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Results for “Gene Expression Profiling”

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PubMed2002

Preliminary study of DNA microarray of human placenta gene expression profile.

OBJECTIVE: To prepare human placenta genechip for analyzing differential gene expressions. METHODS: The target gene amplified from Hybrid Hunter cDNA library was dotted onto the slides by the arrayer (PixSys 5500). Total RNA from K562 cells treated with or without arsenic trioxide was extracted, the mRNA purified and cDNA synthesized. Fluorescent labeling of the samples was performed by restriction display PCR, followed by hybridization with the microarray that was subsequently washed and scanned, with the derived signals analyzed by computer. RESULTS: A reliable and specific method for preparing and assessing gene expression profile microarray was established, with which a total of 45 differentially expressed gene fragments were isolated. CONCLUSION: The genechips can be helpful in the analysis of differential gene expressions.

Female↗

PubMed2005

Influence of inhalation anesthesia assessed by comprehensive gene expression profiling.

Although general anesthesia is routinely used as an essential surgical procedure and its harmlessness has been evaluated and endorsed by clinical outcomes, little is known about its comprehensive influence that is not reflected in mortality and morbidity. In this paper, we have shown that inhalation anesthesia affected the expression of <1.5% of >10,000 genes, by analyzing the expression profiles for multiple organs of rats anesthetized with sevoflurane. The small number of transcripts affected by the inhalation anesthesia comprised those specific to single and common in multiple organs. The former included genes mainly associated with drug metabolism in the liver and influenced by agents such as amphetamine in the brain. The latter contained multiple circadian genes. In the brain, we failed to detect the alteration of the clock gene expression with the exception of Per2, assuming that anesthesia perturbs circadian rhythms. Our findings provide the first assessment for the influence of inhalation anesthesia by approaches of experimental biology and genome science.

Anesthetics, Inhalation↗

PubMed2002

Gene expression profile analysis of rheumatoid synovial fibroblast cultures revealing the overexpression of genes responsible for tumor-like growth of rheumatoid synovium.

To elucidate the aberrant growth properties of rheumatoid synoviocytes, we have examined the gene expression profile of rheumatoid synovial fibroblasts (RSFs) and compared with that of normal synovial fibroblasts (NSF). Gene expression profile analysis was conducted with synoviocyte cultures obtained from five rheumatoid arthritis (RA) patients and five control cases using a commercial cDNA array containing the defined 588 cancer-related genes. The results were confirmed by real-time RT-PCR. Gene expression levels for the platelet-derived growth factor receptor alpha (PDGFRalpha), plasminogen activator inhibitor-1 (PAI-1), and stromal cell derived factor 1A (SDF1A) are constitutively augmented in RSF compared with NSF. The mRNA levels of PDGFRalpha, PAI-1, and SDF1A in RSF over NSF were 4.6-, 14-, and 2.8-fold, respectively, by real-time RT-PCR. In fact, we found that RSFs showed greater sensitivity to the cell proliferative effect of PDGF. T his aberrant gene expression profile suggests that RSF may have retained the premature phenotype of primordial synoviocytes.

Adult↗

PubMed2004

cDNA microarray analysis of bovine embryo gene expression profiles during the pre-implantation period.

BACKGROUND: After fertilization, embryo development involves differentiation, as well as development of the fetal body and extra-embryonic tissues until the moment of implantation. During this period various cellular and molecular changes take place with a genetic origin, e.g. the elongation of embryonic tissues, cell-cell contact between the mother and the embryo and placentation. To identify genetic profiles and search for new candidate molecules involved during this period, embryonic gene expression was analyzed with a custom designed utero-placental complementary DNA (cDNA) microarray. METHODS: Bovine embryos on days 7, 14 and 21, extra-embryonic membranes on day 28 and fetuses on days 28 were collected to represent early embryo, elongating embryo, pre-implantation embryo, post-implantation extra-embryonic membrane and fetus, respectively. Gene expression at these different time points was analyzed using our cDNA microarray. Two clustering algorithms such as k-means and hierarchical clustering methods identified the expression patterns of differentially expressed genes across pre-implantation period. Novel candidate genes were confirmed by real-time RT-PCR. RESULTS: In total, 1,773 individual genes were analyzed by complete k-means clustering. Comparison of day 7 and day 14 revealed most genes increased during this period, and a small number of genes exhibiting altered expression decreased as gestation progressed. Clustering analysis demonstrated that trophoblast-cell-specific molecules such as placental lactogens (PLs), prolactin-related proteins (PRPs), interferon-tau, and adhesion molecules apparently all play pivotal roles in the preparation needed for implantation, since their expression was remarkably enhanced during the pre-implantation period. The hierarchical clustering analysis and RT-PCR data revealed new functional roles for certain known genes (dickkopf-1, NPM, etc) as well as novel candidate genes (AW464053, AW465434, AW462349, AW485575) related to already established trophoblast-specific genes such as PLs and PRPs. CONCLUSIONS: A large number of genes in extra-embryonic membrane increased up to implantation and these profiles provide information fundamental to an understanding of extra-embryonic membrane differentiation and development. Genes in significant expression suggest novel molecules in trophoblast differentiation.

Animals↗

PubMed2005

Genomic sequences encoding two types of medaka hemopexin-like protein Wap65, and their gene expression profiles in embryos.

Medaka genomic BAC clones, which contained two types of medaka hemopexin-like protein gene (Wap65), mWap65-1 and mWap65-2, were screened and their genomic sequences were determined by the shotgun strategy. The exon-intron organizations were highly conserved between both mWap65s and human hemopexin genes. The 5'-flanking regions of mWap65-1 and mWap65-2 contained various putative transcription factor binding sites including elements for developmental regulation. The expression patterns of mWap65s during embryonic development were examined by quantitative real-time PCR, demonstrating that both mWap65 transcripts were observed in early embryonic stages, but their expression patterns were different. Interestingly, in situ hybridization revealed that mWap65-2 transcripts were restricted to liver, whereas mWap65-1 transcripts were detected along the edge of pectoral fin buds and the median fin fold of tail buds in embryos at stage 32. Furthermore, we generated transgenic medaka expressing GFP driven by mWap65-1 and mWap65-2 promoters and observed GFP expression patterns during ontogeny. Although localizations of GFP varied among individuals, embryos uniformly expressed GFP 1 day after injection of mWap65-1-hrGFP and mWap65-2-hrGFP constructs, suggesting that mWap65-1 and mWap65-2 promoters were activated in very early stages. The differences between mWap65-1 and mWap65-2 in their expression profiles indicate their distinct roles during ontogeny.

Animals↗

PubMed2002

Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer.

The increasing availability and maturity of DNA microarray technology has led to an explosion of cancer profiling studies. To extract maximum value from the accumulating mass of publicly available cancer gene expression data, methods are needed to evaluate, integrate, and intervalidate multiple datasets. Here we demonstrate a statistical model for performing meta-analysis of independent microarray datasets. Implementation of this model revealed that four prostate cancer gene expression datasets shared significantly similar results, independent of the method and technology used (i.e., spotted cDNA versus oligonucleotide). This interstudy cross-validation approach generated a cohort of genes that were consistently and significantly dysregulated in prostate cancer. Bioinformatic investigation of these genes revealed a synchronous network of transcriptional regulation in the polyamine and purine biosynthesis pathways. Beyond the specific implications for prostate cancer, this work establishes a much-needed model for the evaluation, cross-validation, and comparison of multiple cancer profiling studies.

Adenosine Monophosphate↗

PubMed2002

Integrating cytogenetics and gene expression profiling in the molecular analysis of multiple myeloma.

Multiple Myeloma (MM), is a currently incurable malignancy of a terminally differentiated antibody secreting plasma cell (PC) that can be controlled with high dose therapy and stem cell support. Conventional cytogenetic analysis has revealed a genomic instability that sets MM apart from the other blood cell cancers. In spite of this "genomic chaos" recurrent structural rearrangements and ploidy changes have aided the identification of important molecular mechanisms of disease etiology and that have also proved to be useful clinical landmarks. Yet, abnormal cytogenetics, present in only 30% of cases, combined with other clinical parameters, only account for 20% of the variability in clinical outcome, which can range from 2 months to > 10 years. Thus, the genomic chaos may mask a unifying chromosome abnormality, e.g. Philadelphia chromosome in CML, or may indicate that MM is a broad descriptor of constellation of many distinct clinical and molecular entities. The advent of microarray profiling of global gene expression patterns is providing evidence that both of these possibilities may be true. We will discuss how the integration of conventional and molecular cytogenetics with gene expression profiling has confirmed past observations and, yet fundamentally changed the way we view the disease.

Chromosome Aberrations↗

PubMed2006

Gene expression profiling as novel tool in experimental asthma research.

With the advances achieved in decoding of the genetic structures of species and the novel possibilities of simultaneous measurements of the regulation of all genes of a given tissue, the last 10 years have seen a massive increase of our knowledge about genetic regulation of diseases. Additionally, the possibilities to control transcriptional processes within the cells will speed up the process of disentangling the various pathways leading to disease.

Animals↗

PubMed2002

Gene expression profiling diagnosis through DNA molecular computation.

Gene expression profiling is the characterization of cells based on the level of gene activity represented by concentrations of complementary DNA reverse transcribed from messenger RNA. The spectrum of cDNA concentrations, the expression profile, is determined using a DNA microarray. Although this approach is valuable for research, a simpler scheme that would give answers on a shorter time-scale for clinical applications is needed. An Adleman DNA self-assembly computer that would use cDNA as input might be ideal for clinical cell discrimination and a neural network architecture would be appropriate for making the necessary classifications. Preliminary experimental results suggest that expression profiling should be feasible using a DNA neural network that acts directly on cDNA.

Algorithms↗

PubMed2004

Gene expression profiling in uveal melanoma reveals two molecular classes and predicts metastatic death.

Melanomas are notoriously difficult to classify because of a lack of discrete clinical and pathological stages. Here, we show that primary uveal melanomas surprisingly cluster into two distinct molecular classes based on gene expression profile. Genes that discriminate class 1 (low-grade) from class 2 (high-grade) include highly significant clusters of down-regulated genes on chromosome 3 and up-regulated genes on chromosome 8q, which is consistent with previous cytogenetic studies. A three-gene signature allows biopsy-size tumor samples to be assigned accurately to tumor classes using either array or PCR platforms. Most importantly, this molecular classification strongly predicts metastatic death and outperforms other clinical and pathological prognostic indicators. These studies offer new insights into melanoma pathogenesis, and they provide a practical foundation for effective clinical predictive testing.

Chromosome Aberrations↗

PubMed2005

Gene expression profiling of the ageing rat vibrissa follicle.

BACKGROUND: The application of gene expression profiling to the study of chronological ageing has the potential to illuminate the molecular mechanisms underlying a complex and active process. For example, ageing of the skin and its constituent organs has myriad phenotypic consequences, and a better understanding of the means by which these changes arise has important corollaries for intervention strategies. OBJECTIVES: We used a transcriptional profiling approach to investigate changes in gene expression associated with ageing of the large vibrissa follicle of the Wistar rat. METHODS: Follicle mRNA isolated from male Wistar rats at 1 and 18 months of age was hybridized to Clontech Atlas 1.2 Rat cDNA macroarrays. Confirmation of array results was provided by the use of Northern blotting and immunohistochemistry. RESULTS: Seven transcripts displayed at least a 1.6-fold increase in expression with age, of which APOD (2.5-fold), GSTM2 (2.0-fold) and NPY (1.8-fold) showed the greatest increases. Decreased expression was found in 19 transcripts, most notably in ALOX12 (13.3-fold) and GAP43 (12.6-fold) expression. CONCLUSIONS: Follicular ageing is characterized by transcriptional changes associated with diverse aspects of keratinocyte metabolism, proliferation and development.

Aging↗

PubMed2005

Gene expression profiling of mantle cell lymphoma cells reveals aberrant expression of genes from the PI3K-AKT, WNT and TGFbeta signalling pathways.

Microarray studies have revealed the differential expression of several genes in mantle cell lymphoma (MCL), but it is unknown which of these differences are dependent on the transformed MCL cell itself or on the tumour microenvironment. To investigate which genes and signalling pathways are aberrantly expressed in MCL cells we used oligonucleotide microarrays to perform gene expression profiling of both purified leukaemic MCL cells and their normal counterparts, the naive B cells. A total of 106 genes were differentially expressed at least threefold in MCL cells compared with naive B cells; 63 upregulated and 43 downregulated. To validate the microarray results in a larger set of samples, we selected 10 differentially expressed genes and quantified their expression by real-time polymerase chain reaction in peripheral blood of MCL patients (n=21), purified MCL cells (n=6) and naive B cells (n=4), obtaining fully concordant results. A computer-assisted approach was used to procure specific molecular signalling pathways that were aberrantly expressed in MCL cells. Several genes related to apoptosis and to the PI3K/AKT, WNT and tumour growth factor beta signalling pathways were altered in MCL cells when compared with naive B cells. These pathways may play a significant role in the pathogenesis of MCL and deserve further investigation as candidates for new therapeutic targets.

Adult↗

PubMed2002

Analysis of 2,3,7,8-tetrachlorodibenzo-p-dioxin-induced gene expression profile in vivo using pathway-specific cDNA arrays.

In the current study, we used pathway-specific cDNA arrays to detect the transcriptional signature induced by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in vivo by studying simultaneously the expression profiles of 83 genes involved in apoptosis, cytokine production and angiogenesis. To this end, C57BL/6 mice were injected i.p. with 50 microg/kg body weight of TCDD and 1 or 3 days later, the thymus was analyzed for gene expression profiles. In the thymus, 23 out of 37 apoptotic genes screened were up-regulated by TCDD by a factor of two or more when compared to the vehicle-treated controls. In contrast, in the spleen, 20 out of 22 and in the liver, 16 out of 37 apoptotic genes were up-regulated. In the thymus, several genes encoding caspases, and members of the TNF family, including Fas ligand, were induced. Also, in the thymus, eight out of 23, and in the spleen, six out of 23 cytokine genes were up-regulated. In the liver and to a lesser extent in the thymus, certain angiogenesis genes were induced while others were repressed. When mice were injected with 0.1, 1, 10 or 50 microg/kg body weight of TCDD and the thymus was analyzed for apoptotic genes 1 day later, a dose-dependent response was not seen with most apoptotic genes. However, certain apoptotic genes were induced in the thymus even at low doses of 0.1 microg/kg body weight of TCDD. These data demonstrate that TCDD alters the expression of a large array of genes involved in apoptosis, cytokine production and angiogenesis. Thus, pathway-specific cDNA arrays may help in the identification of specific gene expression profiles induced by xenobiotics and to delineate the molecular mechanisms of toxicity.

Animals↗

PubMed2001

Gene expression profile in BALB/c-3T3 cells transformed with beryllium sulfate.

Differential gene expression was studied to understand the potential molecular mechanism responsible for cell transformation and tumorigenesis induced by beryllium. Cell lines were derived from tumors developed in nude mice injected subcutaneously with BALB/c-3T3 cells morphologically transformed with beryllium sulfate. Using the Atlas mouse 1.2 cDNA expression microarray, the expression profiles of 1176 genes, belonging to several different functional categories, were studied in the tumor cells as well as in the nontransformed control cells. Expression of 18 genes belonging to two functional groups was found to be consistently and reproducibly different (at least twofold) in the tumor cells compared with the control cells. The functional groups and the differentially expressed genes are as follows: The cancer-related genes (nine genes) were the ets-related transcription factor activated by ras, colony-stimulating factor, A-myb, sky, cot1, c-fos, c-jun, c-myc, and R-ras proto-oncogenes. The DNA synthesis, repair, and recombination genes (nine genes) were the DNA replication licensing factor MCM4, the DNA replication licensing factor MCM5, the DNA mismatch repair gene PMS2, the DNA excision repair gene, the DNA mismatch repair gene MSH2, the ultraviolet excision repair gene Rad23 DNA ligase 1, Rad51, and Rad52. The differential gene expression profile was confirmed with reverse transcription-polymerase chain reaction using primers specific for the differentially expressed genes. In general, expression of the cancer-related genes was upregulated, while expression of genes involved in DNA synthesis, repair, and recombination was downregulated in the tumor cells compared with the control cells. Using c-fos and c-jun, two of the differentially expressed genes, as model genes, we have found that in the nontransformed BALB/c-3T3 cells, the beryllium-induced transcriptional activation of these genes was dependent on pathways of protein kinase C and mitogen-activated protein kinase and independent of reactive oxygen species. These results indicate that beryllium-induced cell transformation and tumorigenesis are accompanied by and are possibly a product of alterations in expression of genes related to cancer and to DNA synthesis, repair, and recombination.

3T3 Cells↗

PubMed2002

Gene expression profiling of follicular lymphoma and normal germinal center B cells using cDNA arrays.

Follicular lymphomas (FLs) are neoplastic counterparts of normal germinal center (GC) B cells. FLs are characterized by t(14;18) with deregulation of the Bcl-2 (BCL2) gene. The presence of t(14;18) and overexpression of Bcl-2 is necessary, but not sufficient, to cause this disease. An array containing 588 complementary DNAs (cDNAs) was used to compare the gene expression between GC B cells and FL cells. To specifically monitor genes expressed in normal GC B and FL cells and not the entire tissue compartment, normal and malignant B cells were purified from tissues. Using the array, 37 genes were up-regulated and 28 were down-regulated in FL cells as compared to normal GC B cells. The expression level of each differentially expressed gene was verified by quantitative polymerase chain reaction. Following these studies 24 genes were up-regulated and 8 genes down-regulated with a P value less than.1. Included among the genes that were up-regulated in FLs were cell cycle regulator proteins CDK10, p120, p21CIP1, and p16INK4A; transcription factors/regulators Pax-5 and Id-2, which are involved in normal B-cell development; and genes involved in cell-cell interactions, tumor necrosis factor, interleukin-2R gamma (IL-2R gamma), and IL-4R alpha. Among the genes that were down-regulated in FLs were MRP8 and MRP14, which are involved in adhesion. Interestingly, several of these genes are localized within chromosomal regions already described to be altered in FLs. These findings provide a basis for future studies into the pathogenesis and pathophysiology of FL and may lead to the identification of potential therapeutic targets as well as antigens for immunotherapeutic strategies.

B-Lymphocytes↗

PubMed2004

Gene expression profiling of inflamed human endothelial cells and influence of activated protein C.

BACKGROUND: During systemic inflammation, activation of vascular endothelium by proinflammatory cytokines leads to hypotension, microvascular thrombosis, and organ damage. Recent data suggest a link between coagulation and inflammation through the activated protein C (APC) pathway. We studied gene expression profiles in human coronary artery endothelial cells (HCAECs) exposed to proinflammatory stimuli and the influence of APC on expression of candidate genes regulated by these stimuli. METHODS AND RESULTS: HCAECs were stimulated with interleukin-1beta, interferon-gamma, and tumor necrosis factor-alpha. In gene expression profiling, 400 of 8400 genes were regulated >2-fold. Verification of selected candidate genes was achieved by measuring expression of mRNA species by real-time polymerase chain reaction, cytokine secretion by ELISA, and metabolites of tetrahydrobiopterin (BH4) biosynthesis by high-performance liquid chromatography. BH4 synthesis, interleukin-6, interleukin-8, monocyte chemotactic protein-1 (MCP-1), and intercellular adhesion molecule-1 (ICAM-1) were downregulated by APC at the transcriptional and protein level. Endothelial nitric oxide synthase, endothelial adhesion molecule, and vascular cell adhesion molecule-1 were not affected by APC. Activities of transcription factors c-Fos, FosB, and c-Rel were inhibited by APC in inflamed HCAECs. CONCLUSIONS: Our study revealed a novel antiinflammatory mechanism of APC-dependent gene regulation in HCAECs since c-Fos-dependent induction of MCP-1 and ICAM-1 was suppressed. APC downregulates expression and activity of genes related to inflammation, most pronounced under intermediate or mild inflammatory conditions.

Biopterins↗

PubMed2004

[Differences in gene expression profile between high and low metastatic human colorectal cancer cell lines].

OBJECTIVE: To analyze the gene expression profiles in colorectal cancer cell lines including high metastatic LoVo and SW620 cell lines and low metastatic SW480 and LS174T cells lines using cDNA microarray for tumor metastasis-associated gene and to screen specific colorectal cancer metastasis-associated genes. METHODS: The cDNAs reversely transcribed from the mRNA derived respectively from the 4 cell lines and normal colorectal tissues were labeled with cy3 and cy5 prior to hybridization with the microarray containing 399 genes. The acquired image was analyzed by software. RESULTS: There were significant differences in gene expression profiles between high- and low- metastatic cell lines, and 44 up-regulated genes and 60 down-regulated genes were found to have statistical significance. CONCLUSIONS: The complex alterations in gene expression underlie the development of metastasis of colorectal cancer. The genes that are expressed differentially in high- and low- metastatic cell lines are probably related to the high metastatic potentials.

Cell Line, Tumor↗

PubMed2006

Specific gene expression profiles distinguish among functional allelic variants of the mouse Pthlh gene in transfected human cancer cells.

The mouse parathyroid hormone-like hormone (Pthlh) gene encodes three allelic variants characterized by amino acid substitutions that are associated with susceptibility (Pthlh(Pro)) or resistance (Pthlh(Thr) and Pthlh(SerAspTyr)) to two-stage skin carcinogenesis and to modulation of cell migration in vitro in transfected human cancer cells. cDNA microarray hybridization analysis of 8473 transcript clones revealed a similar gene expression profile for the Pthlh(Thr) and Pthlh(SerAspTyr) alleles but a distinct pattern for the Pthlh(Pro) allele, suggesting an association between a specific gene expression profile and biological function of the Pthlh alleles. Some of the genes modulated by the Pthlh alleles, e.g., ANXA1, CCL2, FN1 and TFF3, play a role in cell migration and may represent candidate targets for this Pthlh function. Our study demonstrates the potential usefulness of gene expression profiling of genetic variants for the functional characterization of candidate cancer modifier genes.

Alleles↗