Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression profiles of cervical cancers for novel molecular classification

ABSTRACT: Cervical cancers is the second most malignancy in women. It has been clinically important histological variants such as squamous cell carcinoma (SCC) and adenocarcinoma (AC) and adenosquamous carcinomas (ASC). It has been postulated that AC and ASC has a worse prognosis than pure SCC. However, many of the mixed or other types confuses its diagnosis and aggressive/resistant behavior of some tumors has resulted in debate for prognostic role of empirical pathological classification. In addition, the prognosis of adenosquamous carcinoma is still under debate. To establish a novel molecular classification of cervical cancer, we investigated intrinsic characteristics using expression profile. A total of 80 cevical cancer samples of following histology were included in this study: 54 SCC, 18 ASC, 6 AC, and 2 others. Replicate number: 2. No control/no reference sample was included. One-color.

ORGANISM(S): Homo sapiens

SUBMITTER: Shuhei Noda

PROVIDER: E-GEOD-20167 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Subtypes of cervical adenosquamous carcinomas classified by EpCAM expression related to radiosensitivity.

Imadome Kaori K Iwakawa Mayumi M Nakawatari Miyako M Fujita Hidetoshi H Kato Shingo S Ohno Tatsuya T Nakamura Etsuko E Ohkubo Yu Y Tamaki Tomoaki T Kiyohara Hiroki H Imai Takashi T

Cancer biology & therapy 20101115 10

Adenosquamous carcinoma (ASC) is a relatively uncommon histological subtype of cervical cancer (CC). A point of controversy is the relative prognosis of ASC compared to squamous cell carcinoma (SCC). We hypothesized that ASC could be classified into two intrinsic molecular subtypes with different outcomes. We examined 143 biopsy samples of CC patients to identify a molecule for classification using microarray expression analysis and immunohistochemical analysis (IHA). We found specific expressio ...[more]

PMID: 20855955

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Project description:Cytokines are implicated in the development of inflammatory diseases such as endometriosis. This project was designed to test the hypothesis that specific cytokines that are secreted by macrophages, such as tumor necrosis factor ? (TNF?) and interleukin 1 beta (IL1?), cause gene expression changes in endometrial stromal cells. Telomerase-immortalized human endometrial stromal cells (T-HESC) were treated with TNF? (5ng/ml) ± IL1? (1ng/ml). DNA microarray and real time RT-PCR were used to study the gene expression changes in T-HESC cells. Two hundred and nineteen genes featuring in various gene ontologies were found to be differentially expressed in T-HESC cells treated with TNF? ± ILI?. 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Keywords: cytokines, endometrial stromal cells, endometriosis Experimental factors: cytokine treatment Experimental design: The telomerase immortalized - human endometrial stromal cell line (T-HESC, ATCC #CRL-4003, Manassas, VA) was used for all experiments. The cells were treated with vehicle or with the cytokines, TNF? (5ng/ml) ± IL1? (1ng/ml). Three different passages of cells were collected for each treatment group to provide biological replicates. Quality control steps: The cRNA that was synthesized from each cell culture sample was used for hybridization to a single CodeLink (Applied Microarrays, Tempe, AZ) whole human genome microarray. Only one sample was hybridized with each slide and only one dye (Alexa 647) was used so no dye swaps were necessary. Bacterial control spikes were used as per manufacturer's instructions. Samples used, extract preparation and labeling: The origin of each biological sample: The samples were cultured cells of the telomerase-immortalized human endometrial stromal cell (T-HESC) line obtained from ATCC (CRL-4003). Manipulations of biological samples and protocols used: The telomerase immortalized - human endometrial stromal cell line (T-HESC, ATCC #CRL-4003, Manassas, VA) was used for all experiments. The cells were routinely maintained in Dulbecco’s modified Eagle’s medium (DMEM, Sigma, St. Louis, MO) with 10% fetal bovine serum albumin (FBS, Hyclone, South Logan, UT), insulin, selenious acid, transferrin, bovine serum albumin and linoleic acid (ITS+ Premix, BD Biosciences, Bedford, MA), puromycin (Cellgro, Manassas, VA) and penicillin/ streptomycin (Hyclone, South Logan, UT). After the cells reached 80% confluence they were starved for 24 hours in T-HESC starvation medium (DMEM+ ITS+ puromycin+ penicillin/streptomycin) before treatment. The cells were treated with vehicle or with TNF? (5ng/ml) alone, IL1? (1ng/ml) alone, or with the two cytokines combined at the same concentrations for 48 hours. Total RNA was then isolated from the cell cultures for use in the DNA microarray experiments. Each treatment was carried out with 3 different passages of cells. Technical protocols: The cultured endometrial cells were rinsed with PBS and TRI reagent (MRC) was added. The cells were scraped into tubes and centrifuged in the presence of bromochloropropane and sodium acetate. The RNA-containing layer was removed and the RNA purified on an RNeasy extraction column (Qiagen). The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen). The purity and quantity was evaluated with the RNA 6000 NanoLabChip in an Agilent Bioanalyzer. 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Project description:Objective: To examine the effects of the phytoestrogen metabolite, equol, on gene expression in the monkey iliac artery. Design: Eight ovariectomized cynomolgus monkeys were on a high fat diet for 6.5 years. The left iliac artery was biopsied prior to randomization to equol (0.0237 g/100 g chow, n=4) or vehicle (n=4) for 8 months. The right iliac artery was obtained at necropsy. Gene expression in the iliac arteries in response to equol was determined by DNA microarray and confirmed by real time RT-PCR. Results: Atherosclerotic lesions in the iliac arteries ranged in size from 0.113-1.003 mm2 in equol-treated animals and from 0-0.873 mm2 in control animals. 59 genes were down-regulated and 279 were up-regulated in response to equol. Comparison of these data to previous work identified 10 genes regulated in opposite directions by equol compared to presence of atherosclerosis plaque. 55 genes were differentially expressed in the same direction in response to both equol and estradiol. Conclusions: Similar responses of genes to both equol and estradiol may reflect the extent to which equol serves as a natural selective estrogen receptor modulator in the arteries. Opposite responses of 10 genes to equol versus the presence of atherosclerosis implicates those genes in the potential protective effects of equol in the vasculature. Experiment Design: Goal of the experiment: To examine differential gene expression in the iliac arteries of ovariectomized cynomolgous monkeys on a high fat diet in response to treatment with equol. Brief description of the experiment: Objective: To examine the effects of the phytoestrogen metabolite, equol, on gene expression in the monkey iliac artery. Design: Four ovariectomized cynomolgous monkeys were on a high fat diet for 6.5 years. The left iliac artery was biopsied prior to randomization to equol (0.0237 g/100 g chow, n=4 or vehicle (n=4) for 8 months. The right iliac artery was obtained at necropsy. Gene expression in response to equol was determined by CodeLink Whole Human Genome DNA microarrays and confirmed by real time RT-PCR. Results: Atherosclerotic lesions in the iliac arteries ranged in size from 0.113-1.003 mm2 (mean 0.512 ± 0.19 mm2) in pretreatment arteries and 0.025-1.217 mm2 (mean 0.748 ± 0.22 mm2) post-equol treatment. 59 genes were down-regulated and 279 were up-regulated in response to equol. Comparison of these data to previous work identified 10 genes regulated in opposite directions by equol compared to presence of atherosclerosis plaque. 55 genes were differentially expressed in the same direction in response to both equol and estradiol. Conclusions: Similar responses of genes to both equol and estradiol may reflect the extent to which equol serves as a natural selective estrogen receptor modulator in the arteries. Opposite responses of 10 genes to equol versus the presence of atherosclerosis implicates those genes in the potential protective effects of equol in the vasculature. Keywords: nonhuman primate, equol treatment, soy isoflavones Experimental factors: equol treatment Experimental design: Female cynomolgous monkeys (n=4) had been ovariectomized for 4 years and on a high fat diet for 6.5 years. The left iliac artery was removed at surgical biopsy. Animals were treated with equol for 8 months, then necropsied. The right iliac artery was obtained at necropsy. The presence and size of atherosclerotic plaque was quantified in the iliac arteries. Arterial tissue from the iliac arteries was used for DNA microarray analysis of gene expression. Quality control steps: The cRNA that was synthesized from each iliac artery was used for hybridization to a single CodeLink (Applied Microarrays, Tempe, AZ) whole human microarray. Only one sample was hybridized with each slide and only one dye (Alexa 647) was used so no dye swaps were necessary. Bacterial control spikes were used as per manufacturer's instructions. Samples used, extract preparation and labeling: The origin of each biological sample: The samples were iliac arterial tissue from cynomolgous monkeys. Manipulations of biological samples and protocols used: Cynomolgous monkeys were placed on a high fat diet 6.5 years before the experiment and ovariectomized 4 years prior to the experiment to induce a surgical menopause. The left iliac artery was surgically removed from each animal in the study before treatment with equol, the the right iliac artery was removed after the treatment period at necropsy. 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The first strand of cDNA was synthesized with first strand buffer, dNTP mix, RNase inhibitor, and reverse transcriptase for 2 h at 42C. The second strand cDNA synthesis reaction was prepared using second strand buffer, dNTP mix, DNA polymerase mix, and RNase H; the reaction was carried out for 2h at 16C. The double-stranded cDNA was purified on QIAquick columns (Qiagen) and the eluent was dried down in a SpeedVac concentrator. The double-stranded cDNA was resuspended in a mixture containing T7 reaction buffer, T7 ATP, T7 GTP, T7 UTP, T7 CTP, biotin-11-UTP, and T7 enzyme mix for the synthesis of cRNA. The cRNA synthesis reaction was terminated after 14h at 37C by purifying the cRNA on RNeasy columns (Qiagen). The concentration of cRNA was determined by spectrophotometry. Hybridization procedures and parameters: 10 micrograms of cRNA was mixed with fragmentation buffer and heated to 94C for 20 min. The fragmented cRNA was mixed with CodeLink hybridization buffer, loaded on the microarray slides, and hybridized for 18 hours at 37C. The slides were washed in 0.75x TNT (Tris-HCl, NaCl, Tween-20) at 46C for 1h then incubated with streptavidin-Alexa 647 fluorescent dye for 30 min at room temperature. The Alexa fluor was prepared in TNB blocking buffer (0.1M Tris-HCl, 0.15M NaCL, 0.5% NEN Blocking Reagent-PerkinElmer) The slides were then washed 4 times for 5 min each in 1x TNT and twice in 0.05% Tween 20 for 5 sec each. The slides were dried by centrifugation and scanned in an Axon GenePix 4000B scanner.

Project description:Objective: To examine the effect of estradiol on gene expression in the monkey iliac arteries. Design: Eight ovariectomized cynomolgus monkeys were on a high fat diet for 6.5 years. The left iliac artery was biopsied before randomization to estradiol (1 mg Estrace® per day, n=4) or vehicle (n=4) for 8 months. The right iliac artery was obtained at necropsy. Gene expression in the iliac arteries in response to estradiol was determined by DNA microarray and confirmed by real time RT-PCR. Results: Atherosclerotic lesions in the iliac arteries ranged in size from 0-0.61 mm2 in estrogen-treated animals and from of 0-0.873 mm2 in controls. 106 genes were shown to be down-regulated and 26 genes were up-regulated in the monkey iliac arteries in response to estradiol. Among the genes shown to be up-regulated by DNA microarray and confirmed by real time RT-PCR were components of the insulin-like growth factor (IGF) pathway, IGF-1, IGF binding protein 4 (IGFBP4) and IGFBP5. Components of the Wnt signaling pathway were also up-regulated, including secreted frizzled-related protein 2 (SFRP2), SFRP4, low density lipoprotein receptor-related protein 6 (LRP6), and Wnt 1 inducible signaling pathway protein 2 (WISP2). Conclusions: The modest effect of estradiol on gene expression in monkey iliac arteries reported herein may reflect a reduction in response to estradiol as a result of the effect of the altered environment of the artery containing atherosclerotic plaque. Experiment Design: Goal of the experiment: To examine differential gene expression in the iliac arteries of ovariectomized cynomolgous monkeys on a high fat diet in response to treatment with estradiol. Brief description of the experiment: Objective: To examine the effect of estradiol on gene expression in the monkey iliac arteries. Design: Four ovariectomized cynomolgous monkeys were on a high fat diet for 6.5 years. The left iliac artery was biopsied before randomization to estradiol (1 mg Estrace® per day, n=4) for 8 months. The right iliac artery was obtained at necropsy after treatment. Gene expression in response to estradiol was determined by CodeLink Whole Human (Applied Microarrays, Tempe, AZ) DNA microarray and confirmed by real time RT-PCR. Results: Atherosclerotic lesions in the iliac arteries ranged in size from 0-0.61 mm2 (mean 0.34 ± 0.13 mm2) in pretreatment arteries and 0-1.411 (mean 0.789 ± 0.31mm2) in post-estrogen treated arteries. 106 genes were shown to be down-regulated and 26 genes were up-regulated in the monkey iliac arteries in response to estradiol. Among the genes shown to be up-regulated by DNA microarray and confirmed by real time RT-PCR were components of the insulin-like growth factor (IGF) pathway, IGF-1, IGF binding protein 4 (IGFBP4) and IGFBP5. Components of the Wnt signaling pathway were also up-regulated, including secreted frizzled-related protein 2 (SFRP2), SFRP4, low density lipoprotein receptor-related protein 6 (LRP6), and Wnt 1 inducible signaling pathway protein 2 (WISP2). Conclusions: The modest effect of estradiol on gene expression in monkey iliac arteries reported herein may reflect a reduction in response to estradiol as a result of the effect of the altered environment of the artery containing atherosclerotic plaque. Keywords: nonhuman primate, hormone replacement Experimental factors: hormone treatment Experimental design: Female cynomolgous monkeys (n=4) had been ovariectomized for 4 years and on a high fat diet for 6.5 years. The left iliac artery was removed at surgical biopsy. Animals were treated with estradiol for 8 months, then necropsied. The right iliac artery was obtained at necropsy. The presence and size of atherosclerotic plaque was quantified in the iliac arteries. Arterial tissue from the iliac arteries was used for DNA microarray analysis of gene expression. Quality control steps: The cRNA that was synthesized from each iliac artery was used for hybridization to a single CodeLink (Applied Microarrays, Tempe, AZ) whole human microarray. Only one sample was hybridized with each slide and only one dye (Alexa 647) was used so no dye swaps were necessary. Bacterial control spikes were used as per manufacturer's instructions. Samples used, extract preparation and labeling: The origin of each biological sample: The samples were iliac arterial tissue from cynomolgous monkeys. Manipulations of biological samples and protocols used: Cynomolgous monkeys were placed on a high fat diet 6.5 years before the experiment and ovariectomized 4 years prior to the experiment to induce a surgical menopause. The left iliac artery was surgically removed from each animal in the study before treatment with estradiol, the the right iliac artery was removed after the treatment period at necropsy. The presence and size of atherosclerotic plaque was quantified in the iliac arteries Experimental factor: hormone treatment Technical protocols: The iliac arteries were homogenized in TRI reagent, bromochloropropane and sodium acetate were added, and the samples were centrifuged to separate the phases. The RNA-containing layer was removed and the RNA purified on an RNeasy extraction column (Qiagen). The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen). The purity and quantity of RNA were evaluated by an Agilent Bioanalyzer using the RNA 6000 Nanoassay LabChip. Labeled cRNA was prepared using the MessageAmp II-Biotin enhanced kit (Ambion). 0.275 microgram of total iliac artery RNA was mixed with bacterial control RNA spikes and primed with T7 oligo(dT) primer for 10 min at 70C. (The bacterial control spikes included araB, entF, fixB, gnd, hisB, and leuB.) The first strand of cDNA was synthesized with first strand buffer, dNTP mix, RNase inhibitor, and reverse transcriptase for 2 h at 42C. The second strand cDNA synthesis reaction was prepared using second strand buffer, dNTP mix, DNA polymerase mix, and RNase H; the reaction was carried out for 2h at 16C. The double-stranded cDNA was purified on QIAquick columns (Qiagen) and the eluent was dried down in a SpeedVac concentrator. The double-stranded cDNA was resuspended in a mixture containing T7 reaction buffer, T7 ATP, T7 GTP, T7 UTP, T7 CTP, biotin-11-UTP, and T7 enzyme mix for the synthesis of cRNA. The cRNA synthesis reaction was terminated after 14h at 37C by purifying the cRNA on RNeasy columns (Qiagen). The concentration of cRNA was determined by spectrophotometry. Hybridization procedures and parameters: 10 micrograms of cRNA was mixed with fragmentation buffer and heated to 94C for 20 min. The fragmented cRNA was mixed with CodeLink hybridization buffer, loaded on the microarray slides, and hybridized for 18 hours at 37C. The slides were washed in 0.75x TNT (Tris-HCl, NaCl, Tween-20) at 46C for 1h then incubated with streptavidin-Alexa 647 fluorescent dye for 30 min at room temperature. The Alexa fluor was prepared in TNB blocking buffer (0.1M Tris-HCl, 0.15M NaCL, 0.5% NEN Blocking Reagent-PerkinElmer) The slides were then washed 4 times for 5 min each in 1x TNT and twice in 0.05% Tween 20 for 5 sec each. The slides were dried by centrifugation and scanned in an Axon GenePix 4000B scanner.

Project description:Estrogen is a reproductive steroid hormone that has both beneficial and detrimental effects on the cardiovascular system. Selective estrogen receptor modulators (SERMs) exhibit partial estrogen agonist/antagonist activity in estrogen target tissues. Since we still have an incomplete picture of the gene targets of estrogen in the vasculature, and our understanding of SERM gene targets in the vasculature is even less well-developed, it is important to broaden the available information on this subject. The present study tested the hypothesis that estrogens (ethinyl estradiol, estradiol benzoate, and equilin) and SERMs (tamoxifen and raloxifene) cause differential gene and protein expression in the vasculature. DNA microarray and real-time RT-PCR were used to investigate gene expression in the mesenteric arteries of estrogen and SERM treated ovariectomized rats. The genes shown to be differentially expressed included stearoyl-CoA desaturase (SCD), soluble epoxide hydrolase (sEH), secreted frizzled related protein-4 (SFRP-4), insulin-like growth factor-1 (IGF-1), phospholipase A2 group 1B (PLA2-G1B), and fatty acid synthase (FAS). Western blot further confirmed the differential expression of sEH, SFRP-4, FAS, and SCD protein. These results reveal that estrogens and SERMs cause differential gene and protein expression in the mesenteric artery. Consequently, the use of these agents may be associated with a unique profile of functional and structural changes in the mesenteric arterial circulation. Goal of the experiment: To examine the effects of three formulations of estrogen (ethinyl estradiol, equilin, and estradiol benzoate) and of the selective estrogen receptor modulators, tamoxifen and raloxifene, on gene expression in the mesenteric arteries of the rat. Keywords: rat, artery, gene expression, mesentery, estrogen, tamoxifen, raloxifene Experimental factors: hormone treatment, drug treatment Experimental design: Prepubertal female Sprague Dawley rats (Harlan, Indianapolis, IN) were ovariectomized at 4 weeks of age, prior to the initiation of regular ovarian cycles. The animals were allowed to recover for 2 weeks before the experimental protocol was initiated. The rats were randomly divided into 6 groups (n=3-4/group) and treated by daily gavage for 3 weeks with the vehicle (20% 2-hydroxypropyl-β-cyclodextrin, Sigma, St Louis, MO), ethinyl estradiol (EE, 0.15 mg/kg; Sigma), estradiol benzoate (EB, 0.15 mg/kg; Sigma), equilin (EQ, 0.15 mg/kg; Sigma), tamoxifen (TAM, 3 mg/kg; Sigma), or raloxifene (RAL, 3 mg/kg; Eli Lilly & Co., Indianapolis, IN). After 3 weeks of treatment, the rats were euthanized and the mesentery obtained. Total RNA was extracted from each individual sample and used for the synthesis of labeled cRNA for microarray analysis. After the final gavage treatment on day 21, the rats were deeply anesthetized with isoflurane and euthanized by decapitation. The mesenteric arterial tree was isolated and harvested and stored in RNAlater (Ambion) at -80ºC. The mesenteric arteries were dissected free from veins and surrounding fat and homogenized in TRI reagent (MRC, Cincinnati, OH). Mesenteric artery RNA was extracted and purified using an RNeasy Mini Kit (Qiagen). Any potentially contaminating DNA was removed by treatment with RNase-free DNase (Qiagen) on the RNeasy column. Total RNA was quantified and RNA integrity was assessed using the Agilent Bioanalyzer (Santa Clara, CA). Following analysis, the RNA was stored at -80ºC until it was used for gene expression studies. DNA microarray: CodeLink Whole Rat Genome Bioarrays (Applied Microarrays, Tempe, AZ) were used. Five μg total RNA was used from each mesenteric arterial sample for the microarray analysis. Complementary RNA was synthesized per company protocol (Ambion). A set of bacterial RNAs was added to each total RNA sample and carried through the synthesis and labeling reactions as controls and for nor¬malization of the data. The microarrays were scanned with the GenePix 4000B (Axon Instruments, Union City, CA) with GenePix Pro 5.0 software (Axon Instruments). Analysis of the microar¬rays was performed with the CodeLink Expression Analysis software (Applied Microarrays) and Acuity 3.1 software (Axon), and statistical analysis was performed with GeneSpring 7.1 software (Agilent, Santa Clara, CA). A sample of n=3 was completed with the microarrays for each treatment. Quality control steps: The cRNA that was synthesized from each mesenteric artery treatment sample was used for hybridization to a single CodeLink (Applied Microarrays) whole rat genome microarray. Only one sample was hybridized with each slide and only one dye (streptavidin-Alexa 647) was used so no dye swaps were used. Bacterial control spikes were used per manufacturer's instructions. Samples used, extract preparation and labeling: The origin of each biological sample: The samples were isolated mesenteric arteries from individual Sprague Dawley rats that had been treated by daily gavage for 3 weeks with the vehicle (20% 2-hydroxypropyl-β-cyclodextrin, Sigma, St Louis, MO), ethinyl estradiol (EE, 0.15 mg/kg; Sigma), estradiol benzoate (EB, 0.15 mg/kg; Sigma), equilin (EQ, 0.15 mg/kg; Sigma), tamoxifen (TAM, 3 mg/kg; Sigma), or raloxifene (RAL, 3 mg/kg; Eli Lilly & Co., Indianapolis, IN). Manipulations of biological samples and protocols used: Ovariectomized female rats were treated by daily gavage for 3 weeks with the vehicle (20% 2-hydroxypropyl-β-cyclodextrin, Sigma, St Louis, MO), ethinyl estradiol (EE, 0.15 mg/kg; Sigma), estradiol benzoate (EB, 0.15 mg/kg; Sigma), equilin (EQ, 0.15 mg/kg; Sigma), tamoxifen (TAM, 3 mg/kg; Sigma), or raloxifene (RAL, 3 mg/kg; Eli Lilly & Co., Indianapolis, IN). After the final gavage treatment on day 21, the rats were deeply anesthetized with isoflurane and euthanized by decapitation. The mesenteric arterial tree was isolated, harvested, and stored in RNAlater (Ambion) at -80ºC. The mesenteric arteries were dissected free from veins and surrounding fat and homogenized in TRI reagent (MRC, Cincinnati, OH). Experimental factor: hormone treatment, drug treatment Technical protocols: The mesenteric arteries were minced with scalpels and TRI reagent (MRC) was added. The tissue was homogenized with a Polytron homogenizer. Bromochloropropane and sodium acetate were added, and the samples were centrifuged to separate the phases. The RNA-containing layer was removed and the RNA purified on an RNeasy extraction column (Qiagen). The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen). The purity and quantity were evaluated by an Agilent Bioanalyzer using the RNA 6000 Nanoassay LabChip. Labeled cRNA was prepared using the Message Amp II-Biotin Enhanced Kit from Ambion, following the manufacturer's Instruction Protocol. 5.0 microgram of rat mesenteric artery total RNA was mixed with bacterial control RNA spikes and primed with T7 oligo(dT) primer for 10 min at 70C. (The bacterial control spikes included araB, entF, fixB, gnd, hisB, and leuB.) The first strand of cDNA was synthesized with first strand buffer, dNTP mix, RNase inhibitor, and reverse transcriptase for 2 h at 42C. The second strand cDNA synthesis reaction was prepared using second strand buffer, dNTP mix, DNA polymerase mix, and RNase H; the reaction was carried out for 2h at 16C. The double-stranded cDNA was purified on spin columns included in the Ambion kit. The double-stranded cDNA was mixed with T7 reaction buffer, T7 ATP, T7 GTP, T7 UTP, T7 CTP, biotin-11-UTP, and T7 enzyme mix for the synthesis of cRNA. The cRNA synthesis reaction was terminated after 14h at 37C by purifying the cRNA on spin columns from the Ambion kit. The concentration of cRNA was determined by spectrophotometry. Hybridization procedures and parameters: 10 micrograms of biotinylated cRNA was mixed with fragmentation buffer and heated to 94C for 20 min. The fragmented cRNA was mixed with CodeLink hybridization buffer, loaded on the microarray slides (CodeLink Whole Rat Genome Bioarrays), and hybridized for 18 hours at 37C. The slides were washed in 0.75x TNT (Tris-HCl, NaCl, Tween-20) at 46C for 1h then incubated with streptavidin-Alexa 647 fluorescent dye for 30 min at room temperature. The streptavidin-Alexa 647 fluor was prepared in TNB blocking buffer (0.1M Tris-HCl, 0.15M NaCL, 0.5% NEN Blocking Reagent-PerkinElmer) The slides were then washed 4 times for 5 min each in 1x TNT and twice in 0.05% Tween 20 for 5 sec each. The slides were dried by centrifugation and scanned in an Axon GenePix 4000B scanner.

Project description:Endometriosis is an inflammatory disease and bone marrow-derived cells are abundant in endometriotic lesions and in the peritoneal fluid of women with the disease. This study tested the hypothesis that reciprocal communication occurs between macrophages and cultured human endometrial stromal cells and that this communication contributes to the pathology of endometriosis. Changes in gene expression elicited by exposure to factors secreted by the opposing cell type were measured by DNA microarray to test this hypothesis. 716 named genes were differentially expressed in cultured endometrial stromal cells in response to factors secreted by macrophages. Genes that were up-regulated included IL8/CXCL8, MMP3, phospholamban, CYR61/CCN1, CTGF/CCN2, tenascin C, and NNMT, whereas integrin alpha 6 was down-regulated. In contrast, 15 named genes were differentially expressed in macrophages in response to factors secreted by cultured endometrial stromal cells. The data document reciprocal communication between macrophages and endometrial stromal cells and suggest that interaction with macrophages stimulates the expression of genes in endometrial stromal cells that contribute to migration, adhesion, invasion, neovascularization and mitosis of endometrial cells that may support the establishment of endometriosis. Experiment Design: Goal of the experiment: To examine reciprocal communication between a telomerase-immortalized human endometrial stromal cell line (THESC, ATCC #CRL-4003) and U-937 macrophages (ATCC #CRL-1593.2 treated with phorbol ester to stimulate differentiation), and also to assess the response of THESC cells to estrogen plus progesterone. Keywords: human, cultured endometrial stromal cell line, macrophage Experimental factors: hormone treatment and treatment with macrophage-conditioned medium of endometrial stromal cells, treatment of macrophages with endometrial stromal cell conditioned medium Experimental design: T HESC cells were grown in phenol red-free DMEM/F12 medium supplemented with 1% ITS+, 10% charcoal-dextran treated fetal bovine serum albumin, 1% pen/strep, and 500 ng/ml puromycin. THESC cells were treated for 8 days with vehicle (0.1% ethanol) or estradiol (10-8 M) plus progesterone (10-7 M medroxyprogesterone acetate). On day 6, serum was removed from the culture medium. On day 7, half of the cells were treated with U-937 macrophage-conditioned medium for 24 hours. The cells were harvested and RNA extracted on day 8. The experiment was repeated with three different passages of cells (passages 9, 11, and 13) to yield an experimental n of 3. The four groups of cells were vehicle-treated control, estradiol + progesterone, control + macrophage-conditioned medium, and estradiol + progesterone + macrophage-conditioned medium. The monocytic cell line, U-937, was maintained in suspension in RPMI-1640 with 10% fetal bovine serum and 1% pen/strep. The U-937 cells were treated with 32 nM phorbol myristate acetate (PMA) for 48 h to stimulate differentiation into macrophages. The U-937 macrophages were treated with THESC conditioned medium or with non-conditioned control medium. Total RNA was collected after 24 hours. The experiment was repeated with three different passages of cells (passages 7, 9, and 12) to yield an experimental n of 3. The two experimental groups were macrophages treated with non-conditioned control medium and macrophages treated with THESC-conditioned medium. Quality control steps: The cRNA that was synthesized from each cultured cell passage and treatment was used for hybridization to a single CodeLink (Applied Microarrays) whole human genome microarray. Only one sample was hybridized with each slide and only one dye (streptavidin-Alexa 647) was used so no dye swaps were necessary. Bacterial control spikes were used per manufacturer's instructions. Samples used, extract preparation and labelling: The origin of each biological sample: The samples were telomerase-immortalized human endometrial stromal cells and human U-937 monocytic cell line differentiation into macrophages by treatment with phorbol ester. The cell lines were obtained from American Type Culture Collection (#CRL-4003 and #CRL-1593.2). Manipulations of biological samples and protocols used: T HESC cells were grown in culture in phenol red-free DMEM/F12 medium supplemented with 1% ITS+, 2% charcoal/dextran treated fetal bovine serum, 1% penicillin/streptomycin, and 500 ng/ml puromycin. The cells were treated for 8 days with vehicle (0.1% ethanol), estradiol (10-8 M) plus progesterone (10-7 M medroxyprogesterone acetate), vehicle + macrophage-conditioned medium, or estradiol (10-8 M) + progesterone (medroxyprogesterone acetate 10-7 M) + macrophage-conditioned medium. On day 6, serum was removed from the culture medium of all cells. On day 7, half of the cells were treated with macrophage-conditioned medium for 24 hours. The cells were harvested and RNA extracted on day 8. The experiment was repeated with three different passages of cells (passages 9, 11, and 13) to yield an experimental n of 3. The four groups of cells were vehicle-treated control, estradiol + progesterone, control + macrophage-conditioned medium, and estradiol + progesterone + macrophage-conditioned medium. To prepare macrophage-conditioned medium, U-937 (ATCC #CRL-1593.2) cells were grown in RPMI-1640 medium with 10% fetal bovine serum until the cells covered 80% of the flask surface. These U-937 cells were treated with 32 nM PMA for 48 h to stimulate differentiation into macrophages. Differentiated macrophages were maintained in phenol red-free, fetal bovine serum-free DMEM/F12 medium supplemented with 1% penicillin/streptomycin for 48 hours. The cell suspension was centrifuged and the conditioned medium was collected, filtered, and stored at -80C. Before use, macrophage-conditioned medium was supplemented with 1% ITS+ and puromycin. The monocytic cell line, U-937, was maintained in suspension in RPMI-1640 with 10% fetal bovine serum and 1% pen/strep. The U-937 cells were treated with 32 nM PMA for 48 h to stimulate differentiation into macrophages. The differentiated macrophages were treated with THESC conditioned medium or with non-conditioned control medium. Total RNA was collected after 24 hours. Experimental factor: hormone treatment, treatment with macrophage-conditioned medium, and treatment with T-HESC cell conditioned medium Technical protocols: The cells were rinsed and TRI reagent (MRC) was added to the culture flasks. The cells were scraped into centrifuge tubes, bromochloropropane and sodium acetate were added, and the samples were centrifuged to separate the phases. The RNA-containing layer was removed and the RNA purified on an RNeasy extraction column (Qiagen). The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen). The purity and quantity were evaluated by an Agilent Bioanalyzer using the RNA 6000 Nanoassay LabChip. Labelled cRNA was prepared using the Message Amp II-Biotin Enhanced Kit from Ambion, following the manufacturer's Instruction Protocol. 1.0 microgram of T-HESC cell total RNA or 2 micrograms of macrophage total RNA was mixed with bacterial control RNA spikes and primed with T7 oligo(dT) primer for 10 min at 70C. (The bacterial control spikes included araB, entF, fixB, gnd, hisB, and leuB.) The first strand of cDNA was synthesized with first strand buffer, dNTP mix, RNase inhibitor, and reverse transcriptase for 2 h at 42C. The second strand cDNA synthesis reaction was prepared using second strand buffer, dNTP mix, DNA polymerase mix, and RNase H; the reaction was carried out for 2h at 16C. The double-stranded cDNA was purified on spin columns included in the Ambion kit. The double-stranded cDNA was mixed with T7 reaction buffer, T7 ATP, T7 GTP, T7 UTP, T7 CTP, biotin-11-UTP, and T7 enzyme mix for the synthesis of cRNA. The cRNA synthesis reaction was terminated after 14h at 37C by purifying the cRNA on spin columns from the Ambion kit. The concentration of cRNA was determined by spectrophotometry. Hybridization procedures and parameters: 10 micrograms of biotinylated cRNA was mixed with fragmentation buffer and heated to 94C for 20 min. The fragmented cRNA was mixed with CodeLink hybridization buffer, loaded on the microarray slides, and hybridized for 18 hours at 37C. The slides were washed in 0.75x TNT (Tris-HCl, NaCl, Tween-20) at 46C for 1h then incubated with streptavidin-Alexa 647 fluorescent dye for 30 min at room temperature. The streptavidin-Alexa 647 fluor was prepared in TNB blocking buffer (0.1M Tris-HCl, 0.15M NaCL, 0.5% NEN Blocking Reagent-PerkinElmer) The slides were then washed 4 times for 5 min each in 1x TNT and twice in 0.05% Tween 20 for 5 sec each. The slides were dried by centrifugation and scanned in an Axon GenePix 4000B scanner.

Project description:Goal of the experiment: To examine differential gene expression in the iliac arteries of cynomolgous monkeys in the presence of small, medium, or large atherosclerotic plaque. Brief description of the experiment: Objective: To examine global gene expression patterns in the iliac arteries of monkeys containing small, medium, or large atherosclerotic plaque. Design: The left iliac artery of 12 ovariectomized cynomolgous monkeys on a high fat diet for 8 years was biopsied. Gene expression was analyzed by DNA microarray and real time RT-PCR. Results: Significant up- or down-regulation of 986 genes was observed in monkey iliac arteries in the presence of atherosclerotic plaque. Changes in gene expression with atherosclerosis ranged from 0.1-151.9-fold. Differentially expressed genes included many cytokines, chemokines, components of signal transduction pathways, and transcriptional activators and repressors, among others. Real time RT-PCR confirmed down-regulation of estrogen receptor 1 (ESR1), claudin 11, BH protocadherin 7 (PCDH7), and the up-regulation of apolipoprotein E (ApoE), growth differentiation factor 15 (GDF15), superoxide dismutase 2 (SOD2), SET domain, bifurcated 2 (SETDB2), phospholipase A2 group IIA (PLA2IIA), phospholipase A2 group VII (PLA2VII), and ring finger protein 149 (RNF149). Conclusions: The gene expression environment in arteries containing atherosclerotic plaque is profoundly different from that of arteries without atherosclerosis. The data suggest that the changes in gene expression contribute to the disease process in diseased arteries. Experimental factors: presence of disease (atherosclerosis) Experimental design: Female cynomolgous monkeys had been ovariectomized for 4 years and on a high fat diet for 8 years. The left iliac artery was removed at surgical biopsy. The presence and size of atherosclerotic plaque was quantified in the iliac arteries. Samples were divided categories based on plaque size; categories were small (0-0.113mm2, n=4), medium (0.30-0.542 mm2, n=5), and large (0.61-1.003 mm2, n=3) atherosclerotic plaques. Arterial tissue from the iliac arteries was used for DNA microarray analysis of gene expression. Quality control steps: The cRNA that was synthesized from each iliac artery was used for hybridization to a single CodeLink (Amersham/GE) whole human microarray. Only one sample was hybridized with each slide and only one dye (Alexa 647) was used so no dye swaps were necessary. Bacterial control spikes were used as per manufacturer's instructions. Samples used, extract preparation and labelling: The origin of each biological sample: The samples were iliac arterial tissue from cynomolgous monkeys. Manipulations of biological samples and protocols used: Cynomolgous monkeys were placed on a high fat diet 8 years before the experiment and ovariectomized 4 years prior to the experiment to induce a surgical menopause. The left iliac artery was surgically removed from each animal in the study. The presence and size of atherosclerotic plaque was quantified in the iliac arteries Experimental factor: size of atherosclerotic plaque Technical protocols: The iliac arteries were homogenized in TRI reagent, bromochloropropane and sodium acetate were added, and the samples were centrifuged to separate the phases. The RNA-containing layer was removed and the RNA purified on an RNeasy extraction column (Qiagen). The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen). The purity and quantity of RNA were evaluated by an Agilent Bioanalyzer using the RNA 6000 Nanoassay LabChip. Labelled cRNA was prepared using the MessageAmp II-Biotin enhanced kit (Ambion). 0.275 microgram of total iliac artery RNA was mixed with bacterial control RNA spikes and primed with T7 oligo(dT) primer for 10 min at 70C. (The bacterial control spikes included araB, entF, fixB, gnd, hisB, and leuB.) The first strand of cDNA was synthesized with first strand buffer, dNTP mix, RNase inhibitor, and reverse transcriptase for 2 h at 42C. The second strand cDNA synthesis reaction was prepared using second strand buffer, dNTP mix, DNA polymerase mix, and RNase H; the reaction was carried out for 2h at 16C. The double-stranded cDNA was purified on QIAquick columns (Qiagen) and the eluent was dried down in a SpeedVac concentrator. The double-stranded cDNA was resuspended in a mixture containing T7 reaction buffer, T7 ATP, T7 GTP, T7 UTP, T7 CTP, biotin-11-UTP, and T7 enzyme mix for the synthesis of cRNA. The cRNA synthesis reaction was terminated after 14h at 37C by purifying the cRNA on RNeasy columns (Qiagen). The concentration of cRNA was determined by spectrophotometry. Hybridization procedures and parameters: 10 micrograms of cRNA was mixed with fragmentation buffer and heated to 94C for 20 min. The fragmented cRNA was mixed with CodeLink hybridization buffer, loaded on the microarray slides, and hybridized for 18 hours at 37C. The slides were washed in 0.75x TNT (Tris-HCl, NaCl, Tween-20) at 46C for 1h then incubated with streptavidin-Alexa 647 fluorescent dye for 30 min at room temperature. The Alexa fluor was prepared in TNB blocking buffer (0.1M Tris-HCl, 0.15M NaCL, 0.5% NEN Blocking Reagent-PerkinElmer) The slides were then washed 4 times for 5 min each in 1x TNT and twice in 0.05% Tween 20 for 5 sec each. The slides were dried by centrifugation and scanned in an Axon GenePix 4000B scanner. Keywords: nonhuman primate, disease state analysis

Project description:Goal of the experiment: To examine differential gene expression in granulosa cells of women undergoing ovarian stimulation with either recombinant human follicle stimulating hormone or purified human menopausal gonadotropin for in vitro fertilization. Brief description of the experiment: The study was designed to test the hypothesis that human granulosa cell (GC) gene expression response differs between pure recombinant FSH and human menopausal gonadotropin (hMG) stimulation regimens. Women < 35 years-old undergoing in vitro fertilization for tubal or male factor infertility were prospectively randomized to one of two stimulation protocols, Gonadotropin releasing hormone (GnRH) agonist long protocol plus individualized dosages of (1) recombinant follicle stimulating hormone (rFSH) (Gonal-F®) (n=4) or (2) purified human menopausal gonadotropin (hMG; Menopur®; 75 IU FSH/75 IU LH per vial) (n=3). Follicle development was monitored by ultrasound and serum estradiol levels. When two follicles were ≥ 17mm, human chorionic gonadotropin (hCG) (10,000 IU; Novarel®) was administered. Oocytes were retrieved 35 h post-hCG. Following oocyte recovery, GC were immediately collected in RNALater®. Pooled GC from individual patients were washed, centrifuged over 40% Percoll®, resuspended in RNALater, and snap-frozen in LN. Total RNA was extracted and stored at -70C. Biotinylated cRNA was synthesized from total RNA and each sample was run individually on CodeLink Whole Human Genome Bioarrays (Applied Microarrays). Unnamed genes and genes with <2-fold difference in expression were excluded from further analysis. After exclusions, 1736 genes exhibited differential expression between groups. Over 400 were categorized as signal transduction genes, ~180 as transcriptional regulators, and ~175 as enzymes/metabolic genes. Expression of selected genes was confirmed by RT-PCR. Differentially expressed genes included A kinase anchor protein 11 (AKAP11), bone morphogenic protein receptor II (BMPR2), epidermal growth factor (EGF), insulin-like growth factor binding protein (IGFBP)-4, IGFBP-5, basigin, and hypoxia-inducible factor (HIF)-1 alpha. The results suggest that major differences exist in the mechanism by which pure FSH alone versus FSH/LH regulate gene expression in preovulatory GC that could impact oocyte maturity and developmental competence. Experimental design: Women < 35 years-old undergoing in vitro fertilization for tubal or male factor infertility were prospectively randomized to one of two stimulation protocols, Gonadotropin releasing hormone (GnRH) agonist long protocol plus individualized dosages of (1) recombinant follicle stimulating hormone (rFSH) (Gonal-F®) (n=4) or (2) purified human menopausal gonadotropin (hMG; Menopur®; 75 IU FSH/75 IU LH per vial) (n=3). Follicle development was monitored by ultrasound and serum estradiol levels. When two follicles were ≥ 17mm, human chorionic gonadotropin (hCG) (10,000 IU; Novarel®) was administered. Oocytes were retrieved 35 h post-hCG. Following oocyte recovery, GC were immediately collected in RNALater®. Pooled GC from individual patients were washed, centrifuged over 40% Percoll®, resuspended in RNALater, and snap-frozen in LN. Total RNA was extracted and stored at -70C. Biotinylated cRNA was synthesized from total RNA and each sample was run individually on CodeLink Whole Human Genome Bioarrays (Applied Microarrays Quality control steps: The cRNA that was synthesized from the granulosa cells from individual patients was used for hybridization to a single CodeLink (Applied Microarrays) Whole Human Genome microarray. Only one sample was hybridized with each slide and only one dye (Alexa 647) was used so no dye swaps were necessary. Bacterial control spikes were used as per manufacturer's instructions. Samples used, extract preparation and labelling: The origin of each biological sample: Granulosa cells from women < 35 years-old undergoing in vitro fertilization. Manipulations of biological samples and protocols used: Female patients were treated with gonadotropin releasing hormone (GnRH) agonist long protocol plus individualized dosages of (1) recombinant follicle stimulating hormone (rFSH) (Gonal-F®) (n=4) or (2) purified human menopausal gonadotropin (hMG; Menopur®; 75 IU FSH/75 IU LH per vial) (n=3). Follicle development was monitored by ultrasound and serum estradiol levels. When two follicles were ≥ 17mm, human chorionic gonadotropin (hCG) (10,000 IU; Novarel®) was administered. Oocytes were retrieved 35 h post-hCG. Following oocyte recovery, granulosa cells were immediately collected in RNALater®. Pooled GC from individual patients were washed, centrifuged over 40% Percoll®, resuspended in RNALater, and snap-frozen in LN. Experimental factor: treatment with recombinant FSH versus purified human menopausal gonadotropin Technical protocols: Granulosa cells were collected into RNAlater (Ambion) and stored at -80C until processed. The granulosa cells were pelleted by centrifugation to remove the RNAlater. Each cell pellet was homogenized in TRI reagent (Molecular Research Centers). Bromochloropropane and sodium acetate were added, and the samples were centrifuged to separate the phases. The RNA-containing layer was removed and the RNA purified on an RNeasy extraction column (Qiagen). The sample was treated with an on-column DNase treatment (RNase-free DNase, Qiagen). The purity and quantity were evaluated by an Agilent Bioanalyzer using the RNA 6000 Nanoassay LabChip. Labelled cRNA was prepared using the manufacturer's Instruction Protocol (www1.amershambiosciences.com, CodeLink Gene Expression System: Manual Labelled cRNA Target Preparation). The source of reagents was the CodeLink Expression Assay Reagent Kit, Manual Prep, except where specified otherwise. 0.285 micrograms of total granulosa cell RNA was mixed with bacterial control RNA spikes and primed with T7 oligo(dT) primer for 10 min at 70C. (The bacterial control spikes included araB, entF, fixB, gnd, hisB, and leuB.) The first strand of cDNA was synthesized with first strand buffer, dNTP mix, RNase inhibitor, and reverse transcriptase for 2 h at 42C. The second strand cDNA synthesis reaction was prepared using second strand buffer, dNTP mix, DNA polymerase mix, and RNase H; the reaction was carried out for 2h at 16C. The double-stranded cDNA was purified on QIAquick columns (Qiagen) and the eluent was dried down in a SpeedVac concentrator. The double-stranded cDNA was resuspended in a mixture containing T7 reaction buffer, T7 ATP, T7 GTP, T7 UTP, T7 CTP, biotin-11-UTP, and T7 enzyme mix for the synthesis of cRNA. The cRNA synthesis reaction was terminated after 14h at 37C by purifying the cRNA on RNeasy columns (Qiagen). The concentration of cRNA was determined by spectrophotometry. Hybridization procedures and parameters: 10 micrograms of cRNA was mixed with fragmentation buffer and heated to 94C for 20 min. The fragmented cRNA was mixed with CodeLink hybridization buffer, loaded on the microarray slides, and hybridized for 18 hours at 37C. The slides were washed in 0.75x TNT (Tris-HCl, NaCl, Tween-20) at 46C for 1h then incubated with streptavidin-Alexa 647 fluorescent dye for 30 min at room temperature. The Alexa fluor was prepared in TNB blocking buffer (0.1M Tris-HCl, 0.15M NaCL, 0.5% NEN Blocking Reagent-PerkinElmer) The slides were then washed 4 times for 5 min each in 1x TNT and once in 0.05% Tween 20 for 5 sec. The slides were dried by centrifugation and scanned in an Axon GenePix 4000B scanner.

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Gene expression profiles of cervical cancers for novel molecular classification

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Subtypes of cervical adenosquamous carcinomas classified by EpCAM expression related to radiosensitivity.

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