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PubMed2004

A cluster of differentially expressed signal transduction genes identified by microarray analysis in a rat genetic model of alcoholism.

Analyzing gene expression patterns in genetic models of alcoholism may uncover previously unknown susceptibility genes, and point to novel targets for drug development. Here, we compared expression profiles in alcohol-preferring AA rats with the alcohol-avoiding counterpart ANA line, and unselected Wistar rats. Cingulate cortex, Nc. accumbens, amygdala and hippocampus of each line were analyzed using the Afymetrix RN U34 arrays and dChip 1.1 software. Analysis of line-specific expression revealed 48 differentially expressed genes between AA and ANA rats. Elevated hippocampal neuropeptide Y (NPY) was found in ANA rats in agreement with previous studies. A cluster of MAP-kinases indicating altered signal transduction was upregulated within the Nc. Accumbens of the AA line, and is of particular functional interest. Within the amygdala, a more loosely inter-related cluster of cytoskeleton-associated genes may point to structural abnormalities. The observed dysregulations may contribute to the alcohol-preferring phenotype.

Alcoholism↗
PubMed1995

Identification of novel differentially expressed hepatic genes in cholesterol-fed rabbits by a non-targeted gene approach.

Several key genes involved in cholesterol metabolism are known to be directly regulated by cholesterol. The possible indirect effect, however, of increased levels of cellular cholesterol on gene expression and its possible role in cholesterol metabolism and atherosclerosis has not been thoroughly explored. In order to determine the overall effect of cholesterol on gene expression, we isolated differentially expressed genes from a PCR-based subtraction library prepared from the liver of chow-fed and cholesterol-fed rabbits. A total of nine upregulated and four down-regulated cDNA fragments were isolated. As determined by Northern blot analysis, the expression of the isolated cDNAs began to change as early as the first week on the cholesterol-rich diet or as late as 4 weeks, which corresponded with hepatic cholesterol accumulation. Three of the cDNAs were identified by DNA sequence homology, whereas the remaining cDNAs had no significant homology match. CYP1A1, a cytochrome P450 isoenzyme, was found to be down-regulated in hepatocytes by cholesterol feeding. Osteopontin and Mac-2, which are produced by macrophages, were found to be up-regulated in Kupffer cells by cholesterol feeding. Overall these results demonstrate the usefulness of the subtraction library approach for identifying new candidate genes for exploring the pathogenesis of atherosclerosis.

Animals↗
PubMed2005

[Construction and preliminary screening of a forward-subtracted cDNA library for differentially expressed genes in rat liver of prothrombotic state].

OBJECTIVE: To construct and preliminarily screen the forward-subtracted cDNA library of differentially expressed genes in rat liver of prothrombotic state (PTS). METHODS: The forward-subtracted cDNA library for differentially expressed genes in rat liver of PTS was constructed by suppression subtractive hybridization using cDNAs synthesized from mRNA of PTS rat as Tester and cDNAs from mRNA of control rat as Driver. The products from the last PCR amplification of suppression subtractive hybridization were inserted into a T/A plasmid vectors to transform the Escherichia coli JM109 cells. To produce the library, the transformed cells were incubated at 37 C overnight on a LB agar plate containing ampicillin (50 microg/ml), IPTG and X-gal. Forward-subtracted cDNA probes and reverse-subtracted cDNA probes were prepared by nested PCR amplification, which were labeled with HRP. Positive clones were selected by differential screening in which forward-subtracted and reverse-subtracted cDNA probes were separately hybridized with the membranes slot-blotted by plasmid DNAs amplified and isolated from the library. Inserts in the positive clones were submitted to DNA sequencing. Nucleic acid sequence homology search was performed against the GenBank DNA database (non-redundant, and non-mouse and non-human EST entries) using the Standard nucleotide-nucleotide BLAST [blastn] program via a network connection to the National Center for Biotechnology information. RESULTS: The forward-subtracted cDNA library for differentially expressed genes in rat liver of PTS was successfully constructed. Two differentially expressed cDNA fragments were found after preliminary screening. CONCLUSION: The forward-subtracted cDNA library for differentially expressed genes in rat liver of PTS was successfully constructed in the present study.

Animals↗
PubMed2004

Linear models and empirical bayes methods for assessing differential expression in microarray experiments.

The problem of identifying differentially expressed genes in designed microarray experiments is considered. Lonnstedt and Speed (2002) derived an expression for the posterior odds of differential expression in a replicated two-color experiment using a simple hierarchical parametric model. The purpose of this paper is to develop the hierarchical model of Lonnstedt and Speed (2002) into a practical approach for general microarray experiments with arbitrary numbers of treatments and RNA samples. The model is reset in the context of general linear models with arbitrary coefficients and contrasts of interest. The approach applies equally well to both single channel and two color microarray experiments. Consistent, closed form estimators are derived for the hyperparameters in the model. The estimators proposed have robust behavior even for small numbers of arrays and allow for incomplete data arising from spot filtering or spot quality weights. The posterior odds statistic is reformulated in terms of a moderated t-statistic in which posterior residual standard deviations are used in place of ordinary standard deviations. The empirical Bayes approach is equivalent to shrinkage of the estimated sample variances towards a pooled estimate, resulting in far more stable inference when the number of arrays is small. The use of moderated t-statistics has the advantage over the posterior odds that the number of hyperparameters which need to estimated is reduced; in particular, knowledge of the non-null prior for the fold changes are not required. The moderated t-statistic is shown to follow a t-distribution with augmented degrees of freedom. The moderated t inferential approach extends to accommodate tests of composite null hypotheses through the use of moderated F-statistics. The performance of the methods is demonstrated in a simulation study. Results are presented for two publicly available data sets.

Journal Article↗
PubMed2002

[Isolation and identification of cDNA sequence differentially expressed in human lung carcinoma].

BACKGROUND & OBJECTIVE: The molecular mechanism of the pathogenesis of lung carcinoma is unclear; because key genes related to lung carcinoma have not been identified. This study was designed to isolate and identify differentially expressed cDNA sequences in human lung carcinoma for cloning lung carcinoma-related genes. METHOD: Using mRNA differential display method combined with cloning and reserve Northern dot blot and sequencing and RT-PCR, differentially expressed cDNA sequences were isolated between two lung cancer cell lines, two adult lung carcinoma tissue and paired normal tissue of trachea epithelia. RESULT: Sixteen differentially expressed cDNA fragments were isolated, subsequent cloning of sixteen differentially expressed cDNA fragments were confirmed by reverse Northern dot blot and sequencing and BLAST analysis. Two of these were shown to be novel gene sequences that had not been reported. Eight of the remaining cDNA sequences homologize to known genes; additionally two differentially expressed cDNA sequences were confirmed by RT-PCR. CONCLUSION: Using mRNA differentially display, The authors had successfully isolated ten differentially expressed cDNA sequences from human lung carcinoma, these cDNA sequences might be involved in the pathogenesis of lung carcinoma.

Blotting, Northern↗
PubMed2002

[Differentially expressed gene in nasopharyngeal carcinoma cell lines with various metastatic potentialities].

OBJECTIVE: To investigate gene expression profile in nasopharyngeaL carcinoma (NPC) cell lines with different metastatic potentialities, in order to identify new candidate genes related to the development, progress and metastasis of NPC. METHODS: The mRNA expressions of high metastatic NPC cell line 5-8F, tumorigenic but nonmetastatic NPC cell line 6-10B and non-tumorigenic NPC cell line 13-9B (3 sublines of SUNE-1) were investigated by cDNA microarray containing 14 000 cDNA clones. The alterations in gene expression levels were confirmed by reverse-transcription PCR. RESULTS: There were 82 differentially expressed genes comparing 5-8F and 13-9B; 38 differentially expressed genes comparing 6-10B and 13-9B; 54 comparing 5-8F and 6-10B. There were 12 common differentially expressed genes comparing 6-10B, 5-8F and 13-9B; 14 common differentially expressed genes comparing 5-8F and 13-9B, 6-10B. The expressions of the above genes were involved in metabolism, transcription, differentiation, apoptosis and signal transduction. CONCLUSION: The gene expression profile in nasopharyngeal carcinoma cell lines is an important index in the search of new candidate genes related to NPC.

Cell Line↗
PubMed2006

The impact of sample imbalance on identifying differentially expressed genes.

BACKGROUND: Recently several statistical methods have been proposed to identify genes with differential expression between two conditions. However, very few studies consider the problem of sample imbalance and there is no study to investigate the impact of sample imbalance on identifying differential expression genes. In addition, it is not clear which method is more suitable for the unbalanced data. RESULTS: Based on random sampling, two evaluation models are proposed to investigate the impact of sample imbalance on identifying differential expression genes. Using the proposed evaluation models, the performances of six famous methods are compared on the unbalanced data. The experimental results indicate that the sample imbalance has a great influence on selecting differential expression genes. Furthermore, different methods have very different performances on the unbalanced data. Among the six methods, the welch t-test appears to perform best when the size of samples in the large variance group is larger than that in the small one, while the Regularized t-test and SAM outperform others on the unbalanced data in other cases. CONCLUSION: Two proposed evaluation models are effective and sample imbalance should be taken into account in microarray experiment design and gene expression data analysis. The results and two proposed evaluation models can provide some help in selecting suitable method to process the unbalanced data.

Algorithms↗
PubMed1998

[Primary study of differentially expressed cDNA sequences in cell line HNE1 of human nasopharyngeal carcinoma by cDNA representational difference analysis].

OBJECTIVE: To search differentially expressed sequences correlated with pathogenesis of human nasopharyngeal carcinoma (NPC), including the candidates of tumor suppressor genes. METHODS: cDNA representational difference analysis (RDA) was performed to isolate differentially expressed sequences between cDNA from normal human primary cultures of nasopharyngeal epithelial cells and cDNA from NPC cell line HNE1. The sources of differentially expressed products were proved by Southern blot and Northern blot. The fragments were cloned with pGEM-T easy kit and sequenced by the chain termination reaction. RESULTS: Four differentially expressed cDNA fragments were isolated in the fourth subtractive hybridization using cDNA from normal human primary cultures of nasopharyngeal epithelial cells as tester amplicon and cDNA from NPC cell line HNE1 as driver amplicon by cDNA RDA. These differential cDNA fragments revealed that they really came from the tester amplicon and were not expressed or down-regulated in the NPC HNE1 cells. Of these obtained clones, some are the fragments of the human known genes including house-keeping genes, the others are novel genes. CONCLUSION: NPC involves alteration of multiple genes. Some of known genes matched with the differentially expressed sequences have an effective suppressive ability on the carcinoma.

Base Sequence↗
PubMed2004

Identification of genes differentially expressed in human hepatocellular carcinoma by a modified suppression subtractive hybridization method.

To identify differentially expressed genes in human HCC in China, we applied a modified SSH method for cDNA subtraction. Such modification has made the method more effective for subtraction. We have obtained 36 and 24 differentially expressed cDNA fragments after modified SSH from 4 paired samples of human HCC and non-HCC tissues, respectively. Reverse Northern blotting analysis was performed to further identify the genes differentially expressed in the HCC and non-HCC tissue samples. There were 25 genes really overexpressed in HCC, and their corresponding encoding molecules may reflect the events of cell accelerated metabolism, proliferation, angiogenesis, anti-apoptosis, tumorigenesis (TLH107, TFH9) and the potential for metastasis. Of the 25 genes overexpressed in HCC, 5 were novel and their full-length cDNAs were cloned. These 5 novel genes are functionally associated with the occurrence and development of HCC according to the Database analysis. In the paired non-HCC tissues, there were 15 genes lowly or not expressed in HCC, and their encoding proteins function as tumor suppressors (TFA3, TFA11), acute-phase reactive proteins, and the blood plasma proteins that are mainly or exclusively synthesized in the liver. The distinct profiles of the differentially expressed genes in HCC and the paired non-HCC tissues have partially reflected the genetic alterations during HCC tumorigenesis. The novel HCC-specific gene TLH6 and the CT antigen encoding gene TLH107 may have diagnostic and therapeutic potentials in HCC and/or other solid cancers.

Acute-Phase Proteins↗
PubMed2006

[Construction of subtracted cDNA library by suppression subtractive hybridization for differentially expressed genes in eosinophils from asthma patients].

OBJECTIVE: To construct a subtracted cDNA library of differentially expressed genes in eosinophils from asthma patients. METHODS: Suppression subtractive hybridization (SSH) was used to isolate the cDNA fragments of differentially expressed genes in the eosinophils of asthma patients before and after treatment. The cDNA fragments were directly inserted into T/A cloning vector to establish the subtractive library, followed by amplification of the library through E. coli transformation with calcium chloride and screening of blue and white clones of the transformants. One hundred positive bacterial clones were randomly picked and identified by colony PCR. RESULTS: The amplified library contained more than 3,000 positive bacterial clones. Analysis of the randomly selected 100 white clones by PCR showed that 90% of the clones contained 100-500 bp inserts, which might be the cDNA fragments of differentially expressed genes in eosinophils of asthma patients before treatment. CONCLUSION: A subtracted cDNA library of differentially expressed genes in the eosinophils of asthma patients before and after treatment is constructed successfully by SSH and T/A cloning techniques, which lays a solid foundation for screening and cloning new specific differentially.expressed genes in the eosinophils of asthma patients.

Asthma↗
PubMed1993

Protein kinase C beta expression in melanoma cells and melanocytes: differential expression correlates with biological responses to 12-O-tetradecanoylphorbol 13-acetate.

Normal human melanocytes require 12-O-tetradecanoylphorbol 13-acetate (TPA) for prolonged growth in vitro. In contrast, the growth of human malignant melanoma cells is often inhibited by TPA. In this study, we have confirmed and extended these observations. Since protein kinase C (PKC) is an important mediator of the effects of TPA, we have investigated the nature of this differential growth response by examining PKC expression and activity in primary cultures of human neonatal melanocytes and metastatic melanoma cell strains. PKC, when measured by immunoreactivity or a functional assay, was found to be more abundant in melanoma cells than in melanocytes. When specific isotypes were examined by Northern analysis, PKC-alpha and -epsilon were expressed in both melanocytes and melanoma. PKC-beta was expressed in melanocytes, but was undetectable by Northern analysis in 10 out of 11 melanoma cell strains. Southern analysis revealed that no gross deletions or rearrangements of the PKC-beta gene had occurred. These data suggest that down-regulation of the PKC-beta gene occurs frequently during the process of transformation of melanocytes. Furthermore, differential expression of PKC isotypes may explain the different effects of TPA on melanocyte and melanoma cell growth.

Blotting, Northern↗
PubMed2003

[Differentially expressed genes in immunosuppressive and healthy mice after intranasal inoculation of Aspergillus fumigatus].

OBJECTIVE: To screen out the differential expression genes between the immune suppressive host and healthy host after intranasal inoculation of Aspergillus fumigatus (A fumigatus). METHODS: Six immune suppressive mice and 6 healthy mice were inoculated with A, fumigatus intranasally. Three days after the inoculation the mice were killed and autopsied. The total RNA of the lungs was isolated. Gene chip technology was used to examine the differentially expressed genes. RESULTS: 66 differentially expressed genes were screened out of the 4098 genes. In the experimental group the genes encoding CD22, CD53, and 24p3 and the genes related to engulfment and digestion of macrophage or monocytes were up-regulated. The genes encoding surfactant associated protein C, immunoglobulin lambda chain and the genes related to pulmonary metabolism were down-regulated. The genes encoding IL18, CD8, and CD28 were not differentially expressed. CONCLUSION: The up-regulation of CD22 gene may be one of the ways by which the host defense is inhibited. CD53 may take part in the regulation of engulfment of phagocytes. 24p3 protein, an acute stress protein, protects the host from excessive inflammatory response.

Acute-Phase Proteins↗
PubMed2006

Detection of differentially expressed glycogenes in trabecular meshwork of eyes with primary open-angle glaucoma.

PURPOSE: To identify differentially expressed glycogenes in trabecular meshwork (TM) of eyes with primary open-angle glaucoma (POAG). METHODS: Total RNA was isolated from TM of cadaveric eyes derived from donors with diagnosed glaucomas of different etiologies and from normal control subjects. RNA was amplified and hybridized to the GLYCOv2 oligonucleotide microarray that contains probes for carbohydrate-binding proteins, glycosyltransferases, and other genes involved in the regulation of glycosylation. Statistical analysis was used to identify differentially expressed genes between normal and POAG samples. RESULTS: This study revealed that POAG TM and normal TM have distinct gene expression profiles. Of the 2001 genes on the array, 19 genes showed differential expression of greater than 1.4-fold in POAG. Mimecan and activinA, which have been shown to be upregulated in models of glaucoma, were both found to be elevated in POAG TM. Many genes were identified for the first time to be differentially regulated in POAG. Among the upregulated genes were: (1) cell adhesion molecules including platelet endothelial cell adhesion molecule-1 and P-selectin, both of which are targets of NFkappaB, which has been shown to be activated in glaucomatous TM; (2) lumican, a core protein of keratan sulfate proteoglycans; and (3) the receptor for IL6, a cytokine that has been shown to be upregulated in TM in response to elevated intraocular pressure. Among the downregulated genes were chondroitin-4-O-sulfotransferase involved in the synthesis of chondroitin sulfate chains and the receptor for PDGFbeta, a growth factor that has been shown to stimulate both TM cell proliferation and phagocytic activity. Results for several genes were confirmed by RTq-PCR. CONCLUSIONS: Microarray technology was used to show, for the first time, that POAG TM has a distinct glycogene expression profile. Differentially expressed glycogenes identified in this study have not been previously investigated for their role in the pathogenesis of POAG and thus are novel factors for further study of the mechanism of the disease and for their possible use as diagnostic markers.

Aged↗
PubMed2000

Differentially expressed genes in asbestos-induced tumorigenic human bronchial epithelial cells: implication for mechanism.

Although exposure to asbestos fibers is associated with the development of lung cancer, the underlying mechanism(s) remains unclear. Using human papillomavirus-immortalized human bronchial epithelial (BEP2D) cells, we previously showed that UICC chrysotiles can malignantly transform these cells in a stepwise fashion before they become tumorigenic in nude mice. In the present study we used cDNA expression arrays to screen differentially expressed genes among the tumorigenic cells. A total of 15 genes were identified, 11 of which were further confirmed by northern blot. Expression levels of these genes were then determined among transformed BEP2D cells at different stages of the neoplastic process, including non-tumorigenic cells that were resistant to serum-induced terminal differentiation, early and late passage transformed BEP2D cells, five representative tumor cell lines and fused tumorigenic-control cell lines which were no longer tumorigenic. A consistent 2- to 3-fold down-regulation of the DCC (deleted in colon cancer), Ku70 and heat shock protein 27 genes were detected in all the independently generated tumor cell lines while expression levels in early transformants as well as in the fusion cell lines remained normal. In contrast, all the tumor cell lines examined demonstrated 2- to 4-fold overexpression of the insulin receptor and its signal transduction genes. Differential expression of these genes was completely restored in the fusion cell lines examined. No alteration in c-jun or EGF receptor expression was found in any of the cell lines. Our data suggest that activation of the insulin receptor pathway and inactivation of DCC and Ku70 may cooperate in malignant transformation of BEP2D cells induced by asbestos.

Animals↗
PubMed2005

Detecting differentially expressed genes by relative entropy.

DNA microarray experiments have generated large amount of gene expression measurements across different conditions. One crucial step in the analysis of these data is to detect differentially expressed genes. Some parametric methods, including the two-sample t-test (T-test) and variations of it, have been used. Alternatively, a class of non-parametric algorithms, such as the Wilcoxon rank sum test (WRST), significance analysis of microarrays (SAM) of Tusher et al. (2001), the empirical Bayesian (EB) method of Efron et al. (2001), etc., have been proposed. Most available popular methods are based on t-statistic. Due to the quality of the statistic that they used to describe the difference between groups of data, there are situations when these methods are inefficient, especially when the data follows multi-modal distributions. For example, some genes may display different expression patterns in the same cell type, say, tumor or normal, to form some subtypes. Most available methods are likely to miss these genes. We developed a new non-parametric method for selecting differentially expressed genes by relative entropy, called SDEGRE, to detect differentially expressed genes by combining relative entropy and kernel density estimation, which can detect all types of differences between two groups of samples. The significance of whether a gene is differentially expressed or not can be estimated by resampling-based permutations. We illustrate our method on two data sets from Golub et al. (1999) and Alon et al. (1999). Comparing the results with those of the T-test, the WRST and the SAM, we identified novel differentially expressed genes which are of biological significance through previous biological studies while they were not detected by the other three methods. The results also show that the genes selected by SDEGRE have a better capability to distinguish the two cell types.

Acute Disease↗
PubMed2003

Identification of differentially expressed genes in isogenic highly metastatic and poorly metastatic cell lines of R3230AC rat mammary adenocarcinoma.

Tumour metastasis occurs as a result of a cascade of events including alterations in the expression of various genes. The identification of such genes is essential to understanding formation of metastasis. In a previous study, highly metastatic (LN4.D6) and poorly metastatic (CAb.D5) cell lines were obtained from the rat mammary adenocarcinoma cell line R3230AC. Subtractive hybridization was used to identify differentially expressed genes between these two cell lines. We identified eight cDNA clones in CAb.D5 and six cDNA clones in LN4.D6 that were differentially expressed. One of the cDNA clones in each cell line had no homology with known sequences. Expression patterns of these differentially expressed genes were examined in a pair of rat mammary and prostate adenocarcinoma cell lines. Compared with cell lines examined, cDNA FF-10 was only expressed in CAb.D5; however, cDNA RB-8, RE-1, RF-5 were only expressed in the highly metastatic LN4.D6. No correlation was observed between expression patterns of the differentially expressed genes and metastatic potential of these cells. However, differential expression of genes, especially cytokeratins (CK8 and CK5) and collagens (III and IV) between highly metastatic and low metastatic rat mammary adenocarcinoma cell lines might initiate further investigation of these genes in metastatic process.

Adenocarcinoma↗
PubMed2006

On the identification of differentially expressed genes: improving the generalized F-statistics for Affymetrix microarray gene expression data.

It has been shown that the generalized F-statistics can give satisfactory performances in identifying differentially expressed genes with microarray data. However, for some complex diseases, it is still possible to identify a high proportion of false positives because of the modest differential expressions of disease related genes and the systematic noises of microarrays. The main purpose of this study is to develop statistical methods for Affymetrix microarray gene expression data so that the impact on false positives from non-expressed genes can be reduced. I proposed two novel generalized F-statistics for identifying differentially expressed genes and a novel approach for estimating adjusting factors. The proposed statistical methods systematically combine filtering of non-expressed genes and identification of differentially expressed genes. For comparison, the discussed statistical methods were applied to an experimental data set for a type 2 diabetes study. In both two- and three-sample analyses, the proposed statistics showed improvement on the control of false positives.

Computer Simulation↗
PubMed2004

Expression profiling using random genomic DNA microarrays identifies differentially expressed genes associated with three major developmental stages of the protozoan parasite Leishmania major.

To complete its life cycle, protozoan parasites of the genus Leishmania undergo at least three major developmental transitions. However, previous efforts to identify genes showing stage regulated changes in transcript abundance have yielded relatively few. Here we used expression profiling to assess changes in transcript abundance in three stages: replicating promastigotes and infective non-replicating metacyclics, which occur in the sand fly vector, and in the amastigote stage residing with macrophage phagolysosomes in mammals. Microarrays were developed containing 11,484 PCR products that included a number of known genes and 10,464 random 1 kb genomic DNA fragments. Arrays were hybridized in triplicate and genes showing two-fold or greater changes in 2/3 experiments were scored as differentially expressed. Remarkably, only about one percent of the DNAs expression varied by this criteria, in either stage comparison. Northern blot analysis confirmed the predicted change in mRNA abundance for most of these (68%). This set of genes included most of those previously identified in the literature as differentially regulated as well as a number of novel genes. Notably, Leishmania maxicircle transcripts showed strong up-regulation in metacyclic and amastigote parasites, probably associated with changes in parasite energy metabolism. However, current data suggest that expression profiling using shotgun DNA libraries significantly underestimates the extent of regulated transcripts.

Animals↗