title: The lncRNA PCAT29 inhibits oncogenic phenotypes in prostate cancer

city: Ann Arbor

first: Arul

last: Chinnaiyan

state: Michigan

address: 1500 E Medical Center Drive

department: Pathology

institute: University of Michigan

summary: Long noncoding RNAs (lncRNAs) have recently been associated with the development and progression of a variety of human cancers. However, to date, the interplay between known oncogenic or tumor suppressive events and lncRNAs has not been well described. Here the novel lncRNA, Prostate Cancer-Associated Transcript 29 (PCAT29), is characterized along with its relationship to the androgen receptor (AR). PCAT29 is suppressed by dihydrotestosterone (DHT) and up-regulated upon castration therapy in a prostate cancer xenograft model. PCAT29 knockdown significantly increased proliferation and migration of prostate cancer cells, while PCAT29 overexpression conferred the opposite effect and suppressed growth and metastases of prostate tumors in chick chorioallantoic membrane (CAM) assays. Finally, in prostate cancer patient specimens, low PCAT29 expression correlated with poor prognostic outcomes. Taken together, these data expose PCAT29 as an androgen regulated tumor suppressor in prostate cancer

overall_design: PCAT29 was knockdown using shRNA in two prostate cancer cell lines VCaP and LNCaP.

first: Rohit

last: Malik

first: Yang

last: Shi

first: Xiaojun

last: Jing


title: Global hepatic transcript data from LRH-1 WT and LRH-1 K289R jejunums

status: Public on Jul 11 2014

city: Lausanne

first: Kristina

last: Schoonjans

address: Station 15

department: SV IBI GR-SCH

country: Switzerland

institute: Ecole Polytechnique Fédérale de Lausanne

summary:
Transcript data from LRH-1 WT and LRH-1 K289R jejunums from mice fed ad libitum and sacrificed at 7 am
We used microarrays to detail the global programme of gene expression underlying jejunal function in ad libitum fed mice.

overall_design: 19-21-week-old mice were fed ad libitum, sacrificed at 7 am, and jejunums snap-frozen in liquid nitorgen for RNA extraction and hybridization on Affymetrix microarrays.

first: Sokrates

last: Stein


title: Screening of a heptamer-type sgRNA library for therapeutic agents against hematological malignancies.

status: Public on Jun 30 2014

city: Niigata

first: Masayuki

last: Nashimoto

state: Niigata

address: Higashijima 265-1, Akihaku

country: Japan

institute: Niigata University of Pharmacy and Applied Life Sciences

summary: tRNase ZL-utilizing efficacious gene silencing (TRUE gene silencing) is an RNA-mediated gene expression control technology that has therapeutic potential. This technology is based on the properties of tRNase ZL that it can cleave any target RNA at any desired site under the direction of an appropriate artificial small guide RNA (sgRNA) and that cytosolic tRNase ZL can modulate gene expression by cleaving mRNA under the direction of cellular 5′-half-tRNA or microRNA as sgRNA. In order to estimate a number of potential therapeutic heptamer-type sgRNAs for hematological malignancies, we constructed an sgRNA library composed of 156 heptamer-type sgRNAs, and examined how the sgRNAs affect viability of leukemia and myeloma cells. And we found that 20 of the 156 sgRNAs can efficiently induce apoptosis in at least one of the cancer cell lines. Furthermore, we demonstrated that 4 of the 20 effective sgRNAs can reduce growth rates of HL60 cells in mouse xenograft models. DNA microarray analysis for changes in an mRNA profile by these four heptamer-type sgRNAs suggested at least one candidate target mRNA that contains a potential tRNase ZL target site for each sgRNA.

overall_design:
Changes in gene expression in HL60 cells were measured after 18-hour incubation in the absence or presence of one of five different heptamer-type sgRNAs.
*Heptamer sequences requested but not provided by submitter

last: Takahashi


title: Global transcript analysis of livers and/or jejunums of liver-specific Lrh-1 knockout as well as Lrh-1 K289R knockin mice

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

overall_design: Refer to individual Series


title: Genes Differentially Expressed as a result of a fluconazole-resistant variant Candida albicans strain CaLY188 with trisomy of Chromosome R.

status: Public on Jun 24 2014

city: Shanghai

first: xingxing

last: li

address: Guohe Road

country: China

institute: Second Military Medical University

summary: Transcriptional profiling of Candida albicans CaLY188 compared to the wild type SN152

overall_design: A fluconazole-resistant variant Candida albicans strain CaLY188 with trisomy of Chromosome R was selected to carry out the expression profile microarray. Two-condition experiment, CaLY188 vs.SN152. Biological replicates: 2 control, 2 transfected, independently grown and harvested. One replicate per array.

first: Xingxing

last: Li

first: Dedong


title: Phosphatome profiling of estrogen receptor negative breast cancer

city: Torrevieja

first: Ramon

middle: G

last: Manzano

state: Alicante

address: Partida la Loma s/n

department: Unidad de Consejo Genetico, Plataforma de Oncologia

country: Spain

institute: Hospital Quiron Torrevieja

summary:
Purpose: To characterize the expression of phosphatases in estrogen receptor negative breast cancer
Little is known about the role of phosphatases in the major estrogen receptor negative breast cancer phenotypes (i.e. those overexpressing ERBB2 and the triple negative). We carried out microarray phosphatome profiling in 41 estrogen receptor negative (ER-) breast cancer patients (as determined by immunohistochemistry (IHC)) containing both ERBB2+ and ERBB2- in order to characterize the differences between these groups by Statistical Analysis of Microarrays (SAM). Our findings point to the importance of the MAPK and PI3K pathways in ER- BCs as some of the most differentially expressed phosphatases (like DUSP4 and DUSP6) share ERK as substrate, or regulate the PI3K pathway (INPP4B, PTEN). These observations are also confirmed by pathway and GSEA analysis. It is shown that both ER- ERBB2+ and triple negative breast cancers have a distinctive pattern of phosphatase RNA expression.

overall_design: Surgical specimens from primary breast cancers that were estrogen receptor negative according to immunohistochemistry

first: Elena

middle: M

last: Martinez-Navarro

first: Jeronimo

last: Forteza

first: Antonio

last: Brugarolas


title: Gene expression analysis of CD11b+Gr-1+ myeloid cells and epithelial cells purified from Pten KO prostate tumours

status: Public on Jun 13 2014

city: Bellinzona

first: Diletta

last: Di Mitri

state: Switzerland

address: Via Mirasole

institute: IOR-IOSI

summary: Gr-1+ myeloid cells are recruited in prostate conditioanal Pten null tumours (Ptenpc-/-). To identify the secreted factors that may be released by Gr-1+ cells and epithelial cells in the tumour microenvironment, we compared, by gene expression analysis, the cytokine profile of Gr-1+ myeloid cells sorted from Ptenpc-/- tumours with the profile of immune cell-depleted Ptenpc-/-  epithelial cells. qRT-PCR validation for IL-10, IL1rn, IL-1α, IL-6, VEGF, TNFα, CXCL1, CCL2 and CXCL12 was also performed.

overall_design: Pten pc-/- 8 weeks old mice were sacrificed and whole prostates were isolated and processed to single cell suspension. mRNA from sorted Gr-1+ myeloid cells and epithelial cells was used for gene expression analysis. Cells sorted from 3 mice/each experiment were pulled together. 2 independent experiments were performed.

first: D

first: A

last: Toso


title: DAOY human medulloblastoma cells stably expressing a tamoxifen inducible MXD3: Ethanol vs. Tamoxifen

status: Public on Jun 28 2014

city: Davis

first: Elva

last: Diaz

state: CA

address: 451 Health Sciences Drive GBSF 3409A

department: Pharmacology

country: USA

institute: UC Davis

summary: Gene expression profiling of DAOY stable cell lines expressing a tamoxifen inducible MXD3. Data was normalized to a null version of MXD3 (unable to bind DNA). Goal of the study was to identify candidate genes regulated by MXD3.

overall_design: Four condition experiment: two tamoxifen inducible cell lines (ER-MXD3 and ER-MXD3.E66D), each with their own ethanol vs. tamoxifen. Submitted in the matrix sheet is each test condition normalized to reference. Each condition had a dye swap biological repeat, with the normalized opposing dye reference pool of RNA from all samples.

first: Tin

last: Ngo

first: Gustavo

middle: A

last: Barisone

first: Kit

middle: S

last: Lam

middle: D


title: miR-145 transfected PC3 cells

status: Public on Jun 15 2014

city: Istanbul

first: Mustafa

last: Ozen

address: Fatih

department: Medical Genetics

country: Turkey

institute: Istanbul University

summary: It is aimed to reveal overall trancriptional change in prostate cancer PC3 cells after ectopic expression of miR-145

overall_design: Pre-mir-145 transfected PC3 cells were collected at 8, 16 and 24 hours after transfection and control untrasfected PC3 cells were used.

first: Omer

middle: F

last: Karatas

first: Sukru

last: Gulluoglu

last: Bayrak

first: Serfat

last: Sevli

first: Esra

last: Guzel

first: Isin

last: Ekici

first: Turhan

last: Caskurlu

first: Chad

middle: J

last: Creighton

first: Michael

last: Ittmann


title: Gene expression profiles for murine submandibular gland stem cells

status: Public on Jul 01 2014

city: Stanford

first: tori

last: xn

address: 269 Campus Drive

institute: Stanford

summary: To compare the gene expression profile of submandibular gland stem cells to submandibular gland epithelia, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the differential expression in the stem cells and the non-stem cell epithelia.

overall_design: Murine submandibular gland stem cells and non-stem cell epithelia are sorted through FACS

first: N

last: Xiao

first: Q

last: Le


title: Influence of retinol on kidney in 5/6 nephrectomy mice

status: Public on Jun 06 2014

city: fukuoka

first: naoya

last: matsunaga

address: maidashi 3-1-1, higashi-ku

institute: kyushu university

summary: The circadian clock has been found to be associated with various diseases. We showed that 5/6 nephrectomy (5/6Nx) Clk/Clk mice, which show mutation in the gene encoding circadian locomotor output cycles (Clock) do not show aggravation of renal fibrosis because transforming growth factor-1 (Tgf-1) expression is not increased. In wild-type 5/6Nx kidneys, we found that retinoid, a metabolite of retinol, led to alteration of the expresion 24-h rhythm of Clock expression. Renal Tgf-  1 expression is activated by Clock and further aggravates renal dysfunction by causing fibrosis. We also showed that, in 5/6Nx mice fed a retinol-free diet, renal fibrosis and apoptosis are reduced, leading to a marked improvement in serum creatinine levels. Moreover, our study identified hepatic Cyp3a11 and Cyp26a1 as key retinol metabolism-related genes whose expression decreased in 5/6Nx mice. Our data indicated that the negative chain reaction of metabolic clock alteration in between the kidney and liver aggravates renal dysfunction.

overall_design: Differential gene expression between retinol (-) feeding and clock mutant  in 5/6 nephrectomized mouse was measured on the kidney at 8 weeks after operation. Four-week-old male ICR mice (Charles River Japan, Inc., Yokohama, Japan) were housed in a light-controlled room (lights on from Zeitgeber time [ZT] 0 to ZT12) at 24 ± 1°C and 60 ± 10% humidity, with food and water available ad libitum. Mice were synchronized to the lighting conditions for 2 weeks before surgery. Male ICR mice (5 weeks old) were purchased from Charles River Japan, Inc. (Kanagawa, Japan). Clock mutant mice (C57BL/6J-ClockmlJt/J) were purchased from The Jackson Laboratory (Bar Harbor, ME, USA). We placed them in the ICR genetic background to enhance breeding robustness and care of the young. These mice were backcrossed using a Jcl:ICR background for more than eight generations. We prepared mouse models of CRF by 5/6Nx operation (Ope) under sodium pentobarbital (40 mg/kg, i.p.) or diethyl ether anesthesia. 5/6Nx was performed in two stages. In the first surgical procedure (at 6 weeks of age), two-thirds of the left kidney was removed by cutting off both poles. Seven days later, the right kidney was completely removed. After the operation, mice were housed for 8 weeks (until they were 16 weeks old) in order to achieve CRF. Sham-operated (Sham) mice were subjected to laparotomy on the same days as the procedure in the 5/6Nx mice. This method was also used for treating Clk/Clk mice.  Retinol-free food (A minus) was purchased form KBT ORIENTAL CO., LTD. To investigate the influences of retinol-free feeding on kidney, mice were fed from the fourth week to the eighth week after an operation.

first: Naoya

last: Matsunaga

first: Atsushi

last: Doi

first: Kaori

last: Yasuda

first: Shigehiro

last: Ohdo


title: Gene expression signatures in uteri from nuclear and membrane effects of Estradiol on Estrogen receptor ERα

city: Toulouse

first: Francoise

middle: B.

last: LENFANT

address: 1 avenue J. Poulhès

department: Team 9- I2MC

country: France

institute: INSERM U1048

summary: To further study gene expression regulated by 17b-estradiol in uteri, we have employed whole gene microarray profiling to identify genes specifically regulated by the Estrogen receptor ERα localized either at the plasma membrane or in the nucleus. Two mice models have been used, the mice named ERa-AF2° (named AF2_KO and on C57BL6/J background) in which 7 aminoacids have been deleted in the AF2 domain and the mice C451A-ERa (named MISS_KO and on C57BL6/N background) mutated for the C451 into Ala on ERa. Control littermates were used for each mutant mice respectively name AF2_WT or MISS_WT.

overall_design: 17b-estradiol induced gene expression in  uteri from ovariectomized mice was measured after 6 hours exposure to 0 (PLB) and 8µg/kg of 17b-estradiol (E2) injected subcutaneously in castor oil.

first: Anne

last: Abot

first: Marine

last: Adlanmerini

first: Jean-François

last: Arnal

first: Françoise

last: Lenfant

first: Yannick

last: Lippi

first: Pascal

last: Martin


title: DNA microarray analysis following gefinitib/luteolin administration to PC-3 cells

status: Public on Jun 29 2014

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: To further investigate the molecular mechanism of cell death induction by luteolin and/or gefitinib, we performed DNA microarray analysis, which may reveal the change of gene expression pattern following treatment with these chemicals. We examined PC-3 cells after 24h of treatment with 60μM luteolin and/or 60μM gefitinib because subG1 population has not appeared yet at this timing, which helps to avoid the secondary effects of apoptosis on the alteration of the gene expression pattern.

overall_design: PC-3 cells were treated for 24h with DMSO, 60μM luteolin (Lut), 60μM gefitinib (Gef) or their co-administration (Lut+Gef). To calculate the fold change, we compared the hybridization signal intensity between time zero (before addition of any reagents to PC-3 cells) and 24h after addition of DMSO, luteolin, gefitinib and luteolin+gefitinib. Each sample was run in duplicate.

first: Hiroshi

last: Nojima


title: Microarray analysis following gefinitib/luteolin administration to PC-3 cells

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


title: Influence of DEN in mice liver

summary: Hepatocellular carcinoma is the third leading cause of cancer death worldwide, and it is necessary to elucidate the mechanism of hepatocarcinogenesis. Hepatocellular carcinoma (HCC) has a high mortality rate and develops based on the chronic inflammatory hepatic disease. Therefore, novel prophylactic or therapeutic strategies are required to improve outcome. In this study, influence of diethylnitrosamine (DEN) and retinoic acid (ATRA) on hepatocarcinogenesis was investigated in mouse. These results suggest that the control of NF-κB signaling during the early stage of HCC development is important for the prevention of malignant transformation in hepatocytes.

overall_design:
Genes induced by the following treatments in mice liver were investigated at 2 days or 7 days after treatment;
DEN: diethylnitrosamine (treatment of DEN (drinking water 80 mg/L))
ATRA: retinoic acid (treatment of ATRA (drinking water 30 mg/L))
G0s2 siRNA : G0s2 knockdown mouse liver (treatment of G0s2 siRNA)
Control siRNA: treatment of scramble siRNA (negative control)


title: MOF-associated complexes have overlapping and unique roles in regulating pluripotency in embryonic stem cells and during differentiation [array]

status: Public on Jun 04 2014

city: Illkirch

first: Sarina

last: Ravens

address: 1 Rue Laurent Fries

institute: IGBMC

summary: The histone acetyltransferase (HAT) Mof is essential for mouse embryonic stem cells (mESC) pluripotency and early development. Mof is the enzymatic subunit of two different HAT complexes, MSL (Male-Specific Lethal) and NSL (Non-specific lethal). The individual contribution of MSL and NSL complexes to transcription regulation in mESCs is not well understood. Our genome-wide analysis of MSL and NSL localization show that i) MSL and NSL bind to specific and common sets of expressed genes, ii) NSL binds at promoters, iii) while MSL binds in gene bodies. Knockdown of Msl1 leads to a global loss of histone H4K16ac indicating that MSL is the main HAT acetylating H4K16 in mESCs. MSL was enriched at many mESC-specific genes, but also at bivalent domains. Thus, NSL and MSL HAT complexes differentially regulate specific sets of expressed genes in mESCs. Furthermore, MSL is essential for the regulation of key mESC-specific and bivalent developmental genes.

overall_design: Gene expression was analysed through microarrays in mESCs infected with shRNA vectors expressing either a non-target control, shRNA against Nsl1 or Msl1 to knockdown Nsl1 or Msl1.

first: Marjorie

last: Fournier

first: Tao

last: Ye

first: Matthieu

last: Stierle

first: Doulaye

last: Dembele

first: Virginie

last: Chavant

first: Laszlo

last: Tora


title: Changes in gene expression during epithelial-mesenchymal transition in a breast cancer primary culture

status: Public on Jun 02 2014

city: Cefalù

first: Valentina

last: Bravatà

address: Contrada Pietrapollastra Pisciotto

country: Italy

institute: IBSBC CNR

summary: Epithelial-Mesenchymal Transition (EMT) is an important process during normal development, but also co-opted by various cancer cells to enable them to invade and form metastases at distant sites. In this study, we examinated  changes in gene expression during EMT in breast cancer using primary culture named BCpc.

overall_design: Changes in gene expression in primary cells from breast tumour specimen (named BCpc) were analyzed as two-color hybridizations using Agilent Technologies whole human genome 4x44K microarrays


title: Murine CD8 T cell gene expression in reponse to type I interferon

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

country: Germany

institute: University of Duesseldorf

summary: To investigate type I interferon regulated genes in CD8+ T cells, we used microarray analyses after stimulation of primary murine T cell cultures. Negatively sorted T cells from naive C57Bl/6 mice were incubated with PBS or anti-CD3 in presence or absence of type I interferon (IFN-4a, 500U/mL). After 6h total RNA was extracted from the primary T cell cultures and microarrays were performed after RNA quality control. Among significantly regulated genes, we identified NK cell receptor ligands to be affected by exposure to type I interferon.

overall_design: 10^6 negatively sorted CD8+ T cells were stimulated with anti-CD3 antibody in the presence or absence of IFN-4a. Additionally, CD8+ cells were mock treated with PBS in the presence or absence of IFN-4a. After 6h, total RNA was extracted from cell suspensions and microarray analyses were performed. All experiments were carried out in triplicates.

first: Haifeng

last: Xu

first: Melanie

last: Grusdat

first: René

last: Deenen

last: Köhrer

last: Lang

first: Philipp


title: ROCK Inhibition extends passage of human embryonic stem cell derived retinal pigmented epithelium

city: Santa Barbara

first: Roxanne

middle: H

last: Croze

address: UCSB: NRI Bldg. 571 Room 5166

department: Molecular, Cellular and Developmental Biology

institute: UCSB

summary: Human embryonic stem cell derived retinal pigmented epithelial cells (hESC-RPE) are in clinical trials for the treatment of macular diseases. Currently, these cells take over three months to derive and subsequent months to mature and characterize. After only five to six passages the cells begin to undergo an epithelial-to-mesenchymal transition and are unsuitable for cellular therapies. We describe a novel passaging protocol and show that inhibition of Rho-associated, coiled coil containing protein kinases (ROCK1 and ROCK2) using Y-27632, allows extended passage of hESC-RPE in serum-free culture with maintenance of the RPE phenotype. After 30 population doublings, hESC-RPE at passage 13 maintain normal karyotype, display typical, polarized epithelial morphology, and continue to express RPE-specific genes. Passage 13 hESC-RPE show protein localization patterns similar to passage 2 cells, and display similar levels of growth factor secretion and phagocytosis of photoreceptor outer segments. Microarray analysis from day 2 cells shows several key pathways are altered by ROCK inhibition, including stimulation of the cell cycle and suppression of TGFβ and Wnt signaling. These findings describe a means to greatly increase the yield of functional hESC-RPE for use in research and clinical trials.

overall_design:
Two-condition experiment, Control vs Y-27632 treated hESC-RPE passage 5. Biological replicates: 4 control, 4 Y-27632.

The experiments were technically carried out as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but processed as though they are single channel (Cy3 and Cy5 signals are calculated; Cy3/Cy5 ratios are not calculated). Therefore, there are 4 raw data files for total 8 samples.

first: Monte

last: Radeke

first: Dennis

middle: O

last: Clegg

first: Peter

last: Coffey


title: Side population cells in human primary melanoma

status: Public on May 27 2014

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: Melanoma remains the most lethal skin cancer, mainly because of high resistance to therapy. Side population (SP) cells are found in many types of cancer and are usually enriched in therapy-resistant as well as tumorigenic cells. Here, we identified a Hoechst dye-effluxing SP in a large series of human melanoma samples representing different progression phases. The SP size did not change with disease stage but was correlated with the prognostic “Breslow’s depth” in the primary (cutaneous) tumors. When injected into immunodeficient mice, the SP generated larger tumors than the bulk “main population” (MP) melanoma cells in two consecutive generations, and showed tumorigenic capacity at lower cell numbers than the MP. In addition, the SP reconstituted the heterogeneous composition of the human A375 melanoma cell line, and its clonogenic activity was 2.5-fold higher than that of the MP. Gene-expression analysis revealed upregulated expression in the melanoma SP (versus the MP) of genes associated with chemoresistance and anti-apoptosis. Consistent with these molecular characteristics, the SP increased in proportion when A375 cells were exposed to the melanoma standard chemotherapeutic agent dacarbazine, and to the aggravating condition of hypoxia. In addition, the SP showed enhanced expression of genes related to cell invasion and migration, as well as to putative (melanoma) cancer stem cells (CSC) including ABCB1 and JARID1B. ABCB1 immunoreactivity was detected in a number of tumor cells in human melanomas, and in particular in clusters at the invasive front of the primary tumors. Together, our findings support that the human melanoma SP is enriched in tumorigenic and chemoresistant capacity, considered key characteristics of CSC. The melanoma SP may therefore represent an interesting therapeutic target.

overall_design: Four primary melanomas (subtype SSMM) were dissociated into single cells. From each of these single cell suspensions, side population (SP) and bulk \main population\ (MP) cells were isolated based on their Hoechst-effluxing capability using fluorescence-activated cell sorting. Gene expression of SP cells is analyzed relative to the gene expression of the corresponding MP cells.

first: Jasper

last: Wouters

first: Marguerite

last: Stas

first: Lies

last: Gremeaux

first: Olivier

last: Govaere

first: Anke

last: Vandenbroeck

first: Hannelore

last: Maes

first: Patrizia

last: Agostinis

first: Tania

last: Roskams

first: Joost

last: vandenOord

first: Hugo

last: Vankelecom


title: Impact of high-phosphate diet on aortic gene expression

status: Public on May 26 2014

city: Graz

first: Birgit

last: Gallé

address: Stiftingtalstr. 24

country: Austria

institute: ZMF

summary:
Uremic media calcification is not only driven by systemic factors such as hyperphosphatemia, but also crticially dependent on vascular smooth muscle cells per se.  We hypothesized that the different developmental origins of vscular smooth muscle cells might lead to a heterogeneous susceptibility to develop media calcification.
Upon high-phosphate diet, the transcriptional profile revealed an induction of an inflammatory vascular smooth muscle phenotype only in the abdominal, but not in the thoracic aorta. Thus, smooth muscle cells from different lineages responded differently to morphogenetic cues in vivo.

overall_design: We analyzed 3-4 replicates of the thoracic and abdominal aorta, which were previously exposed to either high-phosphate diet (HPD) or standard chow diet (SCD), respectively.

first: Alexander

last: Kirsch

last: Eller


title: NS1-mediated inhibition of c-Abl results in acute lung injury and priming for bacterial co-infections; insights into 1918 H1N1 pandemic

status: Public on Nov 03 2014

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: NS1 proteins from avian influenza viruses like the 1918 pandemic NS1 are capable of inhibiting the key signaling integrator c-Abl (Abl1), resulting in massive cytopathic cell alterations. In the current study, we addressed the consequences of NS1-mediated alteration of c-Abl on acute lung injury and pathogenicity. Comparing isogenic strains that differ only in their ability to inhibit c-Abl, we observed elevated pathogenicity for the c-Abl-inhibiting virus. NS1-mediated block of c-Abl resulted in severe lung pathology and massive edema formation and facilitated secondary bacterial pneumonia. This phenotype was independent of differences in replication and immune responses, defining it as an NS1 virulence mechanism distinct from its canonical functions. Microarray analysis revealed extensive down-regulation of genes involved in cell integrity and vascular endothelial regulation. In conclusion, NS1 protein-mediated blockade of c-Abl signaling drives acute lung injury and primes for bacterial co-infections revealing potential insights into the pathogenicity of the 1918 pandemic virus.

overall_design: Lung transcription analysis of Influenza A virus infected mice.

first: Eike

middle: R

last: Hrincius

first: Swantje

last: Liedmann

last: Vogel

first: Shane

last: Gansebom

first: Christina

last: Ehrhardt

first: Stephan

last: Ludwig

last: Hains

first: Richard

last: Webby

first: Jonathan

last: McCullers


title: Role of the polypeptide N-acetylgalactosaminyltransferase 3 in ovarian cancer progression: possible implications in abnormal mucin O-glycosylation

status: Public on May 22 2014

city: Quebec

first: Dimcho

last: Bachvarov

state: Quebec

address: 9, rue McMahon

country: Canada

institute: CHU-Q, Centre de recherche-HDQ

summary: Previously, we have identified the polypeptide N-acetylgalactosaminyltransferase 3 (GALNT3) gene as notably hypomethylated in low-malignant potential (LMP) and high-grade (HG) serous epithelial ovarian tumors, compared to normal ovarian tissues. Here we show that GALNT3 is strongly overexpressed in both LMP and HG serous EOC tumors, thus suggesting that epigenetic mechanisms might be implicated in GALNT3 overexpression in serous epithelial ovarian cancer (EOC). Moreover, GALNT3 expression significantly correlated with shorter progression-free survival (PFS) periods in serous EOC patients with advanced disease. Knockdown of the GALNT3 expression in EOC cells led to sharp decrease of cell proliferation and induced S-phase cell cycle arrest. Additionally, GALNT3 suppression significantly inhibited EOC cell migration and invasion. Gene expression profiling and consecutive network and pathway analyses confirmed these findings, as numerous genes and pathways known previously to be implicated in ovarian tumorigenesis, including EOC tumor invasion and metastasis, were found to be downregulated upon GALNT3 suppression, while some tumor suppressor genes were induced. Moreover, GALNT3 downregulation was associated with reduced MUC1 protein expression in EOC cells, probably related to destabilization of the MUC1 protein due to lack of GALNT3 glycosylation activity.Taken together, our data are indicative for a strong oncogenic potential of the GALNT3 gene in advanced EOC and identify this transferase as a novel EOC biomarker and putative EOC therapeutic target. Our findings also suggest that GALNT3 overexpression might contribute to ovarian etiology through aberrant mucin O-glycosylation.

overall_design: To better understand the molecular mechanisms of GALNT3 gene action in ovarian cancer cells, we employed the Agilent Whole Human Genome microarrays, containing ~ 44,000 genes to identify global gene expression changes upon GALNT3 suppression in A2780s cells. We compared the gene expression of the previously selected clone shRNA- GALNT3-knockdown clones 1 & 2 (sh-cl1 & sh-cl2) against the corresponding control (ctrl) clone. The microarray experiments were performed in duplicates, as four hybridizations were carried out for the GALNT3-suppressing cell clones against the corresponding control, using a fluorescent dye reversal (dye-swap) technique.


title: Oncogenic MyD88 Mutants Require Toll-like Receptors

status: Public on May 21 2014

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

summary: In the activated B-cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL), the most frequent gain-of-function mutations target MyD88, a signaling adapter for Tolllike receptors (TLRs). The most prevalent oncogenic mutant, MyD88 L265P, occurs in 29% of cases and is the most active in engaging the NF-kappaB pathway. Here we show that MyD88 mutants do not function autonomously, but rather require TLR7, TLR9, and to a lesser extent, TLR4 to promote the survival of ABC DLBCL cells. Unlike wild type MyD88, MyD88 mutants associate constitutively with TLR7 and TLR9 in ABC DLBCL cells. Like ligand-induced TLR7/9 signaling in normal immune cells, the survival of ABC DLBCL cell lines depends upon translocation of TLR7 and TLR9 to acidic endolysosomes, where proteolytic processing of their ligand binding ectodomains is required for their oncogenic signaling. ABC DLBCL viability also depends upon CD14, a co-receptor for TLR7 and TLR9 that promotes engagement of nucleic acid ligands by these receptors. Point mutations in the TLR7 or TLR9 ectodomains that abrogate ligand binding and/or signaling were incapable of sustaining ABC DLBCL survival. An inhibitory oligonucleotide that suppresses TLR9 responses in normal B cells blocked NF-kappaB signaling and survival of ABC DLBCL lines. Together, these data suggest that an endogenous TLR ligand may play a pathogenic role in ABC DLBCL and provide a rationale for targeting TLR signaling to improve therapy of this aggressive lymphoma.

overall_design: Gene expression was analyzed using Agilent human 2-color 4X44K oligo gene expression arrays. Cell line, TMD8 ABC-DLBCL, was infected with control (shControl, Cy3), shLTR7 (Cy5) or shLTR9 (Cy5) and changes in gene expression were monitored on day 1 and day 2 after induction of the shRNA with doxycycline, co-hybridizing control and experimental samples (Cy3+Cy5), for a total of 4 arrays.


title: Exogenous H2S administration does not regulate gene expression in primary murine alveolar type II cells

status: Public on May 20 2014

city: Bad Nauheim

first: Rory

last: Morty

address: Parkstr. 1

department: W.G. Kerckhoff-Institut

institute: MPI für Herz- und Lungenforschung

summary: Primary alveolar type II cells were either treated with vehicle or NaHS for 6 h and 24 h (RS-266 samples). Primary alveolar type II cells treated with GYY4137 at 100 µM concentration were exposed to either 21% O2 or 85% O2 for 24 h (RS-284 samples). Overall no changes in gene expressionwere found in the corrected p values of both microarray studies.

overall_design: Four vehicle samples at 6 h of exposure, four NaHS treated samples at 6 h of exposure, four vehicle samples at 24 h of exposure and four NaHS treated samples at 24 h of exposure were used for the RS-266 microarray study. four GYY4137 100 µM samples in 21% O2 after 24 h of exposure were compared to four GYY4137 100 µM samples in 85% O2 after 24 h of exposure and used for the RS-284 microarray study.

first: Alicia

last: Madurga

middle: E


title: Identification of differentially expressed RNAs of lung cancer cells.

city: Taoyuang

first: Kou-Juey

last: Wu

state: Taiwan

address: No.15, Wenhua 1st Road, Gueishan Dist

department: Cancer Genome Research Center

country: Taiwan

institute: Chang Gung Memorial Hospital at Linkou

summary: Twist1 induces cancer metastasis. Identification of Twist1 downstream targets should help to delineate the mechanisms of Twist1-induced cancer metastasis.

overall_design: Expression profiles of H1299 control cells vs. H1299 with knockdown of Twist1 were compared to identify Twist1 downstream targets.

first: Wu

last: Kou-Juey


title: Taurine transporter (SLC6A6)-deficient skeletal muscle

status: Public on May 08 2014

city: Kobe

first: Takashi

last: Ito

state: Hyogo

address: 1-3-6 Minatojima, Chuo-ku

department: Pharmacy

institute: Hyogo University of health Sciences

summary: Analysis of skeletal muscle from taurine transporter (TauT) knockout mice at 3 or 18 months of age. Knocking out TauT result in a decrease in muscle cell size, impaired exercise capacity and accelerated muscle aging.  Results provide molecular insights into physiological role of taurine.

overall_design: Sample: 12


title: Classification of a frameshift/extended and a stop mutation in WT1 as gain of function mutations which activate cell cycle genes and promote Wilms tumor cell proliferation

status: Public on May 12 2014

first: Brigitte

last: Royer-Pokora

address: Universitätsstr. 1

institute: Institute of Human Genetics and Anthropology, Heinrich-Heine-University Duesseldorf

summary: The Wilms tumor 1 (WT1) gene encodes a zinc finger transcription factor important for normal kidney development. WT1 is a suppressor for Wilms tumor development and an oncogene for diverse malignant tumors. We recently established cell lines from primary Wilms tumors and identified the corresponding WT1 mutations (see GSE18058). To investigate the function of mutant WT1 proteins we performed WT1 knockdown experiments in primary Wilms tumor cell lines with a frameshift/extension (p.V432fsX87 = Wilms3) and a stop mutation (p.P362X = Wilms2) of WT1, followed by genome wide gene expression analysis. A detailed analysis of these gene expression data using MetaCore enabled us to classify the WT1 mutations as gain of function mutations. The mutant WT1Wilms2 and WT1Wilms3 proteins acquired an ability to modulate the expression of a highly significant number of genes from the G2/M phase of the cell cycle, and WT1 knockdown experiments showed that they are required for Wilms tumor cell proliferation. Data from the literature show that p53 negatively regulates the activity of a large number of these genes which are also part of a core proliferation cluster in diverse human cancers. Our data strongly suggest that mutant WT1 proteins facilitate expression of these cell cycle genes by antagonizing transcriptional repression mediated by p53. In light of this it is important to note that mutant WT1 has an ability to physically interact with the tumor suppressor p53. Together the findings show for the first time, that mutant WT1 proteins have a gain of function and act as oncogenes for Wilms tumor development by regulating Wilms tumor cell proliferation.

overall_design: siWT1 mediated knockdown in two Wilms tumor cell lines one and two days after transfection versus non-silencing controls

first: Maike

last: Busch

first: Heinrich

last: Schwindt

first: Artur

last: Brandt

first: Manfred

last: Beier

first: Nicole

last: Görldt

first: Paul

last: Romaniuk

first: Eneda

last: Toska

first: Stefan

last: Roberts

first: Hans-Dieter

last: Royer


title: Gene expression profiles of Liuwei Dihuang Pill treatment postmenopausal osteoporosis with kidney Yin deficiency

status: Public on May 06 2014

city: Fuzhou

first: LH

last: Xie

address: 282hao,Wusi Road ,Gulou distract

institute: Fujian Academy of Traditional Chinese Medicine

summary: Investigate gene expression profiles of Liuwei Dihuang Pill treatment postmenopausal osteoporosis with kidney Yin deficiency in peripheral blood

overall_design: Liuwei Dihuang Pill (LDP), a classic Chinese medicinal formula, has been used to treat PMO with kidney YIN deficiency for three months. Whole human genome oligo microarray were applied to explore the differentially expressed genes before and after LDP treatment.

first: Jirong

last: Ge

first: Lihua

first: Shengqiang

last: Li

first: Juan

last: Chen

first: Huijuan

last: Xu


title: Loss of Runx3 in osteoblasts provokes severe congenital osteopenia

status: Public on May 01 2014

city: Rehovot

first: Omri

last: Bauer

address: Herzl

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary:
Murine Runx3 is expressed in developing bone osteoblasts (OBLs) and its deletion in these cells culminates in severe congenital osteopenia. We demonstrate that Runx3 is non-redundantly involved in the proliferation of early pre-committed OBL progenitor cells, a critical step in the generation of adequate numbers of bone-forming OBLs. Thus, in the absence of Runx3 in cells of this lineage, the number of mature/active OBLs is significantly diminished, providing a mechanistic explanation to the observed osteopenia.
This experiment was aimed at identifying genes that are likely regulated by Runx3 along osteoblastogenesis.

overall_design: To elucidate the Runx3-mediated transcriptional program along OBL differentiation, we compared gene expression profile in WT and Runx3f/f/Col1a1-cre calvarial OBLs. Progenitor cells were purified and RNA extracted, reverse-transcribed, fragmented, labeled and hybridized to GeneChip® Mouse Gene 2.0 ST Array.

first: Amnon

last: Sharir

first: Ayako

last: Kimura

first: Shay

last: Hantisteanu

first: Shu

last: Takeda

first: Yoram

last: Groner


title: Transcriptomics of THP-1 host cells infected with Mycobacterium tuberculosis (Mtb)

status: Public on Dec 31 2014

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary:
Infection is a dialog between the pathogen and the host. Understanding the molecular basis of infection requires understanding the responses and adaptations of both the pathogen and host as a consequence of this dialog. We studied Mtb infection in human THP-1 cells by transcriptomics profiling of host expression over the course of an acute to anestablished infection.
TbSysBio (National Institute of Allergy and Infectious Diseases, National Institute of Health)

overall_design: Microarray experiments were performed as single-color hybridizations using Agilent Technologies whole human genome 4x44K microarrays

first: Anca

last: Dorhoi

last: Kaufmann


title: Opposing Effects of HIF1α and HIF2α on Chromaffin Cell Phenotypic Features and Tumor Cell Proliferation: Insights from MAX [human]

status: Public on Sep 18 2014

city: Madrid

first: Mercedes

last: Robledo

state: Madrid

address: C/ Melchor Fernández Almagro, 3

department: Human Cancer Genetics Program

institute: Spanish National Cancer Research Centre (CNIO)

summary: Pheochromocytomas and paragangliomas (PPGLs) are catecholamine-producing tumors with diverse phenotypic features reflecting mutations in numerous genes, including MYC-associated factor X (MAX). To establish whether PPGL phenotypic differences reflect a MAX-mediated mechanism and opposing influences of HIF2α and HIF1α, we combined observational investigations in PPGLs and gene-manipulation studies in two pheochromocytoma cell lines. In cell lines lacking Max, re-expression of the gene resulted in maturation of phenotypic features and decreased cell cycle progression. In cell lines lacking Hif2α, overexpression of the gene led to immature phenotypic features, failure of dexamethasone to induce differentiation and increased proliferation. HIF1α has opposing actions to HIF2α. These model systems explain the features observed in PPGLs due to mutations of MAX and other PPGL susceptibility genes.

overall_design: 88 samples (primary pheochromocytoma (PCC)/paraganglioma tumors) were hybridized onto a cDNA microarray in order to investigate possible heterogeneity within these tumors. This series of tumors is an expansion of GSE19422 that includes nine additional tumors to examine the role of MAX mutations in PCC/PGL.

last: Qin

first: Aguirre

last: de Cubas


title: Liver transcriptional profile of wild-type and IL-10 knockout mice with colitis

city: Charlestown

first: Bobby

last: Cherayil

state: Massachusetts

address: Building 114, 16th Street

department: Pediatrics

institute: Massachusetts General Hospital

summary:
The goal of the experiment was to compare the liver transcriptional profile of wild-type and IL-10 knockout mice with colitis. Colitis was induced in 6 week old female wild-type and IL-10-deficient C57BL/6 mice by administration of 3% dextran sulfate sodium (DSS) in the drinking water for 7 days.
At necropsy, segments of liver were homogenized in Trizol and total RNA prepared for the transcriptional profiling.

overall_design: Total RNA from 4 wild-type and 4 IL-10 knockout mice with colitis was used to hybridize to Affymetrix Gene Chip Mouse 2.0 ST arrays.


title: Regulation of gene expression in human T lymphoblastic leukemia Molt4 cells by farnesol

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Gene expression profiles of Molt4 cells treated with DMCS (vehicle) or farnesol were compared to understand the mechanism by which farnesol induces apoptosis in these cells.

overall_design: Molt4 cells were treated with 75 uM farnesol for 4 hrs to compare with vehicle-treated Molt4 cells.  RNA from three replicates for each treatment was then isolated for microarray analysis.

first: Joung

last: Joo

first: Eiichiro

last: Ueda

first: Anto

last: Jetten


title: OSLN Reprogramming cells: empty vector vs. HIF2α over-expression

city: Seattle

first: Hannele

last: Ruohola-Baker

state: Washington

address: 850 Republican

department: Biochemistry

institute: University of Washington

summary: Transcriptional profiling of Oct4, Sox2, Lin28 and Nanog (OSLN) reprogramming cell of empty vector compared to HIF2α over-expression at the early stage (day 12) and the late stage(day 30) using fibroblasts MRC5 and IMR90

overall_design: Eight-condition experiment, empty vector vs. HIF2α over-expression cells, at early stage vs. late stage, and fibroblasts MRC5 vs. IMR90

first: Julie

last: Mathieu

first: Wenyu

last: Zhou


title: Gene signature of mouse skin resident macrophages

status: Public on May 30 2014

first: Mirna

last: Perez-Moreno

address: Calle Melchor Fdez Almagro

department: Cancer Cell Biology

institute: CNIO

summary: Skin resident macrophages were isolated by FACS sorting at different ages post natally and RNA was extracted

overall_design: mouse skin resident macrophages

first: D

last: Castellana

first: M


title: Tumor Intrinsic Subtype is Reflected in Cancer-Adjacent Benign Tissue

status: Public on Apr 30 2014

city: Chapel Hill

first: Melissa

last: Troester

address: 135 Dauer Drive, CB 7435

department: Epidemiology

institute: University of North Carolina at Chapel Hill

summary: Introduction: Overall survival of early-stage breast cancer (BC) patients is similar for those who undergo breast conserving therapy (BCT) and mastectomy, however, 10-15% of women undergoing BCT suffer ipsilateral breast tumor recurrence. The risk of recurrence may vary with age or breast cancer subtype. Understanding the gene expression of the cancer-adjacent tissue and/or stromal response to specific tumor subtypes is important for developing clinical strategies to reduce recurrence risk. Methods: We studied gene expression data in cancer-adjacent tissue from 158 BC patients. Complementary in vitro cocultures were used to study cell-cell communication between fibroblasts and specific breast cancer subtypes. Results: Our results suggest that intrinsic tumor subtypes are reflected in histologically normal cancer-adjacent tissue. Gene expression of cancer-adjacent tissues shows that triple negative (Claudin-low or Basal-like tumors) exhibit increased expression of genes involved in inflammation and immune response. While such changes could reflect distinct immune populations present in the microenvironment of different breast cancer subtypes, altered immune response gene expression was also observed in cocultures in the absence of immune cell infiltrates, emphasizing that these inflammatory mediators are secreted by breast-specific cells. In addition, while triple negative BCs are associated with upregulated immune response genes, Luminal breast cancers are more commonly associated with estrogen-response in adjacent tissues. Conclusions: Specific characteristics of BCs are reflected in the surrounding benign tissue. This commonality between tumor and surrounding tissue may underlie second primaries and local recurrences. Biomarkers derived from cancer-adjacent tissue may be helpful in defining personalized surgical strategies or in predicting recurrence risk.

overall_design: reference x sample

first: Patricia

last: Casbas-Hernandez


title: Cardiac-specific YAP activation improve cardiac function and survival in an experimental murine MI model

city: Boston

first: Fei

last: Gu

state: MA

address: 320 Longwood Ave.

department: Cardiology

institute: Childrens hospital boston, Harvard Medical School

summary: In this study, we used a cardiac-specific, inducible expression system to activate YAP in adult mouse heart. Activation of YAP in adult heart promoted cardiomyocyte proliferation and did not deleteriously affect heart function. Furthermore, YAP activation after myocardial infarction (MI) preserved heart function and reduced infarct size. Using adeno-associated virus subtype 9 (AAV9) as a delivery vector, we expressed human YAP in the murine myocardium immediately after MI. We found that AAV9:hYAP significantly improved cardiac function and mouse survival.  AAV9:hYAP did not exert its salutary effects by reducing cardiomyocyte apoptosis. Rather, we found that AAV9:hYAP stimulated adult cardiomyocyte proliferation. Gene expression profiling indicated that AAV9:hYAP stimulated cell cycle gene expression, enhanced TGFβ-signaling, and activated of components of the inflammatory response.Cardiac specific YAP activation after MI mitigated myocardial injury after MI, improved cardiac function and mouse survival. These findings suggest that therapeutic activation of hYAP or its downstream targets, potentially through AAV-mediated gene therapy, may be a strategy to improve outcome after MI.

overall_design: Three groups were involved in this study: sham group, AAV9:Luci+MI group and AAV9-YAP+MI group. Each group contained three biological replicates. The sham group had neither myocardial infarction nor AAV injection. The AAV9:Luci +MI(L for brief) group had myocardial infarction and injected with AAV9:Luic. The AAV9:hYAP+MI(YAP for brief) group had myocardial infarction and injected with AAV9:hYAP. 5 days after MI and AAV injection, the heart apexes were collected and the total RNA were isolated for microarray analysis.

first: Zhiqiang

last: Lin

first: Alexander

last: von Gise

first: Pingzhu

first: Qing

last: Ma

first: Allan

last: Yau

first: Jessica

middle: N

last: Buck

first: Katryna

last: Gouin

first: Pim

last: van Gorp

first: Bin

first: Jinghai

last: Chen

first: Jonathan

last: Seidman

first: Da-zhi

last: Wang

first: William

middle: T

last: Pu


title: Loss of Tet enzymes compromises proper differentiation of embryonic stem cells

status: Public on Apr 14 2014

city: Cambridge

first: Inmaculada

last: Barrasa

address: Nine Cambridge Center

institute: Whitehead Institute

summary: Tet enzymes (Tet1/2/3) convert 5-methylcytosine (5mC) to 5-hydroxy-methylcytosine (5hmC) and are dynamically expressed in various embryonic and adult cell types. While loss of individual Tet enzymes or combined deficiency of Tet1/2 allows for embryogenesis, the effect of complete loss of Tet activity and 5hmC marks in development is not established. We have generated Tet1/2/3 triple knockout (TKO) mouse embryonic stem cells (ESCs) and examined their developmental potential. Combined deficiency of all three Tets depleted 5hmC and impaired ESC differentiation as seen in poorly differentiated TKO embryoid bodies (EBs) and teratomas. Consistent with impaired differentiation, TKO-ESCs contributed poorly to chimeric embryos and could not support embryonic development. Global gene expression and methylome analyses of TKO-EBs revealed promoter hypermethylation and deregulation of genes implicated in embryonic development and differentiation. These findings suggest a requirement for Tet- and 5hmC-mediated DNA demethylation in proper regulation of gene expression during differentiation of ESCs and development.

overall_design: To quantify global gene expression in differentiating embryoid bodies (EBs) derived from wild type (WT) and Tet triple knockout (TKO), TKO and WT mouse embryonic stem cells (ESCs) were differentiated in vitro to EBs and cultured for 10 days. RNA was extracted using Qiagen RNeasy kit and subjected to microarray analysis. Global gene expression profile of two technical replicas of WT embryoid bodies (2 samples in total) was compared to two technical replicas of two independent TKO embryoid bodies (4 TKO samples in total).

first: M

middle: I

first: Meelad

last: Dawlaty

first: Rudolf

last: Jaenisch


title: Role of malignant ascites on human mesothelial cells and their gene expression profiles

first: Dimcho

last: Bachvarov

address: 9, rue McMahon

institute: CHU-Q, Centre de recherche-HDQ

summary: Background: Malignant ascites is often present at diagnostic in women with advanced ovarian cancer (OC) and its presence is associated with a worse outcome. Human peritoneal mesothelial cells (HPMCs) are key components of malignant ascites. Although the interplay between HPMCs and OC cells is believed to be critical for tumor progression, it has not been well characterized. The purpose of this study was to assess the effect of ascites on HPMCs and clarify the role of HPMCs in OC progression.  Methods: Human OC ascites and benign peritoneal fluids were assessed for their ability to stimulate HPMC proliferation. Conditioned medium from ascites- and benign fluid-stimulated HPMCs were compared for their ability to attenuate apoptosis induced by TNF-related apoptosis-inducing ligand (TRAIL). We conducted a comparative analysis of global expression changes in ascites-stimulated HPMCs using Agilent oligonucleotide microarrays.   Results: As compared to benign peritoneal fluids, malignant ascites stimulated the proliferation of HPMCs. TRAIL-induced apoptosis was attenuated in OC cells exposed to conditioned medium from ascites-stimulated HPMCs as compared to OC cells exposed to conditioned medium from benign fluid-stimulated HPMCs. A total of 649 genes were differentially expressed in ascites-stimulated HPMCs. Based on a ratio of more than 1.5-fold and a P < 0.05, 484 genes were up-regulated and 165 genes were down-regulated in ascites-exposed HPMCs. Stimulation of HPMCs with OC ascites resulted in differential expression of genes mainly associated with the regulation of cell growth and proliferation, cell death, cell cycle and cell assembly and organization, compared to benign peritoneal fluids. Top networks up-regulated by OC ascites included Akt and NF-κB survival pathways whereas vascular endothelial growth factor (VEGF) pathway was down-regulated.   Conclusions:  The results of this study not only provide evidence supporting the importance of the interplay between cancer cells and HPMCs but also define the role that the tumor environment plays in these interactions.

overall_design: The expression profiles from human peritoneal mesothelial cells (HPMC) cultures exposed to peritoneal fluids and ovarian cancer ascites were compared using the Agilent Whole Human Genome Oligonucleotide microarrays, containing 44,000 genes.  Microarrays were performed on HPMCs exposed to 3 malignant ascites from women with advanced (stage III/IV) serous OC and two benign peritoneal fluids. First, we generated lists of significantly up-regulated and down-regulated genes that were differentially expressed between OC ascites (OVC346, OVC508 and OVC509) and control OV370 peritoneal fluid. Then, the set of genes that were commonly expressed between control peritoneal fluids (OV370 and OV401) were subtracted from the first list of genes to generate a dataset of differentially expressed genes between malignant ascites and benign peritoneal fluids.


title: Carbon-ion radiotherapy of human lung cancer

status: Public on Apr 20 2014

city: Giessen

first: Jochen

last: Wilhelm

address: Gaffkystrasse 10

department: ECCPS Microarray Unit

institute: Uniklinikum Giessen

summary: Carbon-ion irradiation is an emerging therapeutic option for several tumor entities including lung cancer. Well oxygenated tumor areas compared to a hypoxic environment favor therapeutic photon irradiation efficiency of solid tumors due to increased amounts of DNA damage. The resistance of hypoxic tumor areas towards photon irradiation is enhanced through increased HIF-1 signaling. Here, we compared the effects of oxygen and HIF 1 after photon and carbon-ion irradiation with biological equivalent doses in a human non-small lung cancer model. In hypoxia compared to normoxia, A549 and H1299 cells displayed improved survival after photon irradiation. Knockdown of HIF-1α combined with photon irradiation synergistically delayed tumor growth in vivo. Photon irradiation induced HIF-1α and several of its target genes such as PDK1, GLUT-1, LDHA, and VEGF with subsequent enhanced tumor angiogenesis in vivo, a signaling cascade that was not targeted by carbon-ion irradiation. We present evidence that photons but not carbon-ions induce HIF-1α via mTOR pathway. Importantly, after carbon-ion irradiation in vivo, we observed substantial downregulation of HIF-1α and a drastically delayed tumor growth indicating a considerable higher relative biological effectiveness (RBE) than anticipated from the cell survival data. In sum, our results demonstrate that carbon-ions mediate an improved therapeutic response of tumor treatment compared to photon irradiation that is independent of cell oxygenation and HIF-1 signaling.

overall_design: 16 independent cell cultures were used. Each culture was split into an irradiated and a control plate, yieldin a total of 16 paired samples.  Paired samples were analysed in 16 two-color hybridizations. Factors time (after irradiation) with levels 1h and 4h and factor radiation quality with levels C12 and X-rays were analyzed. Each of the 2x2 combinations was analyzed in 4 independent experiments.

first: Florentine

last: Subtil

first: Ulrike

last: Seay


title: Gene Expression Analysis of Host Immune Responses in CD11b positive cells isolated from lungs of the UV inactivated SARS-CoV-immunized mice following Lethal SARS-CoV Infection

city: Shinnjuku-ku

first: Naoko

last: Iwata-Yoshikawa

state: Tokyo

address: 1-23-1 Toyama

department: Pathology

institute: National institute of infectious diseases

summary: To better understand the biological pathways by which UV inactivated SARS-CoV-induced pulmonary eosinophilia occurs, we examined global transcriptional changes in macrophages from the lungs of mouse.

overall_design: Female BALB/c mice were used at 21 weeks of age.  Mice were subcutaneously immunized with UV inactivated SARS-CoV (UV-V) or UV-V and Toll like receptor (TLR) ligands at 6 and 1 weeks prior to mouse-adapted SARS-CoV (n=6 per group).   Mice were intranasally challenged with 1E+6 TCID50 in 30μL.  MEM was challenged in six mice as control infection.  Mice were sacrificed and collected lungs at 1 days after challenge, then CD11b positive cells were isolated from the lungs of these mice. These cells were used for the analysis of microarray.

first: N

first: A

last: Uda

first: Y

last: Sato

last: Tsunetsugu-Yokota

first: S

last: Morikawa

last: Tashiro

first: T

last: Sata

first: H

last: Hasegawa

last: Nagata


title: Induction of pluripotency in human somatic cells via a primitive streak-like state

status: Public on Apr 24 2014

city: Kyoto

first: Kazutoshi

last: Takahashi

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Center for iPS Cell Research and Application

institute: Kyoto University

summary: During mammalian embryonic development, the primitive streak is initiates the differentiation of pluripotent epiblast cells into germ layers. Pluripotency can be reacquired in committed somatic cells using a combination of handful transcription factors, such as OCT3/4, SOX2, KLF4 and c-MYC (hereafter referred to as OSKM), albeit with low efficiency . Here we   show that, during the OSKM-induced reprogramming process toward pluripotency in human cells, intermediate cells transiently show gene expression profiles resembling mesendoderm, which is a major component of the primitive streak. Based on these findings, we discover that forkhead box H1 (FOXH1), a transcription factor required for anterior primitive streak specification during early development, significantly enhances the reprogramming efficiency of human fibroblasts by promoting their maturation, including the mesenchymal to epithelial transition and the activation of late pluripotent markers. These results demonstrate that during the reprogramming process, human somatic cells go through a transient state that resembles mesendoderm.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Human differentiated progeny derived from pluripotent stem cells, N=13  Human undifferentiated pluripotent stem cells, N=6  Transgenic ESC line, N=6  Human tissues, N=29  Human tissue-derived cells, N=20  Human nascent reprogrammed cells, N=95 Mouse cells, N=12

first: K

last: Tanabe

last: Narita

last: Yamanaka


title: Effect of Aid deletion on the global gene expression iPS cells

status: Public on Apr 10 2014

first: Ren

last: Shimamoto

address: 53 Shogoin Kawahara-cho, Sakyo-ku

department: Dept. of Reprogramming Science

institute: Center for iPS Cell Research and Application (CiRA)

summary:
It has been shown that DNA demethylation has a pivotal role in the generation of induced pluripotent stem (iPS) cells. However, the underlying mechanism is still unclear. Previous reports indicated that activation-induced cytidine deaminase (Aid) is involved in DNA demethylation in several developmental processes and cell fusion-mediated reprogramming. Based on the reports, we hypothesized that Aid may be involved in DNA demethylation during the iPS cell generation. In this study, we examined the function of Aid in iPS cell generation using Aid knockout (Aid-/-) mice expressing a GFP reporter under the control of a pluripotent stem cell marker, Nanog. By the introduction of Oct3/4, Sox2, Klf4 and c-Myc, Nanog-GFP positive iPS cells could be generated from the fibroblasts and primary B cells of Aid-/- mice. The Aid-/- iPS cells showed normal proliferation and gave rise to chimeras, indicating their capacity for self-renewal and pluripotency. Microarray analysis demonstrated that the global gene expression of Aid-/- iPS cells was similar to that of Aid+/+ iPS cells.
Aid+/+ and Aid-/- iPS colonies were generated from Aid+/+ and Aid-/- MEFs and picked up mechanically. The clones were passaged four times on feeder cells and two times on gelatin-coated dishes to exclude the contamination of feeder cells. Subsequently, the RNA was isolated. Six Aid+/+ iPS cell clones and six Aid-/- iPS cell clones were compared by microarray.

overall_design: Samples from Aid+/+ and Aid-/-iPS cells

first: Megumi


title: Gene expression profiling of 4T1-SP and 4T1-NSP cells

status: Public on Apr 01 2014

city: Fukuoka

first: kenzaburo

last: tani

address: 3-1-1 Maidashi

department: Medical Institute of Bioregulation

institute: Kyushu University

summary: Novel therapies targeting cancer stem cells (CSCs), which play critical roles in chemo- and radio-resistance, metastasis, and possibly resistance against cancer immunotherapy including granulocyte-macrophage colony-stimulating factor (GM-CSF) gene-transduced tumor cell vaccines, may provide beneficial clinical outcomes. Here, we used syngeneic immunocompetent mice that allowed precise evaluation of the immunogenicity of the side population (SP) isolated from 4T1 murine breast carcinoma (4T1-SP) cells as putative CSCs. 4T1-SP cells showed various stem cell properties including high capacities for colony formation and tumorigenicity as well as high expression of phosphorylated signal transducer and activator of transcription-3 and vascular endothelial growth factor that are inductive of immune tolerance. Despite these progressive malignant characteristics of 4T1-SP cells, subcutaneous injection of non-transmissible Sendai virus-mediated GM-CSF gene-transduced 4T1-SP (4T1-SP/GM) cells remarkably impaired their tumorigenicity compared with that of the controls. This impairment of tumorigenicity was partially dependent on CD8+ T cells in concert with CD4+ T cells and natural killer cells. Notably, therapeutic vaccinations using irradiated 4T1-SP/GM cells markedly suppressed tumor development of subcutaneously transplanted 4T1-SP cells compared with that of the controls including irradiated 4T1-non-SP/GM cells. Tumor suppression was accompanied by robust accumulation of mature dendritic cells at vaccination sites and systemic Th1-based cellular immunity. Moreover, vaccinations comprising primary 4T1-SP cells isolated from transplanted 4T1-SP tumors elicited antitumor effects. cDNA microarray analysis showed that 4T1-SP cells predominantly expressed genes of cancer-related antigens including cancer/testis antigens. Collectively, we demonstrate that SP cell-based vaccinations induce effective antitumor immunity that may improve the efficacy of SP cell-based immunotherapy.

overall_design: Gene expression profiles were compared between sorted 4T1-SP and 4T1-NSP cells.

first: Chika

last: Sakamoto

first: Hiroyuki

last: Inoue

last: Narusawa

first: Ayumi

last: Watanabe

first: Yosuke

last: Yokota

first: Shohei

last: Miyamoto

first: Yumiko

last: Matsumura

first: Tomotoshi

last: Marumoto

first: Atsushi

first: Makoto

first: Koichi

last: Takayama

first: Mamoru

first: Yoichi

last: Nakanishi

first: Kenzaburo

last: Tani


title: Global transcriptional profiles of WT and HOIL-1L-/- BMDMs in response to LPS and TNFa

status: Public on May 15 2014

city: Los Angeles

first: Mary

last: Rodgers

address: 1450 Biggy St, NRT 5517

department: Molecular Microbiology and Immunology

institute: University of Southern California

summary:
HOIL-1L is an essential member of the linear ubiquitin assembly complex (LUBAC), which targets Nemo for linear ubiquitination during NF-kB activation in response to a variety of simuli, including LPS and TNFa treatment. HOIL-1L has also been suggested to function as a transcription factor.
Here we analyzed changes in the global transcriptional profiles of primary bone marrow derived macrophage (BMDMs) from WT and HOIL-1L-/- mice upon treatment with NF-kB activating simuli.

overall_design: BMDMs were differentiated for 1 week and then treated with mock (untreated), 10ng/ml LPS, or 1ng/ml TNFa for 4 hours. RNA was immediately collected and analyzed in biological duplicates by the Agilent 8x60 mouse array.

first: Jae

middle: U

last: Jung


title: Gene expression profiling reveals activation of the FA/BRCA pathway in advanced squamous cervical cancer with intrinsic resistance and therapy failure

status: Public on Mar 31 2014

city: Cluj-Napoca

first: Ovidiu

last: Balacescu

state: Cluj

address: 34-36 Republicii

department: Functional Genomics, Proteomics and Experimental Pathology

country: Romania

institute: The Oncology Institute I. Chiricuta

summary: Twenty-one patients with locally advanced squamous cell carcinoma were enrolled in this study. Primary biopsies harvested prior to therapy were divided according to the patient’s 6 months clinical response and analyzed for whole human gene expression (Agilent). A 2859-gene signature was identified to distinguish between responder and non-responder patients. ‘DNA Replication, Recombination and Repair’ represented one of the most important mechanisms activated in non-responsive cervical tumors, and ‘Role of BRCA1 in DNA Damage Response’ was predicted to be the most significantly altered canonical pathway involved in intrinsic resistance. The microarray results were validated by qRT-PCR and immunohistochemistry. An additional set of 24 formalin-fixed paraffin-embedded cervical cancer samples was used for independent validation of the proteins of interest.  Immunohistological staining confirmed increased expression of BRCA1, BRIP1, FANCD2 and RAD51 in non-responsive compared with responsive advanced squamous cervical cancer, both in the initial set of 21 cervical cancer samples and the second set of 24 samples.

overall_design:
Twenty-one patients with locally advanced squamous cell carcinoma (FIGO stage IIB-IIIB) were enrolled in the genomics study. A tissue fragment from a primary biopsy specimen was harvested from each patient prior to the therapy. Tissue samples were stored in liquid nitrogen until use for RNA extraction.
One-color microarray experiment was performed to measure differences in gene expression between cervical cancer samples with 6-month complete response (12  patients ) and non-complete response (9 patients).  Complet response group was considered as reference.

first: Loredana

first: Oana

last: Tudoran

first: Nicolae

last: Todor

first: Meda

last: Rus

first: Rares

last: Buiga

first: Sergiu

last: Susman

first: Bogdan

last: Fetica

first: Laura

last: Pop

last: Maja

first: Simona

last: Visan

first: Claudia

last: Ordeanu

first: Ioana

last: Berindan-Neagoe

first: Viorica

last: Nagy


title: Global transcriptome analysis on Ankrd2 deficient or overexpressing differentiating primary myoblasts

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

institute: University of Padova

summary: To provide insights into the role of Ankrd2 in the pathways controlling myogenic differentiation, the gene networks that are disturbed in Ankrd2 knockout or overexpressing primary cells were explored during differentiation. Ankrd2 plays an important role in myogenic differentiation by modulating the activity of its interacting partners (i.e p53). Since Ankrd2 binds to numerous transcription factors many signaling pathways remained to be explored to determine the functional significance of crosstalk between Ankrd2 and the activation of transcriptional programmes that regulate muscle remodeling. In contrast to previous gene expression studies in which we and others have studied the effect of Ankrd2 silencing in mouse differentiating C2C12 cells (Series GSE7542) and human differentiated CHQ5B muscle cells (Belgrano et al., 2011), we here used an in vivo experimental model in which the expression of Ankrd2 was completely abrogated. Furthermore, since Ankrd2 is known to be strongly upregulated in response to various stress stimuli, we studied the effect of Ankrd2 rescue and acute overexpression in KO and WT cells by adenoviral infection 20 hours prior to collection of cells. The pathways that change significantly are involved in distinct inflammatory response phases having NF-kB as a central node. Based on these results Ankrd2 is emerging for the first time as a repressor of immune and inflammatory responses.

overall_design: Gene expression profiling experiments have been performed using the SurePrint G3 Mouse 8x60K array by Agilent with 8 subarrays, each containing 39,430 60mer oligonucleotide probes for Entrez Gene RNAs, 16,251 for lincRNAs, 96 x 10 control probes, and 32 x 10 spike-in control probes. The Agilent platforms with one-color approach were selected to make possible the all-to all experiments comparison. The animal model, created and characterized in the laboratory of Dr.ML Bang, directed at knocking out Ankrd2 function was used. The adenovirus expressing Ankrd2-HA was produced using the AdEasy strategy (Agilent Technologies). Primary muscle cultures derived from wild type (WT) and Ankrd2-knockout (KO) mice infected with adenovirus expressing Ankrd2 or control GFP were collected at three different stages: proliferating, fusing and differentiated myoblasts. Three biological replicates per condition were included and a total of 36 microarray experiments were thus performed. First, the over-expression of Ankrd2 was checked by Western blot analysis. Then RNA was extracted from each sample and the relative transcriptional profiles were carried out using updated microarrays from Agilent technologies. Information from probe features was extracted from microarray scan data with the Feature Extraction Software (Agilent). Only arrays with at least 8/9 quality control metrics in range were used for the following data analyses. Intra-array normalization was performed with the Feature Extraction Software. Quantile inter-arrays normalization was performed using the Expander software (Sharan et al., 2003).

first: Camilla

last: Bean

first: Narendra

middle: K

last: Verma

first: Daniel

last: Yamamoto

first: Francesco

last: Chemello

first: Caterina

last: Millino

first: Marie-Louise

last: Bang


title: PI3K/AKT pathway is activated by miRNA-22 in the proliferative CLL subset (mRNA)

city: Montevideo

first: Tamara

last: Fernandez-Calero

state: Montevideo

address: Mataojo 2020

department: Bioinfomatics Unit

country: Uruguay

institute: Institut Pasteur de Montevideo

summary: Understanding the crosstalk between malignant B-cells and their milieu could provide clues on the molecular and clinical biology of Chronic Lymphocytic Leukemia (CLL). Aiming to generate novel therapeutic strategies, different groups have studied different CLL proliferative fractions. We previously, identified one of these proliferative subsets in the peripheral blood from progressive unmutated CLL patients. Since the presence of this small subset appears to be a hallmark of a proliferative disease in which B lymphocytes are being constitutively activated in the proliferative centers of these patients, we performed gene expression analysis comparing the global mRNA and microRNAs expression of this leukemic subpopulation. Our results suggest that the proliferative behaviour of this fraction appears to depend on microRNA-22 over-expression, which induces PTEN downregulation and PI3K/AKT pathway activation. Transfection experiments demonstrated that miR-22 overexpression in CLL B-cells switches on PI3K/AKT leading to FOXO1 inactivation, p27-Kip1 downregulation, and overexpression of Survivin and Ki-67 proteins. We also demonstrated that this pathway could be triggered by microenvironment signals like CD40L/IL4 and more importantly, that this regulatory loop is also present in lymph nodes from progressive UM patients. Altogether, these results underline the key role of PI3K/AKT pathway in the generation of the CLL proliferative pool and provide rationale for the usage of PI3K inhibitors.

overall_design: Two-subset of B cells, QF vs PF. 8 samples of 4 patients.

first: Florencia

last: Palacios

first: Cecilia

last: Abreu

last: Prieto

first: Santiago

last: Ruiz

first: Pablo

last: Morande

first: Hugo

last: Naya

first: Gabriela

last: Libisch

first: Carlos

last: Robello

first: Ana

last: Landoni

first: Raúl

last: Gabús

first: Guillermo

last: Dighiero

last: Oppezzo


title: PI3K/AKT pathway is activated by miRNA-22 in the proliferative CLL subset

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

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

overall_design: Refer to individual Series


title: Sall1 co-operated with Six2 to actively maintain nephron progenitors in the embryonic kidney

status: Public on Mar 24 2014

city: Kumamoto

first: Ryuichi

last: Nishinakamura

address: Honjo 2-2-1

department: IMEG

institute: Kumamoto Univ.


title: Therapeutic Targeting of BET Bromodomain Proteins in Castration-Resistant Prostate Cancer (microarray)

status: Public on Apr 25 2014

city: Ann Arbor

first: Marcin

middle: Piotr

last: Cieslik

state: Michigan

address: 500 S State St

institute: University of Michigan

summary: Men who develop metastatic castration-resistant prostate cancer (CRPC) invariably succumb to the disease.  The development and progression to CRPC following androgen ablation therapy is predominantly driven by unregulated androgen receptor (AR) signaling1-3.  Despite the success of recently approved therapies targeting AR signaling such as abiraterone4-6 and second generation anti-androgens MDV3100 (enzalutamide)7,8, durable responses are limited, presumably due to acquired resistance. Recently JQ1 and I-BET, two selective small molecule inhibitors that target the amino-terminal bromodomains of BRD4, have been shown to exhibit antiproliferative effects in a range of malignancies9-12.  Here we show that AR signaling-competent CRPC cell lines are preferentially sensitive to BET bromodomain inhibition. BRD4 physically interacts with the N-terminal domain of AR and can be disrupted by JQ111,13. Like the direct AR antagonist, MDV3100, JQ1 disrupted AR recruitment to target gene loci.  In contrast to MDV3100, JQ1 functions downstream of AR, and more potently abrogated BRD4 localization to AR target loci and AR mediated gene transcription including induction of TMPRSS2-ERG and its oncogenic activity.  In vivo, BET bromodomain inhibition was more efficacious than direct AR antagonism in CRPC xenograft models.  Taken together, these studies provide a novel epigenetic approach for the concerted blockade of oncogenic drivers in advanced prostate cancer.

overall_design: Two-color experiment, in duplicates

first: Irfan

last: Asangani


title: Loss of HDAC11 leads to reduced secretion of MCP-1 and less severe EAE

city: Tampa

first: Ed

last: Seto

state: FL

address: 12902 Magnolia Dr.

department: Molecular Oncology

institute: H. Lee Moffitt Cancer Center

summary:
HDAC11 regulates IL-10 expression and overexpression of HDAC11 in antigen presenting cells (APCs) leads to a pro-inflammatory phenotype. Conversely, loss of HDAC11 leads to upregulation of IL-10 and immune tolerance. HDAC11 overexpression is also associated with inflammatory diseases including multiple sclerosis. Hence we wished to determine the inflammatory mediators regulated by HDAC11.
We used microarray to determine gene expression profile of macrophages from WT and HDAC11 knockout mice.

overall_design: Thioglycollate induced-peritoneal macrophages obtained from WT and HDAC11 knockout mice were used for total RNA extraction to determine changes in gene expression levels in macrophages from WT and HDAC11 knockout mice.

first: Elphine

last: Telles


title: Global changes in gene expression during sub-zero acclimation of three Arabidopsis thaliana accessions

status: Public on Mar 12 2014

city: Potsdam-Golm

first: Majken

last: Pagter

address: Am Mühlenberg 1

institute: Max Planck Intitute of Molecular Plant Physiology

summary:
During cold acclimation plants increase their freezing tolerance in response to low non-freezing temperatures. This is accompanied by many physiological, biochemical and molecular changes that have been extensively investigated. In addition, many cold acclimated plants become more freezing tolerant during exposure to mild, non-damaging sub-zero temperatures. There is hardly any information available about the molecular basis of this adaptation. However, Arabidopsis thaliana is among the species that acclimate to sub-zero temperatures. This makes it possible to use the molecular and genetic tools available in this species to identify components of sub-zero signal transduction and acclimation. Here, we have used microarrays and a qRT-PCR primer platform covering 1880 genes encoding transcription factors to monitor changes in gene expression in the accessions Columbia-0, Rschew and Tenela during the first three days of sub-zero acclimation at -3°C. The results indicate that gene expression during sub-zero acclimation follows a tighly controlled time-course. Especially AP2/EREBP and WRKY transcription factors may be important regulators of sub-zero acclimation, although the CBF signal transduction pathway seems to be less important during sub-zero than during cold acclimation. Globally, we estimate that approximately 5% of all Arabidopsis genes are regulated during sub-zero acclimation. Particularly photosynthesis-related genes were down-regulated and genes belonging to the functional classes of cell wall biosynthesis, hormone metabolism and RNA regulation of transcription were up-regulated. Collectively, these data provide the first global analysis of gene expression during sub-zero acclimation and allow the identification of candidate genes for forward and reverse genetic studies into the molecular mechanisms of sub-zero acclimation.
We used whole genome microarrays to monitor changes in gene expression in the Arabidopsis thaliana accessions Columbia-0, Rschew and Tenela during three days of acclimation to sub-zero temperature at -3°C after cold acclimation

overall_design: Plants from Arabidopsis thaliana accessions Columbia-0, Rschew and Tenela were cold acclimated at 4°C for two weeks. Detached leaves were then sub-zero acclimated at -3°C for 8 h, 1 d or 3 d at -3°C. Leaves of cold acclimated plants and sub-zero acclimated leaves were collected for RNA extraction and hybridization on Affymetrix ATH1 microarrays in order to explore temporal transcriptome changes during sub-zero acclimation. For each sample total RNA was isolated from a pool of three leaves from three different plants. The experiment was performed in three idenpendent biological replicates.

first: Mai

middle: Q

last: Le

first: Dirk

last: Hincha


title: Modulation of gene expression induced by cylindrospermopsin in human intestinal Caco-2 cells

status: Public on Mar 11 2014

city: Fougères

first: Antoine

last: Huguet

address: 10B rue Claude Bourgelat

institute: Anses

summary: Cylindrospermopsin (CYN) is a cyanotoxin that has been recognised as an emerging potential public health risk. Although CYN toxicity has been demonstrated, the mechanisms involved have not been fully characterised. To identify some key pathways related to this toxicity, we studied the transcriptomic profile of human intestinal Caco-2 cells exposed to a sub-toxic concentration of CYN (1.6 µM for 24hrs) using a non-targeted approach. CYN was shown to modulate different biological functions which were related to growth arrest (with down-regulation of cdkn1a and uhrf1 genes), and DNA recombination and repair (with up-regulation of aptx and pms2 genes). Our main results reported an increased expression of some histone-modifying enzymes (histone acetyl and methyltransferases MYST1, KAT5 and EHMT2) involved in chromatin remodelling, which is essential for initiating transcription. We also detected greater levels of acetylated histone H2A (Lys5) and dimethylated histone H3 (Lys4), two products of these enzymes. In conclusion, CYN overexpressed proteins involved in DNA damage repair and transcription, including modifications of nucleosomal histones. Our results highlighted some new cell processes induced by CYN.

overall_design: Modulation of gene expression in differentiated Caco-2 cells was measured at 24 hours after exposure to doses of 0 and 1.6 µM of cylindrospermopsin. Six independent experiments were performed, but only 11 samples (5 controls and 6 exposed to cylindrospermopsin) had an RNA quality indicator ≥ 9 and were used for the microarray experiments.


title: Expression profiles of X-ray responsive miRNA in human cells [mRNA data]

status: Public on Mar 14 2014

city: Chiba

first: Ken-ichi

last: Ishikawa

state: Chiba

address: 4-9-1, Anagawa, Inage-ku

department: Research Center for Charged Particle Therapy

institute: National Institute of Radiological Sciences

summary: MicroRNA (miRNA) is a type of non-coding RNA that regulates the expression of its target genes by interacting with the complementary sequence of the target mRNA molecules. Recent evidence has shown that genotoxic stress induces miRNA expression, but the target genes involved and role in cellular responses remain unclear. We examined the role of miRNA in the cellular response to X-ray irradiation by studying the expression profiles of radio-responsive miRNAs and their target genes in cultured human cell lines. We found that expression of miR-574-3p was induced in the lung cancer cell line A549 by X-ray irradiation. Overexpression of miR-574-3p caused delayed growth in A549 cells. A predicted target site was detected in the 3'-untranslated region of the enhancer of the rudimentary homolog (ERH) gene, and transfected cells showed an interaction between the luciferase reporter containing the target sequences and miR-574-3p. Overexpression of miR-574-3p suppressed ERH protein production and delayed cell growth. This delay was confirmed by knockdown of ERH expression. Our study suggests that miR-574-3p may contribute to the regulation of the cell cycle in response to X-ray irradiation via suppression of ERH protein production.

overall_design: mRNA expression were compared between the A549 cell overexpressing a radio-responsive miRNA and in the A549 cells suppressing the miRNA. Five miRNAs (miR-181d, miR-565, miR-574-3p, miR-629* and miR-766) were examined. Microarray experiments were performed with triplicate for each experiment.

first: Atsuko

first: Takashi

last: Imai


title: Direct reprogramming of human fibroblasts to functional hepatocyte-like cells

status: Public on Mar 06 2014

city: Shanghai

first: Lijian

last: Hui

address: Yueyang Road 320

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences, Chinese Academy for Sciences

summary: Plasticity of differentiated cells has been proved by nuclear transfer, induced pluripotent cells and transdifferentiation. Here we show that by transduction of 3 factors (FOXA3, HNF1A and HNF4A), human fetal fibroblasts can be converted to hepatocyte-like cells (hiHep cells), expressing hepatic marker genes, and acquiring many mature hepatocyte functions in vitro and in vivo.

overall_design: Human fetal fibroblasts (HFF) were tranfected with 3 liver enriched transcription factors (FOXA3, HNF1A, HNF4A), and converted to hepatocyte-like cells (hiHep cells). HFF and primary human hepatocytes (PHH) serve as control.

first: Pengyu

last: Huang

first: Ludi

last: Zhang

first: Yimeng

last: Gao

first: Zhiying

last: He


title: Feedback control of Set1 protein levels is important for proper H3K4 methylation patterns

status: Public on Feb 28 2014

city: Montpellier

first: Marta

last: Radman-Livaja

address: 1919 route de Mende

department: IGMM

institute: CNRS

type: Genome binding/occupancy profiling by array

summary: Methylation of histone H3 lysine 4 by the Set1 subunit of COMPASS correlates withactive transcription. Here we show that Set1 levels are regulated by protein degradation in response to multiple signals. Set1 levels are greatly reduced when COMPASS recruitment to genes, H3K4 methylation, or transcription is blocked. The degradation sequences map to N-terminal regions that overlap a previously identified auto-inhibitory domain, as well as the catalytic domain. Truncation mutants of Set1 that cause under- or over-expression produce abnormal H3K4 methylation patterns on transcribed genes. Surprisingly, SAGA-dependent genes are more strongly affected than TFIID-dependent genes, reflecting differences in their chromatin dynamics. We propose that careful tuning of Set1 levels by regulated degradation is critical for establishment and maintenance of proper H3K4 methylation patterns.

overall_design: Genome binding/occupancy profiling of H3K4me2 and H3K4me3 in yeast

first: Luis

middle: M

last: Soares

first: Sherry

middle: G

last: Lin

first: Oliver

last: Rando

first: Stephen

last: Buratowski


title: Gene profiling reveals specific molecular pathways in the pathogenesis of atherothrombosis in Antiphospholipid syndrome, Systemic Lupus Erythematosus and Lupus with Antiphospholipid Syndrome

city: Cordoba

first: Rosario

last: Lopez Pedrera

address: Avda. Menendez Pidal s/n

institute: IMIBIC

summary: The present gene expression array study of comparative gene profile in monocytes from patients with primary Antiphospholipid Syndrome, Systemic Lupus Erythematosus and Lupus with Antiphospholipid Syndrome demonstrates that the gene expression profiling allows the segregation of these highly related autoimmune diseases, with specific signatures explaining the pro-atherosclerotic, pro-thrombotic and inflammatory changes.

overall_design: One hundred and twenty six patients, forty one with APS, thirty one with SAPS and fifty four with SLE, as well as sixty one healthy donors were included in the study. Monocytes were purified from peripheral blood samples (non-monocytes depleting kit, Miltenyi Biotech, Bergisch Galdbach, Germany). Total RNA from monocytes was extracted using TRIzol reagent. RNA quality control was performed in a 2100 Bioanalyzer. Complementary RNAs from 3 APS patients, 3 SAPS patients, 3 SLE patients, and 3 healthy donors were prepared for hybridization in an Agilent G4112F platform (Whole human Genome microarray 44K) using the One-color gene expression system (Agilent technologies).

first: Chary


title: Sall1CreER E13.5 110228

first: Ryuichi

last: Nishinakamura

summary: We have employed whole genome microarray expression profiling to identify genes  regulated by Sall1 in the kidney.

overall_design: Kidneys at E13.5 were obtained from inducible Sall1 deletion 24 hrs after tamoxifen treatment (2 set).


title: Role of Pfn-1 phosphorylation in gene expression in glioma-associated endothelial cells

status: Public on Feb 25 2014

city: Cleveland

first: Yi

last: Fan

address: 9500 Euclid Avenue

institute: Cleveland Clinic

summary:
Analysis of gene expression in glioma-associated endothelial cells in Tie2-Cre,Pfn1fl/fl:Y129F and Pfn1fl/fl:Y129F mice
We detected different gene expression patterns in the tumor-associated endothelial cells in Tie2-Cre,Pfn1fl/fl:Y129F and Pfn1fl/fl:Y129F mice

overall_design: We analyzed RNA expression from 6 samples using the Affymetrix Mouse 2.0 ST platform.

first: Alka

middle: A

last: Potdar

first: Paul

middle: L

last: Fox


title: Triploid causes genome instability in tumorigenesis

city: osaka

first: Hisakatsu

last: Nawata

department: Medicine

institute: Kyoto University

summary: To examain effects of triploidy on gene expression in mouse cells, we have employed whole genome microarray expression profiling. To study the effects of aneuploidy in mouse cells, we isorated diploid, triploid and tetraploid cells from p53-/- mouse embryonic cells

overall_design: Gene expression in diploid cells (RRI2, 15 and 2-1), triploid cells (RRI2-5, 2-12 and 2-15) and tetraploid cells (RRI2-2, 2-4 and 2-6).

first: Kazuhiro

last: Daino

first: Yoshiya

last: Shimada

first: Genro

last: Kashino

first: Keizo

last: Tano

first: Masami

last: Watanabe


title: Effects of PAMAM dendrimers in the mouse brain after a single intranasal instillation

status: Public on Mar 26 2014

city: tsukuba

first: Sone

last: Hideko

state: ibaraki

department: Center for Environmental Risk Research

institute: National Institute for Environmental Studies

summary:
The in vivo effects of nasal exposure to polyamidoamine (PAMAM) dendrimers on their effects on gene expression in the mouse brain.
A single dose of PAMAM dendrimers or saline (control) was intranasally administered to 8-week old male BALB/c mice.

overall_design: PAMAM-induced gene expression in the olfactory bulb, hippocampus, and cerebral cortex was measured at 24 hours after exposure to doses of 0, 0.15 mg/kg b.w.  Pooled RNA from six independent experiments were analyzed at each time.

first: Hideko

last: Sone

first: Hiroko

last: Nansai


title: Nanog is Dispensable for the Generation of Induced Pluripotent Stem Cells

status: Public on Jan 28 2014

city: Boston

first: Benjamin

last: Schwarz

address: 185 Cambridge St.

department: Molecular Biology

institute: MGH

summary: Cellular reprogramming from somatic cells to induced pluripotent stem cells (iPSCs) can be achieved through forced expression of the transcription factors Oct4, Klf4, Sox2 and c-Myc (OKSM). These factors, in combination with environmental cues, induce a stable intrinsic pluripotency network that confers indefinite self-renewal capacity on iPSCs. In addition to Oct4 and Sox2, the homeodomain-containing transcription factor Nanog is an integral part of the pluripotency network. Although Nanog expression is not required for the maintenance of pluripotent stem cells, it has been reported to be essential for the establishment of both embryonic stem cells (ESCs) from blastocysts and iPSCs from somatic cells. Here we revisit the role of Nanog in direct reprogramming. Surprisingly, we find that Nanog is dispensable for iPSC formation under optimized culture conditions. We further document that Nanog-deficient iPSCs are transcriptionally highly similar to wild-type iPSCs and support the generation of teratomas and chimeric mice. Lastly, we provide evidence that the presence of ascorbic acid in the culture media is critical for overcoming the previously observed reprogramming block of Nanog knockout cells.

overall_design: Comparison of Nanog KO iPSCs to WT pluripotent cells.

first: Ori

last: Bar-Nur

first: Jose

last: Silva

first: Konrad

last: Hochedlinger


title: Comparative gene expression profiles induced by PPARγ and PPARα/γ agonists in human hepatocytes

status: Public on Feb 09 2014

city: RENNES

first: rogue

last: alexandra

address: 2 av du professeur leon bernard

institute: inserm

summary:
Transcriptomic profiling of primary human hepatocytes after treatment  with 2 glitazones (TRO and ROSI) and 2 glitazars (MURA and TESA)
Singe-Channel Samples: We have analysed changes in gene expression profiles in primary human hepatocytes after a 24 h treatment with various concentrations of glitazones and glitazars
Dual-Channel Samples: We have analysed changes in gene expression profiles in primary human hepatocytes and differentiated human hepatoma HepaRG cells after a 24 h treatment with various concentrations of glitazones and glitazars

overall_design:
Singe-Channel Samples: 5 condition experiments, control, TRO (3 concentrations) , ROSI  (3 concentrations) , MURA (3 concentrations)  and TESA  (1 concentration) , biological replicates:2 to 4
Dual-Channel Samples: 5 condition experiments, control, TRO (3 concentrations) , ROSI  (4 concentrations) , MURA (4 concentrations)  and TESA  (1 concentration) , biological replicates: 3

first: Alexandra

last: Rogue


title: Gene expression changes in liver tissues from alcohol treated PPARa-null mice

status: Public on Jan 14 2014

city: Washington

first: Henghong

last: Li

state: DC

address: 3970 Reservoir Rd., NW

department: Biochemistry

institute: Georgetown University

summary: transcriptomic changes in wild typw and PPARa-null mice fed the Lieber-Decarli liquid diet with or without alcohol for up to four months to identify biomarkers for the early stage of alcohol induced liver damage. Mice were sampled after 1, 2 and 4 months treatment.

overall_design: single-color experiment using Agilent Mouse GE 8x60K Microarray Cat.# G4858A-028005

first: Heng-Hong


title: Expression data from mouse E14.5 fetal liver SLAM LSKs

city: Philadelphia

first: dawson

last: gerhardt

address: BRB2/3 421 Curie Blvd.

institute: University of Pennsylvania

summary: To determine genes in FL HSCs that are sensitive to Notch signagling, E14.5 FL cells were cultured on DL1( to stimulate Notch signaling). Cells were cultured in the presence of DMSO (vehicle control)  or gamma secretase inhibitor (1uM)  for 4 hrs or 10hrs. Gamma secretase inhibitor was used to inhibit Notch signaling. SLAM-LSKs were sorted and used for RNA preparation.

overall_design: 7 biological replicates (14 totalt samples) were collected for cells cultured for 4hrs. 4 biological replicates (8 total samples) were collected from cells cultured for 10hrs. Each replicate consisted of a DMSO and GSI treated sample

first: Dawson

last: Gerhardt

first: Warren

middle: S

last: Pear


title: Analysis of age-related vascular gene expression in mice

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

institute: University of Duesseldorf

summary: Analyses of the age-related changes that occur at a gene expression level and transcriptional profile have not been elucidated in depth. To determine the changes of the vascular transcriptome, we conducted gene expression microarray experiments on aortas of adult and old mice, in which age-related vascular dysfunction was confirmed by increased stiffness and associated systolic hypertension

overall_design: C57BL/6 mice  obtained from Janvier (Saint Berthevin, France) were aged 6 months (n=6) and 20 (n=6) months and water and standard rodent chow were fed ad libitum. Briefly, the vessel was flushed thoroughly with ice-cold phosphate-buffered saline (PBS), through the left ventricle of the heart, cleaned of periadventitial fat and connective tissues, and snap-frozen in liquid nitrogen and stored at -80 °C.

first: Christos

last: Rammos

first: Ulrike

middle: B

last: Hendgen-Cotta

first: Rene

last: Deenen


title: Comparison of  B-MSCs from young and old mice

status: Public on Feb 18 2014

city: Pittsburgh

first: Maria

last: Kapetanaki

state: PA

address: 200 Lothrop Str, BSTW 1200

institute: University of Pittsburgh

summary: Total RNA of B-MSCs from young and old mice were compared using Agilent microarrays.

overall_design: Bone marrow cells from old and young mice were labeled and sorted.

first: Martha

last: Bustos

first: Mauricio

last: Rojas


title: Gene expression profiles of oxaliplatin resistant colorectal cancer and ovarian cancer cell lines

status: Public on Mar 01 2014

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

summary: Oxaliplatin resistance was induced in 2 colorectal cancer cell lines (LoVo-92, wt-p53 and LoVo-Li, functionally inactive p53) and one ovarian cancer cell line (A2780, wt-p53). Resistance was induced by weekly exposure to oxaliplatin for 4 hrs or 72 hrs with increasing concentrations for a period of 7 months.

overall_design: After RNA isolation, 500ng of RNA of the resistant and parental cell line were linearly amplified and fluorescently labeled with either Cy3-CTP or Cy5-CTP with the Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies, Amstelveen, The Netherlands). Equal amounts (1µg) of Cy3-CTP and Cy5-CTP labeled samples were hybridized to Agilent 4x44K Whole Human Genome arrays (Agilent Technologies) according to the manufacturer. Equal amounts (1µg) of Cy3-CTP and Cy5-CTP labeled samples were hybridized to Agilent 44K Whole Human Genome arrays (Agilent Technologies, Part Number G4112A) according to manufacturer's instructions. Microarrays were scanned using an Agilent DNA Microarray Scanner, and scans were quantified using Agilent Feature Extraction software (version 8.5.1). Raw expression data generated by the Feature Extraction software was imported into R using the LIMMA package in Bioconductor (http://www.bioconductor.org). As overall background levels were very low, no background correction was performed. The intensity distributions within and between arrays were normalized using the quantile scaling algorithm in LIMMA. After normalization, the separate intensity channels were extracted from the ratio measurements and combined to the intensities of the reference. The parental cell line was used as reference.

first: Paul

last: Noordhuis

first: Adrie

middle: C

last: Laan

first: Nienke

last: Losekoot

first: Kasper

last: van de Born

last: Eijk

first: Bauke

last: IJlstra

first: Godefridus

middle: J

last: Peters