title: Oncogenic BRAF regulates oxidative metabolism via PGC1α and MITF

status: Public on Mar 07 2013

city: Boston

first: Hans

last: WIDLUND

state: MA

address: 77 Avenue Louis Pasteur

department: Dermatology

institute: Brigham and Women's Hospital

summary:
Gene expression signatures were measured in logarithmic growing cultures
Affymetrix HG-U133AV2 expression arrays were performed according to the manufacturer's directions using RNA extracted by Qiagen RNeasy from engineered human melanoma cells

overall_design: Resulting expression signatures where derived based on phenotypic properties: tumor-like endpoints driven by MITF overexpression

last: Widlund

first: David

last: Fisher


title: Expression Data from pancreatic cancer cell lines and orthotopic tumors grown with and without MEK inhibitor

status: Public on Apr 04 2013

city: San Francisco

first: Stephan

middle: Christoph

last: Gysin

state: California

address: 1450 3rd Street

department: HDFCCC

country: USA

institute: UCSF

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

overall_design: Refer to individual Series

first: Jesse

last: Paquette

first: Martin

last: McMahon


title: Transcriptome profiling of endometrial biopsies  inflammatory response to Chlamydia trachomatis genital tract infection

status: Public on Mar 01 2013

city: Pittsburgh

first: Stephen

middle: Alan Kenneth

last: Harvey

state: PA

address: 203 Lothrop St

department: Ophthalmology

institute: University of Pittsburgh School of Medicine

summary:
Chlamydia trachomatis is an obligate intracellular Gram-negative bacterium that frequently causes an asymptomatic genital tract infection, gradually cleared by host immunity
Transcriptome profiles were made of endometrial tissue from women with or without genital tract C. trachomatis infection, to characterize host responses to infection.
Profiles showed that infection polarized host defense toward Type 2 immune responses. Responses included fibrin deposition, enhanced wound repair, and tissue remodeling.

overall_design: Trans-cervical endometrial biopsy specimens were collected from 10 women with no identified upper or lower genital tract infection and 12 women with C. trachomatis endometrial infection.

first: Thomas

middle: L

last: Cherpes

first: Rodolfo

middle: D

last: Vicetti Miguel

middle: A

first: William

last: LaFramboise


title: Profiling A375P melanoma cells following PGC1a suppression

status: Public on Feb 25 2013

first: Pere

last: Puigserver

address: 450 Brookline Av. CLSB-11144

institute: Dana-Farber Cancer Institute

summary: PGC1a is a transcriptional coactivator that regulates energy metabolism. PGC1a is highly expressed in a subset of melanoma tumors and cell lines. We generated gene-expression profile of control and PGC1alpha depleted A375P melanoma cells, a melanoma cell line that expresses very high levels of PGC1a to investigate the role of this gene in melanoma.

overall_design: Lentivirus were used to generate stable cell lines expressing two shRNAs against PGC1alpha or two shRNAs controls. Cells were selected with purmycin for 48h and RNA was harvested 48h after selection and gene-expression arrays were generated.

first: Francisca

last: Vazquez


title: Gene regulation following MIF / IL-8 stimulation

city: Rehovot

first: Idit

last: Shachar

address: 2 Hersel st

country: Israel

institute: Weizmann Institute of Science

summary: Chronic lymphocytic leukemia (CLL) is characterized by the accumulation of CD5+ B lymphocytes in peripheral blood, lymphoid organs and BM. The main feature of the disease is accumulation of the malignant cells due to decreased apoptosis. CD84 belongs to the Signaling Lymphocyte Activating Molecule (SLAM) family of immunoreceptors, and has an unknown function in CLL cells. Here, we show that the expression of CD84 is significantly elevated from the early stages of the disease, and is regulated by macrophage migration inhibitory factor (MIF) and its receptor, CD74. Activation of cell surface CD84 initiates a signaling cascade that enhances CLL cell survival. Both immune-mediated neutralization or blockade of CD84 induce cell death in vitro and in vivo. In addition, analysis of samples derived from an on-going clinical trial, in which human subjects were treated with humanized anti-CD74 milatuzumab shows a decrease in CD84 mRNA levels milatuzumab-treated cells. This downregulation was correlated with reduction of Bcl-2 and Mcl-1 message. Thus, our data show that overexpression of CD84 in CLL is an important survival mechanism that appears to be an early event in the pathogenesis of the disease. These findings suggest novel therapeutic strategies based on the blockade of this CD84-dependent survival pathway.

overall_design: 3 samples; incubated with PBS, MIF, or IL-8.

first: Binsky

last: Inbal


title: Expression data from human pluripotent stem cells and differentiated cells treated with pluripotent-specific inhibitors

status: Public on Jan 22 2013

city: Jerusalem

first: Uri

last: Ben-David

address: Givat-Ram

department: Genetics

institute: Hebrew University

summary: The use of human pluripotent stem cells (hPSCs) in cell therapy is hindered by the tumorigenic risk from residual undifferentiated cells. Here we performed a high-throughput screen of over 52,000 small molecules, and identified 15 highly selective cytotoxic inhibitors of hPSCs (PluriSIns). Cellular and molecular analyses revealed that the most selective compound, PluriSIn #1, is a pluripotent-specific inhibitor of stearoyl-coA desaturase (SCD1), the key enzyme in the biosynthesis of monounsaturated fatty acids (MUFA). SCD1 inhibition in hPSCs induced ER stress, protein synthesis attenuation, and apoptosis of these cells, revealing that MUFA biosynthesis is crucial for their survival. PluriSIn #1 was also cytotoxic toward the ICM cells of mouse embryos, indicating that the dependence on SCD1 is inherent to the pluripotent state. Finally, application of PluriSIn #1 prevented teratoma formation from tumorigenic undifferentiated cells. Our novel method to eliminate undifferentiated cells from culture should thus increase the safety of hPSC-based treatments.

overall_design: Expression data from undifferentiated and differentiated human embryonic stem cells. Total RNA was isolated from undifferentiated human pluripotent stem cells grown on matrigel with mTeSR1 medium, or from early endodermal progenitor cells differentiated from human embryonic stem cells.

first: Nissim

last: Benvenisty


title: Transcriptomic survey of lymph node-positive vs. - negative ductal breast cancer

status: Public on Mar 05 2013

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: Lymph node involvement is a major prognostic variable in breast cancer. Whether the molecular mechanisms that drive breast cancer cells to colonize lymph nodes are shared with their capacity to form distant metastases is yet to be established. In a transcriptomic survey aimed at identifying molecular factors associated with lymph node involvement of ductal breast cancer, we found that luminal differentiation, assessed by the expression of estrogen receptor (ER) and/or progesterone receptor (PR) and GATA3, was only infrequently lost in node-positive primary tumors and in matched lymph node metastases. The transcription factor GATA3 critically determines luminal lineage specification of mammary epithelium and is widely considered a tumor and metastasis suppressor in breast cancer. Strong expression of GATA3 and ER in a majority of primary node-positive ductal breast cancer was corroborated by quantitative RT-PCR and immunohistochemistry in the initial sample set, and by immunohistochemistry in an additional set from 167 patients diagnosed of node-negative and –positive primary infiltrating ductal breast cancer, including 102 samples from loco-regional lymph node metastases matched to their primary tumors, as well as 37 distant metastases. These observations suggest that loss of luminal differentiation is not a major factor driving the ability of breast cancer cells to colonize regional lymph nodes.

overall_design: The transcriptomic study comprises 16 samples from Lymph node metastasis from infiltrating ductal breast carcinoma, 18 samples from Primary node-positive infiltrating ductal,7 samples from  Primary node-negative infiltrating ductal and 3 samples from Unaffected lymph node were included. Their RNA was isolated and prepared for hybridization to human Affymetrix GeneChip arrays.

first: P

last: Fernandez

first: J

last: Calvo

first: T

middle: M

last: Thomson

first: L

last: Sanchez-Cid

middle: J


title: Expression data from Bovine leukemia virus (BLV) Tax-transfected HeLa cells

status: Public on Jan 03 2013

city: Wako

first: Yoko

last: Aida

state: Saitama

address: 2-1 Hirosawa

department: Advanced Science Institute

country: Japan

institute: RIKEN

summary: Bovine leukemia virus (BLV) Tax is a transcriptional activator of viral replication and a key contributor to oncogenic potential. We previously identified interesting mutant forms of Tax with elevated (TaxD247G) or reduced (TaxS240P)  transactivation effects on BLV replication and propagation. In this study, to identify genes that play a role in the cascade of signal events regulated by wild-type and mutant Tax proteins, we used a large-scale host cell gene-profiling approach.

overall_design: HeLa cells transiently transfected with the pCAGGS vector for the control sample was compared with HeLa cells transiently transfected with the pCAGGS-Tax-FLAG vector. These cells were incubated for 30h after transfection and total RNA was isolated.

first: Mariluz

last: Arainga-Ramirez

first: Keisuke

last: Fukumoto


title: Microarray-based gene expression profiling in patients with cryopyrin-associated periodic syndromes defines a disease-related signature and IL-1-responsive transcripts.

status: Public on Jan 16 2013

city: bethesda

first: abdel

last: elkahloun

state: MD

address: 50 south dr

institute: nih

summary:
To analyse gene expression patterns and to define a specific gene expression signature in patients with the severe end of the spectrum of cryopyrin-associated periodic syndromes (CAPS). The molecular consequences of interleukin 1 inhibition were examined by comparing gene expression patterns in 16 CAPS patients before and after treatment with anakinra.
Many DEG include transcripts related to the regulation of innate and adaptive immune responses, oxidative stress, cell death, cell adhesion and motility. A set of gene expression-based models comprising the CAPS-specific gene expression signature correctly classified all 17 samples from an independent dataset. This classifier also correctly identified 15 of 16 post-anakinra CAPS samples despite the fact that these CAPS patients were in clinical remission. We identified a gene expression signature that clearly distinguished CAPS patients from controls. A number of DEG were in common with other systemic inflammatory diseases such as systemic onset juvenile idiopathic arthritis. The CAPS-specific gene expression classifiers also suggest incomplete suppression of inflammation at low doses of anakinra.

overall_design: We collected peripheral blood mononuclear cells from 23 CAPS patients with active disease and from 14 healthy children. Transcripts that passed stringent filtering criteria (p values ≤ false discovery rate 1%) were considered as differentially expressed genes (DEG). A set of DEG was validated by quantitative reverse transcription PCR and functional studies with primary cells from CAPS patients and healthy controls. We used 17 CAPS and 43 non-CAPS patient samples to create a set of gene expression models that differentiates CAPS patients from controls and from patients with other autoinflammatory conditions.

first: James

middle: E

last: Balow

first: John

middle: G

last: Ryan

first: Jae

last: Chae

first: Matthew

last: Booty

first: Ariel

last: Bulua

first: Deborah

last: Stone

first: Hong-Wei

last: Sun

last: Greene

first: Beverly

last: Barham

first: Raphaela

last: Goldbach-Mansky

first: Daniel

last: Kastner

first: Ivona

last: Aksentijevich


title: FAT1 knockdown in immortalized astrocyte and glioma cell lines

status: Public on Jan 10 2013

city: New York

first: Luc

middle: GT

last: Morris

state: NY

address: 1275 York Avenue

institute: Memorial Sloan-Kettering Cancer Center

summary:
The FAT1 gene was knocked down using 2 independent siRNAs, in immortalized human astrocytes and U87 and U251 glioma cell lines.

A non-targeted scramble siRNA was used as a control.

overall_design: Scramble, FAT1 siRNA#1 and FAT1 siRNA#2 were transfected into each cell line, in duplicate, and RNA analyzed using the Affymetrix U133A 2.0 platform.

first: Timothy

last: Chan


title: Expression data from Y12-3 and A24-39 roots

status: Public on Jan 01 2013

first: Zvi

last: Peleg

address: P.O.Box 12

department: Inst. of Plant Sciences

summary: Roots adaptation to drought stress was analyzed using transcriptome and metabolomics profiles in two wild emmer wheat (Triticum turgidum ssp. dicoccoides) genotypes: Y12-3 (drought resistance) and A24-39 (drought susceptible).

overall_design: Roots samples of Y12-3 and A24-39 genotypes grown under well-watered (control) and water-stressed (7 days of withholding water) were collected for RNA extraction and hybridization on Affymetrix wheat microarrays chip.

first: Tzion

last: Fahima

first: Tamar

last: Krugman


title: Gene expression profiling of human endometrial stromal cells transduced with BMP2- and WNT4-adenovirus.

status: Public on Feb 08 2013

city: Urbana

first: Quanxi

last: Li

state: IL

address: 2001 S lincoln Avenue

department: Comparative Bioscience

institute: Universit of Illinois at Urbana-Champaign

summary:
Our previous studies have shown that bone morphogenetic protein 2 (BMP2), a morphogen belonging to the TGFβ superfamily, is markedly induced in human primary endometrial stromal cells (HESC) as they undergo differentiation in response to steroid hormones and cAMP. WNT4 is a downstream target of BMP2 regulation in these cells.
To identify the common downstream targets of BMP2 and WNT4 in human endometrial stromal cells, we performed gene expression profling of human ensometrial stromal cell transduced with BMP2 or WNT4 adenovirus. Gene expression profiling revealed that FOXO1, a forkhead family transcription factor and a known regulator of HESC differentiation, is a common downstream mediator of both BMP2 and WNT4 signaling. These studies uncovered a linear pathway involving BMP2, WNT4, and FOXO1 that operates in human endometrium to critically control decidualization.

overall_design: Human endometrial stromal cells were transduced with recombinant adenovirus expressing BMP2, WNT4, or a negative control GFP at MOI 50:1 in 2 ml of culture medium. After transduction for 24 h, the viral particles were removed and the cells were treated with E+P for 3 days to induce decidualization (n=3 for each treatment), pooled total RNA from these cells was then hybridized to high density affymetrix microarrays according to the Affymetrix protocol (Human Genome HG-U133 A2.0 Array) .

first: Indrani

middle: C

last: Bagchi


title: Pathways leading to phosphorylation of p450c17 and to the post-translational regulation of androgen biosynthesis

status: Public on Feb 15 2013

last: Tee

address: HSE1401, 513 Parnassus Ave

summary: Cytochrome P450c17 (P450c17) is the single enzyme that catalyzes steroid 17alpha-hydroxylase and 17,20 lyase activities and hence is the crucial decision-making step that determines the class of steroid made in a steroidogenic cell. Although both activities are catalyzed on a single active site, the ratio of these activities is regulated by posttranslational events. Serine phosphorylation of P450c17 increases 17,20 lyase activity by increasing the enzyme's affinity for its redox partner, P450 oxidoreductase. We searched for the relevant kinase(s) that phosphorylates P450c17 by microarray studies and by testing of kinase inhibitors. Microarrays show that 145 of the 278 known serine/threonine kinases are expressed in human adrenal NCI-H295A cells, only six of which were induced more than 2-fold by treatment with 8-Br-cAMP. Key components of the ERK1/2 and MAPK/ERK kinase (MEK)1/2 pathways, which have been implicated in the insulin resistance of PCOS, were not found in NCI-H295A cells, implying that these pathways do not participate in P450c17 phosphorylation. Treatment with various kinase inhibitors that probe the protein kinase A/phosphatidylinositol 3-kinase/Akt pathway and the calcium/calmodulin/MAPK kinase pathway had no effect on the ratio of 17,20 lyase activity to 17alpha-hydroxylase activity, appearing to eliminate these pathways as candidates leading to the phosphorylation of P450c17. Two inhibitors that target the Rho-associated, coiled-coil containing protein kinase (ROCK)/Rho pathway suppressed 17,20 lyase activity and P450c17 phosphorylation, both in NCI-H295A cells and in COS-1 cells transfected with a P450c17 expression vector. ROCK1 phosphorylated P450c17 in vitro, but that phosphorylation did not affect 17,20 lyase activity. We conclude that members of the ROCK/Rho pathway act upstream from the kinase that phosphorylates P450c17 in a fashion that augments 17,20 lyase activity, possibly acting to catalyze a priming phosphorylation.

overall_design: NCI-H295A adrenocortical cells were grown on 10-cm plates in RPMI 1640 with 2% fetal calf serum, gentamicin, insulin, and selenium. Three nearly confluent plates were incubated in the presence and absence of 1 mM 8-Br-cAMP for 18 h; the cells were washed with PBS and lysed with 1 ml Trizol (Invitrogen, Carlsbad, CA). Total RNA was purified further using RNeasy columns (QIAGEN, Valencia, CA), and 4 μg RNA was used to synthesize double-stranded cDNA using the MessageAmp II-Biotin Enhanced Kit (Ambion, Austin, TX) with oligo-dT primer [5′-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-(dT)24] to incorporate a T7 RNA polymerase promoter. Antisense cRNA was labeled with biotin-UTP using T7 RNA polymerase (Ambion), and the cRNA was fragmented to 35–200 nucleotides (nt) at 94 C for 35 min in 40 μl 40 mm Tris-acetate (pH 8.1), 100 mm KOAc, 30 mm MgOAc. The integrities of total RNAs, cRNAs, and fragmented cRNAs were assessed on a Bio-Rad (Hercules, CA) Experion BioAnalyzer. Each sample of fragmented cRNA was initially hybridized with Affymetrix (Santa Clara, CA) Test3 arrays to determine the quality of the labeled probe before hybridization to Affymetrix U133A plus 2.0 arrays. The chips were stained and washed using an Affymetrix GeneChip Fluidics Station 450, and the arrays were scanned using a GCS 3000 scanner with auto-loader in the Genomics Core laboratory. Hybridization intensity signals from the scanned images were analyzed using Affymetrix GeneChip Operating Software (GCOS, version 1.3) to provide qualitative detection calls and quantitative estimates of gene expression levels (signal values). Raw data were exported to Microsoft Excel for analysis. Transcripts displaying a cAMP-induced increased or decreased signal were selected for further analysis only if they had a mean ± 2.0-fold change and were statistically significant (P < 0.05) in three separate experiments; transcripts displaying no signal change relative to controls in at least three experiments were excluded from further analysis.

first: Meng

middle: K

first: Qing

last: Dong

first: Walter

last: Miller


title: Three human cell types respond to multi-walled carbon nanotubes and titanium dioxide nanobelts with cell-specific transcriptomic and proteomic expression

status: Public on Dec 15 2012

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University


title: Three human cell types respond to multi-walled carbon nanotubes and titanium dioxide nanobelts with cell-specific transcriptomic and proteomic expression [SAE cells]

summary:
To identify key biological pathways that define toxicity or biocompatibility after nanoparticle exposure, three human cell types were exposed in vitro to two high aspect ratio nanoparticles for 1 hr or 24 hr and collected for global transcriptomics.
Transcriptional responses were measured by global microarray analysis of cells in culture.

overall_design: Groups (N=3 biological replicates) of SAE cells exposed to 0, 10 or 100 ug/ml MWCNT or TiO2-NB nanoparticles for 1 or 24 hr.

first: Galya

last: Orr


title: Airborne particulate matter affects gene expression in BEAS-2B bronchial epithelial cells.

status: Public on Dec 21 2012

city: Erlangen

first: Roland

last: Lang

address: Wasserturmstr. 3-5

country: Germany

institute: University Hospital Erlangen

summary:
Background: In classrooms high concentrations of particulate matter PM10 were measured. It is unknown whether the hazard of indoor particles is similar to that of the better studied outdoor particles. This study therefore analyzed adverse biological effects of classroom in comparison to outdoor PM10.

Methods: Samples were taken from six schools during teaching hours. Genome-wide gene expression in human bronchial BEAS-2B  epithelial cells was analyzed, and regulated genes were verified by quantitative PCR. Polycyclic aromatic hydrocarbons (PAH), endotoxin, and cat allergen Fel d 1 were analyzed with standard methods. Enhancement of allergic reactivity by PM10 was confirmed with CD63 upregulation in human primary basophils. Acceleration of human blood coagulation was determined with supernatants of PM10-exposed human peripheral blood monocytes.

Results: Indoor PM10 induced SERPINB2 (involved in blood coagulation) and inflammatory genes (like CXCL6, CXCL1, IL6, IL8, all p<0.001). Outdoor PM10 induced xenobiotic metabolizing enzymes (CYP1A1, CYP1B1, TIPARP, all p<0.001). The induction of inflammatory genes by indoor PM10 could be explained by endotoxin (indoor 128.5±42.2EU/mg versus outdoor 13.4±21.5EU/mg, p<0.001), the induction of CYP by outdoor PAH (indoor 8.3±4.9ng/mg versus outdoor 16.7±15.2ng/mg, p<0.01). The induction of SERPINB2 was confirmed by a more rapid human blood coagulation (p<0.05). Indoor PM10 had no effect on the allergic reactivity from human primary basophils, except in cat allergic individuals. This was explained by varying Fel d 1 concentrations in indoor PM10 (p<0.001).

Conclusions: Indoor PM10, compared to outdoor PM10, was 6 times higher, had a different composition, and on an equal weight basis induced more inflammatory and allergenic reactions, and accelerated blood coagulation. Outdoor PM10 had significantly lower effects, but induced detoxifying enzymes. Therefore, preliminary interventions for the reduction of classroom PM10 seem reasonable, perhaps by intensified ventilation.

overall_design:
For genome-wide gene expression analysis, BEAS-2B cells (passage 41) were incubated with 10µg/ml PM10 (school 4 indoor and outdoor) for 4, 10 or 24h, all in triplicate.
experiment type : time course

first: Sebastian

last: Oeder

first: Jeroen

last: Buters


title: Rhabdomyosarcoma cells (SJRH30) response to hypoxia: time course

status: Public on Dec 31 2012

city: Bunkyo-ku

first: Soichi

last: Ogishima

state: Tokyo

address: Yushima 1-5-45

department: Medical Research Institute

institute: Tokyo Medical and Dental University

summary:
Under hypoxic condition, solid tumor cells are known to involve gene expressions for adopting low O2 condition. We examined chronic hypoxia environment of human rhabdomyosarcoma cell (SJRH30), which is important for understanding characteristic of cancer in the body.
We used microarrays to detail time development of gene expression by using new gene-set analysis called GSMTA and identified up/down-regulated gene sets during hypoxic stress.

overall_design: We measured gene expressions at four time-points during 24 hours (0h, 6h, 12h and 24h) under 1% hypoxic condition by Affymetrix GeneChip. GSMTA identified novel differentially-expressed gene set under hypoxic stress at each time point.

first: Satoru

last: Oshiro


title: PIAS3 induction of apoptosis in non-small cell lung cancer cells is p53-independent and has STAT3-independent mediator.

status: Public on Dec 19 2012

city: Cleveland

first: yu

last: liu

address: 11900 Euclid

institute: Case Western Reserve University

summary: Protein inhibitor of activated STAT3 (PIAS3) is an endogenous inhibitor of STAT3 that negatively regulates STAT3 transcriptional activity and cell growth and demonstrates limited expression in the majority of human squamous cell carcinomas of the lung. In the present study we sought to determine if PIAS3 inhibits cell growth in non-small cell lung cancer (NSCLC) cell lines by induction of apoptosis and further determine the dependence of PIAS3 activity on p53 status by using both wild-type and p53-null cells. Our results demonstrate that over-expression of PIAS3 promotes caspase 3 activation and PARP cleavage. Furthermore, the expression of pro-survival family members Bcl-xL and Bcl-2 is decreased. These effects were observed after both transient and regulated expression of exogenous PIAS3 and were independent of p53 status. Furthermore, while p53 can promote apoptosis by inhibition of STAT3 activity, PIAS3 inhibition of STAT3 activity was also p53 independent. Microarray experiments were performed to further investigate the STAT3-dependence of PIAS3-induced apoptosis by comparing the apoptotic gene expression signature induced by PIAS3 over-expression with that induced by STAT3 siRNA. The results showed that a subset of apoptotic genes, including CIDEC and DAPK2, were uniquely expressed only after PIAS3 expression. Thus, PIAS3 may represent a promising lung cancer therapeutic target because of its p53-independent efficacy as well as its potential to synergize with direct STAT3 inhibitors.

overall_design:
The expression profiles of genes related to apoptosis in A549 cell line transfected with pCMV5 vector encoding human PIAS3 compared with that induced by STAT3 siRNA
Cells in all three groups were grown in serum-free medium, then stimulated with EGF, then one group transfected with pCMV5 vector encoding human PIAS3, second group was induced by STAT3 siRNA, third group considered as control.

first: Snehal

last: Dabir

first: Amy

last: Kluge

first: Yu

last: Liu

first: Balazs

last: Halmos

first: Gary

last: Wildey

first: Afshin

last: Dowlati


title: Three human cell types respond to multi-walled carbon nanotubes and titanium dioxide nanobelts with cell-specific transcriptomic and proteomic expression [Caco-2/HT29-MTX cells]

overall_design: Groups (N=3 biological replicates) of Caco-2/HT29-MTX cells exposed to 0, 10 or 100 ug/ml MWCNT or TiO2-NB nanoparticles for 1 or 24 hr.


title: Determination of molecular markers for BRCA1 and BRCA2 heterozygosity using gene expression profiling

city: jerusalem

first: tamar

last: zahavi

address: Ein-Kerem

department: Oncology

institute: Hadassah

summary:
Approximately 5% of all breast cancers can be attributed to an inherited mutation in one of two cancer susceptibility genes, BRCA1 and BRCA2. We searched for genes that have the potential to distinguish healthy BRCA1 and BRCA2 mutation carriers from non-carriers based on differences in expression profiling. Using expression microarrays we compared gene expression of irradiated lymphocytes from BRCA1 and BRCA2 mutation carriers versus control non-carriers. We identified 137 probe sets in BRCA1 carriers and 1345 in BRCA2 carriers with differential gene expression. Gene Ontology analysis revealed that most of these genes relate to regulation pathways of DNA repair processes, cell cycle regulation and apoptosis. Real-time PCR was performed on the 36 genes which were most prominently differentially expressed in the microarray assay; 21 genes were shown to be significantly differentially expressed in BRCA1 or BRCA2 mutation carriers  as compared to controls (p<0.05). Based on a validation study with 40 mutation carriers and 17 non-carriers, a multiplex model that included six or more coincidental genes of 18 selected genes was constructed in order to predict the risk of carrying a mutation. The results using this model showed sensitivity 95% and specificity 88%.   In summary, our study provides insight into the biological effect of heterozygous mutations in BRCA1 and BRCA2 genes in response to ionizing irradiation induced DNA damage. We also suggest a set of 18 genes that can be used as a prediction and screening tool for BRCA1 or BRCA2 mutational carriers by using easily obtained lymphocytes.
Using expression microarrays we compared gene expression of irradiated lymphocytes from BRCA1 and BRCA2 mutation carriers versus control non-carriers

overall_design: Fresh blood samples were obtained from 9 BRCA1 and  8 BRCA2 mutation carriers and  9 mutation-negative women. Lymphocytes were collected from fresh blood samples, and RNA was extracted one hour after γ-irradiation

first: Asher

middle: Y

last: Salmon

first: Mali

last: Salmon-Divon

first: Tamar

last: Zahavi

first: Yulia

last: Barash

first: Jasmine

last: Jacob-Hirsch

last: Peretz


title: Three human cell types respond to multi-walled carbon nanotubes and titanium dioxide nanobelts with cell-specific transcriptomic and proteomic expression [THP-1 cells]

first: Susan

last: Tilton

overall_design: Groups (N=3 biological replicates) of THP-1 cells exposed to 0, 10 or 100 ug/ml MWCNT or TiO2-NB nanoparticles for 1 or 24 hr.

first: Galya

last: Orr


title: CXCL12 and IGF1 select for cancer cell populations with enhanced bone metastasis ability

status: Public on Dec 10 2012

city: Houston

first: Xiang

last: Zhang

state: TX

address: One Baylor Plaza, BCM600

department: Lester and Sue Smith Breast Center

institute: Baylor College of Medicine

summary: CXCL12 and IGF1 confer on cancer cells survival advantage. Src potentiates cancer cells' reponse to CXCL12 and IGF1 by strengthening AKT activation. Long-term incubation of CXCL12 and IGF1 select for cancer cells with enhanced Src activity and bone metastasis potential.

overall_design: MDA-MB-231 cells were incubated for three weeks in growth medium of reduced  serum concentration (0.2%) with or without CXCL12 (30 ng/ml) and IGF1 (10 ng/ml). Cell populations survive under these condidtions are expanded by regular growth medium with 10% serum. Two biological replicates were profiled for each condition.

middle: H

first: Xin

last: Jin

first: Joan

last: Massague


title: Expression data from alveolar rhabdomyosarcoma cell lines

status: Public on Dec 06 2012

city: Zurich

first: Beat

middle: W

last: Schafer

address: Steinwiesstrasse 75

country: Switzerland

institute: University Childrens Hospital

summary: We aimed to find gene signatures associated with different subgroups of alveolar rhabdomyosarcoma cell lines defined by differences in detection of pro-apoptotic stress

overall_design: RNA from cultured cell lines was isolated the same day and used for subsequent expression profiling

last: Schaefer

first: Marco

last: Wachtel


title: The androgen receptor induces a distinct transcriptional program in castration resistant prostate cancer in man

status: Public on Jan 04 2013

city: Cambridge

first: Suraj

last: Menon

address: Li Ka Shing Center, Robinson Way

country: United Kingdom

institute: Cambridge Research Institute, Cancer Research UK

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The androgen receptor (AR) is the major transcriptional driver of prostate cell growth in man. For the first time, we define AR targets in prostate cancer (PC) tissue representing progression from treatment-naive to castrate-resistant disease (CRPC). We employed chromatin immunoprecipitation with high through-put sequencing (ChIP-seq) in human tissue, with cell-line and xenograft studies. We uncovered an AR transcriptional network not observed in cultured cells, with significant over-representation of MYC, E2F and STAT binding sites, progenitor cell gene signatures and targets which regulate metabolism, cell cycle and steroid biosynthesis. We identified AR targets unique to CRPC tissue, with a subset over-expressed in CRPC and predictive of clinical outcome, highlighting persistence of AR signalling. Our data support a model whereby endocrine and paracrine signals converge on the AR in PC tissue to drive oncogenic transcriptional programs, highlighting the critical role of cellular context in the regulation of target selection and gene expression.

first: Naomi

last: Sharma

first: Rory

last: Stark


title: Transcriptional Alterations of Hamstring Muscle Contractures in Children with Cerebral Palsy

status: Public on Nov 21 2012

city: San Diego

first: Lucas

middle: Robert

last: Smith

state: CA

address: 3350 La Jolla Village Drive Mail Code 151

department: Bioengineering

institute: University of California San Diego

summary: Cerebral palsy is primarily an upper motor neuron disease that results in a spectrum of progressive movement disorders.  Secondary to the neurological lesion, muscles from patients with cerebral palsy are often spastic and form debilitating contractures that limit range of motion and joint function.  With no genetic component, the pathology of skeletal muscle in cerebral palsy is a response to aberrant neurological input in ways that are not fully understood.  This study was designed to gain further understanding of the skeletal muscle response to cerebral palsy using microarrays and correlating the transcriptional data with functional measures.  Hamstring biopsies from gracilis and semitendinosus muscles were obtained from a cohort of patients with cerebral palsy (n=10) and typically developing patients (n=10) undergoing surgery.  Affymetrix HG-U133A 2.0 chips (n=40) were used and expression data was verified for 6 transcripts using quantitative real-time PCR, as well as for two genes not on the microarray.  Chips were clustered based on their expression and those from patients with cerebral palsy clustered separately.  Significant genes were determined conservatively based on the overlap of three summarization algorithms (n=1,398).  Significantly altered genes were analyzed for over-representation among gene ontologies, transcription factors, pathways, microRNA and muscle specific networks.  These results centered on an increase in extracellular matrix expression in cerebral palsy as well as a decrease in metabolism and ubiquitin ligase activity.  The increase in extracellular matrix products was correlated with mechanical measures demonstrating the importance in disability.  These data lay a framework for further studies and novel therapies.

overall_design: Skeletal muscle biopsies from both the gracilis and semitendinosus were obtained during surgery for 20 pediatric subjects for affymetrix microarray analysis.  We obtained a group of 10 patients undergoing medial hamstring lengthening in the cerebral palsy group and 10 patients undergoing ACL reconstruction with hamstring autograft in the control group.  This provided 40 microarrays in 4 groups to analyze the effect of cerebral palsy and also differences between muscles.

middle: R

first: Henry

last: Chambers

first: Shankar

last: Subramaniam

first: Richard

last: Lieber


title: Estrogen receptor prevents p53-dependent apoptosis in breast cancer

status: Public on Nov 02 2012

city: Boston

first: Shannon

middle: Terrell

last: Bailey

address: 450 Brookline Avenue, D728

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: More than two thirds of breast cancers express the estrogen receptor (ER) and depend on estrogen for growth and survival. Therapies targeting ER function including aromatase inhibitors that block the production of estrogens and ER antagonists that alter ER transcriptional activity play a central role in the treatment of ER+ breast cancers of all stages. In contrast to ER- breast cancers, which frequently harbor mutations in the p53 tumor suppressor, ER+ breast cancers are predominantly wild type for p53. Despite harboring wild type p53, ER+ breast cancer cells are resistant to chemotherapy-induced apoptosis in the presence of estrogen. Using genome-wide approaches we have addressed the mechanism by which ER antagonizes the pro-apoptotic function of p53. Interestingly both ER agonists such as estradiol and selective ER modulators (SERM) such as tamoxifen promote p53 antagonism. In contrast the full ER antagonist fulvestrant blocks the ability of ER to inhibit p53-mediated cell death. This suggests an improved strategy for the treatment of ER+ breast cancer utilizing antagonists that completely block ER action together with drugs that activate p53-mediated cell death.

overall_design: MCF7 cells were hormone-depleted for 3 days and then treated with 10 uM doxorubicin for 12 hours

middle: T

first: Hyunjin

last: Shin

first: Thomas

last: Westerling

first: X

middle: S

last: Liu

first: Myles

last: Brown


title: Gene Profiling of Narrow-band UVB-induced Skin Injury Defines Cellular and Molecular Innate Immune Responses

status: Public on Oct 30 2012

first: Mayte

last: Suarez-Farinas

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

summary: We sought to define the cutaneous response at 24 hours following erythemogenic doses of narrow-band UVB (NB-UVB, 312 nm peak) exposure and determine the differences between irradiated and non-irradiated skin.

overall_design: Comparison of Transcriptome between NB-UVB irradiated (2MED) and non-irradiated skin (NON IRRAD).

first: Judilyn

last: Fuentes-Duculan

last: Suárez-Fariñas

first: James

last: Krueger


title: Developmental transcriptional profiling of Triticeae reproductive development

status: Public on Nov 01 2012

city: Ottawa

first: Frances

last: Tran

address: 960 Carling Avenue

country: Canada

institute: Agriculture & Agri-Food Canada

summary: Despite their importance, there remains a paucity of large scale expression-based studies of reproductive development in the species belonging to the Triticeae.  As a first step to address this deficiency, a gene expression atlas of triticale reproductive development was generated using the 55K Affymetrix GeneChip® Wheat Genome Array. The global transcriptional profiles of the anther/pollen, ovary and stigma were analyzed at concurrent developmental stages and co-regulated as well as preferentially expressed genes were identified.  Data analysis revealed both novel and conserved regulatory factors underlying Triticeae floral development and function.

sample_organism: Secale cereale x Triticum turgidum subsp. durum

overall_design: Triticale reproductive tissues (anther, ovary, stigma) were collected at 4 successive stages using pollen development as a developmental reference: tetrad (TET), uninucleate microspore (UNM), bi-cellular pollen (BCP), and tri-cellular pollen (TCP). Mature pollen grains (MPG) were also collected.  Three biological replicates were analyzed for each  tissue using the 55K Affymetrix GeneChip® Wheat Genome Array.

first: Carolyn

last: Penniket

first: Rohan

middle: V

last: Patel

first: Nicholas

last: Provart

first: André

last: Laroche

first: Owen

last: Rowland

first: Laurian

last: Robert


title: TREM-1 is a novel therapeutic target in Psoriasis

status: Public on Nov 17 2012

summary: Our group recently described a population of antigen presenting cells that appear to be critical in psoriasis pathogenesis, termed inflammatory myeloid dendritic cells (CD11c+ BDCA1-). Triggering receptor expressed on myeloid cells type-1 (TREM-1) signaling was a major canonical pathway in the published transcriptome of these cells. TREM-1 is a member of the immunoglobulin superfamily, active through the DAP12 signaling pathway, with an unknown ligand. Activation through TREM-1 induces inflammatory cytokines including IL-8, MCP/CCL2 and TNF. We now show that TREM-1 was expressed in the skin of healthy and psoriatic patients, and there was increased soluble TREM-1 in the circulation of psoriasis patients. In psoriasis lesions, TREM-1 was co-localized with dendritic cells as well as CD31+ endothelial cells. TREM-1 expression was reduced with successful NB-UVB, etanercept and anti-IL-17 treatments. An in vitro model of PGN-activated monocytes as inflammatory myeloid DCs was developed to study TREM-1 blockade, and treatment with a TREM-1 blocking chimera decreased allogeneic Th17 activation, as well as IL-17 production. Furthermore, TREM-1 blockade of ex vivo psoriatic dendritic cells in an alloMLR also showed a decrease in IL-17. Together, these data suggest that the TREM-1 signaling pathway offers a novel therapeutic target to prevent the effects of inflammatory myeloid DCs in psoriasis.

overall_design:
Monocytes were isolated by plastic adherence, treated with TLR agonists overnight, washed twice and harvested in RTL-buffer. RNA was extracted and processed for microarray.
3 groups and 3 replicates with a paired structure across replicates

first: Michelle

last: Lowes


title: Tetraspanin TSPAN12 regulates tumor growth and metastasis and inhibits β-catenin degradation

status: Public on Oct 29 2012

city: Clayton

first: Konstantin

last: Knoblich

state: VIC

address: 15 Innovation Walk

department: Biochemistry and Molecular Biology

country: Australia

institute: Monash University

summary: Ablation of tetraspanin protein TSPAN12 from human MDA-MB-231 cells significantly decreased primary tumor xenograft growth, while increasing tumor apoptosis. Furthermore, TSPAN12 removal markedly enhanced tumor-endothelial interactions and increased metastasis to mouse lungs. TSPAN12 removal from human MDA-MB-231 cells also caused diminished association between FZD4 (a key canonical Wnt pathway receptor) and its co-receptor LRP5. The result likely explains substantially enhanced proteosomal degradation of β-catenin, a key effecter of canonical Wnt signalling. Consistent with disrupted canonical Wnt signaling, TSPAN12 ablation altered expression of LRP5, Naked 1 and 2, DVL2, DVL3, Axin 1 and GSKβ3 proteins. TSPAN12 ablation also altered expression of several genes regulated by β-catenin (e.g. CCNA1, CCNE2, WISP1, ID4, SFN, ME1) that may help to explain altered tumor growth and metastasis. In conclusion, these results provide the first evidence for TSPAN12 playing a role in supporting primary tumor growth and suppressing metastasis. TSPAN12 appears to function by stabilizing FZD4-LRP5 association, in support of canonical Wnt-pathway signaling, leading to enhanced β-catenin expression and function.

overall_design: 4 samples = 2 Control + 2 TSPAN12KD

first: Chandan

last: Sharma

first: Hong-Xing

last: Wang

first: Anne

middle: L

last: Fletcher

last: Turley

first: Martin

last: Hemler


title: TRANSCRIPTIONAL EFFECTS OF INHIBITING EGFR IN KERATINOCYTES

status: Public on Oct 19 2012

first: Miroslav

last: Blumenberg

address: 455 First Ave #874

institute: NYU School of Medicine

summary: EGFR activation is important in human epithelial malignancies, including cutaneous squamous cell carcinoma, lung, colon, pancreatic and other cancers. Therapies targeting EGFR are currently used to treat such cancers, but one significant drawback to EGFR inhibitor therapies is the associated skin toxicity. This toxicity usually presents as papular or pustular folliculitis, dry skin with pruritus and hair and nails abnormalities. The side effects often limit the usefulness of EGFR inhibitors in cancer treatment. The transcriptional changes caused by EGFR inhibition in epidermal keratinocytes have not been extensively explored. To define the transcriptional changes caused by inhibition of EGFR in primary human epidermal keratinocytes, we treated these cells with Tyrphostin and compared treated and control cultures in parallel, using Affymetrix microarrays. Using metaanalysis approaches, we integrated the observed changes with a large set of already existing data on transcriptional profiling in epidermal keratinocytes. We found that EGFR inhibition suppresses expression of genes associated with keratinocyte proliferation, attachment and motility. Apoptosis is facilitated by both induction of proapoptotic and suppression of antiapoptotic genes. Surprisingly, EGFR inhibition induces expression of markers of epidermal differentiation.

overall_design: Time course of human epidermal keratinocytes treated with Tyrphostin (AG1478) and untreated controls

first: Alix

last: Gazel


title: Gene expression analysis of H9 hESC derived neuron stem cells (NSC) harboring pathogenic LRRK2 (G2019S) mutation

status: Public on Oct 17 2012

city: La Jolla

first: Fei

last: Yi

address: 10010 North Torrey Pines Road

institute: Salk Institute

summary:
Genetic mutations on leucine-rich repeat kinase 2 (LRRK2) have been associated with an increased risk of Parkinson's disease. The Gly2019Ser (G2019S) mutation on LRRK2 gene is a relatively common cause of familial Parkinson's disease in Caucasian population.
In this study, we generated H9 hESC harboring LRRK2 (G2019S) mutation by gene knockin. Wildtype and LRRK2 mutant hESC were differentiated into NSC using a chemically defined protocol.

overall_design: LRRK2 mutant NSC were treated with or without the LRRK2 kinase specific inhibitor (LRRK2-IN-1). Global gene expression analysis was performed to assess the overall similarity of gene expression profiles among three NSC groups (wildtype; LRRK2 mutant; LRRK2 mutant with inhibitor treatment).

first: Guanghui

last: Liu

first: JC

last: Izpisua Belmonte


title: Gene expression analysis of human iPSC generated from pathogenic LRRK2 (G2019S) mutation bearing patients

summary:
Genetic mutations on leucine-rich repeat kinase 2 (LRRK2) have been associated with an increased risk of Parkinson's disease. The Gly2019Ser (G2019S) mutation on LRRK2 gene is a relatively common cause of familial Parkinson's disease in Caucasian population. In this study, we generated human induced pluripotent stem cell (iPSC) lines from LRRK2 (G2019S) bearing patient fibroblasts by cell reprogramming.
We performed global gene expression profiling of LRRK2 (G2019S) heterozygous and homozygous patient iPSC lines, and the corresponding fibroblast lines they originated from. An age-matched wildtype human fibroblast line and H1 human embryonic stem cell (ESC) line were used as controls.

overall_design: Microarray gene expression profiling was done to:  (1) Compare global gene expression differences between wildtype fibroblasts and fibroblasts from patients bearing homozygous and heterozygous LRRK2 (G2019S) mutation;  (2) Compare global gene expression differences between wildtype iPSC and iPSC generated from LRRK2 (G2019S) homozygous and heterozygous patients; (3) Check that all iPSC generated from wildtype and patients fibroblasts are in fact similar to human pluripotent ESC.


title: Gene expression profiling of C/EBPβ- and STAT3-deficient human endometrial stromal cells (HESC)

status: Public on Oct 11 2012

first: Wei

address: 2001 S Lincoln Ave.

department: comparative biosciences

institute: University of Illinois

summary: Our previous studies have shown that C/EBPβ plays a critical role in human endometrial stromal decidualization. In order to identify the molecular pathways regulated by C/EBPβ during decidualization, we performed gene expression profiling using RNA isolated from normal and C/EBPβ-deficient human endometrial stromal cells. The microarray results revealed that several key regulators of stromal differentiation, such as BMP2, Wnt4, IL-11Rα and STAT3, operate downstream of C/EBPβ during decidualization. Further studies revealed that STAT3 is a direct target of C/EBPβ and plays an important role in cytokine signal during the decidualization process. Gene expression profiling, using STAT3-deficient HESCs, showed an extensive overlap of pathways downstream of STAT3 and C/EBPβ  during stromal cell differentiation.

overall_design: We employed a siRNA strategy to suppress C/EBPβ or STAT3 mRNA expression in HESCs and then performed  microarray analysis to identify its downstream target genes. Further, using a similar strategy, we focused on STAT3, a C/EBPβ target gene, and identified the commone pathways downstream of both C/EBPβ and STAT3.

first: Milan

last: Bagchi

first: Indrani


title: Resistance to Irreversible EGFR Tyrosine Kinase Inhibitors through a Multistep Mechanism Involving the IGF1R Pathway

status: Public on Oct 01 2012

first: Pasi

last: Janne

address: 44 Binney Street Dana 820

summary: The clinical efficacy of EGFR kinase inhibitors gefitinib and erlotinib is limited by the  development of drug resistance. The most common mechanism of drug resistance is the  secondary EGFR T790M mutation. Strategies to overcome EGFR T790M mediated drug  resistance include the use of mutant selective EGFR inhibitors, including WZ4002, or by the  use of high concentrations of irreversible quinazoline EGFR inhibitors such as PF299804. In  the current study we develop drug resistant versions of the EGFR mutant PC9 cell line which  reproducibly develops EGFR T790M as a mechanism of drug resistance to gefitinib. Neither  PF299804 resistant (PFR) or WZ4002 resistant (WZR) clones of PC9 harbor EGFR T790M.  Instead, they demonstrate activated IGF1R signaling as a result of loss of expression of  IGFBP3 and the IGF1R inhibitor, BMS 536924, restores EGFR inhibitor sensitivity.  Intriguingly, prolonged exposure to either PF299804 or WZ4002 results in the emergence of a  more drug resistant subclone which contains ERK activation. A MEK inhibitor, CI-1040,  partially restores sensitivity to EGFR/IGF1R inhibitor combination. Moreover, an IGF1R or  MEK inhibitor used in combination with either PF299804 or WZ4002 completely prevents  the emergence of drug resistant clones in this model system. Our studies suggest that more  effective means of inhibiting EGFR T790M will prevent the emergence of this common drug  resistance mechanism in EGFR mutant NSCLC. However, multiple drug resistance  mechanisms can still emerge. Preventing the emergence of drug resistance, by targeting  pathways activated in resistant cancers before they emerge, may be a more effective clinical  strategy.

overall_design: Total of three samples with duplicate or triplicate each were analyzed.

middle: A

last: Jänne


title: Reactivation of ERK signaling causes resistance to EGFR kinase inhibitors

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array
Expression profiling by array

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

overall_design: Refer to individual Series


title: Phevalin (aureusimine B) production by Staphylococcus aureus biofilm and impacts on human keratinocyte gene expression

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

department: Microbiology

institute: Montana State University

summary:
Staphylococcus aureus produces the cyclic dipeptides tyrvalin and phevalin (aureusimine A and B, respectively).
A previous study reported that S. aureus mutants not capable of producing these compounds were less virulent in vivo through the deranged regulation of virulence factor genes. These findings, however, have been questioned as an unknown mutation in an operon that regulates virulence was discovered in the mutant strain.
Here, we report that S. aureus biofilms produce greater amounts of phevalin than their planktonic counterparts. When administered to human keratinocytes, phevalin had no substantial effect on gene expression. Phevalin had no obvious impact on the extracellular metabolome of S. aureus.
However, conditioned medium from S. aureus spiked with phevalin resulted in significant differences in keratinocyte gene expression compared to conditioned medium alone.
A role for phevalin in manipulating host responses is apparent. Additionally, phevalin is a potential biomarker and/or therapeutic target for chronic, biofilm-based infections.

overall_design: Secreted factors from S. aureus biofilm and planktonic cultures with equivalent population sizes were placed in contact with human HaCaT keratinocytes for 4 hours. Keratinocytes were grown to ~90% confluency.

first: Patrick

last: Secor

first: Laura

last: Jennings

first: Garth

last: James

first: Kelly

last: Kirker

first: Robin

last: Gerlach

first: Tom

last: Livinghouse

first: Jonathan

last: Hilmer

first: Brian

last: Bothner

first: Philip

last: Fleckman

first: John

middle: E

last: Olerud

last: Stewart


title: Aberrant ERK signaling causes resistance to EGFR kinase inhibitors

summary:
The clinical efficacy of EGFR kinase inhibitors is limited by the development of drug resistance. The irreversible EGFR kinase inhibitor WZ4002 is effective against the most common mechanism of drug resistance mediated by the EGFR T790M mutation. Here we show that in multiple complementary models harboring EGFR T790M, resistance to WZ4002 develops through aberrant activation of ERK signaling caused by either an amplification of MAPK1 or by downregulation of negative regulators of ERK signaling. Inhibition of MEK or ERK restores sensitivity to WZ4002, and the combination of WZ4002 and a MEK inhibitor prevents the emergence of drug resistance. The WZ4002 resistant MAPK1 amplified cells also demonstrate an increase both in EGFR internalization and a decrease in sensitivity to cytotoxic chemotherapy compared to the parental counterparts. Our findings provide insights into mechanisms of drug resistance to EGFR kinase inhibitors and highlight rational combination therapies that should be evaluated in clinical trials.

Our study identifies ERK signaling as a mediator of resistance to irreversible pyrimidine EGFR inhibitors in EGFR T790M-bearing cancers. We further provide a therapeutic strategy to both treat and prevent the emergence of this resistance mechanism.

overall_design: To generate drug-resistant NCI-H1975 cell lines, non-small cell lung cancer (NSCLC) cells were exposed to increasing concentrations of WZ4002 similar to previously described methods. Individual clones from WZ4002-resistant (WZR) cells were isolated and confirmed to be drug resistant. Clone #6, designated as WZR6, was used in this study. For expression analysis, samples were prepared in triplicate from parental NCI-H1975 and NCI-H1975 WZR6 cells.


title: Differentially Expressed Genes Regulating the Progression of Ductal Carcinoma In Situ to Invasive Breast Cancer (Group 2)

status: Public on Sep 29 2012

city: St Louis

first: Sangjun

last: Lee

state: MO

address: 4940 Parkview Place

department: Pathology

institute: Washington University at St. Louis

summary: We used gene expression profiling of human DCIS and IBC to discover uniquely expressed genes that may also regulate progression.

overall_design: RNA from human samples were extracted, purified, amplified, and evaluated for gene expression using Affymetrix U95Av2 gene expression arrays.

first: D

last: Allred


title: Differentially Expressed Genes Regulating the Progression of Ductal Carcinoma In Situ to Invasive Breast Cancer (Group 1)


title: Differentially Expressed Genes Regulating the Progression of Ductal Carcinoma In Situ to Invasive Breast Cancer (Group 3)


title: Genes up and down regulated in LNCaP cells overexpressing MED1

status: Public on Sep 26 2012

city: New Brunswick

last: Langenfeld

state: NJ

address: One Robert Wood Johnson Place

department: Surgery

institute: Rutgers-RWJMS

summary: To identify MED1 target genes involved in prostate tumorigenesis.

overall_design: LNCap cells were transiently transfected with a MED1 expression vector or and empty vector control for 24 hours. Total RNA was extracted and gene microarray carried out. Experiment was performed in duplicate. Four samples total.

first: Feng

last: Jin

first: Joseph

middle: D

last: Fondell


title: Gene expression data from MDA-MB231 cells stably transduced with lentiviral vectors encoding a control shRNA (shscramble) or two shRNAs targeting Coco (shco2 and shco4)

status: Public on Aug 16 2012

city: New York

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary:
Metastatic relapse of breast cancer and other tumor types usually occurs several years after surgical resection of the primary tumor. Early dissemination of tumor cells followed by an extended period of dormancy is thought to explain this prevalent clinical behavior. By using a gain-of-function retroviral cDNA screen in the mouse, we found that Coco, a secreted antagonist of TGF-beta ligands, induces solitary mammary carcinoma cells that have extravasated in the lung stroma to exit from dormancy. Mechanistic studies demonstrate that Coco awakens dormant metastasis-initiating cells by blocking stroma-derived Bone Morphogenetic Proteins. Inhibition of canonical BMP signaling reverses the commitment to differentiation of these cells and enhances their self-renewal and tumor-initiation capacity. Expression of Coco induces a discrete gene expression signature strongly associated with metastatic relapse to the lung but not to the bone or brain in primary patients’ samples. Accordi ngly, silencing of Coco does not inhibit metastasis to the bone or brain in mouse models. These findings suggest that metastasis-initiating cells require the self-renewal capability typically associated with stem cells in order to exit from dormancy and identify Coco as a master regulator of this process.
The Affymetrix HG-U133A and Agilent platforms, which were used to build MSK82 [GSE2603], EMC192 [GSE12276], EMC286 [GSE2034], and NKI295 [van 't Veer et al., 2002; van de Vijver et al.,2002; Fan et al., 2006] datasets, do not contain probes for Coco, preventing a direct analysis of the correlation of the expression of Coco with metastatic relapse. We therefore examined the changes in gene expression caused by silencing of Coco in MDA-MB231 cells in vitro and used the resulting signature as a proxy of Coco expression.

overall_design:
Compare the gene expression profile between shscramble with shCoco knockingdown MDA-MB231 cells
Coco shRNA #2 corresponds to TRCN0000149666 and Coco shRNA #4 corresponds to TRCN0000148148.

first: Hua

last: Gao

first: Ai

middle: P

last: Lee-Lim

first: Goutam

last: Chakraborty

first: Qianxing

last: Mo

first: Markus

last: Decker

first: Alin

last: Vonica

first: Ronglai

last: Shen

first: Ali

last: Brivanlou

first: Filippo

middle: G

last: Giancotti


title: Host gene expression response to Toxoplasma gondii infection is not different between RH∆ku80 and RH∆ku80∆rop5 parasites

status: Public on Sep 13 2012

first: Michael

middle: Sean

last: Behnke

address: 660 S. Euclid Ave

department: Molecular Microbiology

institute: Washington University School of Medicine

summary: The normally virulent type-I RH parasite is rendered avirulent when lacking ROP5. The avirulent phenotype is a consequence of interaction with the host innate immune system. We sought to understand if ROP5 alters host gene expression in order to escape host defenses. We saw no gene expression differences between host cells infected with wt (RH∆ku80) or RH∆ku80∆rop5 parasites. We have included uninfected HFF samples that were harvested in parallel with the infected samples.

overall_design: Host gene expression in response to infection with Toxoplasma gondii. Two independent samples per sample type. Three sample types: HFF infected with RH∆ku80, HFF infected with RH∆ku80∆rop5, and uninfected HFF.

first: L

last: Sibley


title: Lr1-mediated leaf rust resistance pathways of transgenic wheat lines

status: Public on Sep 14 2012

city: Winnipeg

first: Sylvie

last: Cloutier

state: MB

address: 195 Dafoe Road

institute: Agriculture and Agri-Food Canada

summary:
The wheat gene Lr1 imparts resistance to certain races of the leaf rust pathogen Puccinia triticina. However, the biological basis underlying the complex resistance mechanisms remains largely unknown. Gene expression profiling analyses using the Affymetrix GeneChip® Wheat Genome Array were performed with six independent Lr1 transgenic lines sampled before inoculation (0h) and at 6 and 24 h after inoculation with the avirulent P. triticina race CCDS. For the 6 and 24 h time points, 3 384 probe sets corresponding to 2 978 transcripts were differentially expressed as compared to the plants before inoculation. Genes involved in defence signalling were triggered as early as 6 h post inoculation (HPI) and included COI1, the primary component of jasmonic acid signalling. By 24 HPI, a shift in plant cellular metabolism, namely carbon conservation, was notable. The enzymes of glycolysis and gluconeogenesis were down-regulated, however, enzymes linked to alternative carbon sequestration processes such as the glyoxylate cycle were up-regulated. Also at 24 HPI, various secondary signalling molecules belonging to the various hormone signalling pathways were triggered. These microarray data suggest that the Lr1 mediated leaf rust resistance is achieved by early onset of defence signalling followed by co-ordinated interplay of metabolism alteration and elicitation of defence responses.
We used microarrays to detail the early gene expression events underlying Lr1-mediated resistance to Puccinia triticina pathogen in wheat.

overall_design: Three biological replicates with six independent Lr1 transgenic lines were used in this study to eliminate the possibility of false discovery of genes due to copy number variation or the position of insertion of the transgene  Lr1. Early time points of 6 and 24 HPI were compared to 0 h (prior to inoculation) to capture the early signalling events involved in Lr1-mediated response to rust infection.

first: Santosh

last: Kumar

first: Zining

last: Wang

first: Travis

last: Banks

first: Mark

middle: C

last: Jordan

first: Brent

last: McCallum


title: Effect of integrin alphaV on transcription in 2d or 3d

status: Public on Jul 11 2012

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

summary: M21 or M21L cells were grown either in a 2-dimensional culture (on plastic) or in a 3-dimensional-collagen model.

overall_design: 2x2 design, in triplicate.

first: Enge

last: Martin

first: Wenjie

last: Bao


title: A mesenchymal stromal cell gene signature for donor age

status: Public on Jul 21 2012

city: Enschede

first: Nathalie

last: Groen

address: Drienerlolaan 5

department: Tissue Regeration

country: Netherlands

institute: University of Twente - MIRA – Institute for Biomedical Technology and Technical Medicine

summary:
Human aging is associated with loss of function and regenerative capacity. Human bone marrow derived mesenchymal stromal cells (hMSCs) are involved in tissue regeneration, evidenced by their capacity to differentiate into several lineages and therefore are considered the gold standard for cell-based regeneration therapy. Tissue maintenance and regeneration is dependent on stem cells and declines with age and aging is thought to influence therapeutic efficacy, therefore, more insight in the process of aging of hMSCs is of high interest. We, therefore, hypothesized that hMSCs might reflect signs of aging. In order to find markers for donor age, early passage hMSCs were isolated from bone marrow of 61 donors, with ages varying from 17-84, and clinical parameters, in vitro characteristics and microarray analysis were assessed. Although clinical parameters and in vitro performance did not yield reliable markers for aging since large donor variations were present, genome-wide microarray analysis resulted in a considerable list of genes correlating with human age. By comparing the transcriptional profile of aging in human with the one from rat, we discovered follistatin as a common marker for aging in both species. The gene signature presented here could be a useful tool for drug testing to rejuvenate hMSCs or for the selection of more potent, hMSCs for cell-based therapy.
We used microaray gene expression profiling to find expressed genes that correlated with the donor age of bone-marrow derived mesenchymal stromal cells (hMSCs)

overall_design: Human mesenchymal stem cells (hMSC) were biopsied from bone marrow from 61 different donors aging from 17 - 89 years old. The genome wide expression profiles was assessed using Affymetrix microarrays. The expression of genes was correlated with the age of the donors.

first: Hugo

last: Alves

first: Jetty

last: van Ginkel

first: Marc

last: Hulsman

first: Anouk

last: Mentink

first: Marcel

last: Reinders

first: Clemens

last: van Blitterswijk

first: Jan

last: de Boer


title: DNA methylation alterations and transcriptional gene silencing induced by IDH1 R132H mutation [Affymetrix]

status: Public on Aug 14 2012

city: Atlanta

first: Benjamin

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

summary: The cytosolic NADP+-dependent isocitrate dehydrogenase IDH1 is frequently mutated in human cancers. Recent studies have shown that IDH1 mutant primary glioblastomas (GBM) and acute myeloid leukemias (AML) display robust association with CpG island methylator phenotype (CIMP).  Such observations bring into question whether IDH1 mutations directly contribute to the development of CIMP or if the hypermethylation phenotype precedes acquisition of IDH1 mutations.  To reveal the effects of IDH1 mutations on DNA methylation and gene expression, we introduced the most frequently observed IDH1 mutation, R132H, into a human cancer cell line through gene targeting.  We profiled changes in methylation at over 27,000 CpG dinucleotides spanning 14,475 unique gene regions and characterized genome-wide gene expression alterations resulting from IDH1R132H knockin.  We observed consistent changes in both DNA methylation and gene expression when comparing two independent IDH1R132H knockin clones to their wild-type parent, and report hypermethylation of over 2,000 loci, the majority of which contained preexisting methylation in IDH1WT parental cells. These loci exhibit the same trend in primary TCGA glioblastoma tumors with mutant IDH1 as compared to those with wild-type IDH1 and have significant overlap with genes hypermethylated in glioma-CIMP+ tumors. Furthermore, we identify specific DNA methylation and gene expression alterations which correlate with IDH1 mutations in our cell-line model as well as primary glioblastomas, including hypermethylation and transcriptional silencing of RBP1.  The presented data provide insight on epigenetic alterations induced by IDH1 mutations and support a contributory role for IDH1 mutants in regulation of DNA methylation and gene expression in human cancer cells.

overall_design: Comparison of IDH1 R132H and wild-type HCT116 cells

first: Christopher

last: Duncan

first: Paula

last: Vertino

first: Hai

last: Yan


title: GEP data from BCWM.1 cells treated with LNA antimiR-155 or scramble control

status: Public on Jul 10 2012

first: Yong

last: Zhang

state: MA

address: 450 Brookline Ave

summary:
microRNA-155 acts as an oncogenic miRNA in B-cell lymphoproliferative disorders including Waldenstrom Macroglobulinemia (WM) and Chronic Lymphocytic Leukemia (CLL).
we used an 8-mer LNA (locked nucleic acid) phosphorothioate oligonucleotide targeting the seed region of miR-155 to effectively antagonize in vitro tumor growth in WM.

overall_design: We performed gene expression profiling (GEP) analysis on BCWM.1 cells after treatment with LNA antimiR-155 or scramble control for 48 hours.

first: Irene

middle: M

last: Ghobrial


title: Expression data from U2OS ER-E2F1 cells after FOXO knockdown and E2F1 activation

status: Public on Jul 06 2012

city: Durham

first: Igor

last: Shats

state: NC

address: 101 Science Drive

institute: Duke University

summary: Effect of FOXO knockdown on E2F1-mediated transcription

overall_design:
U2OS cells stably expressing ER-E2F1 were infected with two different lentiviruses both targeting  FOXO1 and FOXO3 or control virus encoding scrambled sequence.
Twenty four hours post infection medium was replaced to serum-free DMEM for 24 hours. Then medium was replaced to serum-free DMEM with or without 20 nM 4-hydroxy tamoxifen for 6 hours.

first: Joseph

last: Nevins


title: Time series data of HCV (JC1) infection of Huh7 cells

status: Public on Jun 15 2012

city: Vienna

first: Kumaran

last: Kandasamy

state: Vienna

address: Lazarettgasse 14, AKH BT25.3

country: Austria

institute: Center for Molecular Medicine

summary:
Huh7/5-2 cells (Binder et al., Hepatology 2007) were mock infected (DMEM) (time points 4 and 48 h) or  infected with the chimeric HCV virus Jc1 (Pietschmann et al., PNAS 2006) (all time points).
Multiplicity of infection was 15 (TCID50). Cells were lysed after 4, 12, 24, 48 and 72 hours post infection and total cellular RNA was prepared.

overall_design: Mock infected cells serve as controls for the infected samples. The whole experiment was repeated on independent days (2 biological replicates).

first: Marco

last: Binder

first: Ralf

last: Bartenschlager

first: Martin

last: Trippler

first: Andreas

last: Pichlmair

first: Giulio

last: Superti-Furga


title: DNA methylation alterations and transcriptional gene silencing induced by IDH1 R132H mutation

status: Public on Aug 13 2012

type:
Expression profiling by array
Methylation profiling by array


title: Differentially Expressed Genes Regulating the Progression of Ductal Carcinoma In Situ to Invasive Breast Cancer

first: Sangjun

last: Lee


title: Phosphorylated and Sumoylation-Deficient Progesterone Receptors Drive Proliferative Gene Signatures During Breast Cancer Progression (Affymetrix gene expression analysis)

status: Public on Jun 07 2012

city: Minneapolis

first: Todd

last: Knutson

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

summary: Anlaysis of the differential gene expression between T47D cells expressing wild type (WT) progesterone receptor isoform B (PR) or SUMOylation-deficient PR molecules.

overall_design: Total RNA obtained from T47D breast cancer cells induced (with AP21967) to express either iWT PR-B or mutant PR-B (iK388R, SUMO-deficient), treated with or without synthetic PR ligand R5020 for 6 h. Each sample had 1 replicate.

first: Kevin

last: Silverstein


title: Highly Pathogenic Avian Influenza Viruses Avoid Effective Inflammatory Response of Human Macrophages

status: Public on May 29 2012

city: Hannover

first: Dorothee

last: Viemann

state: Deutschland

address: Carl-Neuberg-Straße 1

department: Department of Pediatric Pulmonology, Allergy and Neonatology

institute: Hannover Medical School

summary:
Macrophages were infected with low (PR8) and high pathogenic influenza viruses (FPV and H5N1). To our surprise a genome-wide comparative systems biology approach revealed that in contrast PR8 infections with HPAIV H5N1 and FPV result in a reduced immune response of human macrophages contradicting a primary role of this cell type for the cytokine storm.
Our data point to a viral strategy of HPAIV to bypass a major amplifier of the initial local inflammatory response thereby hampering antiviral effector mechanisms and facilitating virus spreading and systemic disease.

first: Judith

last: Friesenhagen

first: Johannes

last: Roth

first: Yvonne

last: Börgeling

first: Eike

last: Hrincius

first: Stephan

last: Ludwig


title: Phosphorylated and Sumoylation-Deficient Progesterone Receptors Drive Proliferative Gene Signatures During Breast Cancer Progression


title: MiR-106b-25 cluster targets caspase 7 and focal adhesion in human prostate cancer

status: Public on May 01 2012

city: Bethesda

first: Robert

middle: Scott

last: Hudson

state: MD

address: National Cancer Institute Room Blgd.37/3044

department: NCI

institute: NIH

summary:
We and others previously reported that the miR-106b-25 microRNA cluster is a candidate oncogene in human prostate cancer. Here, we made the novel observation that miR-106b-25 expression is further up-regulated in distant metastasis. Moreover, increased tumor miR-106b expression was associated with early disease recurrence. To identify yet unknown oncogenic functions of the prognostic miR-106b, we overexpressed it in LNCaP human prostate cancer cells to examine miR-106b-induced global expression changes among protein-coding genes. The approach revealed that caspase-7 is a candidate direct target of miR-106b, which was confirmed by Western blot analysis and a 3’UTR reporter assay. Other analyses showed that caspase-7 is down-regulated in primary human prostate tumors and metastatic lesions across multiple datasets and is by itself associated with disease recurrence. Using bioinformatics, we also discovered that miR-106b-25 may specifically influence focal adhesion-related pathways. This observation was experimentally confirmed using miR-106b-25-transduced 22Rv1 human prostate cancer cells. After infection with a miR-106b-25 lentiviral expression construct, 22Rv1 cells showed increased adhesion to basement membrane- and bone matrix-related filaments and enhanced soft agar growth. In summary, miR-106b-25 was found to be associated with prostate cancer progression and metastasis and may do so by altering apoptosis- and focal adhesion-related pathways.
To elucidate the effects miR-106b, we up-regulated miR-106b in LNCaP cells and examined gene expression alterations on a global scale with Affymetrix arrays.

overall_design: LNCaP cells were transfected with pre-miR oligos and 24 hr post-transfection total RNA was collected for microarray anaylsis.

first: Stefan

last: Ambs

first: Ming

last: Yi


title: MDA-MB-231 eIF4E RIP-CHIP

first: Uma

last: Shankavaram

address: 9000 Rockville Pike

summary: Cytoplasmic RNA bound to eIF4E was pulled down from MDA-MB-231 cells to determine the influence of radiation on eIF4E mRNA binding

overall_design: 4 samples were analyzed with 3 biological replicates

first: Thomas

middle: J

last: Hayman

first: Eli

last: Williams

first: Muhammad

last: Jamal

last: Camphausen

first: Philip

last: Tofilon


title: Diverse epigenetic strategies interact to control epidermal differentiation [ChIP-Seq]

status: Public on Jun 24 2012

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

summary: It is becoming clear that interconnected functional gene networks, rather than single genes in isolation, govern stem cell self-renewal and differentiation. To identify potential epigenetic networks that impact on human epidermal stem cells we performed siRNA based genetic screens for 332 chromatin modifiers. We developed a Bayesian mixture model to predict putative functional interactions between those epigenetic modifiers that regulated differentiation. This allowed us to discover a network of genetic interactions involving EZH2, UHRF1 (both known to regulate epidermal self-renewal), ING5 (a MORF complex component), BPTF and SMARCA5 (NURF complex components). Genome-wide localisation and global mRNA expression analysis revealed that these factors impact two distinct but functionally related gene sets, including integrin extracellular matrix receptors that mediate anchorage of epidermal stem cells to their niche. Using a competitive epidermal reconstitution assay we confirmed that ING5, BPTF, SMARCA5, EZH2 and UHRF1 control differentiation under physiological conditions. Thus, regulation of distinct gene expression programs through the interplay between diverse epigenetic strategies protects epidermal stem cells from differentiation.

overall_design: Examination of genome-wide localisation of ING5 in primary human keratinocytes

first: Klaas

middle: W

last: Mulder

first: Fiona

last: Watt


title: SIRT7 is a histone H3 lysine 18 deacetylase that regulates oncogenic transformation

status: Public on May 07 2012

city: Houston

first: Yuanxin

last: Xi

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Center

summary: Sirtuin proteins regulate diverse cellular pathways that influence genomic stability, metabolism, and ageing. SIRT7 is a mammalian sirtuin whose biochemical activity, molecular targets, and physiologic functions have been unclear. Here we show that SIRT7 is an NAD+-dependent, histone H3 acetyl-lysine 18 (H3K18Ac) deacetylase that stabilizes the transformed state of cancer cells. Genome-wide binding studies reveal that SIRT7 binds to promoters of a specific set of gene targets, where it deacetylates H3K18Ac and promotes transcriptional repression. The spectrum of SIRT7 target genes is defined in part by interaction of SIRT7 with the cancer-related ETS transcription factor ELK4, and comprises numerous genes with links to tumour suppression. Notably, selective hypoacetylation of H3K18Ac has recently been linked to oncogenic transformation, and in patients, is associated with aggressive tumour phenotypes and poor prognosis. We find that deacetylation of H3K18Ac by SIRT7 is necessary for maintaining essential features of human cancer cells including anchorage independent growth and escape from contact inhibition. Moreover, SIRT7 is necessary for a global hypoacetylation of H3K18Ac associated with cellular transformation by viral oncoproteins. Finally, SIRT7 depletion markedly reduces the tumourigenicity of human cancer cell xenografts in mice. Together, our work establishes SIRT7 as the first known site-specific H3K18Ac deacetylase and demonstrates a pivotal role for SIRT7 in chromatin regulation, cellular transformation programs, and tumour formation in vivo.

overall_design: SIRT7 ChIP-seq was performed in K562 cell lines under normal conditions. Two replicates were performed for both the SIRT7 ChIP as well as input control.

first: Matthew

middle: F

last: Barber

first: Eriko

last: Michishita

first: Zarmik

last: Moqtaderi

first: Kevin

last: Struhl

first: Wei

last: Li

first: Katrin

last: Chua


title: IL-17A is an essential cytokine to sustain pathogenic cell activation and inflammatory gene circuits in psoriasis vulgaris

status: Public on Apr 30 2012

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

summary: In psoriasis, inflammation and epidermal hyperplasia are thought to be controlled by T cell-derived cytokines. Evidence now suggests that Th17 and Th22 cells infiltrate psoriasis lesions and by secreting IL-17 and IL-22, respectively, may drive disease-specific gene or cell responses. While studies in model systems indicate that IL-22 has a dominant pathogenic role, there is evolving evidence that IL-17 contributes to features of psoriasis. To more fully understand the role of IL-17 in human disease pathogenesis, we examined psoriatic skin lesions obtained from patients treated with an anti-IL-17 (IL-17 A) monoclonal antibody, LY2439821. In a phase 1, randomized, double-blind, placebo-controlled dose escalation trial, patients with chronic psoriasis were randomized to receive 3 doses of subcutaneous LY2439821 at 5 mg (n=8), 15 mg (n=8), 50 mg (n=8), 150 mg (n=8) or placebo (n=8) at weeks 0, 2 and 4. Repeat biopsies were taken from the same lesional area at baseline, week 2 and 6. At week 6, a PASI75 was observed in 0/8, 2/8, 5/7 and 8/8 patients receiving 5 mg, 15 mg, 50 mg or 150 mg LY2439821 respectively and 0/8 patients receiving placebo. The antibody was well-tolerated. In patients receiving the two highest doses, histological and immunohistochemical analyses of biopsies revealed significant reductions from baseline in keratinocyte proliferation, hyperplasia and epidermal thickness after 2 weeks, as well as reduced infiltration into the dermis and epidermis by T-cells (CD3+) and dendritic cells (CD11c and DC-LAMP). Keratinocyte expression of innate defense proteins, S100A7, S100A8, beta-defensin2 and LL37/cathelicidin was also reduced. By week 6, the skin appeared normal with a reversal of disease defining pathological features. Quantitative RT-PCR revealed decreased expression of interferon gamma (IFN-gamma), IL-22 and IL-17, key cytokines from T cell subsets Th1, Th22 and Th17, respectively. In order to explore the extent to which IL-17 blockade influences an even broader set of inflammatory or psoriatic disease related genes, mRNA levels from skin biopsy samples were evaluated using whole genome microarrays. At week 2, the highest dose of LY2439821 modulated over 1500 genes significantly (>1.5 fold change [FC], p<0.05). Of these, 51 genes were strongly suppressed (>7-fold) including IL-19, lipocalin, amphiregulin, granzyme B, and several chemokines. In a separate analysis, those genes known to be synergistically regulated by both IL-17 and TNF-alpha showed the greatest normalization in expression compared to genes known to be regulated by TNF-alpha alone, IFN-gamma or Interferon alpha. Our data suggest that Th17 cells, through the expression of IL-17, mediate psoriasis pathogenesis, and that neutralization of IL-17 with LY2439821 suppresses signaling through multiple inflammatory circuits by inhibiting expression of cytokines from multiple T cell subsets, as well as chemokines, and antimicrobial proteins from keratinocytes.

first: James

last: Krueger

first: Robert

last: Hoffman


title: Transcriptome profiling of reproductive stage flag leaves of wheat from drought susceptible parent WL711, drought tolerant parent C306 and drought susceptible and drought tolerant RIL bulks in irrigated and drought condition

city: new delhi

first: suhas

middle: baliram

last: kadam

state: delhi

address: lbs pusa campas

department: biotechnology

country: India

institute: NRCPb

summary: The aim of the study was to identify candidate genes responsible for drought tolerance trait between a pair of wheat varieties ( WL711 and C306) and correspondng progeny bulks (10 drought susceptible RILs  and 10 drought tolerant  RILs) by combining QTLs analysis with expression analysis.   Microarray analysis of RNA extracted from the flag leaves showed large number of differentially expressed genes.  The number of differentially expressed genes was reduced  to 37 on the basis of their occurance in a major QTL region (responcible for drought tolerance) detected in RIL population derived from WL711 and C306.

overall_design: RNA from the reproductive stage flag leaf of wheat in irrigated and drought condition of drought susceptible parent WL711, drought tolerant parent C306 and drought susceptible and drought tolerant RIL bulks were analysed in three different biological replications  (A , B and C) making total twenty four samples

first: Suhas

middle: B

last: Kadam

first: Vasantrao

middle: N

last: Pawar

first: Kishor

last: Gaikwad

first: Renu

middle: K

last: Chopra

first: Nagendra

last: Singh


title: Global transgenerational gene expression dynamics in two nascent allohexaploid wheat lines analogous in genome constitution to common wheat (Triticum aestivum)

city: changchun

first: bao

last: qi

address: 5268 Renmin Street

country: China

institute: chinese academy of science

summary: Alteration in gene expression accompanying initial stages of allopolyploidy is a prominent feature in plants, but its spectrum and model are highly idiosyncratic. We used multi-colour GISH to identify individuals from two nascent allohexaploid wheat lines between Triticum turgidum and Aegilops tauschii, which had a transgenerationally stable chromosomal constitution mimicking that of common wheat.  We performed genomewide analysis of gene expression for these plants along with their parental species using the Affymetrix GeneChip Wheat Genome-Array.  Comparison with parental species coupled with inclusion of empirical mid-parent values (MPVs) revealed two patterns of alteration in gene expression in the allohexaploid lines: parental dominance expression and nonadditive expression.  Genes involved in each altered pattern could be classified into three distinct groups, stochastic, heritable and persistent, based on their transgenerational heritability and inter-line conservation.  Whereas both altered patterns of gene expression showed a propensity of inheritance, identity of the involved genes is stochastic, consistent with the involvement of diverse Gene Ontology (GO) terms.  Nonetheless, those genes showing nonadditive expression exhibited a significant enrichment for vesicle-function. Our results suggest global alteration in gene expression conditioned by nascent allopolyploidy likely play functional roles in stabilization and establishment of the newly formed plants, and consequential to evolution.

sample_organism:
Triticum aestivum
Triticum turgidum subsp. durum
Aegilops tauschii
Triticum carthlicum

overall_design: We used Affymetrix GeneChip Wheat Genome-Array to compare the expression difference of newly synthetic wheat allopolyploid lines and their parental lines.

first: Bao

last: Qi

last: Huang

first: Bo

last: Zhu

first: Xiaofang

last: Zhong

first: Jianhua

last: Guo

last: Zhao

first: Chunming

last: Xu

first: Jinsong

last: Pang

first: Fangpu

last: Han

first: Moshe

last: Feldman

last: Liu


title: Expression data from intact adipose tissue in human pregnancy

status: Public on Apr 13 2012

city: Cleveland

first: Veronica

last: Resi

state: Ohio

address: MetroHealth Drive 2500

department: Ob/Gyn Department

institute: MetroHealth Medical Center

summary: We performed microarray analysis to evaluate differences in the transcriptome of the adipose tissue before and during pregnancy

overall_design: Biopsies of adipose tissue of the subcutaneous gluteal depots, processed for adipose cell isolation, the remining tissue was snap frozen in liquid nitrogen, adipocytes were isolated by digestion with collagenase


title: Innate immune agonist, dsRNA, induces apoptosis in ovarian cancer cells and enhances the potency of cytotoxic chemotherapeutics

status: Public on Apr 29 2012

city: Richmond

first: Jessica

last: Bell

state: VA

address: 1101 E. Marshall St.

institute: VCU

summary:
This study aimed at characterizing the effect of the innate immune agonist, dsRNA, on ovarian cancer cell lines and ascites-derived ovarian cancer cells.
DsRNA stimulation revealed two sub-populations of ovarian cancer cells, dsRNA sensitive and dsRNA resistant, that could be categorized based upon dsRNA-induced dsRNA receptor expression.

overall_design: Human ovarian cancer cell lines were treated with pI:pC and compared against untreated cells.

first: Catherine

middle: I

last: Dumur

first: Danielle

last: Van


title: Expression data from glioblastoma stem-like cells and their differentiated progeny co-cultured with astrocytes

status: Public on Apr 09 2012

first: Barbara

middle: Helen

last: Rath

address: 10 Center Drive B3B406

department: National Cancer Institute

institute: National Institute of Health

summary: Glioblastoma stem-like cells or their differentiated progeny were co-cultured for 48h with normal human astrocytes to detect if invasion associated genes were influenced

overall_design: Co-cultured samples and controls, a total 24 samples were selected for RNA extraction and hybridization on Affymetrix microarrays.

middle: H

first: Joshlean

last: Fair

first: Kevin

last: Camphausen

first: Philip

last: Tofilon


title: Gene expression profiles of ovarian tumor biopsies from Phase I dasatinib trial

status: Public on Apr 12 2012

city: durham

first: Miao

last: yu

address: Laselle drive

institute: Duke

summary: A phase I trial of a SRC kinase Inhibitor, dasatinib, in combination with paclitaxel and carboplatin in patients with advanced or recurrent ovarian cancer. Background: We conducted a phase I study of dasatinib, an oral SRC tyrosine kinase inhibitor, in combination with paclitaxel and carboplatin in advanced and recurrent epithelial ovarian cancer (EOC). Methods: The primary objective was to determine the maximum tolerated dose (MTD). Secondary objectives included toxicity, response rate (RR), pharmacokinetics and pharmacodynamics. Based on the 3+3 design, cohorts of 3-6 pts received paclitaxel 175 mg/m2 and carboplatin AUC 6 every three weeks with escalating doses of dasatinib (100, 120, 150 mg daily), followed by an 8 patient expansion cohort. Results: Twenty patients were enrolled between 06/07 and 12/09. The median age was 61 yrs (42-82) with a median of 2 prior regimens (0-6), and 71% had platinum-sensitive disease. There were 3-6 pts in each cohort, and 8 in the expansion cohort. Pharmacokinetics were observed over the first 2 cycles of therapy. One DLT was observed in the 100 mg dasatinib cohort (grade 3 myalgia. Other toxicities in all cycles included neutropenia (95% grade 3-4), thrombocytopenia (35% grade 3-4), and fatigue (10% grade 3). The RR was 45% (complete responses, 3/18(17%); partial responses, 5/18(28%)) and 56% (10/18) had stable disease. The PFS6-month actuarial estimate was 86%. The median PFS and OS were 7.8 and 16.2 months, respectively. Conclusions: Due to the high incidence of myelosuppression with subsequent cycles the recommended phase II dose is 150 mg daily of dasatinib in combination with paclitaxel and carboplatin. The combination was safe with evidence of clinical activity in advanced EOC.

overall_design: Global profiles of expression were characterized using unsupervised clustering methods and gene- and pathway-analyses of differential expression.

first: Angeles

middle: A

last: Secord

first: William

middle: T

last: Barry


title: Compilation of expression profiles distinct thyroid neoplasias

status: Public on Jun 01 2012

city: Brussels

first: Gil

last: Tomas

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

summary: A cohort of distinct thyroid neoplasias was hybridized onto the Affymetrix U95 GeneChip

overall_design: We profiled the gene expression of a cohort of 9 Hurthle cell adenomas, 17 follicular adenomas, 9 follicular thyroid carcinomas, 13 follicular variants of papillary thyroid carcinomas, 6 Hashimoto throiditis, 8 thyroid hyperplasias and 9 papillary thyroid carcinomas.

first: Vincent

last: Detours

first: T

last: Fahey III


title: Molecular defense mechanisms of Barrett's metaplasia estimated by an integrative genomics

status: Public on Mar 08 2012

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

summary:
Barrett's esophagus is characterized by the replacement of squamous epithelium with specialized intestinal metaplastic mucosa. The exact mechanisms of initiation and development of Barrett's metaplasia remain unknown, but a hypothesis of successful adaptation against noxious reflux components has been proposed. To search for the repertoire of adaptation mechanisms of Barrett's metaplasia, we employed high-throughput functional genomic and proteomic methods that defined the molecular background of metaplastic mucosa resistance to reflux. Transcriptional profiling was established for 23 pairs of esophageal squamous epithelium and Barrett's metaplasia tissue samples using Affymetrix U133A 2.0 GeneChips and validated by quantitative real-time polymerase chain reaction. Differences in protein composition were assessed by electrophoretic and mass-spectrometry-based methods. Among 2,822 genes differentially expressed between Barrett's metaplasia and squamous epithelium, we observed significantly overexpressed metaplastic mucosa genes that encode cytokines and growth factors, constituents of extracellular matrix, basement membrane and tight junctions, and proteins involved in prostaglandin and phosphoinositol metabolism, nitric oxide production, and bioenergetics. Their expression likely reflects defense and repair responses of metaplastic mucosa, whereas overexpression of genes encoding heat shock proteins and several protein kinases in squamous epithelium may reflect lower resistance of normal esophageal epithelium than Barrett's metaplasia to reflux components. Despite the methodological and interpretative difficulties in data analyses discussed in this paper, our studies confirm that Barrett's metaplasia may be regarded as a specific microevolution allowing for accumulation of mucosal morphological and physiological changes that better protect against reflux injury.
Department of Gastroenterology, Medical Center for Postgraduate Education and Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781 Warsaw, Poland

overall_design: 2 types of tissue sample derived from the same patient:  > Normal squamous epithelium (NE) from patients with longsegment of Barret’s epithelium   > Metaplastic epithelium from Barrett’s esophagus (BE)

first: Jerzy

last: Ostrowski

first: Michał

last: Mikula

first: Jakub

last: Karczmarski

first: Tymon

last: Rubel

first: Lucjan

middle: S

last: Wyrwicz

first: Piotr

last: Brągoszewski

first: Paweł

last: Gaj

last: Dadlez

first: Eugeniusz

last: Butruk

first: Jarosław

last: Reguła


title: Human prolactinoma

city: Los Angeles

first: Yunguang

last: Tong

state: CA

address: 8700 Beverly BLVD

institute: Cedars-Sinai Medical Center

summary: Human prolactinomas (n=4, 3 males and 1 female) were obtained during trans-sphenoidal surgery as part of an ongoing accession of human pituitary tumors.  The study was approved Institutional Review Board (IRB) of Emory University, and informed consent obtained for all subjects. Tumors were microdissected and removed using the surgical microscope, rinsed in sterile saline, snap-frozen in liquid nitrogen, and stored (-80 ℃) until analysis. Each tumor fragment was confirmed independently by a neuropathologist by histology and immunohistochemistry prior to molecular analysis. Three normal pituitary glands from cadavers were obtained from the National Resource Center (NDRI, www.ndriresource.org).   Each human tissue sample was analyzed using Affymetrix Human Genome U95Av2 arrays.

overall_design: 4 prolactinoma and 3 normal pituitaries

first: Nelson

last: Oyesiku


title: Profiling of direct mRNA targets of miR-130a, miR-203 and miR-205 in prostate cancer cell line LNCaP

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

department: Diagnostics

institute: Fraunhofer Institute for Cell Therapy and Immunology

summary: Micro RNAs (miRNAs) miR-130a, miR-203 and miR-205 are jointly downregulated in prostate cancer and act as repressors of AR-signaling.  MiRNAs are small non-coding RNAs that regulate the expression of specific mRNA targets mainly by translational repression, mRNA deadenylation or cleavage. Reconstitution of these lost miRNAs in the LNCaP PCa cell line cause morphology changes, growth arrest, and apoptosis, increasing when the miRNAs were co-expressed. This series identifies direct targets of miR-130a, miR-203, and miR-205 by AGO2-RNA co-immunoprecipitation as described by (Beitzinger et al. 2007) upon miRNA reconstitution in LNCaP cells and analyzing AGO2-bound mRNAs using Affymetrix Genechips. Relative levels of AGO2 bound versus total RNA expression were compared between miRNA reconstituted and miR-scr transfected samples.

overall_design: Three arrays each for AGO2-bound RNA upon reconstitution of miR-130a, miR-203, miR-205, a scramble miRNA, and three arrays each for total RNA upon reconstitution of miR-130a, miR-203, miR-205, a scramble miRNA.

first: Kerstin

last: Boll

first: Nora

last: Mörbt

first: Antje

last: Kretzschmar

first: Katharina

last: Schutt

first: Janina

last: Tomm

first: Gerald

last: Verhaegh

first: Jack

last: Schalken

first: Martin

last: von Bergen

first: Friedemann

last: Horn

first: Jörg

last: Hackermüller


title: Gene expression profiles of fibroblasts and fibroblast-reprogrammed induced pluripotent stem cells (iPSCs) from childhood cerebral adrenoleukodystrophy patients and healthy controls

status: Public on Mar 01 2012

first: Joseph

middle: Gerard

last: Hacia

address: 2250 Alcazar Street, IGM 261

department: Biochemistry and Molecular Biology

institute: University of Southern California

summary:
Although not an affected cell type, skin fibroblasts from individuals with CC-ALD, an early onset X-linked neurological disorder, show defects in very long chain fatty acid (VLCFA) metabolism that provide the basis for clinical diagnostic tests. Skin fibroblasts from CC-ALD patients can be reprogrammed into iPS cells with all the hallmark properties of pluripotency. The iPS cell phenotypes may reflect the tissue-specificity of the lipid metabolic defects found in CC-ALD patients.
We report the gene expression profiles of fibroblasts and fibroblast-reprogrammed iPSCs from childhood cerebral adrenoleukodystrophy patients and healthy controls

overall_design: Dermal fibroblast cultures from 2 CCALD patients and 3 healthy controls were reprogrammed into iPSCs by transfection with retroviruses desinged to express the human OCT4, SOX2, KLF4 and c-MYC cDNA.  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 CCALD patients and healthy controls.

first: Xiao-Ming

last: Wang

middle: G