLX and 15 in BLS-211 cells were obtained, respectively. Some Bacillus Galmette-Guerin(BCG)- associated genes, such as BCG induced integral membrane protein(BIGM103), fibronectin(FN), complement factor B(BF), were over-expressed in BLX cells. And 8 new ESTs(Expressed Sequence Tag) in BLS-211 cells were collected by GenBank dbEST database with the accession number of DY505708-13, DY230447-8. CONCLUSION: SSH is a powerful method for the identification of differentially expressed genes in different cell lines or clones. Some BCG-associated genes, which are differentially expressed in different cells may contribute to the different response to clinical BCG therapy. The identified new ESTs can be cloned for full length to further study their functions.

Carcinoma, Transitional Cell↗

Identification of differentially expressed genes in oral squamous cell carcinoma.

Rapid advances in multimodality therapy have not significantly improved the overall 5-yr survival of oral cancer patients in the past two decades, thereby underscoring the need for molecular therapeutics. The development of new treatment strategies for more effective management of oral cancer requires identification of novel biological targets. Therefore, the aim of this study was to identify novel genes associated with oral tumorigenesis by comparing gene expression profile of oral squamous cell carcinomas (OSCCs) and matched nonmalignant oral epithelial tissues with differential display. Of the 180 differentially expressed cDNAs isolated, reamplified, and cloned into pGEMT-Easy Vector, 26 cDNAs were confirmed to be upregulated in OSCCs by reverse Northern blot analysis. The differentially expressed genes included components of immune system, signaling pathways, angiogenesis, cell structure, proliferation, apoptosis, cell-adhesion, and cellular metabolism. Reverse transcription (RT)-polymerase chain reaction (PCR) analysis of 15 OSCCs and matched nonmalignant oral tissues provided the first evidence that 14-3-3-zeta, melanoma metastasizing clone D (MEMD), KIAA0471, sperm protein 17 (SP17), TC21, and anti-TNF alpha antibody are upregulated in OSCCs. Immunohistochemical analysis confirmed overexpression of 14-3-3-zeta and TC21 protein, a member of the Ras family, in OSCCs as compared to histologically normal oral tissues validating the differential display analysis. Identification of six novel differentially expressed genes in oral tumors adds to the repertoire of genes associated with oral carcinogenesis and provides candidate potential biological targets for diagnosis and/or therapy. Further characterization of the 14 unknown differentially expressed cDNAs identified in this study may provide significant clues for understanding the molecular mechanisms underlying oral tumorigenesis.

14-3-3 Proteins↗

Debt91, a putative zinc finger protein differentially expressed during epithelial morphogenesis.

In a differential screen for genes that might be important in the regulation of epithelial morphogenesis, we identified a novel gene, Debt91 (differentially expressed in branching tubulogenesis), which is up-regulated in an in vitro model of renal tubulogenesis and branching. Debt91 appears to encode a 381 amino acid molecule with high Ser and Thr composition and is highly conserved at its N-terminus across species. Sequence analysis suggests that it is a coiled-coil nuclear phosphoprotein with zinc finger motifs at the N-terminal conserved region, which is rich in cysteine and histidine. Debt91 is located on mouse chromosome 6 at a region that has conserved synteny with human chromosome 2p11.2, and appears to express two transcripts in several mouse cell lines and adult tissues. On whole murine embryo blots Debt91 expresses primarily its small transcript and is differentially regulated during development. Analysis of expression in in vitro cell culture models suggests that Debt91 is an immediate early gene up-regulated during growth factor-induced branching tubulogenesis.

Amino Acid Sequence↗

[Screening differentially expressed genes in denucleated K562 cells with restriction display technique].

OBJECTIVE: To screen differentially expressed genes in cytochalasin B (CB)-induced denucleated K562 cells by restriction display (RD) technique. METHODS: The total RNA was isolated and purified from K562 cells before and after CB (10 mug/ml) treatment. The mRNA from both treated and untreated K562 cells were reversely transcribed into cDNA, and the differentially expressed genes were separated using RD technique combined with polyacrylamide gel electrophoresis and sliver staining, followed by cloning, sequencing and homology analysis against GenBank database of these genes. RESULTS: Seven differentially expressed genes were identified in CB-treated cells including aquaporin 1 (AQP1) gene, which was verified to be up-regulated after CB treatment by RT-PCR. CONCLUSION: AQP1 gene might be in close association with the regulation of denucleation processes and CB-induced proliferation inhibition of K562 cells.

Aquaporin 1↗

Improved method for detecting differentially expressed genes using cDNA indexing.

In cDNA indexing, differentially expressed genes are identified by the display of specific, corresponding subsets of cDNA. Subdivision of the cDNA population is achieved by the sequence-specific ligation of adapters to the overhangs created by class IIS restriction enzymes. However, inadequate specificity of ligation leads to redundancy between different adapter subsets. We evaluate the incidence of mismatches between adapters and class IIS restriction fragments during ligation and describe a modified set of conditions that improves ligation specificity. The improved protocol reduces redundancy between amplified cDNA subsets, which leads to a lower number of bands per lane of the differential display gel, and therefore simplifies analysis. We confirm the validity of this revised protocol by identifying five differentially expressed genes in mouse duodenum and ileum.

Animals↗

[Screening of differentially expressed genes related to laterally spreading tumor by cDNA microarray].

OBJECTIVE: To screen differentially expressed genes between laterally spreading tumor (LST) cell line and common colon carcinoma cell lines, and identify new targets and strategies for exploring the pathogenesis of colorectal tumor. METHODS: The total RNA was extracted from the LST, SW480 and LoVo cells, from which purified mRNAs were obtained. The PCR products of 18 816 genes were blotted onto a fibrous membrane to generate the microarray. The mRNAs from the 3 cell lines were reversely transcribed into cDNA probes and labeled with (33)P before hybridization with the cDNA microarray. After thorough washing, the cDNA microarray was scanned and the 3 samples compared. RESULTS AND CONCLUSIONS: A series of differentially expressed genes were found between the 3 samples, and 58 up-regulated and 39 down-regulated genes were identified among the 97 differentially expressed genes, which suggest different pathogeneses of the laterally spreading tumor. Further analysis of the obtained genes can be helpful in understanding the molecular mechanism of colorectal tumors.

Cell Line, Tumor↗

Differential expression of fibronectin receptors during myeloid differentiation and in marrow- and peripheral blood-derived leukemic cells.

A 125I-labeled 120-kDa fibronectin fragment (FN120) containing the RGD binding site was employed to assess FN120 receptor levels in control and dimethylsulfoxide (DMSO)-differentiated HL60 cells, as well as in leukemic peripheral and bone marrow blast cells from acute lymphoid (ALL) and myeloid (AML) patients. Fibronectin CS1 fragment receptor alpha 4 (VLA4-alpha) and RGD-dependent alpha 5 integrin subunits (VLA5-alpha) were characterized by specific monoclonal antibodies (MoAb). HL60 cells, induced along the granulocytic pathway with DMSO, displayed low FN120 binding level densities (36,070 +/- 5142 sites/cell (s/c) vs. 19,780 +/- 4564 s/c, P < 0.005), respectively, for untreated and treated cells) together with decreased VLA5-alpha expression. Granulocytes displayed low levels of FN120 receptors (3167 +/- 1165 s/c) with weak VLA5-alpha expression and absence of VLA4-alpha. Normal lymphocytes displayed 17,670 +/- 8,705 s/c FN120 receptors and VLA4-alpha and VLA5-alpha. The mean FN120 binding levels and mean VLA5-alpha expression were lower in peripheral blast cells, both in ALL and AML, than in the bone marrow leukemic cells. VLA4-alpha remained the same irrespective of cell localization. FN120 binding sites and differential expression of VLA4-alpha and VLA5-alpha integrin molecules on hemopoietic cells could be related to lineage characteristics or cell type distribution within hemopoietic tissue.

Adolescent↗

Differential expression and characterization of three metallothionein-like genes in Cavendish banana (Musa acuminata).

Metallothioneins (MTs) are cysteine-rich polypeptides that are involved in metal detoxification and homeostasis in both prokaryotes and eukaryotes. In this study, we report the isolation and characterization of three members (MT2A, MT2B and MT3) of the MT-like gene family from ripening banana fruit and their differential expression in various banana organs and during fruit development and ripening. All members of the MT-like gene encode small cysteine-rich polypeptides of 65-79 amino acid residues. MT2A shared a high sequence similarity (54-77%) with several type-2 MTs in plants, while MT3 was highly homologous (51-61%) with type-3 MTs. The three members expressed differentially in various organs but transcripts were generally more abundant in reproductive than vegetative organs. During fruit development, the MT2A transcript was barely detectable in ovary but increased to a high level in young fruit at 20 days after shooting (DAS) and declined gradually thereafter as fruit developed. In contrast, both MT2B and MT3 expressed poorly in young fruits (20-60 DAS) and transcripts were detected only in fruits at later stages of development. As ripening progressed, expression of MT2A decreased but that of MT3 increased. Expression of MT members during ripening appeared to be differentially regulated by ethylene, whose levels were low in FG and TY fruit but surged climacteristically in MG and declined sharply as ripening advanced further. Exogenous application of ethylene at 5 ppm or higher concentrations down-regulated MT2A expression and the inhibitory effect of ethylene could be partially suppressed by the presence of norbornadiene, an inhibitor of ethylene action. Ethylene had no effect on transcript accumulation of MT2B and MT3. However, MT3 expression was greatly enhanced in response to metals such as CdSO4, CuSO4 and ZnSO4. These results suggest that increased MT3 expression may be associated with excess metal ions present in ripening fruit tissues. This study also provided evidence, for the first time, that ethylene and metals play a regulatory role in expression of MT-like genes in banana.

Journal Article↗