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PubMed1995

Identification of melanoma inhibitory activity and other differentially expressed messenger RNAs in human melanoma cell lines with different metastatic capacity by messenger RNA differential display.

The differential display technique was used to identify mRNAs differentially expressed in human melanoma cell lines with different metastatic capacity. We report the isolation of nine different clones, of which four were uniquely expressed in the highly metastatic human melanoma cell line MV3, whereas the other five clones were uniquely expressed in the poorly metastatic human melanoma cell line 530. The differences in expression identified by differential mRNA display were confirmed by Northern blot analyses. DNA sequencing followed by computer search analyses indicated that of the nine differentially expressed clones, five represented novel gene products. The other four were histocompatibility antigen HLA-DR, laminin B2, melanoma inhibitory activity (MIA), and tissue inhibitor of metalloproteinases 3. MIA was also identified in RNA from human melanoma metastasis lesions in a comparison by differential display with pooled human nevi. Northern blot analysis confirmed MIA mRNA expression in nonmetastasizing melanoma cell lines and in melanoma metastasis lesions, while expression was absent in highly metastasizing cell lines and pretumor stages. In the 11 metastasis lesions examined, MIA mRNA expression was apparently inversely correlated with pigmentation.

Amino Acid Sequence↗
PubMed2007

Discovery of differentially expressed genes: technical considerations.

Identification and characterization of differentially expressed genes may be an important first step toward the understanding of both normal physiology and disease. A multitude of techniques belonging to two main categories have been developed to identify the differences in gene expression between samples from different biological origin: selection techniques and global techniques. Whereas the selection techniques strive to identify specific differentially expressed genes, the global techniques analyze the total transcriptome or a major part of the RNA population in a defined biological material. By exploiting the known sequences of the adaptors used in suppressive subtraction hybridization technique, a strategy named novel rescue-suppression-subtractive hybridization was developed. It should facilitate the discovery of differentially expressed genes.

Cloning, Molecular↗
PubMedDate not supplied

Characterization of differentially expressed genes in ovarian cancer by cDNA microarrays.

The molecular events leading to the development and progression of ovarian carcinoma are not completely understood. We performed a large-scale survey for the identification of differentially expressed genes between ovarian carcinoma and normal ovarian tissue by using cDNA microarray analysis. We utilized 512 member human novel putative oncogene and tumor suppressor gene cDNA microarrays to study the differences in gene expression between ovarian carcinoma and normal ovarian tissues. Some differentially expressed genes have been further confirmed by immunohistochemical analysis. A total of 39 differentially expressed genes were identified, of which 16 and 23 were specifically expressed in ovarian cancer and normal ovarian tissue, respectively. The comparison of average signal of differentially expressed genes exhibited at least a twofold difference in expression. The differentially expressed genes may be related to the carcinogenesis and progression of the malignant growth. The use of cDNA microarrays allows simultaneous monitor of the expression of many genes, thereby it speeds up the identification of differentially expressed genes. It is essential for further exploration of the mechanisms of the disease.

Adenocarcinoma↗
PubMed2000

Identification of differentially expressed genes in normal and tumor human gastric tissue.

The search for differentially expressed genes in gastric cancer may help define molecular alterations and molecular diagnosis of gastric cancer. Using the differential display PCR technique, we identified 18 genes that are differentially expressed between normal and tumor human gastric tissues. Their expressions were verified with reverse Northern blot analysis and Northern blot analysis. Oxidative phosphorylation-related genes, antizyme inhibitor of ornithine decarboxylase, protein phosphatase-1beta, 35-kDa peroxisomal membrane protein, and cystic fibrosis transmembrane conductance receptor were highly expressed in tumor tissue, whereas pepsinogen A, Na-K ATPase alpha subunit, nerve growth factor receptor, and alpha-tropomyosin were highly expressed in normal tissue. In addition, 3 unknown genes were found to be differentially expressed in paired gastric tissues. These differentially expressed genes may provide significant opportunities for further understanding of gastric carcinogenesis and the molecular diagnosis of gastric cancer.

DNA, Complementary↗
PubMed2002

Vitreous treatment of cultured human RPE cells results in differential expression of 10 new genes.

PURPOSE: To analyze the differential gene expression in cultured human retinal pigment epithelial (RPE) cells after treatment with vitreous. METHODS: Cultured human RPE cells were incubated for 48 hours with 25% human vitreous from donor eyes. Total RNA from treated and untreated cells was extracted. The gene expression was analyzed by differential expression analysis (DEmRNA-PCR). The differentially expressed genes were identified by gene bank searches. Differential expression was verified by a quantitative real-time RT-PCR fluorescent nucleic acid staining system. The in vivo mRNA expression of these genes in RPE cells was shown by gene-specific RT-PCR. RESULTS: Vitreous treatment of human RPE cells resulted in the reduced expression of NFIB2, KE03 (NY-REN-25ag), PIG-B, DKFZp564BC462, LKHA, G3BP, PAM, UEV-1, and MAP1B calibrated to the expression of GAPDH when compared with their expression in untreated cells. The reduced expression after vitreous treatment was quantified by gene-specific quantitative real-time RT-PCR and varied from 0.69 to 0.17 compared with untreated cells. The mRNA expression of UDP-GalNac mRNA remained constant. The mRNA expression of eight of these genes was demonstrated in this study for the first time in human RPE cells. CONCLUSIONS: Vitreous treatment of cultured RPE cells induces the differential expression of a variety of genes with functions in transcription, mediation of signal transduction and inflammation, glycosylation, ubiquitination and protein-protein interaction. Further examination of these genes may locate additional targets for treatment of diseases caused by contact of RPE cells with vitreous, typical in proliferative vitreoretinopathy.

Cells, Cultured↗
PubMed2003

Expression of biomarkers modulating prostate cancer angiogenesis: differential expression of annexin II in prostate carcinomas from India and USA.

BACKGROUND: Prostate cancer (PCa) incidences vary with genetic, geographical and ethnic dietary background of patients while angiogenesis is modulated through exquisite interplay of tumor-stromal interactions of biological macromolecules. We hypothesized that comprehensive analysis of four biomarkers modulating angiogenesis in PCa progression in two diverse populations might explain the variance in the incidence rates. RESULTS: Immunohistochemical analysis of 42 PCa biopsies reveals that though Anx-II expression is lost in both the Indian and American population with Gleason scores (GS) ranging between 6 and 10, up to 25 % of cells in the entire high grade (GS > 8) PD PCa samples from US show intense focal membrane staining for Anx-II unlike similarly graded specimens from India. Consistent with this observation, the prostate cancer cell lines PC-3, DU-145 and MDA PCa 2A, but not LNCaP-R, LNCAP-UR or MDA PCa 2B cell lines, express Anx-II. Transcriptional reactivation of Anx-II gene with Aza-dC could not entirely account for loss of Anx-II protein in primary PCa. Cyclooxygenase-2 (COX-2) was moderately expressed in most of high grade PIN and some MD PCa and surrounding stroma. COX-2 was not expressed in PD PCa (GS approximately 7-10), while adjacent smooth muscles cells stained weakly positive. Decorin expression was observed only in high grade PIN but not in any of the prostate cancers, atrophy or BPH while stromal areas of BPH stained intensively for DCN and decreased with advancing stages of PCa. Versican expression was weak in most of the MD PCa, moderate in all of BPH, moderately focal in PD PC, weak and focal in PIN, atrophy and adjacent stroma. CONCLUSIONS: Expression of pro- and anti-angiogenic modulators changes with stage of PCa but correlates with angiogenic status. Focal membrane staining of Anx-II reappears in high grade PCa specimens only from US indicating differential expression of Anx-II. COX-2 stained stronger in American specimens compared to Indian specimens. The sequential expression of DCN and VCN in progressive stages was similar in specimens from India and USA indicating no population-based differences. The mechanistic and regulatory role of Anx-II in PCa progression warrants further investigation.

Annexin A2↗
PubMed2006

A powerful method for detecting differentially expressed genes from GeneChip arrays that does not require replicates.

BACKGROUND: Studies of differential expression that use Affymetrix GeneChip arrays are often carried out with a limited number of replicates. Reasons for this include financial considerations and limits on the available amount of RNA for sample preparation. In addition, failed hybridizations are not uncommon leading to a further reduction in the number of replicates available for analysis. Most existing methods for studying differential expression rely on the availability of replicates and the demand for alternative methods that require few or no replicates is high. RESULTS: We describe a statistical procedure for performing differential expression analysis without replicates. The procedure relies on a Bayesian integrated approach (BGX) to the analysis of Affymetrix GeneChips. The BGX method estimates a posterior distribution of expression for each gene and condition, from a simultaneous consideration of the available probe intensities representing the gene in a condition. Importantly, posterior distributions of expression are obtained regardless of the number of replicates available. We exploit these posterior distributions to create ranked gene lists that take into account the estimated expression difference as well as its associated uncertainty. We estimate the proportion of non-differentially expressed genes empirically, allowing an informed choice of cut-off for the ranked gene list, adapting an approach proposed by Efron. We assess the performance of the method, and compare it to those of other methods, on publicly available spike-in data sets, as well as in a proper biological setting. CONCLUSION: The method presented is a powerful tool for extracting information on differential expression from GeneChip expression studies with limited or no replicates.

Algorithms↗
PubMed2006

A unified approach for simultaneous gene clustering and differential expression identification.

Although both clustering and identification of differentially expressed genes are equally essential in most microarray studies, the two tasks are often conducted without regard to each other. This is clearly not the most efficient way of extracting information. The main aim of this article is to develop a coherent statistical method that can simultaneously cluster and detect differentially expressed genes. Through information sharing between the two tasks, the proposed approach gives more sensible clustering among genes and is more sensitive in identifying differentially expressed genes. The improvement over existing methods is illustrated in both our simulation results and a case study.

Animals↗
PubMed2005

[A cDNA microarray study of the differential expression of genes in signal transduction pathway during hepatocarcinogenesis in tree shrews].

OBJECTIVES: To study the differential expression of genes in signal transduction pathway (STP) during the hepatocarcinogenesis in tree shrews induced by AFB1 and/or HBV and to elucidate the molecular mechanism of hepatocellular carcinoma (HCC) development. METHODS: Adult tree shrews were divided into three groups: Group A was fed AFB1 only, Group B was infected firstly with HBV then fed AFB1 as in Group A, Group C served as the normal control. Liver biopsies were obtained at the 30th, 60th and 90th week of the experiment or until HCC occurred and the animals were sacrificed. Tree shrew-specific cDNA microarray was applied for detecting the differential expression of corresponding genes in each group at different time points during the experiment, and real time RT PCR was applied to verify the results of the cDNA microarray. RESULTS: Genes of IGF-II, C-rel, and NF-kappaB2 were differentially expressed between para-cancerous tissues and HCC tissues in both group A and group B, and the differential expression of bcl-2, cyclin A and CNTF was only seen in group B. Between the experimental groups A and B and the control group C, there were differential expressions of CNTF and cyclin A in the early 30th week and middle 60th week stage of hepatocarcinogenesis in tree shrews. Real time RT PCR results showed that the expression level of IGF-II and C-Rel in group A and of IGF-II in group B in HCC tissues were significantly lower than that in the adjacent non-cancerous tissues and in the biopsies taken at the 30th and 60th week of the experiment. Nevertheless, there were no significant differences between the para-cancerous tissues and the cancer tissues at the 30th and 60th week. These results were consistent with the cDNA microarray assay. The expression levels of C-Rel and CNTF in group B were not obviously altered in the para-cancerous tissues, HCC and at the 60th week, but they were significantly lower in these tissues than that in the tissues at the 30th week. In group A, the expression levels of CNTF in adjacent liver and HCC tissues were higher than that in para-cancerous lesions, but the difference did not reach a statistically significant level. In group C, the expression level of IGF-II, C-Rel and CNTF at different stages showed no significant differences, which was consistent with the cDNA microarray results. CONCLUSIONS: To apply the tree shrew-specific cDNA microarray to detect the differential expression of genes related to signal transduction pathway during tree shrew hepatocarcinogenesis could be a valuable utility for further comprehending the mechanism of HCC. IGF-II, NF-kappaB2, C-rel, Bcl-2, and cyclin A. CNTF may be involved in the occurrence and progress of HCC in tree shrews.

Animals↗
PubMed2004

Actin expression is induced and three isoforms are differentially expressed during germination in Zea mays.

Previous analysis of actin in a dicotyledonous plant, Phaseolus vulgaris (or common bean), showed very low actin levels in cotyledons but they were concentrated in the embryo axis. Upon imbibition, actin expression increased 5-fold and a maximum of four actin isoforms were observed, two of them transient and two major ones were steadily expressed. In this work, analysis of the actin expression in a monocotyledonous plant, Zea mays (or maize), and over a longer period of germination/growth, showed that striking similarities exist. Actin is present in all the seed components, but it is mainly concentrated in the embryo axis. The expression of maize actin was induced during post-imbibition at both the protein and mRNA levels. Sharp increases in actin appeared from 24-48 h and again from 72-96 h. A more modest and steady actin mRNA increase in expression was observed; however, it did not appear as dramatic as in the case of common bean due to the presence of readily detectable amounts of message in the dry maize seed. The isoform distribution in the dry seed showed a pattern of at least three isovariants of pIs approximately 5.0, 5.1, and 5.2, which were differentially expressed at the various post-imbibition times analysed. Two of the actin isoforms at 48 h post-imbibition cross-reacted with a phosphotyrosine-specific antibody and they are the product of three expressed genes as shown by in vitro translation assays. These data indicate that maize actin protein and mRNA expression is induced upon the trigger of germination, and the isoform expression kinetics and patterns resemble those from bean, suggesting that, in both species, actin expression at these early germination/growth stages is a highly regulated event.

Actins↗
PubMed2004

Microarray analysis identified differentially expressed genes in keratocytes from keratoconus patients.

PURPOSE: To identify differentially expressed genes in human keratoconus keratocyte by cDNA microarray. METHODS: Normal and keratoconic cornea were cultured for keratocytes. RNA was extracted. cDNA probe labeled with fluorescence dye was made from Poly A+ RNA, hybridized with microarray slide, containing 164 human apoptosis genes. Signal intensity was measured. Expression ratio between keratoconus and normal was determined using ImaGene Ver.3.0. Identified genes were further evaluated by RT-PCR and real-time PCR. RESULTS: Five over-expressed and four under-expressed genes were identified. Of these, differential expression of tumor necrosis factor alpha-induced protein 6 (TNFAIP6), human insulin-like growth factor binding protein 5 (IGFBP5), and IGFBP3 were verified and confirmed by RT-PCR. Real-time PCR showed TNFAIP6 increased by 3.3 folds, while IGFBP5, IGFBP3 decreased by 14 and 11 folds respectively. CONCLUSIONS: The identified genes could be important and deserve further investigation. Significant differential expression of TNFAIP6, IGFBP5, and IGFBP3 may indicate an important role of these genes in the mechanism underlying stromal thinning.

Adult↗
PubMed2005

Construction of a hepatic stellate cells subtracted cDNA library of differentially expressed genes in normal mice and mice with Schistosomiasis japonica.

To construct a hepatic stellate cells (HSCs) subtracted cDNA library to find differentially expressed genes in normal mice and mice infected with Schistosoma japonicum (S. japonicum). Suppression subtractive hybridization (SSH) was used. The cDNA fragments of normal mouse were compared to those of schistosoma-infected mice to find differentially expressed genes. Then differentially expressed cDNA fragments were directly inserted into T/A cloning vector to set up the subtractive library. Amplification of the library was carried out with transformation of DH5alpha. The amplified library contained more than 400 positive bacterial clone, which were then hybridized with forward and backward subtracted probes for differential screening. One hundred positive bacterial clones were randomly selected for sequencing and BLAST analysis. Finally, virtual Northern Blot confirmed such differential expression. The subtracted cDNA library of differentially expressed genes of HSCs was constructed successfully, the library is efficient and lays foundation for screening and cloning new and specific genes of schistosomiasis.

Animals↗
PubMed1999

Identification and isolation of differentially expressed genes from very small tissue samples.

Identification of differentially expressed genes from tissue samples weighing only a few milligrams has remained a major challenge. Here, we describe a novel and simple strategy that uses standard molecular biology equipment and commercially available kits. The approach combines isolation of total RNA by silica-gel binding, reverse transcription using anchored modified, 5' end enhancers oligonucleotides, exponential amplification of the single-stranded cDNA and hybridization to high-density cDNA filter arrays. The method was tested by comparing genes expressed on freshly isolated human trabecular meshwork tissue with those expressed in corresponding primary cells at third passage. Validation was achieved by using two biological properties: (i) hybridization, to identify the differentially expressed genes, and (ii) PCR amplification, to confirm their distinct expression. The strategy presented allows the identification of differentially expressed genes and/or uncharacterized expressed sequence tags (ESTs) in very small tissue samples, including those from clinical specimens.

Biotechnology↗
PubMed1997

Genes differentially expressed with malignant transformation and metastatic tumor progression of murine squamous cell carcinoma.

Molecular changes occurring with tumor formation and metastasis need to be identified in order to define novel markers and targets for chemoprevention and therapy. Cell lines from a multistage model of murine squamous cell carcinoma were analyzed for differences in gene expression using mRNA differential display. mRNA was isolated from primary keratinocytes, an in vitro transformed keratinocyte line (Pam 212), and three metastatic cell lines derived from Pam 212 following tumor progression in vivo. cDNA was synthesized by reverse transcription and amplified by PCR using 72 primer combinations to screen and compare approximately 3,600 sequences. Five cDNAs with a differential expression pattern confirmed by Northern blot analysis were cloned and sequenced, revealing homology with known genes. The gene encoding tropomyosin alpha was preferentially expressed in primary keratinocytes; genes for tyrosine kinase Yes-associated protein (YAP65) and ribosomal protein L18a were preferentially expressed in transformed and metastatic tumor cell lines; and genes for the Gro-alpha family cytokine KC and antigen Sp17 exhibited increased expression in the three metastatic cell lines. The structure and function of the genes identified suggest that they may possibly be linked to cell shape and motility, signal transduction, protein synthesis, growth, granulocyte chemotaxis, and angiogenesis. This study demonstrates the ability of mRNA differential display to detect altered gene expression in this tumor progression model of murine squamous cell carcinoma, and the potential usefulness of this approach for identification of candidate genes as chemoprevention markers and targets.

Amino Acid Sequence↗
PubMed2004

An empirical bayes adjustment to increase the sensitivity of detecting differentially expressed genes in microarray experiments.

MOTIVATION: Detection of differentially expressed genes is one of the major goals of microarray experiments. Pairwise comparison for each gene is not appropriate without controlling the overall (experimentwise) type 1 error rate. Dudoit et al. have advocated use of permutation-based step-down P-value adjustments to correct the observed significance levels for the individual (i.e. for each gene) two sample t-tests. RESULTS: In this paper, we consider an ANOVA formulation of the gene expression levels corresponding to multiple tissue types. We provide resampling-based step-down adjustments to correct the observed significance levels for the individual ANOVA t-tests for each gene and for each pair of tissue type comparisons. More importantly, we introduce a novel empirical Bayes adjustment to the t-test statistics that can be incorporated into the step-down procedure. Using simulated data, we show that the empirical Bayes adjustment improved the sensitivity of detecting differentially expressed genes up to 16%, while maintaining a high level of specificity. This adjustment also reduces the false non-discovery rate to some degree at the cost of a modest increase in the false discovery rate. We illustrate our approach using a human colon cancer dataset consisting of oligonucleotide arrays of normal, adenoma and carcinoma cells. The number of genes with differential expression level declared statistically significant was about 50 when comparing normal to adenoma cells and about five when comparing adenoma to carcinoma cells. This list includes genes previously known to be associated with colon cancer as well as some novel genes. AVAILABILITY: R code for the empirical Bayes adjustment and step-down P-value calculation via resampling are available from the supplementary web-site. SUPPLEMENTARY INFORMATION: http://www.mathstat.gsu.edu/~matsnd/EB/supp.htm

Algorithms↗
PubMed1985

Clustered homeo boxes are differentially expressed during murine development.

A murine homeo box (m6-12) known to be expressed during differentiation of embryonal carcinoma cells lies within a cluster of homeo boxes located in 30 kilobase pairs of genomic DNA. We have established the organization of the boxes within this complex, as well as the nucleotide sequence of a second box, m5-4. Similar to the m6-12 box, expression of novel m5-4 transcripts is induced upon differentiation of embryonal carcinoma cells. Transcripts of genes containing m6-12 were found in embryonic tissue during almost all stages of prenatal development studied, whereas expression of m5-4 was detected only in 12 day embryonic tissue. Finally, we have described the differential expression of these homeo-box-containing regions in various adult tissues.

Amino Acid Sequence↗
PubMed2005

Correlation between gene expression levels and limitations of the empirical bayes methodology for finding differentially expressed genes.

Stochastic dependence between gene expression levels in microarray data is of critical importance for the methods of statistical inference that resort to pooling test statistics across genes. The empirical Bayes methodology in the nonparametric and parametric formulations, as well as closely related methods employing a two-component mixture model, represent typical examples. It is frequently assumed that dependence between gene expressions (or associated test statistics) is sufficiently weak to justify the application of such methods for selecting differentially expressed genes. By applying resampling techniques to simulated and real biological data sets, we have studied a potential impact of the correlation between gene expression levels on the statistical inference based on the empirical Bayes methodology. We report evidence from these analyses that this impact may be quite strong, leading to a high variance of the number of differentially expressed genes. This study also pinpoints specific components of the empirical Bayes method where the reported effect manifests itself.

Journal Article↗
PubMed2002

Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis.

BACKGROUND: Oligonucleotide microarrays measure the relative transcript abundance of thousands of mRNAs in parallel. A large number of procedures for normalization and detection of differentially expressed genes have been proposed. However, the relative impact of these methods on the detection of differentially expressed genes remains to be determined. RESULTS: We have employed four different normalization methods and all possible combinations with three different statistical algorithms for detection of differentially expressed genes on a prototype dataset. The number of genes detected as differentially expressed differs by a factor of about three. Analysis of lists of genes detected as differentially expressed, and rank correlation coefficients for probability of differential expression shows that a high concordance between different methods can only be achieved by using the same normalization procedure. CONCLUSIONS: Normalization has a profound influence of detection of differentially expressed genes. This influence is higher than that of three subsequent statistical analysis procedures examined. Algorithms incorporating more array-derived information than gene-expression values alone are urgently needed.

Animals↗