title: Expression Data from  Allogeneic Human Mesenchymal Stem Cells and Primary Cultures of Human Alveolar Epithelial Type II Cells

status: Public on Jul 08 2015

city: San Francisco

first: Michael

last: Matthay

state: California

address: 513 Parnassus Ave

department: CVRI

institute: UCSF

summary:
Acute lung injury (ALI) or acute respiratory distress syndrome (ARDS) is a severe syndrome affecting more than 200,000 patients annually in the U.S.  New studies are needed to understand the biological and clinical mechanisms that impair alveolar epithelial function. Also, innovative  therapies are needed for the resolution of pulmonary edema in ARDS. We and other investigators have reported that bone marrow derived mesenchymal stem cells (MSCs) are effective in preclinical models of ALI due to their ability to secrete several paracrine factors that can regulate lung endothelial and epithelial permeability, including growth factors, anti-inflammatory cytokines, and antimicrobial peptides. So in this study we will test the therapeutic value of human MSCs in an in vitro model of acute lung injury induced by pro-inflammatory cytokines.
We will identify differentially expressed genes in primary cultures of human alveolar epithelial type II cells and human bone marrow derived mesenchymal stem cells using Affymetrix gene expression arrays.

overall_design: Human mesenchymal stem cells (MSCs) and human alveolar epithelial type II cells were co-cultured in a transwell system. The cells were stimulated with cytomix (a combination of different pro-inflammatory cytokines) under different conditions. Cells were harvested for  Affymetrix gene expression arrays. Total 25 samples are analyzed, 3~5 replicates are included.

first: Ritu

last: Roy

first: Jaewoo

last: Lee

first: xiaohui

last: Fang


title: Expression data from insulin-treated human primary fibroblasts and effects of U0126 on insulin-induced gene expression

status: Public on Aug 03 2015

city: Ann Arbor

first: Isabel

middle: Xiaorong

last: Wang

state: Michigan

address: 210 washtenaw ave

department: Pediatrics&Genetics

country: USA

institute: HHMI/University of Michigan

summary:
We carried out a high throughput analysis of insulin-induced kinase signaling pathways in primary fibroblasts from 35 unrelated individuals.  We found that extensive individual variation exists in induction of various signaling pathways.  ERK signaling displayed the greatest variation, which led to extensive variation in expression of downstream target genes.
Our results suggest that phenotypic variation in kinase signaling mediates variation in downstream processes of insulin response.  Future study of such phenotypic variation is important to linking genetic variants to individual susceptibility to complex diseases such as diabetes.

overall_design:
Passage-matched primary fibroblasts from 35 unrelated newborns (foreskin) were treated with 100 nM insulin.   We measured gene expression levels in each of 35 individuals at baseline, and 1 hour and 6 hours after insulin treatment using expression arrays.
In order to examine effects of ERK inhibition on insulin-induced gene expression, we treated fibroblasts from 4 individuals with DMSO or 10uM of U0126 for 1 hour, followed by insulin treatment for one hour and 6 hours.  We then harvested cells and measured gene expression in each sample using expression arrays.

middle: X

first: Vivian

middle: G

last: Cheung


title: Genome-wide mRNA level and mRNA translation analysis of eIF4E silencing in MCF10A cells

status: Public on Jun 19 2015

city: New York

first: Robert

middle: J

last: Schneider

state: NY

address: 550 First Ave, MSB 238

department: Microbiology

institute: NYU School of Medicine

type:
Expression profiling by array
Other

summary: Translation initiation factor eIF4E is overexpressed early in breast cancers in association with disease progression and reduced survival.  Much remains to be understood regarding the role of eIF4E in human cancer. Using immortalized human breast epithelial cells, we report that elevated expression of elF4E translationally activates the TGFβ pathway, promoting cell invasion, loss of cell polarity, increased cell survival and other hallmarks of early neoplasia.  Overexpression of eIF4E is shown to facilitate selective translation of integrin β1 mRNA, which drives the translationally controlled assembly of a TGFβ receptor signaling complex containing α3β1 integrins, β-catenin, TGFβ receptor I, E-cadherin and phosphorylated Smads2/3.  This receptor complex acutely sensitizes non-malignant breast epithelial cells to activation by typically sub-stimulatory levels of activated TGFβ.  TGFβ can promote cellular differentiation or invasion and transformation.  As a translational coactivator of TGFβ, eIF4E confers selective mRNA translation, reprogramming non-malignant cells to an invasive phenotype by reducing the set-point for stimulation by activated TGFβ.  Overexpression of eIF4E may be a pro-invasive facilitator of TGFβ activity.

overall_design: MCF10A cells were subjected to consitutive silencing with a non-silencing control shRNA or an shRNA to eIF4E.  Total RNA, light polysomal RNA (2-3 ribosome fraction) and heavy polysomal RNA (greater than or equal to 4 ribosome fraction) were purified and used for hybridization to Affymetrix 133 2.0 Plus arrays. Data analysis was conducted using MicroArray Suite Software from Affymetrix. To remove probe sets with insignificant differences between perfect match and mismatch data, which creates a more robust data set of greater clarity without a high level of background noise, discrimination values for each probe pair were calculated for low intensity ratios using Wilcoxon signed rank test to assess significance and data re-assigned as either changed or unchanged mRNAs. Data sets were compared using Expressionist Suite software. Significance of mRNAs were assessed using fold changes and the FDRs estimated based on t-tests.


title: Host plant adaptation of a polyphagous herbivore shapes transcriptome of both herbivore and host

status: Public on Jul 21 2015

city: Gent

first: Nicky

last: Wybouw

address: Coupure Links 653

department: Department of Crop Protection

country: Belgium

institute: University of Ghent

summary:
In an experimental evolutionary set-up, we transferred a genetically diverse strain of the spider mite Tetranychus urticae from its common host bean to tomato where replicated populations were allowed to adapt.
By sampling the transcriptomes of non-adapted and adaptes mites feeding on bean and tomato, we identified gene-expression changes in the spider mite affiliated with tomato adaptation.
Transcriptional analysis revealed that both constitutive gene-expression levels as well as the transcriptional plasticity of genes were affected.
Specifically, tomato adaptation resulted in a large set of constitutively down-regulated genes of unknown function in adapted mites compared to non-adapted mites. Additionally, upon tomato exposure, adapted mites exhibited an increased transcriptional plasticity of genes coding for detoxifying enzymes and xenobiotic transporters. Remarkably, adapted mites further exhibited a differential effect on host plant physiology compared to non-adapted mites. Adapted mites induced a greater chlorotic area on tomato leaves and triggered attenuated induced responses relative to those induced by non-adapted mites.

overall_design: 12 comparisons were investigated; 3 biological replicates for 4 conditions: (1) NonAdapted-Induced (non-adapted 24 hrs on tomato vs non-adapted on bean); (2) Adapted-Tomato (adapted on tomato vs non-adapted on bean); (3) Adapted-2G Bean (adapted 2 generations on bean vs non-adapted on bean); (4) Adapted-2G Bean-Induced (adapted 2 generations on bean, 24 hrs on tomato vs non-adapted on bean).

first: Vladimir

last: Zhurov

first: Vojislava

last: Grbic

first: Thomas

last: Van Leeuwen


title: Large scale analysis of apple mealiness within IM apple progeny

status: Public on Jun 25 2015

city: Beaucouzé

first: Mathilde

last: ORSEL

address: 42, rue Georges Morel

country: France

institute: IRHS

summary: Based on sensorial analysis over 4 years, 6 apple genotypes with contrasted fruit texture (mealy or not) were selected among a progeny. Apple samples were collected at 100 days after flowering (100 DAF), harvest (H), after 2 and 4 months of cold storage (60DAH and 120DAH respectively).

overall_design: 6 apple hybrids were analysed in dye-switch. Biological replicates are fruits from 2 to 4 different harvest years. Each mealy hybrid was compared to a non-mealy hybrid from the same harvest year in 12 dye-swap 3 pairs at 4 four time points).

first: Sandrine

last: Mikol

first: Maryline

last: Bruneau

first: Jean-Marc

last: Celton

first: Céline

last: Gourdon

first: Jean-Pierre

last: Renou

last: Orsel


title: Gene Expression Data in Pediatric Burkit lymphoma patients

status: Public on Jun 04 2015

city: Valhalla

first: Sanghoon

address: 40 Sunshine Cottage Road, Vos 145

department: Pediatrics

institute: New York Medical College

summary: Gene expression profiling of Peditric Burkitt lymphoma (PBL) patients samples were performed to analyze the comparative genomic signature and to investigate targetable signaling pathways in PBL

overall_design: 11 primary tumor specimens were obtained from Pediatric Burkitt lymphoma (PBS) patients and samples were hybridized to HGU133A2. Genechip (Affymetrix)

first: S

first: N

middle: S

last: Day

first: R

middle: R

last: Miles

middle: L

last: Perkins

first: M

last: Lim

first: J

last: Ayello

first: C

last: van de Ven

first: W

last: Sanger

first: L

last: Harrison

last: El-Mallawany

last: Goldman

last: Cairo


title: The phosphorylated prodrug FTY720 is a histone deacetylase Q15 inhibitor that reactivates ERα expression and enhances hormonal therapy for breast cancer

status: Public on Jun 03 2015

city: Jacksonville

first: Catherine

last: Dumur

state: FL

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

summary: Nuclear FTY720-P is a potent inhibitor of class I histone deacetylases (HDACs) that enhances histone acetylations and regulates expression of a restricted set of genes independently of its known effects on canonical signaling through sphingosine-1-phosphate (S1P) receptors. We found that FTY720 is phosphorylated in Era-negative breast cancer cells by nuclear sphingosine kinase 2 and accumulates these cells.

overall_design: To determine whether FTY720-P inhibits HDACs in Era-negative breast cancer cells and in tumors to regulate histone acetylation and gene expression, and it can re-express ERα in these aggressive breast carcinoma for hormonal therapies.

first: Sarah

last: Spiegel

first: Nitai

last: Hait

middle: I


title: Gene expression profiles after induced Id3 levels in A431 squamous carcinoma cells

status: Public on Jun 30 2015

city: Washington

first: Rosenthal

last: Dean

state: DC

address: 3900 Reservoir Rd., NW

department: Biochemistry and Molecular & Cellular Biology

institute: Georgetown University

summary:
Previously it has been shown that Id3 can act as an apoptosis-inducer gene in immortalized human keratinocytes.  To further investigate the role of Id3 in the progression of skin cancer, the role of Id3 in A431 cells is investigated through ectopic induction of Id3.
Microarray analysis is used to guide us the genes and pathways that are significantly altered after Id3 induction.

overall_design: 4 groups are included in this study, each with one sample.  There are two cell lines: A431 cells stably transfected with Id3 or control vector.  In each cell line, there are two conditions: induced and un-induced with tetracycline.

first: You-Shin

last: Chen

first: Fen-Pi

last: Chou

first: Cynthia

middle: M

last: Simbulan-Rosenthal

first: Dean

last: Rosenthal


title: Gene expression during early infection of the resistant winter wheat cultivar Dream with Fusarium graminearum, the major causal agent of fusarium head blight in wheat

city: Ottawa

first: Thérèse

last: Ouellet

state: ON

address: 960 Carling Ave, room 2091

department: Eastern Cereal and Oilseed Research Centre

country: Canada

institute: Agriculture and Agri-Food Canada

summary: Fusarium head blight (FHB) is a major disease of cereal crops caused by the fungus Fusarium graminearum (Fg). FHB affects the flowering heads (or spikes).  This study compare the gene expression profile in wheat spikelets from the resistant winter wheat cultivar Dream inoculated with water (H2O) or Fg.

overall_design: We used the Affymetrix wheat array to compare wheat spikelets from the resistant winter wheat cultivar Dream inoculated with water (H) or Fg, using the point inoculation method; samplings were done at 0 and 4 days (d) after inoculation, for 3 biological replicates

first: Sigrun

last: Gulden


title: Gene expression during early infection of the resistant spring wheat cultivar NuyBay with Fusarium graminearum, the major causal agent of fusarium head blight in wheat

summary: Fusarium head blight (FHB) is a major disease of cereal crops caused by the fungus Fusarium graminearum (Fg). FHB affects the flowering heads (or spikes).  This study compare the gene expression profile in wheat spikelets from the resistant spring wheat cultivar NuyBay inoculated with water (H2O) or Fg.

overall_design: We used the Affymetrix wheat array to compare wheat spikelets from the resistant spring wheat cultivar NuyBay inoculated with water (H) or Fg, using the point inoculation method; samplings were done at 1, 2 and 4 days (d) after inoculation, for  2 biological replicates

first: Li

last: Wang


title: Gene expression in near isogenic spring wheat lines carrying or not the 2DL FHB resistance QTL during early infection with Fusarium graminearum, the major causal agent of fusarium head blight in wheat

summary: Fusarium head blight (FHB) is a major disease of cereal crops caused by the fungus Fusarium graminearum (Fg). FHB affects the flowering heads (or spikes).  This study compare the gene expression profile in wheat spikelets from near isogenic spring wheat lines carrying or not the FHB resistance QTL 2DL, after inoculation with water (H2O) or Fg; two inoculation methods were also compared, point and spray inoculation.

overall_design: We used the Affymetrix wheat array to compare wheat spikelets from the near isogenic spring wheat lines 2-2890 (nul for FHB resistance QTLs 2DL, 3BS and 5A), 2-2618 (carrying 2DL QTL; nul for QTLs 3BS, 5A; sister line to 2-2890) and 2-2674 (nul for QTLs 2DL, 3BS and 5A), after inoculation with water (H2O) or Fg. Two inoculation methods were also compared, point and spray inoculation.  Samplings were done at 4 days (d) after inoculation, for 2 (point inoculation) or 3 (spray inoculation) biological replicates


title: Gene expression in near isogenic spring wheat lines carrying different combinaison of the FHB resistance QTLs 2DL, 3BS and 5A during early infection with Fusarium graminearum, the major causal agent of fusarium head blight in wheat

summary: Fusarium head blight (FHB) is a major disease of cereal crops caused by the fungus Fusarium graminearum (Fg). FHB affects the flowering heads (or spikes).  This study compare the gene expression profile in wheat spikelets from near isogenic spring wheat lines carrying different combinaison of the FHB resistance QTLs 2DL, 3BS and 5A, after inoculation with water (H2O) or Fg; the point inoculation method was used.

overall_design: We used the Affymetrix wheat array to compare wheat spikelets from the near isogenic spring wheat lines (all sister lines) 2890 (null for FHB resistance QTLs 2DL, 3BS and 5A), 2618 (carrying 2DL QTL; null for QTLs 3BS, 5A), 2598 (carrying 3BS QTL; null for QTLs 2DL, 5A), 2543 (carrying 2DL and 3BS QTLs; null for QTL 5A), 2557 (carrying 2DL and 5A QTLs; null for QTL 3BS), and 2614 (carrying 2DL, 3BS and 5A QTLs), after inoculation with water (H2O) or Fg.  the point inoculation method was used.  Samplings were done at 4 days (d) after inoculation, for 2 or 3 biological replicates.


title: Gene expression during early infection of the susceptible spring wheat cultivar Roblin with Fusarium graminearum strains producing or not DON.

summary: Fusarium head blight (FHB) is a major disease of cereal crops caused by the fungus Fusarium graminearum (Fg). FHB affects the flowering heads (or spikes).  This study compare the gene expression profile in wheat spikelets from the very susceptible spring wheat cultivar Roblin inoculated with either water (H2O), a Fg strain (GZ3639) producing the mycotoxin deoxynivalenol (+DON), or a GZ3639-derived Fg strain which has been inactivated at the Tri5 locus  (-DON).

overall_design: We used the Affymetrix wheat array to compare wheat spikelets from the very susceptible spring wheat cultivar Roblin inoculated with either water (H), a Fg strain (GZ3639; also called DAOM 233423) producing the mycotoxin deoxynivalenol (+DON,) or a GZ3639-derived Fg strain (Tri5-; also called DAOM 221141) which has been inactivated at the Tri5 locus  (-DON), using the point inoculation method; samplings were done at 2 and 4 days (d) after inoculation, for 2 (H) or 3 (+DON and -DON) biological replicates.

first: Margaret

last: Balcerzak


title: Gene expression in wheat heads treated with Fusarium graminearum mutants that produce a priming-induced resistance to fusarium head blight

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Gene expression in wheat heads treated  with the mutant noxABΔ of Fusarium graminearum, which produces a priming-induced resistance to fusarium head blight

status: Public on Jun 02 2015

summary:
Fusarium head blight (FHB) is a major disease of cereal crops caused by the fungus Fusarium graminearum (Fg). FHB affects the flowering heads (or spikes) and developing seeds.  This study compares the gene expression profile of heads from the susceptible cultivar Roblin after inoculation with either water (dH2O) or the disarmed Fg strain noxABΔ (NoxAB).  noxABΔ is a double deletion mutant of NoxA and NoxB, which function are component of the NADPH oxidase enzyme complex converting molecular oxygen in a stepwise reduction to superoxides leading to the production of H2O2.
Deletion mutants of Nos A and B have been described in more details in Li Wang, Christopher Mogg, Sean Walkowiak, Manisha Joshi & Rajagopal Subramaniam (2014).  Characterization of NADPH oxidase genes NoxA and NoxB in Fusarium graminearum. Can. J. Plant Pathol. 36: 12-21, DOI: 10.1080/07060661.2013.868370.   This manuscript characterizes the role of the catalytic subunit (gp91phox) of Nox, NoxA and NoxB in F. graminearum. Targeted deletion of NoxA and NoxB show that these genes differentially regulate the production of superoxides during mycelia development. The nitro blue tetrazolium staining revealed that both the single noxA mutant and the double noxA/B mutant strains are restricted in the production of superoxides. This limitation, however, did not affect their ability to synthesize 15-ADON in culture. Deletion analyses also revealed that NoxA, but not NoxB is involved in perithecia development and ascospore production.  An in-vitro based cellophane breach assay indicated that both NoxA and NoxB contribute to virulence. The pathogenicity tests performed on a susceptible variety of wheat, ‘Roblin’ confirmed that these two genes act synergistically to promote virulence. Cumulatively, we provide evidence that the Nox homologues have non-redundant functions in F. graminearum.

overall_design: We used the Affymetrix wheat array to compare gene expression in wheat spikelets from the susceptible cultivar Roblin.  One central spikelet (F0) per head was inoculated with either water (dH2O) or the disarmed Fg strain noxABΔ (NoxAB) using a point inoculation method.  Sampling was done at 48 hours after inoculation. Spikelets F0 and F2 relative to inoculation point were sampled separately. Three biological replicates were done for each condition.

first: Rajagopal

last: Subramaniam


title: Gene expression during early infection by Fusarium graminearum in wheat lines susceptible and resistant to fusarium head blight


title: A novel combination of serum microRNAs for detecting breast cancer in the early stage

status: Public on Jan 21 2016

city: Kanagawa

first: Satoko

last: Takizawa

state: Kamakura

country: Japan

institute: Toray Industries, Inc.

summary: MicroRNAs (miRNAs), which are stably present in serum, have been reported to be potentially useful for detecting cancer. In the present study, we examined the expression profiles of serum miRNAs in large cohorts to identify the miRNAs that can be used to detect breast cancer in the early stage. We comprehensively evaluated serum miRNA expression profiles using highly sensitive microarray analysis. A total of 1,280 serum samples of breast cancer patients stored in the National Cancer Center Biobank were used. Additionally, 2,836 serum samples were obtained from non-cancer controls and 514 from patients with other types of cancers or benign diseases. The samples were divided to a training cohort including non-cancer controls, other cancers and breast cancer and a test cohort including non-cancer controls and breast cancer. The training cohort was used to identify a combination of miRNAs that detect breast cancer, and the test cohort was used to validate that combination. miRNA expression was compared between breast cancer and non-breast cancer serum , and a combination of five miRNAs (miR-1246, miR-1307-3p, miR-4634, miR-6861-5p, and miR-6875-5p) was found to detect breast cancer. This combination had a sensitivity of 97.3%, specificity of 82.9%, and accuracy of 89.7% for breast cancer in the test cohort Additionally, the combination could detect breast cancer in the early stage (sensitivity of 98.0% for T0).

overall_design: 1280 breast cancer serums (74 in training cohort, 1206 in test cohort), 54 benign breast diseases serums in test cohort, 2836 non-cancer control serums (1493 in training cohort, 1343 in test cohort), 514 non-breast benign diseases serums in training cohort. 150 of the non-cancer control serums in training cohort and 412 of the non-breast benign diseases serums in training cohort have been uploaded previously and are avaialable under GSE59856 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59856).

first: Akihiko

last: Shimomura

first: Sho

last: Shiino

first: Junpei

last: Kawauchi

first: Hiromi

last: Sakamoto

first: Makiko

last: Ono

first: Fumitaka

last: Takeshita

first: Shumpei

last: Niida

first: Chikako

last: Shimizu

first: Yasuhiro

last: Fujiwara

first: Takayuki

last: Kinoshita

first: Kenji

last: Tamura

first: Takahiro

last: Ochiya

first: Juntaro

last: Matsuzaki


title: Gene expression during early infection of the resistant spring wheat cultivar Wuhan1 with Fusarium graminearum, the major causal agent of fusarium head blight in wheat

first: Thérèse

last: Ouellet

summary: Fusarium head blight (FHB) is a major disease of cereal crops caused by the fungus Fusarium graminearum (Fg). FHB affects the flowering heads (or spikes).  This study compare the gene expression profile in wheat spikelets from the resistant spring wheat cultivar Wuhan1 inoculated with water (H2O) or Fg.

overall_design: We used the Affymetrix wheat array to compare wheat spikelets from the resistant spring wheat cultivar Wuhan1 inoculated with water (H) or Fg, using the point inoculation method; samplings were done at 1, 2 and 4 days (d) after inoculation, for 1 (1d) or 2 (2 and 4d) biological replicates

first: Li

last: Wang


title: Gene expression during early infection of the susceptible spring wheat cultivar Roblin with Fusarium graminearum, the major causal agent of fusarium head blight in wheat

summary: Fusarium head blight (FHB) is a major disease of cereal crops caused by the fungus Fusarium graminearum (Fg). FHB affects the flowering heads (or spikes).  This study compare the gene expression profile in wheat spikelets from the very susceptible spring wheat cultivar Roblin inoculated with water (H2O) or Fg.

overall_design: We used the Affymetrix wheat array to compare wheat spikelets from the very susceptible spring wheat cultivar Roblin inoculated with water (H) or Fg, using the point inoculation method; samplings were done at 1, 2 and 4 days (d) after inoculation, for 2 biological replicates


title: Gene expression profiles of hepatocyte-like cells derived from induced pluripotent stem cells (iPSCs) from donors with the Zellweger spectrum of peroxisome biogenesis disorders (PBD-ZSD) and healthy controls

status: Public on May 21 2015

city: Los Angeles

first: Joseph

middle: Gerard

last: Hacia

state: CA

address: 2250 Alcazar Street, IGM 261

department: Biochemistry and Molecular Biology

institute: University of Southern California

summary:
Skin fibroblasts from individuals with PBD-ZSD, a rare autosomal recessive disorder caused by peroxisome assembly defects, show defects in lipid metabolism that provide the basis for clinical diagnostic tests, but are not among the cell types most affected by disease. To explore phenotypes of more clinically relevant cell types, skin fibroblasts from PBD-ZSD patients and healthy controls were reprogrammed into iPS cells with all the hallmark properties of pluripotency. Subsequently, iPSCs were differentiated into ASGPR-positive hepatocyte-like cells that were subject to flow cytometry and subject to gene expression profiling.
We report the gene expression profiles of hepatocyte-like cells derived from iPSCs that were themselves derived from skin fibroblasts from PBD-ZSD patient donors and healthy controls.

overall_design: The overall goal was to evaluate gene expression biomarkers of hepatocyte-like cells derived from PBD-ZSD patients and healthy controls. Dermal fibroblast cultures from 2 PBD-ZSD patients and 1 healthy control were reprogrammed into iPSCs by transfection with retroviruses designed to express the human OCT4, SOX2, KLF4 and c-MYC cDNA (see GEO entry GSE43996). Hepatic cell lineages were derived following the protocol of Duan (Duan Y, Catana A, Meng Y, Yamamoto N, He S, Gupta S et al. Stem Cells. 2007;25:3058-68; Duan Y, Ma X, Zou W, Wang C, Bahbahan IS, Ahuja TP et al. Stem Cells. 2010;28:674-86) with modifications. Total RNA samples from flow-sorted ASGPR-positive candidate hepatocyte-like cells obtained from healthy (control1) and PBD-ZSD patient (PBD_PEX1ms1 and PBD_PEX1fs1) donors were processed and analyzed on Affymetrix Human Genome 133A 2.0 microarrays.

first: Xiao-Ming


title: caArray_golub-00142: Gene expression correlates of clinical prostate cancer behavior

status: Public on May 15 2015

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

summary: Prostate tumors are among the most heterogeneous of cancers, both histologically and clinically. Microarray expression analysis was used to determine whether global biological differences underlie common pathological features of prostate cancer and to identify genes that might anticipate the clinical behavior of this disease. While no expression correlates of age, serum prostate specific antigen (PSA), and measures of local invasion were found, a set of genes was identified that strongly correlated with the state of tumor differentiation as measured by Gleason score. Moreover, a model using gene expression data alone accurately predicted patient outcome following prostatectomy. These results support the notion that the clinical behavior of prostate cancer is linked to underlying gene expression differences that are detectable at the time of diagnosis.

overall_design:
golub-00142
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HG_U95Av2
Organism: Homo sapiens (ncbitax)


title: caArray_golub-00392: Gefitinib (Iressa) induces myeloid differentiation of acute myeloid leukemia

status: Public on May 16 2015

summary: Cure rates for patients with acute myeloid leukemia (AML) remain low despite ever-increasing dose intensity of cytotoxic therapy. In an effort to identify novel approaches to AML therapy, we recently reported a new method of chemical screening based on the modulation of a gene expression signature of interest. We applied this approach to the discovery of AML-differentiation-promoting compounds. Among the compounds inducing neutrophilic differentiation was DAPH1 (4,5-dianilinophthalimide), previously reported to inhibit epidermal growth factor receptor (EGFR) kinase activity. Here we report that the Food and Drug Administration (FDA)-approved EGFR inhibitor gefitinib similarly promotes the differentiation of AML cell lines and primary patient-derived AML blasts in vitro. Gefitinib induced differentiation based on morphologic assessment, nitro-blue tetrazolium reduction, cell-surface markers, genome-wide patterns of gene expression, and inhibition of proliferation at clinically achievable doses. Importantly, EGFR expression was not detected in AML cells, indicating that gefitinib functions through a previously unrecognized EGFR-independent mechanism. These studies indicate that clinical trials testing the efficacy of gefitinib in patients with AML are warranted.

overall_design:
golub-00392
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HG-U133A, HG-U133A_2
Organism: Homo sapiens (ncbitax)
Material Types: cell, total_RNA, synthetic_RNA, organism_part, whole_organism*Cell Types:
Disease States: Acute Myeloid Leukemia, Normal, Acute Myeloid Leukemia


title: In vivo gene expression changes in EW5 Ewing sarcoma xenografts after IGF-1R or mTOR blockade

status: Public on Apr 02 2015

city: Houston

middle: A.

last: Ludwig

state: Texas

department: Sarcoma Medical Oncology

institute: UT-MD-Anderson Cancer Center

summary: Ewing Sarcoma is caused by a pathognomonic genomic translocation that places an N-terminal EWSR1 gene in approximation with one of several ETS genes (typically FLI1). This aberration, in turn, alters the transcriptional regulation of more than five hundred genes and perturbs a number of critical pathways that promote oncogenesis, cell growth, invasion, and metastasis. Among them, translocation-mediated up-regulation of the insulin-like growth factor receptor 1 (IGF-1R) and mammalian  target of rapamycin (mTOR) are of particular importance since they work in concert to facilitate IGF-1R expression and ligand-induced activation, respectively, of proven importance in ES transformation. When used as a single agent in Ewing sarcoma therapy, IGF-1R or mTOR inhibition leads to rapid counter-regulatory effects that blunt the intended therapeutic purpose. Therefore, identify new mechanisms of resistance that are used by Ewing sarcoma to evade cell death to single-agent IGF-1R or mTOR inhibition might suggest a number of therapeutic combinations that could improve their clinical activity.

overall_design: Male non-obese diabetic (NOD)-SCID-IL-2Rgnull mice were used to generate EW5 explants (2 mm). Mice bearing subcutaneous tumors were randomized into treatment and control groups when their tumors reached a diameter of 6 mm and received MK-8669 (mTOR inhibitor, 5mg/kg per dose, once weekly), MK-0646 (IGF-1R inhibitor monoclonal antibody, 0.5mg IP twice weekly), or a placebo control (sterile buffer). Animals were treated either until their tumors reached 1500 mm3 in volume. Affymetrix Geneship profiling of EW5 xenografts treated in vivo either with MK-0646, MK-8669, and control and compared each other using extracted RNA and hybridized on Affymetrix microrrays ( Affymetrix Human Genome U133A 2.0 cartridge arrays).

first: Salah-Eddine

last: Lamhamedi-Cherradi

first: Brian

middle: A

last: Menegaz

first: Vandhana

last: Ramamoorthy


title: Transcriptome analysis in nutrient deficient wheat roots

status: Public on Apr 01 2015

city: Harpenden

first: Astrid

last: Gruen

address: Rothamsted Research

department: Plant Biology and Crop Science

country: United Kingdom

institute: Rothamsted Research

summary:
Microarrays were used to identify transcriptional responses in field-grown root material of wheat in order to dissect specific gene expression responses to limited macronutrient availability, particularly phosphate.
This study fills the gap between the transcriptome studies on model plants and the lack of studies on soil-grown wheat aiming to identify candidate genes for enhancing nutrient uptake efficiency.
The work at Rothamsted Research is supported via the 20:20 Wheat® Programme by the UK Biotechnology and Biological Sciences Research Council. The contribution was supported by BIONUT-ITN and the research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement no. 264296.

overall_design: T. aestivum cv. Hereward root material was excavated in triplicates in May 2011 at booting stage from sections 0 and 1 plots representing continuous wheat plots of the “Broadbalk” field experiment at Rothamsted Research, UK (http://www.rothamsted.ac.uk/sample-archive/guide-classical-and-other-long-term-experiments-datasets-and-sample-archive). The distinct peculiarity of these plots, including a control plot with nutrient replete wheat plants, is the withdrawal of N, P, K, Mg and S fertilizers exposing the plants to multiple long-term nutrient deficiencies and  representing 6 treatments ; 12 samples were analysed.

first: Peter

last: Buchner

first: Malcolm

last: Hawkesford

first: Martin

last: Broadley


title: Gene expression during priming-induced resistance to fusarium head blight in wheat as revealed by two distinct mutants of Fusarium graminearum

status: Public on May 28 2015

summary: Fusarium head blight (FHB) is a major disease of cereal crops caused by the fungus Fusarium graminearum (Fg). FHB affects the flowering heads (or spikes) and developing seeds.  This study compare the gene expression profile in wheat spikelets (spk 2) inoculated with either water (mock treatment) or a pathogenic strain of Fusarium graminearum (WT); spikelets 2 were inoculated 24 hrs after a neighbour spikelet (spk 0) was treated with either water or F. graminerum mutant strain Tri6Δ or NoxABΔ. Spikelets 2 were sampled 8 and 24 hrs after the second treatment.

overall_design: We used the Affymetrix wheat array to compare gene expression in wheat spikelets from the susceptible cultivar Roblin. Individual Roblin heads were inculated first in a spikelet at mid anthesis (spk 0) with water (H20) or F. graminerum mutant strain Tri6Δ or NoxABΔ , followed 24 hrs later by a second inoculation in spikelet 2 (spk 2) of the same heads with either water or a pathogenic strain of F. graminearum (WT). Point inoculation was used for the treatments; sampling of spikelets 2 was done at 8 and 24 hrs after the second inoculation, with  3 biological replicates for each treatment combination.

first: Michael

last: Ravensdale

first: Hélène

last: Rocheleau

first: Rajagopal

last: Subramaniam


title: CD34 negative populations are associated with an increased relapse risk in childhood AML and harbor chemo-resistant leukemia stem cells

status: Public on Mar 01 2015

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

institute: Durham University

summary: Differences in chemo-sensitivity of subpopulations of AML stem cells could have important clinical implications. Using in vitro cytotoxicity, xenograft models and colony forming assays, we compared chemotherapy sensitivity between Lineage (Lin-)CD34-CD38-, Lin-CD34-CD38+, Lin-CD34+CD38- and Lin-CD34+CD38+ populations from 26 primary AMLs (19 paediatric and 7 adult). We identified a common recurring pattern of chemo-response associated with a poor clinical outcome: In each of 16/26 (62%) AMLs, Lin-CD34-CD38- cells were the most chemoresistant of the four subpopulations to daunorubicin in vitro. Cytarabine-resistant colonies formed only from Lin-CD34-CD38- populations following tertiary passages through both NOG mice and methylcellulose in these AMLs The presence of chemo-resistant Lin-CD34-CD38- populations was signficantly associated with reduced relapse-free survival in childhood AML. Consistently, CD34 negativity was significantly associated with an increased risk of relapse in a larger retropsective cohort (n=89). Samples enriched for chemo-resistant Lin-CD34-CD38- LSCs with a stem cell profile and an undifferentiated genotype revealed pathways likely to confer chemo-resistance, These strongly indicated dependence of chemo-resistant Lin-CD34-CD38- LSCs on their niche environment as well as deregulated DNA damage responses, lipid and Notch1 signalling, Our findings have major implications for the risk stratification of childhood AML and could lead to the development of novel therapeutic approaches.

overall_design: 3 subpopulations of leukemia stem cells from 9 patients with primary childhood AML were analysed. We compared gene expression profiles of Lin-CD34+CD38- (Q1), Lin-CD34+CD38+ (Q2) and Lin-CD34-CD38- (Q3) cells between 3 AMLs in which the CD34+ cells were most chemo-resistant (AML-1P, AML-6P and AML-10P) and the same cells from the remaining AMLs in which the Lin-CD34-CD38- cells were the most chemo-resistant population. We also compared the gene expression profiles of Lin-CD34-CD38- (Q3) cells in the 3 samples with the highest LC50 values (AML-15P, AML-17P and AML-19P) with that of the 3 AMLs exhibiting the lowest LC50 values (AML-2P, AML-5P and AML-11P).

first: Victoria

last: Weston

first: Tracey

last: Perry

first: Katie

last: Brown

first: Khaleda

last: Yasmeen

first: Shaun

last: Wilson

first: Sally

last: Jeffries

first: Jenny

last: Jesson

first: Lisa

last: Eyre

first: Philip

last: Short

first: Oliver

last: Ziff

first: Francis

last: Mussai

first: Daniel

last: White

first: Adam

last: Stevens

first: Mike

last: Griffiths

first: A

last: Taylor

first: Tatjana

last: Stankovic

first: Stefan

last: Meyer

first: Sarah

last: Lawson

first: Pamela

last: Kearns


title: caArray_becic-00235: Gene expression alterations in prostate cancer predicting tumor aggression and preceding development of malignancy

status: Public on May 06 2015

first: Mervi

last: Heiskanen

summary: The incidence of prostate cancer is frequent, occurring in almost one-third of men older than 45 years. Only a fraction of the cases reach the stages displaying clinical significance. Despite the advances in our understanding of prostate carcinogenesis and disease progression, our knowledge of this disease is still fragmented. Identification of the genes and patterns of gene expression will provide a more cohesive picture of prostate cancer biology. PATIENTS AND METHODS: In this study, we performed a comprehensive gene expression analysis on 152 human samples including prostate cancer tissues, prostate tissues adjacent to tumor, and organ donor prostate tissues, obtained from men of various ages, using the Affymetrix (Santa Clara, CA) U95a, U95b, and U95c chip sets (37,777 genes and expression sequence tags). RESULTS: Our results confirm an alteration of gene expression in prostate cancer when comparing with nontumor adjacent prostate tissues. However, our study also indicates that the gene expression pattern in tissues adjacent to cancer is so substantially altered that it resembles a cancer field effect. CONCLUSION: We also found that gene expression patterns can be used to predict the aggressiveness of prostate cancer using a novel model.

overall_design:
becic-00235
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HG_U95A, HG_U95Av2, HG_U95B, HG_U95C
Organism: Homo sapiens (ncbitax)
Material Types: synthetic_RNA, organism_part, whole_organism, total_RNA
Disease States: Normal, Prostate_Adenocarcinoma


title: Gene expression in wheat heads treated  with the mutant tri6Δ of Fusarium graminearum, which produces a priming-induced resistance to fusarium head blight

first: Thérèse

last: Ouellet

summary: Fusarium head blight (FHB) is a major disease of cereal crops caused by the fungus Fusarium graminearum (Fg). FHB affects the flowering heads (or spikes) and developing seeds.  This study compares the gene expression profile of heads from the susceptible cultivar Roblin after inoculation with either water (W) or the disarmed Fg strain tri6Δ (T6). Tri6 is a global transcription regulator affecting the trichothecene biosynthesis pathway.

overall_design: We used the Affymetrix wheat array to compare gene expression in wheat spikelets from the susceptible cultivar Roblin.  One central spikelet (F0) per head was inoculated with either water (W) or the disarmed Fg strain tri6Δ (T6) using a point inoculation method.  Sampling was done at 0, 24 and 48 hours after inoculation. Spikelets F0, F2 and F4 relative to inoculation point were sampled separately. Three biological replicates were done for each condition.

first: Hélène

last: Rocheleau

first: Rajagopal

last: Subramaniam


title: InVERT molding for scalable control of tissue micro-architecture

status: Public on Jan 04 2015

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

summary: Complex tissues contain multiple cell types that are hierarchically organized within morphologically and functionally distinct compartments. Construction of engineered tissues with optimized tissue architecture has been limited by tissue fabrication techniques, which do not enable versatile microscale organization of multiple cell types in tissues of size adequate for physiologic studies and tissue therapies. Here, we present an ‘Intaglio-Void/Embed-Relief Topographic (InVERT) molding’ method for microscale organization of many cell types, including induced pluripotent stem cell (iPS)-derived progeny, within a variety of synthetic and natural extracellular matrices and across tissues of sizes appropriate for in vitro, pre-clinical, and clinical biologic studies. We demonstrate that compartmental placement of non-parenchymal cells relative to primary or iPS-derived hepatocytes and hepatic compartment microstructure and cellular composition modulate hepatic functions. Configurations found to be optimal in vitro also result in superior survival and function after transplantation into mice, demonstrating the importance of architectural optimization prior to implantation.

overall_design: Two replicates of iPS-Hepatocytes cultured alone for 1 day or co-cultured with mouse  J2 stromal cells for 1 day. One replicate of a mixture of iPS-Hepatocytes cultured alone for 1 day and then combined with J2 stromal cell RNA after RNA purification. Pure J2 stromal cell RNA was also hybridized to they Human chips but those hybridizations did not produce usable data and have not been included in this study.

first: K

first: M

middle: D

last: Ungrin

first: R

middle: E

last: Schwartz

first: B

last: Carvalho

last: Christine

last: Chaturvedi

first: C

middle: Y

last: Li

first: P

middle: W

last: Zandstra

last: Chen

first: S

middle: N

last: Bhatia


title: Expression data of PGR isoforms, PRA and PRB, regulated genes in differentiating human endometrial stromal cells

status: Public on Apr 27 2015

city: Urbana

first: Milan

middle: K

last: Bagchi

state: IL

address: 407 S. Goodwin Ave

department: MIP

institute: UIUC

summary: gene expression at 6h of differentiation of Human endometrial stromal cell expressing either or both of PRA and PRB

overall_design: Endogenous PGR expression is silenced with siRNA mediated knockdown. Then, cells are transduced with adenovirus exressing flag tagged PRA or flag tagged PRB. Human endometrial stromal cell expressing one or both isoforms are treated with differentiation cocktail for 6h.

first: Hatice

last: Kaya

first: Indrani


title: Transcription profiling of human skin squamous cell carcinoma (SCC)

status: Public on Dec 31 2014

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

country: Italy

institute: Fondo Edo Tempia

summary: Skin squamous cell carcinomas are among the most frequent human cancers. In this study we compared the expression profiles of 10 skin SCCs with a set of 3 normal human epidermis controls.

overall_design: Total RNA from 10 surgically excised skin SCCs were analyzed in parallel with a set of 3 normal human epidermis controls.

first: Yang

last: Brooks

first: Gian

last: Dotto


title: Integrating mRNA and miRNA Co-Expression Networks with eQTLs in the Nucleus Accumbens of Human Chronic Alcoholics

status: Public on May 22 2015

city: Richmond

first: Vladimir

last: Vladimirov

state: VA

address: 800 E Leigh ST

department: Psychiatry

institute: Virginia Commonwealth University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Alcohol consumption is known to lead to gene expression changes in the brain. After performing gene co-expression network analysis (WGCNA) of genome-wide mRNA and microRNA expressions in the Nucleus Accumbens (NAc) from subjects with alcohol dependence (AD) and matched controls six mRNA and three miRNA modules significantly correlated with AD after Bonferroni correction (adj. p≤ 0.05) were identified. Cell-type-specific transcriptome analysis revealed two of the mRNA modules to be enriched for neuronal specific marker genes and downregulated in AD, whereas the remaining four were enriched for astrocyte and microglial specific marker genes and were upregulated in AD. Using gene set enrichment analysis, the neuronal specific modules were enriched for genes involved in oxidative phosphorylation, mitochondrial dysfunction and MAPK signaling, while the glial-specific modules were enriched mostly for genes involved in processes related to immune functions, i.e. reactome cytokine signaling in immune system (all adj. p≤ 0.05). In the mRNA and miRNA modules, 461 and 25 candidate hub genes were identified, respectively. In contrast to the expected miRNAs’ biological functions, the correlation analyses between mRNA and miRNA hub genes revealed a significantly higher number of positive than negative correlations (chi-square p≤ 0.0001). At FDR≤ 0.1, integration of the mRNA and miRNA hubs genes expression with genome-wide genotypic data identified 591 cis-eQTLs and 62 cis-eQTLs for the mRNA and miRNA hubs, respectively. Adjusting for the number of tests, the mRNA cis-eQTLs were significantly enriched for AD GWAS signals in the Collaborative Study on Genetics of Alcohol (COGA) sample (adj. p=0.024), providing a novel biological role for these association signals. In conclusion, our study identified coordinated mRNA and miRNA co-expression changes in the NAc of AD subjects, and our genetic (cis-eQTL) analysis provides novel insights into the etiological mechanisms of AD.

platform_organism:
Homo sapiens
synthetic construct

overall_design: Tissue samples were received from the Australian Brain Donor Programs New South Wales Tissue Resource Centre, which is supported by The University of Sydney, National Health and Medical Research Council of Australia, Schizophrenia Research Institute, National Institute of Alcohol Abuse and Alcoholism, and the New South Wales Department of Health. Cases were excluded if they had an infectious disease (i.e. HIV/AIDS, hepatitis B or C, or Creutzfeldt-Jakob disease), an unsatisfactory agonal status determined from the circumstances surrounding the death, post-mortem delays >48 hours, or significant head injury. In addition to case status, age, sex, ethnicity, brain weight, brain pH, post-mortem interval (PMI), tissue hemisphere, clinical cause of death, blood toxicology at time of death, smoking status, neuropathology and liver pathology were also provided for each subject. MiRNA and mRNA expression in 18 matched case-control pairs (N=36) with sample RINs ≥6  were assessed on the Affymetrix GeneChip® Human Genome U133A 2.0 (HG-U133A 2.0) and Affymetrix GeneChip miRNA 3.0 microarray.

first: Brien

middle: P

last: Riley


title: Celecoxib, rofecoxib treated human smooth muscle cells microarray timecourse

status: Public on Apr 20 2015

city: Philadelphia

first: Emanuela

last: Ricciotti

state: PA

address: 3400 Civic Center Blvd.

department: Department of Pharmacology/Institute for Translational Medicine and Therapeutics

institute: University of Pennsylvania

summary: The aim of this data set is to measure the effect of rofecoxib and celecoxib on the transcription profile in an in vitro inflammation model. Transcription profiling was carried out using Affymetrix HG U-133A v2 microarrays.

overall_design: Human aortic smooth muscle cells (3F1243) were pre-treated with rofecoxib (500 nM) or celecoxib (500 nM) for two hours and subsequently exposed to IL-1beta (10 ng/ml). Transcription profiling was carried out at several time points of IL-1beta exposure: Four samples at -2 hours. Four samples each of control, celecoxib, and rofecoxib at each time point 0hr, 2hr, 8hr and 24hr. 52 samples in total.

first: Tilo

last: Grosser

first: Thomas

last: Price

first: Garret

last: Fitzgerald


title: Distinct human stem cell populations in small and large intestine

status: Public on Jan 15 2015

city: Pittsburgh

first: William

middle: Armand

last: LaFramboise

address: 5230 Centre Avenue

department: Pathology

institute: University of Pittsburgh

summary: The intestine is composed of an epithelial layer, containing rapidly proliferating cells that mature into two distinct anatomic regions, the small and the large intestine. Although previous studies have identified stem cells as the cell-of-origin for the whole intestine, no studies have compared stem cells derived from the small and large intestine. Here, we report intrinsic differences between these two populations of cells.  Primary epithelial cells isolated from human fetal small and large intestine and expanded with Wnt agonist, R-spondin 2, displayed differential expression of stem cell markers and separate hierarchical clustering of gene expression involved in differentiation, proliferation and disease pathways. Using a three-dimensional in vitro differentiation assay, single cells derived from small and large intestine formed distinct organoid architecture with cellular hierarchy similar to that found in primary tissue. Our characterization of human fetal intestinal stem cells defies the classical definition proposed by most where small and large intestine are repopulated by an identical epithelial stem cell and raises the question of the importance of intrinsic and extrinsic cues in the development of intestinal diseases.

overall_design: 12 samples were analyzed. They consisted of human fetal small and large intestine (SI; n=6 and LI; n=6) stem cells, expanded with Wnt agonist and R-spondin 2. Differential expression of genes in epithelial cells from both the large and small intestine were observed.

first: Julie

last: Cramer


title: Comprehensive profiling of amino acid response uncovers unique methionine-deprived response dependent on intact creatine biosynthesis

first: Xiaohu

last: Tang

state: NC

address: CIEMAS Rm 2133, 101 Science Dr.

department: Department of Molecular Genetics and Microbiology

institute: Duke University

summary: Besides being building blocks for protein synthesis, amino acids serve a wide variety of cellular functions, including acting as metabolic intermediates for ATP generation and for redox homeostasis. Upon amino acid deprivation, free uncharged tRNAs trigger GCN2-ATF4 to mediate the well-characterized transcriptional amino acid response (AAR). However, it is not clear whether the deprivation of different individual amino acids triggers identical or distinct AARs. Here, we characterized the global transcriptional response upon deprivation of one amino acid at a time. With the exception of glycine, which was not required for the proliferation of MCF7 cells, we found that the deprivation of most amino acids triggered a shared transcriptional response that included the activation of ATF4, p53 and TXNIP. However, there was also significant heterogeneity among different individual AARs. The most dramatic transcriptional response was triggered by methionine deprivation, which activated an extensive and unique response in different cell types. We uncovered that the specific methionine-deprived transcriptional response required creatine biosynthesis. This dependency on creatine biosynthesis was caused by the consumption of S-Adenosyl-L-methionine (SAM) during creatine biosynthesis that helps to deplete SAM under methionine deprivation and reduces histone methylations. As such, the simultaneous deprivation of methionine and sources of creatine biosynthesis (either arginine or glycine) abolished the reduction of histone methylation and the methionine-specific transcriptional response. Arginine-derived ornithine was also required for the complete induction of the methionine-deprived specific gene response. Collectively, our data identify a previously unknown set of heterogeneous amino acid responses and reveal a distinct methionine-deprived transcriptional response that results from the crosstalk of arginine, glycine and methionine metabolism via arginine/glycine-dependent creatine biosynthesis.

overall_design: RNA was extracted by RNAeasy kits (Qiagen) from the MCF7 or PC3 cells which exposed to the control full DMEM or deprived one (or all) amino acid media for 24 or 48 hours.

first: Jen-Tsan

last: Chi


title: Expression data from human pluripotent stem cells treated with PluriSIn#2

status: Public on Jan 01 2015

city: Jerusalem

first: Uri

last: Ben-David

address: Givat-Ram

department: Genetics

country: Israel

institute: Hebrew University

summary: Pluripotent-specific inhibitors (PluriSIns) make a powerful tool for studying the mechanisms that control the survival of human pluripotent stem cells (hPSCs). Here we characterize PluriSIn#2 as a novel selective indirect inhibitor of topoisomerase II alpha (TOP2A). We find that TOP2A is uniquely expressed in undifferentiated hPSCs, and that its inhibition results in their rapid cell death. These findings reveal a dependency of hPSCs on the activity of TOP2A, which can be harnessed for their selective elimination from culture.

overall_design: Expression data from undifferentiated human embryonic stem cells treated with PluriSIn#2 or vehicle.

first: Nissim

last: Benvenisty


title: Whole-transcript expression data of BRD4 inhibition in uveal melanoma

status: Public on Feb 19 2015

city: New York

first: Grazia

last: Ambrosini

address: 1130 St. Nicholas Ave

institute: Columbia University

summary:
G protein alpha q and 11 are mutated in 80% of uveal melanoma. We observed that treatment with the BRD4 inhibitor JQ1 resulted in different phenotypic responses in G-protein mutant uveal melanoma cell lines and wild type uveal melanoma cell lines.
We used microarrarys to profile the gene expression changes occuring in wild type and mutant cell lines in response to treament with JQ1

overall_design: Uveal melanoma cells were profiled in triplicate on Affymetrix Human Genome U133A 2.0 Array arrays per manufacturer's instructions

first: Elgilda

last: Musi

first: Ashley

last: Sawle

first: Gary

last: Schwartz


title: An Immune and Inflammation Signature in Prostate Tumors of Smokers (part 1)

status: Public on Apr 22 2015

city: bethesda

first: Stefan

last: Ambs

state: md

address: 37 convent cir

institute: NIH

summary: Current smokers develop metastatic prostate cancer more frequently than nonsmokers, suggesting that a tobacco-derived factor induces metastasis. To identify smoking-induced alterations in human prostate tumors, we analyzed gene and protein expression of tumors from current, past, and never smokers and observed distinct molecular alterations in current smokers. Specifically, an immune and inflammation signature was identified in prostate tumors of current smokers that was either attenuated or absent in past and never smokers. Key characteristics of this signature included augmented immunoglobulin expression by tumor-infiltrating B cells, NF-kB activation, and increased interleukin-8 in tumor and blood. In an alternate approach to characterize smoking-induced oncogenic alterations, we explored the effects of nicotine in prostate cancer cells and prostate cancer-prone TRAMP mice. These experiments showed that nicotine increases both invasiveness of human prostate cancer cells and metastasis in tumor-bearing TRAMP mice, indicating that nicotine can induce a phenotype that resembles the epidemiology of smoking-associated prostate cancer progression. In summary, we describe distinct oncogenic alterations in prostate tumors from current smokers and show that nicotine can enhance prostate cancer metastasis.

overall_design: Prostate tissues of cancer patients were selected for RNA extraction and hybridization on Affymetrix microarrays. Gene expression profiles of current, past and never smokers were compared.

first: Wei


title: Expression data from normal myometrium, leiomyomata, and leiomyosarcomas

status: Public on Jan 08 2015

first: Douglas

last: Levine

address: 1275 York Ave.

department: Surgery

institute: MSKCC

summary: The molecular etiology of uterine leiomyosarcoma (ULMS) is poorly understood, which accounts for the wide disparity in outcomes among women with this disease.  We examined and compared the molecular profiles of ULMS, fibroids, and normal myometrium (NL) to identify clinically relevant molecular subtypes.  RNA was hybridized to Affymetrix U133A 2.0 transcription microarrays.  Differentially expressed genes and pathways were identified using standard methods.

overall_design: RNA was extracted from frozen tissues and hybridized to microarrays.  Unsupervised and supervised analyses were performed using standard methods.

first: Jeff

last: Boyd


title: Gene expression profiles of fibroblasts and induced pluripotent stem cells (iPSCs) from individuals with Zellweger spectrum disorder (ZSD), a class of peroxisome biogenesis disorder, and healthy controls

status: Public on Mar 24 2015

first: Joseph

last: Hacia

summary: Zellweger spectrum disorder (PBD-ZSD) is a disease continuum caused by mutations in a subset of PEX genes required for normal peroxisome assembly and function. Their clinical manifestations highlight the importance of peroxisomes in the development and functions of the central nervous system, liver, and other organs. We reprogrammed skin fibroblasts from PBD-ZSD patients into induced pluripotent stem cells (iPSCs) and report their gene expression profiles as well as those of matching healthy controls.

overall_design: Dermal fibroblast cultures from 6 PBD-ZSD patient and 3 healthy control donors were reprogrammed into iPSCs by transfection with retroviruses designed to express the human OCT4, SOX2, KLF4 and c-MYC genes.  Fibroblasts and iPSCs were cultured in 1:1 ratio of DMEM:F12 medium supplemented with 20% KSR at 37°C with 5% CO2 until confluence for RNA extraction. The overall goal was to identify genes that are differentially expressed between PBD-ZSD patient and healthy control cells in order to gain insights into the pathomechanisms of disease.

first: Xiao-Ming

last: Wang

middle: G


title: ECOG 5998, trial of immunosupressives for the treatment of Large Granular Lymphocyte Leukemia

status: Public on Dec 29 2014

city: Hershey

first: Penn State

last: COM

address: 500 University Drive

department: Genome Sciences Facility

institute: Penn State College of Medicine

summary: Eastern Clinical Oncology Group trial number 5998 determined the efficacy of the immunosupressives methotrexate (step 1) and cylophosphamide (step 2) in the treatment of Large Granular Lymphocyte leukemia.  Expression data from pre-treatment samples were evaluated for a priori ability to predict treatment response to Step 1 and for correlation with STAT3 mutation types predictive of response.  Method:  patient PBMCs from Ficoll, normal patient PBMCS enriched for CD3+/CD8+ or CD3+/CD8+/CD45RA+/CCR7- were extracted in Trizol.  Conclusion:  A gene expression profile was associated with response to treatment with evidence of particular STAT3 mutations driving this expression profile and response.

overall_design: Total RNA from patient Peripheral Blood Mononuclear Cells (PBMC) negatively enriched CD3+/CD8+  or negatively enriched CD3+/CD8+/CCR7-/CD45RA+(CD45RO-)

first: Thomas

last: Olson

first: Robert

last: Brucklacher

last: Loughran


title: An Immune and Inflammation Signature in Prostate Tumors of Smokers (part 2)

overall_design: 22RV1 and LnCap in three replicates were treated with 100uM nocotine for 24 hours and then compared the global gene expression profiles.

last: Tang


title: MicroRNA markers for the diagnosis of pancreatic and biliary tract cancers

city: Kamakura

first: Ichikawa

last: Makiko

state: Kanagawa

institute: Toray Industries, Inc.

summary: MicroRNAs from serum samples could detect pancreatic and biliary tract cancer patients more accurately than other traditional markers.

overall_design: Prospective miRNA markers for pancreatic/biliary tract cancer were selected in the training cohort. Using these miRNAs, discriminant analysis was performed, and the diagnostic accuracy, sensitivity and specificity were calculated in the test cohort.

first: Motohiro

last: Kojima

first: Hiroko

last: Sudo

first: Junpei

last: Kawauchi

first: Satoko

last: Takizawa

first: Satoshi

last: Kondou

first: Hitoshi

last: Nobumasa

first: Atsushi

last: Ochiai


title: Expression data of Wnt3a stimulated K562 cells after CXXC5 overexpression or knockdown

status: Public on Mar 20 2015

city: London

first: Andrea

last: Kuehnl

address: Great Maze Pond

institute: King's College London

summary:
CXXC5 inhibits the canonical Wnt signaling pathway
Impact of CXXC5 on Wnt stimulated gene expression in K562 cells

overall_design: K562 cells were incubated with recombinant Wnt3a protein after overexpression (transient transfection of pEGFP-CXXC5 vector) or knockdown of CXXC5 (stable lentiviral infection of  CXXC5 shRNA (pLKO.1; clone TRCN0000144558 and TRCN0000142729)

last: Kuhnl

first: Matthew

last: Arno

first: Erick

last: Nasser


title: Transcriptional profiling of Triticea seed and vegetative tissues

status: Public on Dec 24 2014

city: Lethbridge

first: Carolyn

last: Penniket

state: Alberta

institute: Agriculture & Agri-Food Canada

summary:
Despite their importance, there remains to be few large scale expression-based studies of tissue-specific expression information in the species belonging to the Triticeae.
We used the 55K Affymetrix GeneChip® Wheat Genome Array to generate a gene expression atlas of triticale tissues.  The global transcriptional profiles of seed tissues (embryo, endosperm, crease, pericarp and epiderm) and vegetative tissues (root, coleoptile, stem and leaf) were analyzed and co-regulated as well as preferentially expressed genes were identified. Data analysis revealed both novel and conserved regulatory factors underlying Triticeae tissue development and function.

sample_organism: Secale cereale x Triticum turgidum subsp. durum

overall_design: Triticale seed (embryo, endosperm, crease, pericarp and epiderm) and vegetative tissues (root, coleoptile, leaf and stem) were collected and analyzed using the 55K Affymetrix Wheat Genome array. All seed tissues were collected at the soft dough stage of seed development.  Vegetative tissues were collected at multiple stages of development.  Root and coleoptile tissues  were collected at early development (Zadoks' stage 7), and leaf tissue was collected at five successive stages ranging from seedling to late senescence and stem tissue was collected at four successive stages stages ranging from initial tillering to early senescence. Between two to five biological replicates for each tissue were analyzed.

first: Francis

last: Tran

first: L

middle: B

last: Selinger

first: N

middle: J

last: Provart

middle: S

last: Robert

first: André

last: Laroche


title: Comparative transcriptome analysis of wheat embryo and endosperm response to ABA and H2O2 stresses during seed germination

status: Public on Dec 11 2014

city: Beijing

first: Yonglong

last: Yu

address: 105 Xisanhuan North Road

country: China

institute: College of Life Science, Capital Normal University

summary:
Wheat seed germination directly affects wheat yield and quality. The wheat grains mainly include embryo and endosperm, and both play important roles in seed germination, seedling survival and subsequent vegetative growth. ABA can positively regulate dormancy induction and then negatively regulates seed germination at low concentrations. H2O2 treatment with low concentration can promote seed germination of cereal plants. Although various transcriptomics and proteomics approaches have been used to investigate the seed germination mechanisms and response to various abiotic stresses in different plant species, an integrative transcriptome analysis of wheat embryo and endosperm response to ABA and H2O2 stresses has not reported so far. We used the elite Chinese bread wheat cultivar Zhenmai 9023 as material and performed the first comparative transcriptome microarray analysis between embryo and endosperm response to ABA and H2O2 treatments during seed germination using the GeneChip® Wheat Genome Array
Wheat seed germination includes a great amount of regulated genes which belong to many functional groups. ABA/H2O2 can repress/promote seed germination through coordinated regulating related genes expression. Our results provide new insights into the transcriptional regulation mechanisms of embryo and endosperm response to ABA and H2O2 treatments during seed germination

overall_design: The six groups including embryo and endosperm response to pure water (CK), ABA and H2O2 were havested respectively, which were CK_embryo (CKem), CK_endosperm (CKe), ABA_embryo (ABAem), ABA_endosperm (ABAe), H2O2_embryo (H2O2em), H2O2_endosperm (H2O2e). Three independent experiments were performed for each group.

first: Shu

last: Wang


title: Expression data from BCL-3 overexpression HaCat cells

status: Public on Nov 04 2014

city: Liege

first: Alain

last: Chariot

state: Liege

address: Avenue de l'hopital

institute: University of Liege

summary:
Constitutive activation of EGFR- and NF-kB-dependent pathways is a hallmark of cancer, yet signaling proteins that connect both oncogenic cascades are poorly characterized. Here we define KIAA1199 as a BCL-3- and p65-dependent gene in transformed keratinocytes. KIAA1199 expression is enhanced upon human papillomavirus (HPV) infection and is aberrantly expressed in clinical cases of cervical (pre)neoplastic lesions. Mechanistically, KIAA1199 binds Plexin A2 and protects from Semaphorin 3A-mediated cell death by promoting EGFR stability and signaling. Moreover, KIAA1199 is an EGFR-binding protein and KIAA1199 deficiency impairs EGF-dependent Src, MEK1 and ERK1/2 phosphorylations. Therefore, EGFR stability and signaling to downstream kinases requires KIAA1199. As such, KIAA1199 promotes EGF-mediated epithelial-mesenchymal transition (EMT). Taken together, our data define KIAA1199 as an oncogenic protein induced by HPV infection and constitutive NF-kB activity that transmits pro-survival and invasive signals through EGFR signaling.
We used microarrays to detail the global programme of gene expression upon BCL-3 overexpression

overall_design: We used two experimental conditions, namely HaCat cells infected with a control lentivirus as well as HaCat cells infected with a BCL-3 expressing construct. Both experimental conditions were in triplicates.

first: Xin

last: Zhang

first: Benoît

last: Hennuy


title: Combination of epigenetic, differentiation and DNA damaging agents induce tumor cell death and stem cell depletion in breast cancer

status: Public on Nov 18 2014

city: Baltimore

first: Saraswati

last: Sukumar

address: 1650 Orleans St, CRB 1, Rm 132

department: Breast Cancer Program

institute: Johns Hopkins School of Medicine

summary: Gene expression profiles were performed on MDA-MB-231 TNBC cell line treated with entinostast, all-trans retinoic acid (ATRA), and doxorubicin as single, double, and triple combinations using Illumina.

overall_design: Treatment signatures were made from each drug treatment and integrated to find a comprehensive view of changes associated with the epigenetic, differentiation and chemotherapy combination

first: Vanessa

middle: F

last: Merino

first: Soonweng

last: Cho

first: Nguyen

last: Nguyen

first: Zhe


title: PBMC gene expression of early onset of the first demyelinating event of acute optic neuritis

status: Public on Oct 22 2014

city: Ramat-Gan

first: Michael

last: Gurevich

address: Tel-Hashomer

department: Multiple Sclerosis Center

institute: Sheba Medical Center

summary:
Optic neuritis (ON) is a common manifestation of multiple sclerosis (MS); it appears as the presenting symptom in about 25% of MS patients and occurs in 30–70% of patients with MS during the course of their illness
Purpose. To evaluate the molecular pathways that operate in the early phase of acute ON by studying gene expression profiles of peripheral blood mononuclear cells (PBMCs) subpopulations including CD19+ B cells, CD14+ macrophages, CD4+ and CD8+ T cells.

overall_design: High throughput gene expression analysis was performed on periferal mononuclear blood cells (PBMC) samples from 6 patients within 96 hours of the acute onset of the first demyelinating event of optic neuritis and 9 age matched healthy subjects using Affymetrix Inc. technology

first: Anna

last: Feldman

first: Ruth

last: Huna-Baron

first: Anat

last: Achiron


title: Comparative transcriptional profiling of developing wheat grains with contrasting levels of minerals

status: Public on Oct 31 2014

city: Mohali

first: Sudhir

last: Singh

state: Punjab

address: NABI, C127, Indus Area, Phase8

country: India

institute: National Agri-Food Biotechnology Institu

summary: Transcriptional comparison of developing grains between two wheat genotypes with contrasting levels of minerals in grain, using Affymetrix GeneChip® Wheat Genome Array.

overall_design: Gene expression data of two wheat genotypes with high and low grain mineral concentration at two seed development stages (14, and 28 days after anthesis)

first: Jitendra

last: Kumar

first: Raja

last: Jeet

first: Vishnu

last: Shukla

first: Shrikant

last: Mantri

first: Rakesh

last: Tuli


title: Expression data from cells with siRNA-mediated knockdown of OPG and from HVSMCs incubated with RANKL or TRAIL

status: Public on Sep 22 2014

city: Roskilde

first: Vibe

last: Skov

address: Koegevej 7-13

department: Hematology

country: Denmark

institute: Roskilde Hospital

summary: We used microarrays to assess gene expression changes in cells with siRNA-mediated knockdown of OPG compared to normal cells. Furthermore, we used microarrays to assess gene expression in cells treated with either RANKL or TRAIL compared to vehicle-treated cells.

overall_design: Total RNA was purified from cells and amplified to biotin-labeled aRNA and hybridized to microarray chips.

first: Malene

last: Olesen


title: Expression data from glioblastoma stem-like cells (GSCs) and astrocyte co-cultured GSCs

status: Public on Nov 07 2014

city: Bethesda

first: Barbara

middle: Helen

last: Rath

address: 10 Center Drive B3B406

department: National Cancer Institute

institute: National Institute of Health

summary:
consequences of astrocytes on GSCs, gene expression profiles generated from glioblastoma stem-like cells grown alone (mono-culture) and compared to those generated 48h after the initiation of co-culture with astrocytes
We used microarrays show that astrocytes are capable to modify via a paracrine mechanism  GSC gene expression and thus phenotype.

overall_design:
GSCs were seeded into 6-wellplates  with astrocytes onto the corresponding trans-well inserts.  Co-cultures were initiated by combining the inserts and the 6-well plates; 48h later RNA was collected from GSCs.  RNA was collected from three biological replicates was processed and subjected to microarray analysis on Human Genome U133A 2.0 chips.
NSC11:  glioblastoma stem-like cells isolated from human glioblastoma surgical specimen patient 1
GBAM1: glioblastoma stem-like cells isolated from human glioblastoma surgical specimen patient 2

middle: H

first: Philip

last: Tofilon


title: RECK Controls Breast Cancer Metastasis by Modulating a Convergent, STAT3-dependent Neoangiogenic Switch

status: Public on Sep 01 2014

first: Logan

middle: A

last: Walsh

state: NY

address: 1275 York Ave

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

summary: Metastasis leads to the majority of deaths in breast cancer patients. Here we investigated the molecular and biochemical signaling pathways altered by RECK, a major metastasis suppressor gene in breast cancer.  We overexpressed RECK in 2 highly invasive cell lines and knocked-down RECK expression in 2 poorly invasive cell lines. IPA analysis of differentially expressed genes revealed IL-6, and IL8 signaling alteration with RECK pertubation. This lead us to discover that RECK suppresses metastasis and neoangiogenesis at secondary sites by inhibiting STAT3 dependent VEGF & uPA regulating. This finding is significant because it reveals the biology behind a major metastasis suppressor gene in cancer.

overall_design: Cell lines were obtained from the ATCC or were generous gifts from Dr Joan Massague (MSKCC). Invasive cell lines were stably infected with a constitutively expressing RECK construct or and Empty Vector control. Poorly invasive cell lines were transfected with a Scramble siRNA or siRNA targeting the RECK gene. RNA was extracted using the RNeasy kit (Qiagen) as per the manufacturer’s instructions. Expression analysis was performed using the Affymetrics U133 2.0 microarray (Affymetrix). Affymetrix CEL files were imported into the Partek Genomics Suite (Partek).

first: David

middle: M

last: Roy

first: Marsha

last: Reyngold

first: Dilip

last: Giri

first: Alexandra

last: Snyder

first: Sevin

last: Turcan

first: Chaitanya

middle: R

last: Badwe

first: Jaclyn

last: Lyman

first: Jacqueline

last: Bromberg

first: Tari

last: King

first: Timothy

last: Chan


title: Transcriptome profile of GEN2.2 cell line after CpG stimulation

status: Public on Jul 30 2014

city: Granada

first: Pedro

last: Carmona

address: Avda. de la Ilustración 114

country: Spain

institute: GENYO

summary:
Analysis of expression profile of human GEN2.2 cell line cultured in the presence of CpG for 2 h.
RNA expression profile of the human pDC cell line GEN2.2  after CpG stimulation

overall_design: Total RNA was isolated from GEN2.2 cells growing at log phase with High Pure RNA isolation Kit (Roche Diagnostics, Mannheim, Germany), according with the manufacturer´s instructions in triplicate. GEN2.2 cells were stimulated with 1 µM ODN2006 (Life Technologies) for 2h. A total of 300 ng of total RNA was processed using Illumina TotalPrep RNA Amplification Kit. Hybridization of human samples was performed on Illumina Human-HT12 Version 4.

first: Concepcion

last: Marañon


title: Cellular and Molecular Immune Profiles in Renal Transplant Recipients after Conversion from Tacrolimus to Sirolimus

status: Public on Sep 17 2014

city: Jacksonville

first: Catherine

last: Dumur

state: FL

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

summary:
Tacrolimus and Sirolimus are commonly used to maintain immunosuppression in kidney transplantation.  However, their effects on immune cells and allograft molecular profiles have not been elucidated.
Here we characterized the effects of Tacrolimus to Sirolimus conversion on frequency and function of T cells, and on graft molecular profiles.

overall_design: Samples from 30 renal transplant recipients in a randomized trial of late Sirolimus conversion (n=18) vs. Tacrolimus maintenance (n=12) were utilized.  Peripheral blood was collected at 0- 6- 12 and 24-months post-randomization.  This dataset only contains the 18 arrays corresponding to patients treated with Sirolimus.

first: Valeria

last: Mas

middle: I

first: Daniel

last: Maluf


title: Expression data for miR-33a over-expression in CD133-negative D456MG cells

status: Public on Jul 17 2014

city: Durham

first: Hui

last: Wang

address: 380 Research Drive

institute: Duke University

summary:
MiR-33a is involved in the maintenance of Glioma Initiating Cells (GIC) and tumor progression. MicroRNA-33a could promote GIC growth and self-renewal by regulating two pathways including cAMP/PKA pathway and Notch pathway. We used microarrays to identify the direct target genes of miR-33a in a glioblastoma cell line D456MG.
We used microarrays to detail the global change of gene expression after miR-33a over-expression and identified target genes during this process.

overall_design: Cells were infected with lenti-virus expressing a control vector (pWPXLD) or human primary miR-33a. Then RNA was extracted and gene expression was profiled by Affymetrix microarray.

first: Tao

last: Sun

first: Jing

last: Hu


title: Analysis of global changes in gene expression induced by human polynucleotide phosphorylase (hPNPaseold-35)

status: Public on Jun 01 2014

summary:
Human Polynucleotide Phosphorylase (hPNPaseold-35) is an evolutionarily conserved 3’→5’ exoribonuclease implicated in the regulation of numerous physiological processes like maintenance of mitochondrial homeostasis, mtRNA import and aging-associated inflammation.
From an RNase perspective, little is known about the RNA or miRNA species it targets for degradation or whose expression it regulates; except for c-myc and miR-221.

overall_design: To further elucidate the functional implications of hPNPaseold-35 in cellular physiology, we knocked-down and overexpressed hPNPaseold-35 in melanoma and HeLa cells, resectively, and performed gene expression analyses to identify differentially expressed transcripts. Biological triplicates were run on microarrays.

first: Paul

last: Fisher

first: Upneet

last: Sokhi


title: Expression data from human metastatic melanoma cell lines

status: Public on Jun 10 2014

first: Laura

middle: L

last: Baxter

address: 35A Convent Drive

department: NHGRI

institute: NIH

summary:
The genetic changes underlying metastatic melanoma need to be deciphered to develop new and effective therapeutics.  Previously, genome-wide microarray analyses of human melanoma identified two reciprocal gene expression programs, that included expression of mRNAs  regulated by either transforming growth factor, beta 1 (TGFB1) pathways or microphthalmia-associated transcription factor (MITF)/SRY-box containing gene 10 (SOX10) pathways.  We extend this knowledge to include gene expression analyses of 5 additional human melanoma lines, and show that these lines also fall into either TGFB1 or MITF/SOX10 gene expression groups.
These mRNA expression studies were followed up by miRNA expression analyses.

overall_design: Microarray analyses were performed on 5 metastatic melanoma lines in 3 replicates. Standard Affymetrix protocols were used.

first: Hun-Way

last: Hwang

first: Stacie

last: Loftus

first: Julia

middle: C

last: Cronin

first: Niraj

last: Trivedi

first: Bhavesh

last: Borate

first: William

last: Pavan


title: Whole genome expression profiling of artemsinin-resistant Plasmodium falciparum field isolates [ex vivo]

status: Public on Jul 15 2014

city: Singapore

first: Sachel

last: Mok

address: 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

summary: The objective of our study is to characterize gene expression signatures associated with in vivo artemisinin-resistance phenotype in this large-scale genome-wide association study. To achieve this goal, we employed microarray technology to establish the global gene expression profiles of isolates sampled from 1043 patients, of whom after treatment with ACTs (artemisinin combination therapy) displayed differential rates of parasite clearance.

overall_design: P. falciparum isolates were sampled from the whole blood of 1043 malaria-infected patients. Sampling was done across 14 field sites spanning across South East Asia (Pailin, Pursat, Preah Vihear, Rattanakiri in Cambodia; Mae Sot, Srisakhet, Khun Han, Ranong in Thailand; Shwe Kyin in Myanmar; Binh Phuoc in Vietnam; Attapeu in Laos), to Bangladesh and African DR Congo from 2010 to 2012. Of the 1043 isolates, ex vivo culturing of 19 Pailin, Cambodian isolates were carried out and samples were harvested every 8 hours over the the 48 hour intraerythrocytic developmental cycle (IDC). RNA were extracted and synthesis and amplification of target DNA was carried out as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211 (PMID 22990779), to generate sufficient material for hybridizations against a common RNA reference pool of 3D7 strain using a microarray platform.

first: Zhaoting

last: Lin

first: Kekyee

last: Liong

first: Weiliang

last: Guo

first: Joan

last: Sim

first: Tomas

last: Yeo

first: Zbynek

last: Bozdech


title: Whole genome expression profiling of artemsinin-resistant Plasmodium falciparum field isolates [in vivo]

overall_design: P. falciparum isolates were sampled from the whole blood of 1043 malaria-infected patients prior to ACT treatment. Sampling was done across 14 field sites spanning across South East Asia (Pailin, Pursat, Preah Vihear, Rattanakiri in Cambodia; Mae Sot, Srisakhet, Khun Han, Ranong in Thailand; Shwe Kyin in Myanmar; Binh Phuoc in Vietnam; Attapeu in Laos), to Bangladesh and African DR Congo from 2010 to 2012. RNA were extracted and synthesis and amplification of target DNA was carried out as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211 (PMID 22990779), to generate sufficient material for hybridizations against a common RNA reference pool of 3D7 strain using a microarray platform.


title: Expression profiles of field-grown wheat expressing the Pm3 allele and null segregants

status: Public on May 01 2014

city: Zürich

first: Carolina

last: Diaz Quijano

state: Zürich

address: Universitätstrasse 2

department: Department of Biology

country: Switzerland

institute: ETH Zürich

summary:
It has been demonstrated that wheat overexpressing Pm3b, an allele of the R gene Pm3, has enhanced resistance against powdery mildew under field conditions. A gene expression profile study
using GeneChip® Wheat Genome Array was performed to obtain insights into the mode of action of Pm3b and to elucidate the molecular basis of pleiotropic effects observed in three out of four
independent transgenic events tested under field conditions.

overall_design:
24 samples were analyzed. Three biological replicates of each sample were included. Two independent transformation events and respective null segregants as control treated with fungicide or
artificially inoculated with powdery mildew.

last: Quijano

first: Susanne

last: Brunner

first: Beat

last: Keller

first: Wilhelm

last: Gruissem

first: Christof

last: Sautter


title: Transcriptomal Diversity of Long-Term Glioblastoma Survivors

status: Public on May 02 2014

city: New York

first: Naamit

middle: Kurshan

last: Gerber

address: 1275 York Avenue

institute: Memorial Sloan-Kettering Cancer Center

summary: Glioblastoma (GBM) is a highly aggressive type of glioma with poor prognosis. However, a small number of patients live much longer than the median survival. A better understanding of these long-term survivors (LTS) may provide important insight into the biology of GBM. We identified 7 patients with GBM treated at Memorial Sloan-Kettering Cancer Center (MSKCC) with survival greater than 48 months. We characterized the transcriptome of each patient and determined rates of MGMT promoter methylation and IDH1 and IDH2 mutational status. We identified LTS in two independent cohorts (TCGA and REMBRANDT) and analyzed the transcriptomal characteristics of these LTS.  The median overall survival of our cohort was 62.5 months.  LTS were distributed between the proneural (n=2), neural (n=2), classical (n=2) and mesenchymal (n=1) subtypes.  Similarly, LTS in the TCGA and REMBRANDT cohorts demonstrated diverse transcriptomal subclassification identity.  The majority of the MSKCC LTS (71%) were found to have methylation of the MGMT promoter. None of the patients had an IDH1 or IDH2 mutations, and IDH mutation occurred in a minority of the TCGA LTS as well.  A set of 42 genes was found to be differentially expressed in the MSKCC and TCGA LTS. While IDH mutant proneural tumors impart a better prognosis in the short-term, survival beyond 4 years does not require IDH mutation and is not dictated by a single transcriptional subclass.  In contrast, MGMT methylation continues to have strong prognostic value for survival beyond 4 years.   These findings have substantial impact for understanding GBM biology and progression.

overall_design: All tumors (n = 7) were obtained following surgical resection at the MSKCC as part of routine clinical care, and snap frozen. Tumors were obtained in accordance with Institutional Review Board policies at the MSKCC. Each sample was examined histologically by 3 independent neuropathologists and confirmed to be World Health Organization (WHO) grade IV glioma (GBM).  Before analysis, tumors were sectioned and microdissected. Genomic DNA or RNA was extracted using the DNeasy kit (Qiagen) or RNeasy Lipid Tissue Mini Kit (Qiagen) as per the manufacturer’s instructions. Expression analysis of tumors was performed using the Affymetrics U133 2.0 microarray (Affymetrix). Affymetrix CEL files were imported into the Partek Genomics Suite (Partek).  The TCGA gene expression data (HT-HG-U133A) was accessed from the TCGA data repositories (http://cancergenome.nih.gov, date of download 12/2013).


title: Effect of AZA on gene expression of multiple breast, colon, and ovarian cell lines [expression]

status: Public on May 08 2014

first: Stephen

last: Baylin

state: Maryland

address: 1650 Orleans St CRB I RM 541

department: Oncology

institute: Johns Hopkins UniversityJohns Hopkins Medical Institutions

summary:
Epigenetic therapy is emerging as a potential therapy for solid tumors. To investigate its mechanism of action, we performed integrative expression and methylation analysis of 63 cancer cell lines (breast, colorectal, and ovarian) after treatment with the DNA methyltransferase inhibitor 5-azacitidine (AZA). Gene Set Enrichment Analysis demonstrated significant enrichment for immunomodulatory pathways in all three cancers (14.4-31.3%) including interferon signaling, antigen processing and presentation, and cytokines/chemokines. Strong upregulation of cancer testis antigens was also observed.
An AZA IMmune gene set (AIMs) derived from the union of these immunomodulatory pathway genes classified primary tumors from all three types, into “high” and “low” AIM gene expression subsets in tumor expression data from both TCGA and GEO (GSE42284, GSE10893, and GSE26712 for the colon, breast, and ovarian samples, respectively). Samples from selected patient biopsies showed upregulation of AIM genes after treatment with epigenetic therapy. These results point to a broad immune stimulatory role for DNA demethylating drugs in multiple cancers.

overall_design: control vs. 5'-azacitidine-treated breast, colon, and ovarian cells at different time points (1, 3, 7, 10, 14, 21, or 28 days)

first: Huili

last: Li

first: Katherine

last: Chiappinelli

first: Angela

last: Guzzetta

first: Ray-Whay

last: Yen

first: Rajita

last: Vatapalli

first: Cynthia

last: Zahnow

first: Nita

last: Ahuja


title: Arabidopsis inflorescence stems: upper flanks vs lower flanks after gravi-stimulation at 10 min and 30 min

status: Public on Jun 12 2014

city: Nagoya

first: Miyo

middle: Terao

last: Morita

address: Furocho, Chikusa

department: Graduate School of Bioagricultural Sciences

institute: Nagoya University

summary: Transcriptional profiling of upper flanks and lower flanks of Arabidopsis inflorescence stems after gravistimulation. Candidate genes which were up-regulated in the lower flanks relative to the upper falanks after gravi-stimulation at 30 min were identified.

overall_design: Two time-points experiments, at 10 min and 30 min. Biological replicates: 2 replicates for each experiments (as color swapped data)

middle: T

first: Masatoshi

last: Taniguchi

first: Moritaka

last: Nakamura

first: Masao

last: Tasaka


title: GLOBAL CHANGES IN GENE EXPRESSION OF BARRETT'S ESOPHAGUS COMPARED TO NORMAL SQUAMOUS ESOPHAGUS AND GASTRIC CARDIA TISSUES

status: Public on Apr 15 2014

city: Rockville

first: Paula

middle: Lisa

last: Hyland

address: 6120 Executive Blvd

department: DCEG

institute: NCI, NIH

summary: Barrett’s esophagus (BE) is a metaplastic precursor lesion of esophageal adenocarcinoma (EA), the most rapidly increasing cancer in western societies. While the prevalence of BE is increasing, the vast majority of EA occurs in patients with undiagnosed BE. Thus, we sought to identify genes that are altered in BE compared to the normal mucosa of the esophagus, and which may be potential biomarkers for the development or diagnosis of BE.

overall_design: We performed gene expression analysis using HG-U133A Affymetrix chips on fresh frozen tissue samples of Barrett’s metaplasia and matched normal mucosa from squamous esophagus (NE) and gastric cardia (NC) in 43 BE patients.

first: P

first: N

last: Hu

first: M

last: Rotunno

first: H

last: Su

first: C

last: Wang

first: L

first: R

last: Pfeiffer

first: B

last: Gherman

last: Giffen

last: Dykes

first: S

last: Dawsey

last: Abnet

first: K

last: Johnson

middle: D

last: Acosta

middle: E

last: Young

last: Cash

last: Taylor


title: PAX3-FOXO1 suppresses cellular senescence through RASSF4-mediated restraint of the mammalian Hippo/MST1 pathway

status: Public on May 15 2014

first: Jen-Tsan

last: Chi

address: 101 Science Drive, DUMC 3382

department: Molecular Genetics and Microbiology

summary:
Alveolar rhabdomyosarcoma (aRMS) is an aggressive sarcoma of skeletal muscle characterized by expression of the PAX3-FOXO1 fusion gene. Despite its discovery over almost 20 years ago, PAX3-FOXO1 remains an enigmatic tumor driver. Previously, we reported that PAX3-FOXO1 supports aRMS initiation by enabling bypass of cellular senescence. Here, we show that bypass occurs in part by PAX3-FOXO1-mediated upregulation of RASSF4, a Ras-association domain family (RASSF) member, which then suppresses the evolutionarily conserved mammalian Hippo/Mst1 pathway. RASSF4 loss-of-function activates Hippo/Mst1 and inhibits downstream YAP, causing aRMS cell cycle arrest and senescence. This is the first evidence for an oncogenic role for RASSF4, and a novel mechanism for Hippo signaling suppression in human cancer.
Human skeletal muscle myoblasts (HSMMs) were retrovirally transduced with either an empty vector (Vp, pK1) or PAX3-FOXO1 (PFp, pK1-PAX3-FOXO1) and selected on puromycin. Presenescent (presen) cells were harvested before the senescence checkpoint. Since cells expressing PAX3-FOXO1 can bypass the senescence checkpoint, postsenescent (postsen) cells expressing PAX3-FOXO1 were also harvested.

overall_design: the gene expression affected by the introduction of PAX3-FOXO1

first: Lisa

last: Crose

first: Corinne

last: Linardic


title: Gene expression data of primary human bronchial epithelial cells exposed to crocidolite asbestos and cristobalite silica mineral dusts

status: Public on Oct 29 2014

city: Maastricht

first: Paul

middle: Michel

last: Peeters

state: Limburg

address: universiteitssingel 50

department: Respiratory Medicine

country: Netherlands

institute: Maastricht University

summary: Gene expression microarrays were used to compare gene alterations induced by exposure to equitoxic doses of crocidolite asbestos and cristobalite silica in an isolate of normal human bronchial epithelial cells.

overall_design: Primary human bronchial epithelial cells (NHBE) were exposed to crocidolite asbestos, cristobalite silica, and saline as control for 24 hours. Total RNA was extracted from cell cultures, 3 separate cultures were used for each condition. The isolated RNA was used to analyze mRNA expression via Affymetix GeneChip Human U133A 2.0 arrays.

first: Timothy

last: Perkins

first: Arti

last: Shukla

first: Ingrid

last: Arijs

first: Julie

last: Dragon

first: Emiel

last: Wouters

first: Nicki

last: Reynaert

first: Brooke

last: Mossman


title: A translatable predictor of human radiation injury

status: Public on Oct 21 2014

first: Holly

middle: K

last: Dressman

address: 101 Science Drive

department: IGSP

institute: Duke

summary: The development of a biodosimetric assay based on the combined gene expression analysis of ex vivo-irradiated human peripheral blood (PB) and humans treated with total body irradiation has been developed.  Gene expression profile signature of human radiation injury into a rapid and high-throughput chemical ligation-dependent probe amplification assay (CLPA) has been shown to discriminate 6 radiation dose levels in human PB.  Candidate gene lists were first developed assaying human ex vivo and human TBI samples on the Affymetrix platform.

overall_design:
For the Ex Vivo samples, healthy consented adult donor was randomly assigned to a radiation group and labeled with the target dose of 0 cGy, 150 cGy, 300 cGy, or 600 cGy.  In addition to the radiation exposures, the samples were also treated with either no treatment, GCSF, or LPS at time points 6 hours and 24 hours.  Radiation expire times from the Cs137 irradiator were calculated to achieve target doses specific for tubes filled with blood and inserted in the roaring test tube holder.  The dose rate was 480 cGy/min for the duration of the study. The healthy donors were enrolled to participate in this study following a protocol to collect PB samples that was previously approved by the Duke University Institutional Review Board.
For the TBI samples, adult patients, ages 21 to 66, were evaluated at the Duke University Adult Bone Marrow Transplantation Program enrolled in a Duke IRB-approved protocol to collect PB prior to and post TBI conditioning.  With approval from the Duke University Institutional Review Board (IRB), between 5-12 mL of peripheral blood was collected from consented patients prior to and 6 hours following TBI with 150-200 cGy as part of their pre-transplantation conditioning.  All patients receiving non-myeloablative conditioning were treated with 200 cGy of TBI from a linear accelerator at a dose rate of 20 cGy/min. All patients who underwent TBI-based myeloablative allogeneic or autologous stem-cell transplantation received radiation fractionated at 150 cGy per fraction at 20 cGy/min. All patients had PB collected (50 ml) prior to and 6 hours following exposure to either 200 cGy or 150 cGy radiation treatment.  The dose exposure for TBI patients used in this study were 0 cGy, 150 cGy, 450 cGy and 1050 cGy at 0, 6, 30 and 78 hours post irradiation.   Total RNA was extracted and assayed on the Affymetrix platform.

first: Joseph

last: Lucas

first: Sunil

last: Suchindran

first: Mai

last: Nakamura

first: Nelson

middle: J

last: Chao

first: Heather

last: Himburg

first: Gary

last: Phillips

first: Joel

last: Ross

first: Majid

last: Abedi

first: Robert

last: Terbrueggen

first: John

middle: P

last: Chute


title: Gene expression changes between sensitive and YK-4-279-resistant Ewing's Sarcoma cell lines

status: Public on Sep 04 2014

city: Houston

middle: A.

last: Ludwig

department: Sarcoma Medical Oncology

institute: UT-MD-Anderson Cancer Center

summary:
Microarray gene expression analysis conducted from cell lines in each of three cohorts: (1) Resistant ES cell lines, (2) Sensitive parental ES cell lines treated with YK-4-279 for 72 hours, and (3) untreated sensitive parental ES cell lines (Three replicates from TC32 & TC71 original parental cell lines)
We used microarrays to detail the global programme of gene expression underlying mechanism of resistance to YK-4-279 within parental sensitive and resistant selected Ewing's Sarcoma cell lines. We identified distinct classes of up-regulated genes during this process.

overall_design: Total RNA was extracted from the cell lines using the Qiagen miRNeasy Mini kit. RNA quality was assessed to have an RNA integrity number before amplification and labeling using Affymetrix’s GeneChip GeneChip®3’ IVT Express Kit following manufacturer’s instructions. Amplified and biotinylated cRNAs were hybridized onto Affymetrix GeneChip Human Genome U133A 2.0 cartridge arrays, Washed, and Stained with kit following manufacturer’s instructions. Arrays were scanned using Affymetrix GeneChip Scanner 3000 and the initial raw data were extracted using Affymetrix GeneChip Command Console-Expression software. The statistical analyses of scanned data were performed using default setting on GeneSpring GX 12.1 software (Agilent).

first: Salah-Eddine

last: LAMHAMEDI-CHERRADI

first: Vandhana

last: Ramamoorthy

first: Brian

last: Menegaz