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Results for “differential gene expression”

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PubMed2002

Assessment of differential gene expression in human peripheral nerve injury.

BACKGROUND: Microarray technology is a powerful methodology for identifying differentially expressed genes. However, when thousands of genes in a microarray data set are evaluated simultaneously by fold changes and significance tests, the probability of detecting false positives rises sharply. In this first microarray study of brachial plexus injury, we applied and compared the performance of two recently proposed algorithms for tackling this multiple testing problem, Significance Analysis of Microarrays (SAM) and Westfall and Young step down adjusted p values, as well as t-statistics and Welch statistics, in specifying differential gene expression under different biological states. RESULTS: Using SAM based on t statistics, we identified 73 significant genes, which fall into different functional categories, such as cytokines / neurotrophin, myelin function and signal transduction. Interestingly, all but one gene were down-regulated in the patients. Using Welch statistics in conjunction with SAM, we identified an additional set of up-regulated genes, several of which are engaged in transcription and translation regulation. In contrast, the Westfall and Young algorithm identified only one gene using a conventional significance level of 0.05. CONCLUSION: In coping with multiple testing problems, Family-wise type I error rate (FWER) and false discovery rate (FDR) are different expressions of Type I error rates. The Westfall and Young algorithm controls FWER. In the context of this microarray study, it is, seemingly, too conservative. In contrast, SAM, by controlling FDR, provides a promising alternative. In this instance, genes selected by SAM were shown to be biologically meaningful.

Journal Article↗

PubMed2004

Mycobacterium bovis BCG cell wall-specific differentially expressed genes identified by differential display and cDNA subtraction in human macrophages.

We have analyzed the gene expression profile of monocytes in response to a highly purified cell wall fraction of Mycobacterium bovis BCG, a clinically approved adjuvant known as BCG cell wall skeleton (BCG-CWS). It is composed of mycolic acid, arabinogalactan, and peptidoglycan and confers Toll-like receptor 2 (TLR2)- and TLR4-dependent signaling that induces monocytes to differentiate into antigen-presenting cells (APCs). Here we report differential gene expression analysis with BCG-CWS-stimulated versus nonstimulated monocytes. BCG-CWS exerted massive induction of genes regulated by TLR signaling. Marked gene regulatory characteristics in BCG-CWS-stimulated cells compared to lipopolysaccharide (LPS)-stimulated cells follow. (i) Spliced mRNAs encoding soluble forms of TREM-1 and TREM-2 (recently discovered inflammatory-signal-amplifying receptors) were regulated by BCG-CWS, resulting in their differential expression. (ii) The genes for zinc-iron transporter protein (ZIP)-like family proteins HKE-1 and LIV-1 were induced exclusively by BCG-CWS. (iii) Interleukin-23 (IL-23), rather than IL-12p70, was induced by BCG-CWS, while interferon-inducible genes were induced only by LPS. By Northern and reverse transcription-PCR analyses, we confirmed the differential expression of more than 30 BCG-CWS regulatory genes, and their expression was compared with that of LPS and other known TLR ligands. A battery of genes responded rapidly and for a short time to LPS but for a long time to BCG-CWS. Structural analysis of the identified novel or hypothetical proteins revealed that some are potential candidates as signaling mediators or transcriptional regulators. Hence, BCG-CWS may profoundly modulate APC responses in a way distinct from that of LPS, leading to possible advantages for its adjuvant-active therapeutic potential.

Adjuvants, Immunologic↗

PubMed2003

Mesothelial differentiation as reflected by differential gene expression.

Human mesothelial cells obtained from benign effusions retain their proliferative capacity and grow uniformly either with a fibroblastic or epithelioid morphology in vitro. These cultures therefore provide a model for the process of mesothelial differentiation in vivo. To study this differentiation, we isolated differentially expressed genes obtained by suppression subtractive hybridization. Of the nine genes found to be overexpressed in fibroblastic mesothelial cells, three are matrix-associated (integrin alpha5, collagen binding protein 2, human cartilage glycoprotein 39), whereas the others are associated with a proliferative cell type (14-3-3 epsilon, plexin B2, N33, and three genes encoding ribosomal elements). Seven of the eight genes upregulated in the epithelioid phenotype are related rather to specialized functions, such as metabolism (aldose reductase, lecithin:cholesterol acyltransferase, ATPase 6), cytoskeletal composition (cytokeratins 7 and 8), and regulation of differentiation (granulin, annexin II). Immunohistochemistry with available antibodies to six of the differentially expressed gene products confirmed the differences also in pleural tissues, where submesothelial cells displayed the fibroblastic markers, whereas surface cells displayed the epithelioid markers. In summary, this approach revealed a pattern of genes coordinately regulated during mesothelial differentiation and suggests that mesothelium may regenerate also by recruiting cells from the submesothelial layer. Some of the gene products may also be useful markers for differentiation and activation in serosal tissues.

14-3-3 Proteins↗

PubMed1997

Constitutive modulation of Raf-1 protein kinase is associated with differential gene expression of several known and unknown genes.

BACKGROUND: Raf-1, a cytoplasmic serine/threonine protein kinase, plays an important role in mitogen- and damage-responsive cellular signal transduction pathways. Consistent with this notion is the fact that constitutive modulation of expression and/or activity of Raf-1 protein kinase modifies cell growth, proliferation, and cell survival. Although these effects are controlled at least in part by transcriptional mechanisms, the role of Raf-1 in the regulation of specific gene expression is unclear. MATERIALS AND METHODS: Differential display of mRNA was used to identify the genes differentially expressed in human head and neck squamous carcinoma cells (PCI-06A) transfected with either the antisense c-raf-1 cDNA (PCI-06A-Raf(AS)), or a portion of cDNA coding for the kinase domain of Raf-1 (PCI-06A-Raf(K)). The differentially expressed fragments were cloned and sequenced, and they were used as probes to compare the expression patterns in parent transfectants by Northern blot analysis. In addition, expression patterns of the novel genes were examined in normal tissues and cancer cell lines. RESULTS: Six differentially expressed cDNA fragments were identified and sequenced. Northern blot analysis revealed that four of these fragments representing human alpha 1-antichymotrypsin (alpha 1-ACT), mitochondrial cytochrome c oxidase subunit II (COX-II), and two as-yet unidentified cDNAs (KAS-110 and KAS-111) were relatively overexpressed in PCI-06A-Raf(AS) transfectants compared with PCI-06A-Raf(K) transfectants. The other two cDNA fragments representing human elongation factor-1 alpha (HEF-1 alpha) and ornithine decarboxylase antizyme (OAz) were overexpressed in PCI-06A-Raf(K) transfectants compared with PCI-06A-Raf(AS) transfectants. The KAS-110 (114 bp) and KAS-111 (202 bp) cDNAs did not show significant matches with sequences in the GenEMBL, TIGR, and HGS DNA databases, and these may represent novel genes. The KAS-110 and KAS-111 transcripts, approximately 0.9 kb and approximately 0.5 kb, were observed in most normal tissues and several cancer cell types, indicating their housekeeping function. CONCLUSIONS: This study reports novel components of the Raf-1 signaling pathway. alpha 1-ACT, HEF-1 alpha, COX-II, and OAz have been previously implicated in diverse cellular responses including transformation, energy metabolism, and cell survival. Our data suggest that expression of these genes may play a role in the Raf-1-mediated biological activity of PCI-06A cells. The KAS-110 and KAS-111 cDNAs represent unknown genes, and further investigations are necessary to determine their role in the cellular response. Identification of specific targets may provide useful markers for prognosis and therapy selection in squamous cell carcinoma.

Base Sequence↗

PubMed2005

Differential gene expression in queen-worker caste determination in bumble-bees.

Investigating how differential gene expression underlies caste determination in the social Hymenoptera is central to understanding how variation in gene expression underlies adaptive phenotypic diversity. We investigated for the first time the association between differential gene expression and queen-worker caste determination in the bumble-bee Bombus terrestris. Using suppression subtractive hybridization we isolated 12 genes that were differentially expressed in queen- and worker-destined larvae. We found that the sets of genes underlying caste differences in larvae and adults failed to overlap greatly. We also found that B. terrestris shares some of the genes whose differential expression is associated with caste determination in the honeybee, Apis mellifera, but their expression patterns were not identical. Instead, we found B. terrestris to exhibit a novel pattern, whereby most genes upregulated (i.e. showing relatively higher levels of expression) in queen-destined larvae early in development were upregulated in worker-destined larvae late in development. Overall, our results suggest that caste determination in B. terrestris involves a difference not so much in the identity of genes expressed by queen- and worker-destined larvae, but primarily in the relative timing of their expression. This conclusion is of potential importance in the further study of phenotypic diversification via differential gene expression.

Animals↗

PubMed2006

Differential gene expression in the rat cochlea after exposure to impulse noise.

Understanding the molecular biology of noise trauma is vital to developing effective and timely interventions. In a model of explosion-mediated impulse noise injury, differential gene expression was studied in whole rat cochlea preparations at 3 and 24 h following the exposure. We developed a technique using mRNA from a single cochlea on each oligonucleotide microarray to avoid pooling of mRNA samples. Application of a conservative statistical analysis approach resulted in the identification of 61 differentially expressed genes. Within 3 h after the exposure, there was an up-regulation of immediate early genes, mainly transcription factors and genes involved in the tissue's response to oxidative stress. No genes were found to be significantly down-regulated. At 24 h following the exposure, up-regulated genes included members of inflammatory and antioxidant pathways and one gene involved in glutathione metabolism was down-regulated. A subset of genes was confirmed by real-time reverse transcriptase-polymerase chain reaction (RT-PCR). The present study demonstrates the power of the microarray technique in providing a global view of the gene regulation following noise exposure, and in identifying genes that may be mechanistically important in hearing loss, and thereby serve as a basis for the development of therapeutic interventions.

Acoustic Stimulation↗

PubMed2001

Differentially expressed genes in L6 rat skeletal muscle myoblasts after incubation with inflammatory cytokines.

OBJECTIVE: The mechanism underlying exercise intolerance in chronic heart failure is still unclear. An increased concentration of inflammatory cytokines could be detected in the serum of patients with chronic heart failure (CHF) exhibiting a correlation with the severity of the disease. The variety of molecular alterations triggered by these cytokines in the skeletal muscle is almost unknown. The study was designed to analyze the differential gene expression in skeletal muscle myoblasts after stimulation with inflammatory cytokines. METHODS: L6 rat skeletal muscle myoblasts were incubated for 24 h with a combination of IL-1beta/IFN-gamma and the differential gene expression profile was determined by a PCR-based subtractive hybridization method. RESULTS: Out of 173 picked clones 141 different sequences could be identified. By comparison with Genebank, the identity of 73 genes (51.7%) could be confirmed, whereas the rest did not show a homology to any known gene. Some of the identified genes are known to be altered in patients with CHF. CONCLUSION: In summary, the results of this study provide information about changes in gene expression after exposure of skeletal muscle cells to inflammatory cytokines. This information may yield a new gene pool, worthwhile to be analyzed in skeletal muscle of patients with chronic heart failure.

Animals↗

PubMed2001

Profiling of differential gene expression in activated, allergen-specific human Th2 cells.

Th2 cells play a pivotal role in the pathogenesis of allergic diseases, including asthma, but the molecular basis of the Th1/Th2 dichotomy and the precise molecular pathways leading to Th2-dominant immune responses are still unclear. To this end, we have combined suppression subtractive hybridization (SSH) and high throughput analysis of cDNA arrays spotted with IMAGE clones to determine the profile of differential gene expression in human allergen-specific Th2 cells. Allergen-stimulated Th2 cells were used as the tester, and either resting Th2 cells or stimulated Th1 cells were used as the driver. SSH was used to equalize different mRNA levels and remove common sequences between the tester and the driver. Comparison of cDNA arrays probed with subtracted tester and non-subtracted driver provided a profile of Th2-selective gene expression. Analysis of 77 sequence-confirmed and differentially expressed genes in Th2 cells showed predominant EST sequences, representing 80% of sequences analyzed. The pattern of gene expression in 19 selected sequences was further analyzed in additional Th1 and Th2 clones. A total of 15 sequences showed predominant expression in Th2 cells, while the remaining four EST sequences showed no detectable amplification signal. The database containing Th2-selective genes will further our understanding of Th2 cell function and the genetic basis of allergic diseases.

Allergens↗

PubMed2000

Differential gene expression in the activation and maturation of human monocytes.

Differential-display or RNA fingerprint was applied to identify genes differentially expressed in monocyte maturation induced by an immunomodulating peptide on human peripheral blood mononuclear cells. Two unknown sequences (06c22 and 06c71) and p21 protein (cyclin dependent kinase inhibitor) were repressed, and three genes activated: Cathepsin D, DRP2 (dihydropirimidinase related protein 2), and gp91phox (91-kDa subunit of citochrome b(558)). Phenotype of evolving monocytes was analyzed by flow cytometry and mRNA level of identified genes determined by reverse transcription-PCR. The expression pattern of identified genes seemed to correlate with different monocyte subsets, monocyte-derived cells, and expected functional changes. After peptide addition, immature monocytes were initially activated, increasing the expression of CD25, CD69, and HLA-DR markers. This was accompanied by repression of p21 and the two unknown sequences, along with the simultaneous activation of Cathepsin D and DRP2. Later, the differentiation marker CD16 rose, and gp91phox gene expression activated. Further maturation led certain monocytes to express marker CD23 and gp91phox expression to reach a maximum, while Cathepsin D and DRP2 dropped to preactivation levels. Results reflect part of the evolution of immature monocytes toward macrophages and monocyte-derived dendritic cell precursors.

Base Sequence↗

PubMed2005

Identification of differentially expressed genes in hepatic HepG2 cells treated with acetaminophen using suppression subtractive hybridization.

Acetaminophen (APAP) is widely used for the treatment of pain and fever. Although it is safe at therapeutic doses, APAP is toxic at higher doses and can cause severe damage to the liver. To clarify the mechanism of APAP-related liver damage, we attempted the identification of the differential gene expression in response to APAP treatment in hepatic HepG2 cells. In the present study, we used the technique of suppression subtractive hybridization (SSH) for the identification of the differentially expressed genes between untreated and treated cells and identified 14 candidate genes showing increased expression in response to APAP treatment. RT-PCR and real-time RT-PCR analysis confirmed that the expression of two genes was increased within 24 h following APAP treatment. Among them, only lysyl hydroxylase 2 expression was increased in a time- and dose-dependent manner. Furthermore, the expression of lysyl hydroxylase 2 was shown to be increased in the livers of APAP-treated mice compared to untreated controls. The increased expression of lysyl hydroxylase 2 was also observed when the cells were exposed to other hepatotoxins, ethanol and isoniazid. Since lysyl hydroxylase 2 is known to be a key enzyme of liver fibrosis, the increased expression of lysyl hydroxylase 2 may be involved in hepatotoxins-related liver fibrosis.

Acetaminophen↗

PubMed2000

Large-scale identification of differentially expressed genes during neurogenesis.

We report here a modified mRNA differential display method and its application for the analysis of differential gene expression in NGF-treated PC12 cells and in embryonic rat spinal cord. The optimized protocol is based on low fidelity priming of multiple cDNAs followed by high fidelity amplification. In PC12 cells induction by nerve growth factor (NGF) altered the expression of 4% of the 466 transcripts evaluated. During neurogenesis of the spinal cord we found that 30% of the 288 examined products changed. The differential expression of the characterized genes was confirmed by independent quantitative PCR. We conclude this method is suitable for the identification of increases and decreases of mRNA levels and allows the discovery of differentially expressed unknown transcripts.

Animals↗

PubMed2025

Differential gene expression study in whole blood identifies candidate genes for psychosis in African American individuals.

Genome-wide association has identified regions of the genome that mediate risk for psychosis. It is possible that variants in these regions confer risk by altering gene expression. This work has predominantly been conducted in individuals of European descent and has focused narrowly on schizophrenia rather than psychosis as a syndrome. In the present study we investigated alterations in gene expression in African American individuals with a range of psychotic diagnoses to increase understanding of the etiology in an underserved population. We performed RNA-seq in whole bloody to survey the transcriptome in 126 patients with a psychosis-spectrum disorder and 217 healthy controls and applied differential gene expression analyses across the genome while controlling for age, sex, population stratification and batch. We found 18 differentially expressed genes (DEGs), some of the locations of the corresponding genes overlap with previously implicated regions for psychosis, but many of which were novel associations. Enrichment analysis of nominally significant genes (p < 0.05) revealed overrepresentation of biological processes relating to platelet, immune and cellular function, and sensory perception. Weighted gene co-expression network analysis, applied to identify modules of co-expressed genes associated with psychosis, revealed 10 modules, one of which was significantly associated with psychosis. This module was significantly enriched for DEGs, and for platelet function. These results support the potential role of immune function in the etiology of psychosis, identify novel candidate gene expression phenotypes that correspond to both established and new genomic regions, in individuals of African American ancestry.

Humans↗

PubMed1997

Differentially expressed genes in androgen-dependent and -independent prostate carcinomas.

Differential gene expression between androgen-dependent (LNCaP-FGC) and androgen-independent (LNCaP-LNO) prostate cancer cells has been investigated using RNA arbitrarily primed and differential display PCR of mRNA. Four differentially expressed cDNA transcripts were identified, of which differential expression was confirmed by Northern blot analysis. Sequence analysis revealed two unknown (JC19 and GC79) and two known genes [B-cell translocation gene 1 and UDP-glucuronosyltransferase 2B15 (UGT2B15)]. JC19, GC79, and B-cell translocation gene 1 were more highly expressed in LNCaP-FGC cells compared with LNCaP-LNO cells, whereas UGT2B15 was only expressed in LNCaP-LNO cells. Androgens and 1,25-dihydroxyvitamin D3 were able to down-regulate UGT2B15 mRNA in LNCaP-LNO cells. For GC79 mRNA, down-regulation was only observed with androgens in LNCaP-FGC cells. Expression of JC19 mRNA was studied using a panel of human prostate cancer xenografts. In androgen-dependent xenografts, expression of JC19 mRNA was much higher compared with androgen-independent xenografts, in which significant expression was hardly detectable. The mRNA expression pattern in the xenografts is in good agreement with that observed in the cell culture system. In conclusion, the differential display technique used in the present study allows analysis of gene expression in vitro and in vivo and can be used for the identification of important genes involved in androgen-independent prostate cancer development.

Androgens↗

PubMed2006

Tests for differential gene expression using weights in oligonucleotide microarray experiments.

BACKGROUND: Microarray data analysts commonly filter out genes based on a number of ad hoc criteria prior to any high-level statistical analysis. Such ad hoc approaches could lead to conflicting conclusions with no clear guidance as to which method is most likely to be reproducible. Furthermore, the number of tests performed with concomitant inflation in type I error also plagues the statistical analysis of microarray data, since the number of tested quantities in a study significantly affects the family-wise error rate. It would, therefore, be very useful to develop and adopt strategies that allow quantification of the quality of each probeset, to filter out or give little credence to low-quality or unexpressed probesets, and to incorporate these strategies into gene selection within a multiple testing framework. RESULTS: We have proposed a unified scheme for filtering and gene selection. For Affymetrix gene expression microarrays, we developed new methods for measuring the reliability of a particular probeset in a single array, and we used these to develop measures for a set of arrays. These measures are then used as weights in standard t-statistic calculations, and are incorporated into the multiple testing procedures. We demonstrated the advantages of our methods using simulated data, publicly available spiked-in data as well as data comparing normal muscle to muscle from patients with Duchenne muscular dystrophy (DMD), in which a set of truly differentially expressed genes is known. CONCLUSION: Our quality measures provide convenient ways to search for individual genes of high quality. The quality weighting strategies we proposed for testing differential gene expression have demonstrable improvement on the traditional filtering methods, the standard t-statistic and a regularized t-statistic in Affymetrix data analysis.

Data Interpretation, Statistical↗

PubMed1997

Detection and isolation of differentially expressed genes by differential display.

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Animals↗

PubMed2005

Variations in differential gene expression patterns across multiple brain regions in schizophrenia.

Large-scale gene expression studies in schizophrenia (SZ) have generally focused on the dorsolateral prefrontal cortex. Despite a wealth of evidence implicating multiple other brain regions in the disease, studies of other brain regions have been less frequent and have rarely been performed in the same subjects. We analyzed postmortem gene expression in the frontal, cingulate, temporal, parietal and occipital cortices (Brodmann areas 8, 10, 44, 46, 23/31, 24/32, 20, 21, 22, 36/28, 7 and 17, respectively) as well as in the hippocampus, caudate nucleus and putamen of persons with schizophrenia and control subjects (N's = 13) using Affymetrix GeneChip microarrays. Under identical data filtering conditions, the superior temporal cortex (BA22) of schizophrenia subjects showed the maximal number of altered transcripts (approximately 1200) compared to controls. Anterior and posterior cingulate cortices (BA23/31, 24/32) and the hippocampus followed the superior temporal cortex with two-times lower numbers of altered transcripts. The dorsolateral prefrontal cortex (BA46), a frequent target of SZ-associated studies, showed substantially fewer altered transcripts (approximately 33). These regional differences in differentially expressed genes could not be accounted for by factors such as total numbers of genes expressed or the filtering conditions and criteria used for identification of differentially expressed genes. These findings suggest that the temporal and cingulate cortices and the hippocampal formation represent brain regions of particular abnormality in SZ and may be more susceptible to the disease process(es) than other regions thus far studied.

Aged↗

PubMed1999

Normalization of array hybridization experiments in differential gene expression analysis.

For detecting and confirming differentially expressed genes it is necessary to have a trustworthy reference. So called 'housekeeping genes' are frequently used for this purpose as internal standard. However, if the influence of new experimental conditions is to be analyzed it is not safe to assume a priori that the expression of these genes is not affected. Therefore two synthetic poly(A)-RNAs were generated by PCR and in vitro transcription. They were used as external standards for normalization of northern blots and cDNA arrays where non-regulated genes as internal reference were not available.

Ampicillin Resistance↗

PubMed2005

Identification of differentially expressed genes after partial rat liver ischemia/reperfusion by suppression subtractive hybridization.

AIM: To identify potential diagnostic target genes in early reperfusion periods following warm liver ischemia before irreversible liver damage occurs. METHODS: We used two strategies (SSH suppression subtractive hybridization and hybridization of cDNA arrays) to determine early changes in gene expression profiles in a rat model of partial WI/R, comparing postischemic and adjacent nonischemic liver lobes. Differential gene expression was verified (WI/R; 1 h/2 h) and analyzed in more detail after warm ischemia (1 h) in a reperfusion time kinetics (0, 1, 2 and 6 h) and compared to untreated livers by Northern blot hybridizations. Protein expression was examined on Western blots and by immunohistochemistry for four differentially expressed target genes (Hsp70, Hsp27, Gadd45a and IL-1rI). RESULTS: Thirty-two individual WI/R target genes showing altered RNA levels after confirmation by Northern blot analyzes were identified. Among them, six functionally uncharacteristic expressed sequences and 26 known genes (12 induced in postischemic liver lobes, 14 with higher transcriptional expression in adjacent nonischemic liver lobes). Functional categories of the verified marker genes indicate on the one hand cellular stress and tissue damage but otherwise activation of protective cellular reactions (AP-1 transcription factors, apoptosis related genes, heat shock genes). In order to assign the transcriptional status to the biological relevant protein level we demonstrated that Hsp70, Hsp27, Gadd45a and IL-1rI were clearly up-regulated comparing postischemic and untreated rat livers, suggesting their involvement in the WI/R context. CONCLUSION: This study unveils a WI/R response gene set that will help to explore molecular pathways involved in the tissue damage after WI/R. In addition, these genes especially Hsp70 and Gadd45a might represent promising new candidates indicating WI/R liver damage.

Animals↗