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PubMed2003

Genetic expression profiling of six odontogenic tumors.

Odontogenic tumors are rare neoplasms arising from the odontogenic apparatus. We aimed to identify molecular characteristics associated with odontogenic tumorigenesis and malignancy. To this end, we investigated the expression level of human genes by using, for the first time in odontogenic tumors, the technique of expression profiling. Gene expression alterations common to all six odontogenic tumors were identified by the use of cDNA microarrays containing 19,000 human cDNAs. Statistical analysis on a subset of 4974 cDNAs present in the biopsies identified 506 distinct genes associated with the tumors (p-value < 0.01). Gene ontology analysis of the cellular processes which were differentially regulated in odontogenic tumors was accomplished by the use of a subset of 1409 annotated genes. Finally, 43 cDNAs differentiated the three malignant odontogenic tumors (ameloblastic carcinoma, clear cell odontogenic tumor, granular cell odontogenic tumor) from the three benign ameloblastoma biopsies (p < 0.01). The identified genes might help us better classify borderline odontogenic tumors.

Ameloblastoma↗

PubMed2005

The transcriptome in blood: challenges and solutions for robust expression profiling.

Peripheral blood may be the most feasible tissue source in clinical assessment of differences in gene expression between diseases and drug treatments due to accessibility. Yet, gene expression profiling from blood remains a challenge. Blood is a complicated biological system consisting of a variety of cell types at different stages of development. In addition, blood is also one of the most variable tissue types for gene expression analysis. The success of a blood microarray study depends on the choice of cell isolation method and preparation technique. In this review, we give a brief overview of the current status of using blood as a source for expression profiling and discuss potential applications of this method in the practices of clinical research.

Animals↗

PubMed2003

Novel gene expression profiles define the metabolic and physiological processes characteristic of wood and its extractive formation in a hardwood tree species, Robinia pseudoacacia.

Wood is of critical importance to humans as a primary feedstock for biofuel, fiber, solid wood products, and various natural compounds including pharmaceuticals. The trunk wood of most tree species has two distinctly different regions: sapwood and heartwood. In addition to the major constituents, wood contains extraneous chemicals that can be removed by extraction with various solvents. The composition and the content of the extractives vary depending on such factors as, species, growth conditions, and time of year when the tree is cut. Despite the great commercial and keen scientific interest, little is known about the tree-specific biology of the formation of heartwood and its extractives. In order to gain insight on the molecular regulations of heartwood and its extractive formation, we carried out global examination of gene expression profiles across the trunk wood of black locust (Robinia pseudoacacia L.) trees. Of the 2,915 expressed sequenced tags (ESTs) that were generated and analyzed in the current study, 55.3% showed no match to known sequences. Cluster analysis of the ESTs identified a total of 2278 unigene sets, which were used to construct cDNA microarrays. Microarray hybridization analyses were then performed to survey the changes in gene expression profiles of trunk wood. The gene expression profiles of wood formation differ according to the region of trunk wood sampled, with highly expressed genes defining the metabolic and physiological processes characteristic of each region. For example, the gene encoding sugar transport had the highest expression in the sapwood, while the structural genes for flavonoid biosynthesis were up-regulated in the sapwood-heartwood transition zone. This analysis also established the expression patterns of 341 previously unknown genes.

DNA, Complementary↗

PubMed2004

Comparison of gene expression profiles between Peyronie's disease and Dupuytren's contracture.

OBJECTIVES: To compare the gene expression alterations in human Peyronie's disease (PD) and Dupuytren's disease (DD) to determine whether they share a common pathophysiology. Multiple mRNA expression profiles of human PD have previously shown that genes that regulate fibroblast replication, myofibroblast differentiation, collagen metabolism, tissue repair, and ossification are involved. DD, a palmar fascia fibrosis, may be associated with PD. METHODS: Total RNA samples from PD plaques, normal tunica albuginea, Dupuytren's nodules, and normal palmar fascia (nine samples per group) were subjected to differential gene expression profile analysis (Clontech Atlas DNA microarray) comparing PD with tunica albuginea and DD with normal palmar fascia. Changes of more than 2.0 in PD and DD compared with tunica albuginea and normal palmar fascia, respectively, were recorded. Reverse transcriptase-polymerase chain reactions were performed for some genes whose expression was altered in PD. RESULTS: Some of the gene families upregulated in both PD and DD were (a) collagen degradation: matrix metalloproteinase (MMP), with MMP2 and MMP9, and thymosins (MMP activators), with TMbeta10 and TMbeta4; (b) ossification: osteoblast-specific factors (OSFs) OSF-1 and OSF-2 (DD only); and (c) myofibroblast differentiation: RhoGDP dissociation inhibitor 1. The genes upregulated in PD only were decorin (an inhibitor of transforming growth factor-beta1 and a part of fibroblast replication/collagen synthesis) and early growth response protein. Reverse transcriptase-polymerase chain reaction confirmed these changes. CONCLUSIONS: These data demonstrate that the pattern of alterations in the expression of certain gene families in PD and DD is similar, suggesting that they share a common pathophysiology and may be amenable to the same therapeutic regimens.

Adult↗

PubMed2004

Follicle stimulating hormone-induced growth promotion and gene expression profiles on ovarian surface epithelial cells.

Epidemiologic data have implicated reproductive follicle-stimulating hormone (FSH) as a probable risk factor for ovarian cancer (OC) development. Although pituitary and sex hormones have been reported to regulate OC cell growth, no information is available on the influence of FSH on gene expression profiles during ovarian surface epithelial (OSE) cell proliferation. This study evaluated the effect of FSH treatment on cell proliferation of various OSE cell lines and gene expression profiles with FSH treatment. Follicle-stimulating hormone receptor (FSHR) was found at higher expression at both transcriptional and protein levels in ovarian cancerous tissues compared to normal tissues, and FSH was shown to promote cell growth in 3 OSE cell lines. Furthermore, it was also found that overexpression of FSHR in Chinese hamster ovary (CHO) cells leads to cell proliferation. Using cDNA MicroArray analysis on MCV152 cells with FSH treatment, 91 genes were found upregulated and 68 genes downregulated for more than 2-fold after FSH treatment. Most of the genes were related to metabolism, cell proliferation and oncogenes. Downregulated genes included tumor suppressor genes (RB1, BRCA1, BS69) and the genes related to cell proliferation control. Pathway analysis found that FSH activates certain important enzymes in sterol biosynthesis pathways. FSH-induced gene expression profiles on MCV152 cells support the standing hypothesis that FSH is a probable risk factor for ovarian cancerous development.

Animals↗

PubMed2004

Expression profiling of non-small cell lung carcinoma identifies metastatic genotypes based on lymph node tumor burden.

OBJECTIVE: This study hypothesized that non-small cell lung carcinoma cells from primary tumors isolated by laser capture microdissection would exhibit gene expression profiles associated with graded lymph node metastatic cell burden. METHODS: Non-small cell lung carcinoma tumors (n = 15) were classified on the basis of nodal metastatic cell burden by 2 methods, obtaining 3 groups: no metastasis, micrometastasis, and overt metastasis. We then performed microarray analysis on microdissected primary tumor cells and identified gene expression profiles associated with graded nodal tumor burden using a correlation-based selection algorithm coupled with cross-validation analysis. Hierarchical clustering showed the regrouping of tumor specimens; the classification inference was assessed with Fisher's exact test. We verified data for certain genes by using another independent assay. RESULTS: The 15 specimens clustered into 3 groups: cluster A predominated in specimens with overt nodal metastasis; cluster B had more specimens with nodal micrometastases; and cluster C included only specimens without nodal metastases. Cluster assignment was based on a validated 75-gene discriminatory subset. Notably, genes not previously associated with positive non-small cell lung carcinoma lymph node status were encountered in the profiling analysis. CONCLUSIONS: Microdissection, combined with microarray analysis, is a potentially powerful method to characterize the molecular profile of tumor cells. The 75-gene expression profiles representative of clusters A and B may define genotypes prone to metastasize. Overall, the 3 groups of tumor specimens clustered separately, suggesting that this approach may identify graded metastatic propensity. Further, genes singled out in clustering may yield insights into underlying metastatic mechanisms and may represent new therapeutic targets.

Carcinoma, Non-Small-Cell Lung↗

PubMed2001

Expression profile of protein tyrosine kinase genes in human osteoarthritis chondrocytes.

OBJECTIVE: To determine the expression profile of protein kinase (PK) and protein tyrosine kinase (PTK) genes in human primary osteoarthritis (OA) chondrocytes and to compare it with that of immortalized human chondrocytes T/C 28a4 with a view to learning whether T/C 28a4 cells can be used for elucidating signal transduction pathways in human chondrocytes. DESIGN: We used the Atlas Human cDNA Array and a method based on PCR with degenerate primers to analyse the expression profile of protein kinase genes in primary human OA chondrocytes and compared it with that of immortalized human chondrocyte cell line T/C 28a4 using RT-PCR and Western blotting. RESULTS: A total of 21 PTK genes were identified and several of these have never been shown to be expressed in human OA chondrocytes. Comparative expression analysis of some selected kinase genes showed that the mRNA expression pattern of many protein kinase genes in OA chondrocytes was identical to that of T/C 28a4 cells. However, there were differences in the level of protein expression of selected protein kinases in these cells. For example, mRNA expression of the novel kinase HCK was detected in OA chondrocytes and in the cell lines analysed but by Western blotting HCK protein was not detected in OA chondrocytes. In these studies, we also identified a novel mutant form of the discoidin domain receptor 2 (DDR2) transcript from chondrocyte-like cell line HTB-94. CONCLUSIONS: Our results provide novel information about protein kinase gene expression in OA chondrocytes and indicate that the transformed chondrocyte cell line T/C 28a4 may be suitable for elucidating signal transduction pathways in chondrocytes and to investigate how they regulate chondrocyte function in inflammatory and degenerative joint diseases.

Blotting, Western↗

PubMed2006

Global gene expression profiling of the asymptomatic bacteriuria Escherichia coli strain 83972 in the human urinary tract.

Urinary tract infections (UTIs) are an important health problem worldwide, with many million cases each year. Escherichia coli is the most common organism causing UTIs in humans. The asymptomatic bacteriuria E. coli strain 83972 is an excellent colonizer of the human urinary tract, where it causes long-term bladder colonization. The strain has been used for prophylactic purposes in patients prone to more severe and recurrent UTIs. For this study, we used DNA microarrays to monitor the expression profile of strain 83972 in the human urinary tract. Significant differences in expression levels were seen between the in vivo expression profiles of strain 83972 in three patients and the corresponding in vitro expression profiles in lab medium and human urine. The data revealed an in vivo lifestyle of microaerobic growth with respiration of nitrate coupled to degradation of sugar acids and amino acids, with no signs of attachment to host tissues. Interestingly, genes involved in NO protection and metabolism showed significant up-regulation in the patients. This is one of the first studies to address bacterial whole-genome expression in humans and the first study to investigate global gene expression of an E. coli strain in the human urinary tract.

Amino Acids↗

PubMed2006

Gene expression profiling reveals complex changes following MEK-EE expression in cardiac myocytes.

The activation of the MEK/ERK pathway has been implicated in the proliferative growth of many tissues, however in the heart it has been linked with hypertrophic growth of the individual cardiac myocytes. We have explored the transcriptional consequences of prolonged ERK1/2 activation in cardiac myocytes following the adenoviral overexpression of a constitutively active form of MEK, MEK-EE. Analysis of microarray data obtained using full rat genome arrays showed >2000 gene expression changes in response to MEK-EE overexpression for 24h. We observed similar numbers of genes upregulated and downregulated. The genes were involved in diverse processes including cell structure, metabolism and intracellular signalling. There were also changes in the pro- and ani-apoptotic genes as well as downregulation of the antioxidant enzymes, Mn superoxide dismutase, catalase and thioredoxin 2. Our results reveal the complexity of transcriptional changes that follow the activation of the ERK signalling pathway in these cells and suggest that activation of this MAPK pathway impinges on diverse cellular functions.

Animals↗

PubMed2007

Protein expression profiles in the epidermis of cyclooxygenase-2 transgenic mice by 2-dimensional gel electrophoresis and mass spectrometry.

Exposure of murine skin to tumor-promoting agents such as 12-O-tetradecanoyl-phorbol-13-acetate (TPA) causes up-regulation of cyclooxygenase-2 (COX-2) and increased prostaglandin (PG) synthesis. Pharmacological inhibition of COX-2 significantly reduces skin tumor development. However, we previously demonstrated that K14.COX-2 transgenic (TG) mice that overexpressed COX-2 in the epidermis were unexpectedly resistant to tumor development under the classical 7,12-dimethylbenz[a]anthracene-TPA protocol. In the present study, we employed a proteomic approach of 2-dimensional gel electrophoresis (2-DE) and mass spectrometry to profile differentially expressed proteins in the epidermis of K14.COX-2 TG and wild-type control mice. Various 2-DE approaches were used to identify the maximum number of differentially expressed proteins: 20 for untreated samples, 3 for acetone-treated samples, and 22 for TPA-treated samples. These proteins include 14-3-3 sigma, numerous actin fragments, actin filament related proteins cofilin-1 and destrin, galectin-3, galectin-7, prohibitin, S100A6, S100A9, and many others. The differential expression of galectin-3, galectin-7, S100A9 was validated by Western blot analysis and/or immunohistochemical analysis. The current data suggest that some of the differentially expressed proteins might increase apoptosis and cell cycle arrest, which, in turn, may provide insight into the role of COX-2 in skin tumorigenesis.

Amino Acid Sequence↗

PubMed1999

Expression profiling using cDNA microarrays.

cDNA microarrays are capable of profiling gene expression patterns of tens of thousands of genes in a single experiment. DNA targets, in the form of 3' expressed sequence tags (ESTs), are arrayed onto glass slides (or membranes) and probed with fluorescent- or radioactively-labelled cDNAs. Here, we review technical aspects of cDNA microarrays, including the general principles, fabrication of the arrays, target labelling, image analysis and data extraction, management and mining.

Animals↗

PubMed2005

Expression profile and molecular genetic regulation of cyclin D1 expression in epithelioid sarcoma.

Epithelioid sarcoma is a distinctive, aggressive soft tissue tumor typically presenting as a subcutaneous or deep dermal mass in the distal extremities of young adults. Molecular genetic data of well-characterized cases of epithelioid sarcoma are sparse. A recent cytogenetic study of epithelioid sarcoma by conventional metaphase comparative genomic hybridization reported recurrent gains at chromosome 11q13, a region containing many genes, including the cyclin D1 gene. Cyclin D1 is a positive cell cycle regulator that is overexpressed in a variety of neoplasms, including mantle cell lymphoma and breast carcinoma. The objective of this study was to examine cyclin D1 expression in epithelioid sarcoma. Of 24 cases evaluated, 23 (96%) displayed cyclin D1 nuclear expression using immunohistochemical evaluation. Eight cases, which expressed cyclin D1 by immunohistochemistry, were evaluated by fluorescence in situ hybridization (FISH) and RNA in situ hybridization (RISH) for amplification of the cyclin D1 gene and messenger RNA (mRNA) expression, respectively. Seven of eight cases showed a typical eusomic state. One case showed pseudoamplification due to aneusomy/polysomy. There was no evidence of cyclin D1 gene amplification or messenger RNA overexpression detected by FISH or RNA in situ hybridization analyses, respectively. Our data clearly demonstrate that cyclin D1 protein is upregulated in epithelioid sarcoma, suggesting a role for this cell cycle regulator in the pathogenesis of epithelioid sarcoma. The high level of cyclin D1 protein expression in epithelioid sarcoma appears to be regulated by translational and/or post-translational mechanisms.

Cyclin D1↗

PubMed2001

The effect of TGF-beta1 on differential gene expression profiles in human corneal epithelium studied by cDNA expression array.

PURPOSE: TGF-betas regulate cell proliferation and differentiation, and they play important roles in maintenance of corneal epithelium. However, the precise function of TGF-betas in the corneal epithelium remains unclear. In this study, cDNA expression array technology was used to demonstrate the effect of TGF-beta1 on the simultaneous expression of a large number of genes in cultured human corneal epithelial cells (HCECs). The change in protein level expression of the specific genes influenced by TGF-beta1 was also investigated. METHODS: Human cDNA expression array technology was used to study the simultaneous expression of 1176 specific cellular genes in HCECs incubated with TGF-beta1 (10 ng/ml). Moreover, gene-specific semiquantitative reverse transcription-polymerase chain reaction (RT-PCR) was used to confirm the gene expression pattern measured by the cDNA expression array. Western blot analysis was used to examine protein expression of the specific genes in the presence or absence of TGF-beta1. RESULTS: TGF-beta1 significantly upregulated the expression of 19 genes and significantly downregulated ras-related protein, caspase10, and beta4-integrin in the treated HCECs. The expression of 277 genes including alpha3-integrin, PAI-2, transferrin receptor, and cyclin-D1 was studied. Semiquantitative RT-PCR analysis confirmed the TGF-beta1-mediated changes in expression patterns of these genes. Furthermore, Western blot analysis revealed that TGF-beta1 remarkably decreased PAI-2, transferrin receptor, and integrin alpha3, and increased caspase10 on the protein level. CONCLUSIONS: TGF-beta1 regulates the expression of specific types of genes in HCECs. These results strongly suggest that TGF-beta1 is critically involved in the maintenance of the corneal epithelium through the control of a network of various signal-transduction pathways.

Blotting, Western↗

PubMed2003

[Gene expression profiles in the diagnosis and prognosis of cancer].

DNA-microarray technology can be used to assess the expression of several thousands of genes at the same time. The identification of the gene expression profiles may help to better characterize human cancer. These studies may reveal subclasses of tumor types with similar histopathologic profile but different clinical courses.Furthermore,such studies could help to define therapeutic sensitivity and to estimate prognosis of various cancers. Identification of gene expression profiles of cancer can identify new therapeutic targets or cancer susceptibility genes. The DNA-microarray technology may write a new chapter in molecular oncology.

Antineoplastic Agents↗

PubMedDate not supplied

DEPD, a high resolution gene expression profiling technique capable of identifying new drug targets in the central nervous system.

Digital expression pattern display (DEPD) is an open, automated, PCR-based system of gene expression profiling that is capable of resolving as many as 100,000 transcripts from a single brain tissue cDNA sample. It has a detection sensitivity of better than 1 in 750,000 and it can reliably detect differences in RNA expression levels of less than two-fold. Digital expression pattern display presently is the most sensitive and therefore the only expression profiling method available that is capable of monitoring, in a semi-quantitative fashion, the expression of even the rarest of transcripts found in human brain tissue. Biofrontera applies this proprietary technique, together with state-of-the-art bioinformatics, for the purposes of elucidating pathology pathways of major brain diseases, of analysing the target profiles of drugs presently applied or in development, and of identifying novel targets for drug action.

Animals↗

PubMed2006

[Analysis of differential protein expression profile between retinoic acid resistant and sensitive acute promyelocytic leukemia cells].

BACKGROUND & OBJECTIVE: This study was to compare the protein expression profiles between retinoic acid (RA) resistant and sensitive acute promyelocytic leukemia (APL) cells by proteomic research method. METHODS: Total cellular proteins extracted from a RA sensitive cell line NB4 and a RA resistant cell line MR2 were separated by two-dimensional (2D) polyacrylamide gel electrophoresis (PAGE). High quality 2D-PAGE protein profiles were obtained and analyzed by PDQuest v7.1 analysis software to screen differentially expressed protein spots. Those sports were identified by mass spectrometry. RESULTS: 2-DE patterns of APL cell lines with high-resolution and reproducibility were obtained. The average spots for MR2 and NB4 cells were 890+/-45 and 912+/-56, respectively. 57 significantly differentially expressed protein spots were screened, among which 23 protein spots were identified to be up-regulated and 34 down-regulated in MR2 cells compared with NB4 cells. Ten proteins were identified by mass spectrometry, with a successful identification rate of 70%. The identified proteins could be classified into different categories: oncogenes,cell cycle regulator and signal transducer. CONCLUSION: The utilization of 2D-PAGE is effective in identifying the protein expression profiles between RA resistant and sensitive APL cells, therefore this study may provide a novel clue to elucidate the drug resistant mechanisms of all-trans retinoic acid.

Antineoplastic Agents↗

PubMed2006

[Establishment of protein expression profile of human normal colonic epithelia].

OBJECTIVE: To establish a protein expression profile of human normal colonic epithelia. METHODS: Two-dimensional gel electrophoresis (2-DE) was applied to separate the total proteins of 20 human normal colonic epithelial tissues. The expression proteins in the human normal colonic epithelia were identified by both matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) and electrospray ionization tandem mass spectrometry (ESI-Q-TOF), and the biological function and subcellular locations of the identified proteins were analyzed by bioinformatics. RESULTS: A 2-DE reference map of human normal colonic epithelium was established. On the 2-DE map, 1020+/-50 protein spots were detected, 204 protein spots representing 162 non-redundant proteins were identified, and 37 proteins had posttranslational modification. The identified proteins were categorized into several protein groups according to their functions or subcellular locations, whose data were available at our website (http://www.xyproteomics.org). CONCLUSION: A protein expression profile of human normal colonic epithelia is established for the first time, which provides useful information for investigating the physiological functions and pathologic process of colonic epithelia.

Adult↗

PubMed2004

Tissue-wide expression profiling using cDNA subtraction and microarrays to identify tumor-specific genes.

With the objective of discovering novel putative intervention sites for anticancer therapy, we compared transcriptional profiles of breast cancer, lung squamous cell cancer (LSCC), lung adenocarcinoma (LAC), and renal cell cancer (RCC). Each of these tumor types still needs improvement in medical treatment. Our intention was to search for genes not only highly expressed in the majority of patient samples but which also exhibit very low or even absence of expression in a comprehensive panel of 16 critical (vital) normal tissues. To achieve this goal, we combined two powerful technologies, PCR-based cDNA subtraction and cDNA microarrays. Seven subtractive libraries consisting of approximately 9250 clones were established and enriched for tumor-specific transcripts. These clones, together with approximately 1750 additional tumor-relevant genes, were used for cDNA microarray preparation. Hybridizations were performed using a pool of 16 critical normal tissues as a reference in all experiments. In total, we analyzed 20 samples of breast cancer, 11 of LSCC, 11 of LAC, and 8 of RCC. To select for genes with low or even no expression in normal tissues, expression profiles of 22 different normal tissues were additionally analyzed. Importantly, this tissue-wide expression profiling allowed us to eliminate genes, which exhibit also high expression in normal tissues. Similarly, expression signatures of genes, which are derived from infiltrating cells of the immune system, were eliminated as well. Cluster analysis resulted in the identification of 527 expressed sequence tags specifically up-regulated in these tumors. Gene-wise hierarchical clustering of these clones clearly separated the different tumor types with RCC exhibiting the most homogeneous and LAC the most diverse expression profile. In addition to already known tumor-associated genes, the majority of identified genes have not yet been brought into context with tumorigenesis such as genes involved in bone matrix mineralization (OSN, OPN, and OSF-2) in lung, breast, and kidney cancer or genes controlling Ca(2+) homeostasis (RCN1,CALCA, S100 protein family). EGLN3, which recently has been shown to be involved in regulation of hypoxia-inducible factor, was found to be highly up-regulated in all RCCs and in half of the LSCCs analyzed. Furthermore, 42 genes, the expression level of which correlated with the overall survival of breast cancer patients, were identified. The gene dendogram clearly separates two groups of genes, those up-regulated such as cyclin B1, TGF-beta 3, B-Myb, Erg2, VCAM-1, and CD44 and those down-regulated such as MIG-6, Esp15, and CAK in patients with short survival time.

Adenocarcinoma↗