title: Expression data from A549 cells infected by adenovirus not carrying virus associated sequences in the genome.

city: Kobe

first: Kenji

last: Yoshida

address: 2-2-2, Minatojima Minamimachim Chuo-ku

department: Regenerative & Cellular Medicine

institute: Sumitomo Dainippon Pharma Co.,Ltd.

summary: Non-coding small RNAs are involved in viral life cycles. Adenovirus-encoding small RNAs, virus-associated RNAs (VA RNAs), are transcribed throughout the replication process, and the transcript levels depend on the copy numbers of the viral genome. Although the VA RNA transcription starts immediate early phase, little is known about the function in the early phase. Here we applied replication-deficient adenovirus vectors (AdVs) and novel VA-RNA deleted AdVs to analyze expression change of cellular gene mediated by VA RNAs.

overall_design: Human lung cell, A549, were infected by VA(+) or VA(-) adenoviral vectors. After the designed preiod of infection, cells were harvested and RNA was extacted, followed by DNA microarray analysis.

first: Saki

last: Kondo

first: Yumi

last: Kanegae


title: The functional interplay between the t(9;22)-associated fusion proteins BCR/ABL and ABL/BCR in Philadelphia chromosome positive acute lymphatic leukemia

status: Public on Sep 01 2014

city: Frankfurt am Main

first: Anahita

last: Rafiei

address: Theodor Stern Kai 7

country: Germany

institute: University Clinic Frankfurt

summary: p96ABL/BCR fusion protein plays an important role in the pathogenesis of Ph+ ALL

overall_design: Isolation of murine bone marrow stem cells, transduction of the cells with the desired construct, tranplantation of the cells into lethaly irradiated mice, isolation of RNA from the spleens 12 days after the transplantation, investigation of gene expression profile

first: Claudia

last: Döring


title: Melanoma cell acquired resistance to vinca-alkaloids

status: Public on Sep 03 2014

city: Montpellier

first: Laure-Anais

last: Vincent

address: 15 Avenue Charles Flahault

country: France

institute: IBMM

summary: Malignant melanoma (MM) remains a therapeutic challenge on account of extreme primary resistance to apoptosis and fated acquired chemoresistance. In the current context of molecular classification of MM, the understanding of molecular mechanisms giving rise to these resistances should drive therapeutic choice trough personalized medicine. In order to study mechanisms of MM acquire resistance to VAs, we previously established three VA-resistant cell lines, CAL1R-VCR, CAL1R-VDS, and CAL1R-VRB, by long time exposure of the CAL1-wt MM cell line to IC50 (4nM) of VCR, VDS and VRB respectively. CAL1R-VAs cell lines consisted of polyclonal populations to respect biological diversity of tumour. Then, we searched for determine the resistance process impact on MM cells. We thus performed genome-wide analyses based on comparison of global transcriptomic profile of CAL1R-VAs cells to CAL1-wt. In this way, RNA extracted from each cell line was hybridized to Affimetrix HG-U133 Plus 2.00 GeneChips. After hybridization, microarray data were processed with Robust Multi-array Average (RMA) algorithm. We then performed bioinformatic analyses of microarray data and in vitro investigations in the aim to identify genes and pathways that might predict drug resistance.

overall_design: Melanoma model: CAL1 cell line. Treatments: vinorelbine (VRB), vincristine (VCR), vindesine (VDS). Etablishment of 3 resistant cell lines by long time exposure to vinka-alkaloids (4nM, 6-12 months): CAL1R-VRB, CAL1R-VCR, CAL1R-VDS. RNA extracted from a pooled population of each cell line were hybridized to Affimetrix HG-U133 Plus 2.00 GeneChips. Then, microarray data were processed with Robust Multi-array Average (RMA) algorithm.

first: Chaker

last: Attaoua

first: Pierre

last: Cuq

first: Michel

last: Bellis


title: Gene Expression Following Cardioembolic Stroke

status: Public on Sep 02 2014

city: Sacramento

first: Boryana

last: Stamova

state: California

address: 2805 50th Street

department: Neurology; MIND Institute

country: USA

institute: University of California, Davis Medical Center

overall_design: Blood from subjects with cardioembolic stroke and controls was collected, and the RNA extracted was interrogated and whole genome U133 Affymetrix Arrays. Twenty-three control samples and sixty-nine cardioembolic stroke samples were assayed. Cardioembolic stroke subjects were analyzed at three time points: less than 3 hours, 5 hours, and 24 hours following the event.

middle: B

first: Frank

middle: R

last: Sharp

first: Glen

last: Jickling


title: Gene expression profile of TRAIL-sensitive and -resistant H460 cells

city: Columbus

first: Alessandra

last: Drusco

state: Ohio

address: 460 W 12th Ave

institute: The Ohio State University

summary:
We generated H460 cells with acquired TRAIL resistance by exposing the parental sentisitve cells to subtoxic concentrations of TRAIL for 6 months. Then we compared the gene expression profile of the sensitive versus the resistant cells.
We generated acquired TRAIL-resistant H460 cells from the sentisitve cells by treating subtoxic range of TRAIL for 6 month. And we tried to compare the expressional profile of the genes between two cell types to isolate genes regulating acquired TRAIL-resistance

overall_design: H460 cells were treated with subtoxic concentrations of TRAIL for 6 month. After confirmation of the resistance, the RNA was extracted and the gene expression profile was analyzed.

first: M

last: Garofalo

first: Young-Jun

last: Jeon


title: A set of NF-KB-regulated microRNAs induce acquired TRAIL resistance in lung cancer

type:
Other
Expression profiling by array

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

overall_design: Refer to individual Series


title: TNFR1 controls apoptosis and chronic liver disease in hepatocyte-specific IKKγ (Nemo) mice.

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Death receptor-mediated hepatocyte apoptosis is implicated in a wide range of liver diseases including viral hepatitis, alcoholic hepatitis, ischemia/reperfusion injury, fulminant hepatic failure, cholestatic liver injury and cancer. Deletion of NF-ĸB essential modulator in hepatocytes (NemoΔhepa) causes the spontaneous development of hepatocellular carcinoma preceded by steatohepatitis in mice and thus serves as an excellent model for the progression from chronic hepatitis to liver cancer. In the present study we aimed to dissect the death-receptor mediated pathways that contribute to liver injury in NemoΔhepa mice. Therefore, we generated NemoΔhepa/TRAIL-/- and NemoΔhepa/TNFR1-/- animals and analyzed the progression of liver injury. NemoΔhepa/TRAIL-/- displayed a similar phenotype to NemoΔhepa mice characteristic of high apoptosis, infiltration of immune cells, hepatocyte proliferation and steatohepatitis. These pathophysiological features were significantly ameliorated in NemoΔhepa/TNFR1-/- livers. Hepatocyte apoptosis was increased in NemoΔhepa and NemoΔhepa/TRAIL-/- mice while NemoΔhepa/TNFR1-/- animals showed reduced cell death concomitant with a strong reduction in pJNK levels. Cell cycle parameters were significantly less activated in NemoΔhepa/TNFR1-/- livers. Additionally, markers of liver fibrosis and indicators of tumour progression were significantly decreased in these animals. The present data demonstrate that the death receptor TNFR1 but not TRAIL is important in determining progression of liver injury in hepatocyte-specific Nemo knockout mice.

overall_design: Expression profiling of livers from wild type, NEMO, NEMO-TRIAL, and NEMO-TNFR null mice

first: Anjana

last: Singh

first: Francisco

middle: J

last: Cubero

first: Erawan

last: Borkham-Kamphorst

first: Yulia

middle: A

last: Nevzorova

first: Malika

last: Al Masaoudi

first: Mark

middle: V

last: Boekschoten

first: Nikolaus

last: Gassler

first: Ralf

last: Weiskirchen

first: Tom

last: Luedde

first: Mathias

last: Heikenwalder

first: Michael

last: Müller

first: Christian

last: Liedtke

last: Trautwein


title: Transcriptional programs of lymphoid tissue capillary and high endothelium reveal control mechanisms for lymphocyte homing

status: Public on Aug 31 2014

city: Palo Alto

first: Eugene

middle: C.

last: Butcher

state: CA

address: 3801 Miranda Avenue

department: Pathology

institute: Stanford School of Medicine

summary: This file contains gene microarray data from FACS purified mouse high endothelial cells and capillary endothelial cells from peripheral lymph nodes, mesenteric lymph nodes, and Peyer’s patches. The data will allow for better understanding of the specialization of high endothelial venules (HEV) and their role in lymphocyte recruitment from the blood; the tissue-specific differentiation of lymphoid tissue vasculature; and the specialized features of capillary vs. post-capillary endothelium, including differences in signaling pathways, adhesive properties and mechanisms of hemostasis.

overall_design: We analyzed transcript expression data from vascular endothelial subsets from BALB/c mouse lymphoid tissue.

middle: C

first: Mike

last: Lee


title: Genes regulated by miR-127-3p in glioblastoma cell line

city: hangzhou

first: jie

last: liu

address: yuhangtang road 866

country: China

institute: zcni

summary:
Overexpression of miR-127-3p in LN229 glioblastoma cells promotes their migration and invasion in vitro and in vivo in xenograft models.
We used microarrays to detail the global programme of gene expression in miR-127-3p overexpression LN229 cells compared with mock overexpression LN229 cells

overall_design: MiR-127-3p overexpression LN229 cells and and mock overexpression LN229 cells were cultured in DMEM cell culture media for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the genes regulated by miR-127-3p in glioblastoma cell lines.

first: Huawei

last: Jiang

first: Biaoyang

last: Lin


title: Expression data from hBMSCs cultured on PLLA nanofibers

city: Beijing

first: Wentao

last: Liu

address: 22 Zhongguancun South Avenue

institute: Peking University School and Hospital of Stomatology

summary:
Nanotopographic cues from biomaterials exert powerful effects on the osteogenic differentiation of mesenchymal stem cells because of their niche-mimicking features. However, the biological mechanisms underlying cell lineage determination by surface nanotopography have not been clearly elucidated.
Here, we explored the osteogenic behavior of human bone marrow mesenchymal stem cells (hBMSCs) on PLLA nanofibers with different orientations, and monitored the dynamic changes in global gene expression triggered by topographical cues.

overall_design: The global gene expression of hBMSCs cultured on random and aligned nanofibers and induced with osteogenic supplement (OS) were analysed using microarray company with control at 4, 7, 14 and 21 days.

first: Xuliang

last: Deng


title: Gene expression changes in limb buds of Nipbl-haploinsufficient mice

status: Public on Aug 30 2014

city: Irvine

first: Arthur

middle: D

last: Lander

address: 2638 Biosciences 3

department: Developmental and Cell Biology

institute: University of California Irvine

summary:
Multiple genes are dysregulated in hindlimb buds of Nipbl-deficient embryos.  In all, more than 1000 limb bud genes were found to be significantly altered in expression by microarray analysis of E10.5 mouse hindlimb buds.
Small changes in expression (mostly decreases) were observed for genes involved in FGF, BMP, and SHH pathways, as well as numerous genes involved in the Wnt/planar cell polarity signaling pathway.  Genes involved in the Mediator complex,  Cohesin function, and Hox gene expression and functions  were also dysregulated in Nipbl deficient limb buds.

overall_design: Microarray analysis using RNA extracted from E10.5 hindlimb limb buds harvested from stage-matched Nipbl+/- (n=12) and wildtype (n=12)

first: Martha

middle: E

last: Lopez-Burks


title: Transcriptome analysis of human umbilical cord fibroblasts from babies whose mother experienced preeclampsia

city: Columbia

first: Toshihiko

last: Ezashi

state: MO

address: 240a CS Bond Life Sciences Center

department: Animal Sciences

institute: University of Missouri-Columbia

summary:
In pregnancies involving preeclampsia (PE), there is evidence that the fetal-placental unit is under oxidative stress. Here we examined primary cell lines generated from umbilical cords (UC) delivered by mothers who had either a normal pregnancy or experienced early onset PE to determine whether the two had distinguishable phenotypes. While all UC provided outgrowths when established in 4 % O2, success was less assured for PE cords under ambient (20 % O2) conditions (P < 0.05). Moreover, proliferation rates of established PE lines, although similar to controls in 4 % O2, were significantly lower in 20 % O2.  PE lines grown in 4 % O2 were also more susceptible to the pro-oxidant diethylmaleate than control lines, and unlike controls, were not protected by glutathione.
Transcriptome profiling revealed only a few differentially regulated genes between PE lines and controls in 4 % O2 conditions, but confirmed the more severely stressed phenotype of the PE lines under 20 % O2. We conclude that the primary UC cell lines generated from PE births maintain a susceptibility to oxidative stress that is stable over many cell divisions, but whether the basis of this vulnerability is genetic or epigenetic remains unclear.

overall_design: RNA was isolated from early passages (< p5) of UC fibroblast lines (15 PE and 9 CTL lines, grown in T25 flasks) when they reached ~90% confluency in 4 % O2 conditions. In order to collect RNA from cells under 20 % O2, cell lines at either p 4, 5, or 6 were switched from 4 % O2 conditions to 20 % O2 conditions when they were approximately 20 % confluent. When they reached ~90% confluency (generally 2 days in 4 %  O2 and 3-4 days in 20 % O2 conditions), medium was removed and RNA STAT60  (I ml; Tel-Test, Friendswood, TX) was immediately added to each T25 flask and RNA extracted by following the manufacturer’s instructions. The samples of RNA were submitted to University Texas Southwestern Medical Center Microarray Core Facility (https://microarray.swmed.edu/) and microarray analysis performed with Illumina HumanHT-12 v4 expression BeadChips. Raw intensity data were background subtracted by using BeadStudio software and analyzed further by GeneSpring 12.6 software (Agilent Technologies Inc., Santa Clara CA), according to the advanced workflow protocol: percentile shift and filter by flags (detected).

first: Penghua

last: Yang

first: Danny

last: Schust

last: Roberts


title: DNA methylation analysis of the autistic brain reveals dysregulated biological pathways

city: Safed

first: Evan

last: Elliott

state: Israel

address: Hanrietta Sold 8

department: Faculty of Medicine

country: Israel

institute: Bar Ilan University

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of post-mortem human brain samples from both autistic individuals and nonautistic individuals.  Samples of the frontal cortex (BA10) and cingulate cortex (BA24)  were examined from each individual.

overall_design: Bisulphite converted DNA from the 45 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Nardone

last: Stefano

first: Elliott

last: Evan


title: Paternal poly(ADP-ribose) metabolism modulates retention of inheritable sperm histones and early embryonic gene expression [PJ34_2CE]

city: Logan

first: Ralph

middle: G

last: Meyer

state: UT

address: 4700 Old Main Hill

department: School of Veterinary Medicine

institute: Utah State University

summary: To achieve the extreme nuclear condensation necessary for sperm function, most histones are replaced with protamines during spermiogenesis in mammals.  Mature sperm retain only a small fraction of nucleosomes, which are, in part, enriched on gene regulatory sequences, and recent findings suggest that these retained histones provide epigenetic information that regulates expression of a subset of genes involved in embryo development after fertilization.  We addressed this tantalizing hypothesis by analyzing two mouse models exhibiting abnormal histone positioning in mature sperm due to impaired poly(ADP-ribose) (PAR) metabolism during spermiogenesis and identified altered sperm histone retention in specific gene loci genome-wide using MNase digestion-based enrichment of mononucleosomal DNA.  We then set out to determine the extent to which expression of these genes was altered in embryos generated with these sperm.  For control sperm, most genes showed some degree of histone association, unexpectedly suggesting that histone retention in sperm genes is not an all-or-none phenomenon and that a small number of histones may remain associated with genes throughout the genome.  The amount of retained histones, however, was altered in many loci when PAR metabolism was impaired.  To ascertain whether sperm histone association and embryonic gene expression are linked, the transcriptome of individual 2-cell embryos derived from such sperm was determined using microarrays and RNA sequencing.  Strikingly, a moderate but statistically significant portion of the genes that were differentially expressed in these embryos also showed different histone retention in the corresponding gene loci in sperm of their fathers.  These findings provide new evidence for the existence of a linkage between sperm histone retention and gene expression in the embryo.

overall_design: Seven WT (wild-type) samples of one 2-cell embryo each, all from fathers treated with saline (controls). Each group A, B, D consists of eggs fertilized by the same father (each sample is a single 2 cell embryo, 2CE). Ten samples of 2CE from fathers treated with PJ34 (PARP inhibitor) for 6 weeks, in the same setup (PJ-MTM11-1 to PJ34-MTM14-2, offspring from fathers MTM11, MTM13 or MTM14). All mice are wild-type, strain 129SVE (=129S6/SvEvTac, Taconic).

first: Motomasa

last: Ihara

first: Mirella

middle: L

last: Meyer-Ficca

first: N

last: Leu

first: Shilpa

last: Rao

first: Fan

last: Li

first: Brian

last: Gregory

first: Irina

last: Zalenskaya

first: Richard

middle: M

last: Schultz


title: Paternal poly(ADP-ribose) metabolism modulates retention of inheritable sperm histones and early embryonic gene expression [Parg(110)_KO_2CE]

overall_design: 9 WT samples in 3 groups of 3. Each group consists of 3 eggs fertilized by the same father. 9 KO samples in the same setup. Samples are single 2-cell embryos. All mice are in a 129SVE (=129S6/SvEvTac, Taconic) background.


title: Expression data from mouse embryonic ureteric bud (UB) cells

status: Public on Aug 27 2014

city: Charlottesville

first: Jing

last: Yu

state: VA

address: 1340 Jefferson Park Ave.

department: Cell Biology

institute: University of Virginia School of Medicine

summary:
Dicer-dependent miRNAs are required for UB morphogenesis and differentiation during metanephric kidney development.
We used microarray analysis to identify genes whose expression in the UB epithelium are altered from UB-specific ablation of Dicer.

overall_design: E15.5 UB cells from control and Dicer mutant kidneys were FACS sorted for transcription profiling.

first: Vidya

middle: K

last: Nagalakshmi


title: Polycomb protein EED is required for selective silencing of pluripotency genes upon ESC differentiation

status: Public on Aug 28 2014

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

institute: Institute for Biomedical Engineering

summary: Eed (embryonic ectoderm development) is a core component of the Polycomb Repressive Complex 2 (PRC2) which catalyzes the methylation of histone H3 lysine 27 (H3K27). Trimethylated H3K27 (H3K27me3) can act as a signal for PRC1 recruitment in the process of gene silencing and chromatin condensation. Previous studies with Eed KO ESCs revealed a failure to down-regulate a limited list of pluripotency factors in differentiating ESCs. Our aim was to analyze the consequences of Eed KO for ESC differentiation. To this end we first analyzed ESC differentiation in the absence of Eed and employed in silico data to assess pluripotency gene expression and H3K27me3 patterns. We linked these data to expression analyses of wildtype and Eed KO ESCs. We observed that in wildtype ESCs a subset of pluripotency genes including Oct4, Nanog, Sox2 and Oct4 target genes progressively gain H3K27me3 during differentiation. These genes remain expressed in differentiating Eed KO ESCs. This suggests that the deregulation of a limited set of pluripotency factors impedes ESC differentiation. Global analyses of H3K27me3 and Oct4 ChIP-seq data indicate that in ESCs the binding of Oct4 to promoter regions is not a general predictor for PRC2-mediated silencing during differentiation. However, motif analyses suggest a binding of Oct4 together with Sox2 and Nanog at promoters of genes that are PRC2-dependently silenced during differentiation. In summary, our data further characterize Eed function in ESCs by showing that Eed/PRC2 is essential for the onset of ESC differentiation.

overall_design: RNAs obtained from undifferentiated (d0) wild type and Eed KO ESCs and from day 3 (d3) and day 7 (d7) respective Ebs were subjected to Affymetrix Mouse Gene 1.0 ST Array. 24 samples in total.

first: Nadine

last: Obier

first: Qiong

last: Lin

first: Pierre

last: Cauchy

first: Vroni

last: Hornich

first: Matthias

last: Becker

first: Albrecht

last: Müller


title: Testing gene expression changes in VCaP upon depletion of the mutated ETS transcription factor ERG

city: Cambridge

first: Joshua

last: Korn

state: MA

address: 250 Mass Ave

institute: Novartis

summary:
VCaP cells expressing inducible shRNAs for either ERG or a non-targeting control were treated with Doxycycline for 1, 3, 7 and 10 days prior to collection
This experiment is designed to see which genes and pathways are modulated by ERG knockdown

overall_design: VCaP cells stably expressing a Doxycycline (dox)-inducible control nontargeting shRNA (Pak4) or an ERG shRNA (2217) were exposed to 100ng/ml Dox for the noted days.

first: Zineb

last: Mounir

first: Ray

last: Pagliarini

first: Jenn

last: Rocnik

first: Kim

last: Bellavance


title: Paternal poly(ADP-ribose) metabolism modulates retention of inheritable sperm histones and early embryonic gene expression

first: Ralph

last: Meyer

type: Genome binding/occupancy profiling by genome tiling array


title: Expression data from 20 human colon cancer

status: Public on Aug 26 2014

city: Guangzhou

first: Lekun

last: Fang

address: Yuancunerheng Road

institute: Sun Yat-sen University

summary:
We obtained snap-frozen tissue samples from 20 colorectal cancer (CRC) patients with stage III disease who had undergone curative resection. The expression profiles were determined using Affymetrix Human Genome U133Plus 2.0 arrays.
We used microarrays to identify potential gene deregulation correlated with the outcomes of colon cancer patients.

overall_design: mRNA from 20 primary colorectal tumour samples were extracted and hybridized to HG-U133Plus 2.0 expression arrays. The NexusExp3 procedure was used to make calls of expression. Of the 20 patients, 7 had disease relapse within 3 years after surgery.


title: First ruxolitinib treatment of human alopecia areata patients

status: Public on Aug 17 2014

city: Iowa City

first: Ali

last: Jabbari

state: IA

address: 200 Hawkins Dr, 40025 PFP

institute: University of Iowa

summary:
Two patients with alopecia areata were treated with systemic ruxolitinib.  Skin biopsies were taken before starting treatment and 12 weeks after starting treatment.
We used microarrays to assess changes in gene expression of affected skin before and after starting treatment

overall_design: Two patients with alopecia areata were recruited for our study.  Skin biopsies of affected scalp were taken prior to starting treatment with oral ruxolinitib.  Additional skin biopsies were taken 12 weeks after starting treatment.  Scalp skin biopsies were taken from patients without alopecia areata for comparison.  RNA was extracted, cDNA libraries were made and profiled on affymetrix microarray chips.

first: Jane

last: Cerise

first: Angela

last: Christiano


title: Human Alopecia Areata Skin Profiling

summary: Our goal was to develop a transcriptomic description of affected alopecic scalp skin from patients with alopecia areata.

overall_design: 5 biological replicates of skin samples from 5 separate AA patients compared with 5 similar scalp samples from healthy control patients


city: Jerusalem

first: Uri

last: Ben-David

address: Givat-Ram

department: Genetics

institute: Hebrew University

summary: Human pluripotent stem cells (hPSCs) tend to acquire genomic aberrations in culture, the most common of which is the trisomy of chromosome 12. Interestingly, trisomy 12 is also prevalent in germ cell tumors (GCTs). Here, we aimed to dissect the cellular and molecular implications of trisomy 12 in hPSCs. A genome-wide gene expression analysis revealed that trisomy 12 profoundly affects the global gene expression profile of hPSCs, inducing a transcriptional program very similar to that of CGTs. Direct comparison of the proliferation, replication, differentiation and apoptosis between diploid and aneuploid hPSCs revealed that trisomy 12 significantly increases the proliferation rate of hPSCs. Increased replication largely accounts for the increased proliferation observed, and may explain the selection advantage that trisomy 12 confers to hPSCs. A comparison of the tumors induced by diploid and aneuploid hPSCs further demonstrated that trisomy 12 increases the tumorigenicity of hPSCs, inducing transcriptionally-distinct teratomas, from which pluripotent cells can be recovered. Lastly, a chemical screen of 89 anticancer drugs against diploid and aneuploid hPSCs discovered that trisomy 12 raises the sensitivity of hPSCs to several replication inhibitors, suggesting that the increased proliferation and tumorigenicity of these aberrant cells also makes them more vulnerable, and might potentially be used for their selective elimination from culture. Together, our findings demonstrate the extensive effect of trisomy 12 on the gene expression signature and on the cellular behavior of hPSCs, and highlight the danger posed by this trisomy for the successful use of hPSCs in basic research and in regenerative medicine.

overall_design:
Expression data from diploid and aneuoploid human pluripotent stem cells, teratomas derived from them, and pluripotent-like cells recovered from these teratomas
total RNA was isolated from undifferentiated human pluripotent stem cells grown under standard human ES conditions, or from teratomas derived from them, or from ES-like cells recovered from these teratomas.

first: Juan

last: Biancotti

first: Nissim

last: Benvenisty


title: Thrombospondin-1 type 1 repeats in a model of inflammatory bowel disease: genetic profile and therapeutic effects

city: Rensselaer

first: Sridar

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary:
Thrombospondin 1 (TSP-1) is an anti-angiogenic matricellular protein with regulatory functions in inflammation and cancer. The type 1 repeats (TSR) domains of TSP-1 have been shown to interact with a wide range of proteins that result in the anti-angiogenic and anti-tumor properties of TSP-1. To evaluate potential therapeutic effects of TSRs in inflammatory bowel disease, we conducted clinical, histological and gene microarray analyses on a mouse model of induced colitis.
We used Affymetrix GeneChips to determine the changes in the genetic profile underlying TSR-treatment coincident with induction of colitis using DSS. We identified differentially expressed genes among the treatment groups.

overall_design: Using DSS (dextran sulfate sodium) to induce colitis, wild-type mice were simultaneously injected with either saline or one form of TSP-1 derived peptides, containing either the three domains of the TSR (3TSR), the two last domains (TSR2), or TSR2 with the RFK sequence (TSR2+RFK). Wt mice drinking water only was used as reference.

first: Linda

last: Gutierrez

first: Zenaida

last: Lopez-Dee


title: UBF Is An Epigenetic Factor Required For Ribosomal RNA Gene Activity And Preinitiation Complex Assembly But Not For Nucleolar Body Formation

status: Public on Aug 19 2014

city: Lausanne

first: Eric

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

country: Switzerland

institute: EPFL

summary:
Upstream Binding Factor (UBF) is a unique multi-HMGB-box protein first identified as a co-factor in RNA polymerase I (RPI/PolI) transcription. However, its poor DNA sequence selectivity and its ability to generate nucleosome-like nucleoprotein complexes suggest a more generalized role in chromatin structure. We previously showed that extensive depletion of UBF reduced the number of actively transcribed ribosomal RNA (rRNA) genes, but had little effect on rRNA synthesis rates or cell proliferation, leaving open the question of its requirement for RPI transcription. Using conditional gene deletion in mouse, we now show that UBF is indeed essential for transcription of the rRNA genes.
Unexpectedly, arrest of rRNA synthesis does not affect RPIII transcription of 5S or tRNA genes, nor RPII expression of the hundreds of mRNAs implicated in ribosome biogenesis, but does upreguglate snRNAs and snoRNAs. Thus, rRNA gene activity does not coordinate global gene expression required for ribosome biogenesis.

overall_design: Conditional UBF flox/flox MEFs and immortalized MEFs and isogenic controls all carrying homozygous ER-Cre alleles were treated with 4-HT and mRNA analyzedat 0h and at 24h intervals  posttreatment over 4 days.

first: Tom

last: Moss

first: Nourdine

last: Hamdane

first: Michel

last: Tremblay

first: Victor

last: Stefanovsky


title: Gene expression profiles of murine Runx1;Runx3 double deficient cKit+Sca1+Lin- hematopoietic stem/progenitor cells

city: Singapore

first: Motomi

last: Osato

address: 14 Medical Drive  #12-01

department: Cancer Science Institute of Singapore

country: Singapore

institute: National University of Singapore

summary: The RUNX genes encode for transcription factors involved in development and human disease. RUNX1 and RUNX3 are frequently associated with leukemias, yet the basis for their involvement in leukemogenesis is not fully understood. Here we show that Runx1;Runx3 double knockout (DKO) mice exhibited lethal phenotypes due to bone marrow failure and myeloproliferative disorder. These contradictory clinical manifestations are reminiscent of human inherited bone marrow failure syndromes like Fanconi anemia (FA), caused by defective DNA repair. Indeed, Runx1;Runx3 DKO cells showed mitomycin C hypersensitivity, due to impairment of monoubiquitinated-FANCD2 recruitment to DNA damage foci, although FANCD2 monoubiquitination in the FA pathway was unaffected. RUNX1 and RUNX3 interact with FANCD2 independent of CBFβ, suggesting non-transcriptional role for RUNX in DNA repair. These findings suggest that RUNX dysfunction causes DNA repair defect, besides transcriptional misregulation, and promotes development of leukemias and other cancers.

overall_design: 6 mice were analyzed in this study. 3 Runx1;Runx3 double knockout cKit+Sca1+Lin- hematopoietic stem/progenitor cells were compared with their wild type littermate controls. RNA was isolated from 3 independent Runx1;Runx3 WT KSL samples, each pooled from 3 Runx1;Runx3 WT mice, and 3 independent Runx1;Runx3 DKO KSL samples, using the RNeasy Micro Kit (QIAgen). RNA integrity and quantity was assessed using the Agilent 2000 Bioanalyzer system. 3 μg to 5 μg RNA was processed using WT-Ovation Pico RNA Amplification System (NuGEN) paired with the WT-Ovation Exon Module and FL-Ovation cDNA Biotin Module (NuGEN). A detailed protocol in the user’s guide kit was used without modification. cDNA were prepared for hybridization on GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix) according to the instructions in GeneChip Hybridization Wash and Stain Kit for ST arrays (Affymetrix). Microarray hybridization, scanning and preliminary MAS 5.0 normalizations were completed at the A*STAR Biopolis Shared Facilities (BSF).


title: Effect of AMPK activation by AICAR on MA-10 Leydig cell transcriptome

city: Quebec

first: Jacques

state: Quebec

address: 2705, boulevard Laurier

department: Department of Obstetrics, Gynecology, and Reproduction

country: Canada

institute: Centre de recherche du CHU

summary:
Steroid hormones regulate essential physiological processes and inadequate levels are associated with various pathological conditions. In testosterone-producing Leydig cells, steroidogenesis is strongly stimulated by LH via its receptor leading to increased cAMP production and expression of the steroidogenic acute regulatory (STAR) protein, which is essential for the initiation of steroidogenesis. Leydig cell steroidogenesis then passively decreases following the rapid degradation of cAMP into AMP by phosphodiesterases. In this study, we show that AMP-activated protein kinase (AMPK) is activated following cAMP breakdown in MA-10 and MLTC-1 Leydig cells. Activated AMPK then actively inhibits cAMP-induced steroidogenesis by repressing the expression of key regulators of steroidogenesis including Star and Nr4a1. Similar results were obtained in Y-1 adrenal cells and in the constitutive steroidogenic cell line R2C. Our data identify AMPK as an active repressor of steroid hormone biosynthesis in steroidogenic cells that is essential to preserve cellular energy and prevent excess steroid production.
Steroid hormones regulate essential physiological processes and inadequate levels are associated with various pathological conditions. In testosterone-producing Leydig cells, steroidogenesis is strongly stimulated by LH via its receptor leading to increased cAMP production and expression of the steroidogenic acute regulatory (STAR) protein, which is essential for the initiation of steroidogenesis. Leydig cell steroidogenesis then passively decreases following the rapid degradation of cAMP into AMP by phosphodiesterases. In this study, we show that AMP-activated protein kinase (AMPK) is activated following cAMP breakdown in MA-10 and MLTC-1 Leydig cells. Activated AMPK then actively inhibits cAMP-induced steroidogenesis by repressing the expression of key regulators of steroidogenesis including Star and Nr4a1. Similar results were obtained in Y-1 adrenal cells and in the constitutive steroidogenic cell line R2C. Our data identify AMPK as an active repressor of steroid hormone biosynthesis in steroidogenic cells that is essential to preserve cellular energy and prevent excess steroid production.

overall_design: MA-10 Leydig cells were treated with either DMSO (control), 10 uM forskolin or forskolin+Aicar (1 mM) for 1.5 h before total RNA extraction

first: Houssein

middle: S

last: ABDOU

last: TREMBLAY


title: Expression data from peripheral blood mononuclear cell in patients with type 1 diabetes  compared with normal controls

status: Public on Aug 16 2014

city: shanghai

first: wei

middle: qiong

last: gu

address: 197#,second ruijin road

institute: ruijin hospital

summary:
Type 1 diabetes mellitus (T1D) is a common autoimmune disease mediated by autoimmune attack against pancreatic b  cells.Dys-regualtion of the component of peripheral blood mononuclear cells (PBMCs), including T-cells and B-cells, and smaller amounts of NK cells and dendritic cells, have all been implicated in this process
This study sought to identify T1D associated differently expressed  genes in the peripheral blood mononuclear cell (PBMC).

overall_design: Peripheral blood mononuclear of newly diagnosed type1 diabetes patients and normal controls were purified by LymphoprepTm gradient purification according to the manufacturer’s instructions (Axis-Shield PoC AS, Oslo, Norway) for futher microarray analysis.

first: M

last: Yang

first: L

last: Ye


title: Expression data of  hiPSC-derived anterior foregut endoderm cells (AFECs), ventral anterior foregut cells (VAFECs), EpCAM+CPM+ and EpCAM+CPM- cells and CPM+ cells sorted from VAFECs

status: Public on Aug 25 2014

city: Kyoto

first: Shimpei

last: Gotoh

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Center for iPS cell Research and Application

country: Japan

institute: Kyoto University

summary:
Specific surface marker for NKX2-1+ VAFECs may be helpful for isolating a homogeneous population of alveolar epithelial progenitor cells and distinguishing the differentiation from a thyroid lineage to a lung lineage.
In order to identify specific markers of VAFECs, a microarray analysis was performed to compare the global gene expression patterns between AFECs and VAFECs in 201B7 hiPSCs. We hypothesized that NKX2-1+ cells could be purified by sorting CPM+ VAFECs. After dissociating VAFECs cells on day 14 with Accutase, FACS was performed using anti-EPCAM and anti-CPM antibodies. EPCAM+CPM+ and EPCAM+CPM- cells were then sorted, and the global gene expression patterns of these two populations were examined using a microarray analysis. In addition, MACS was performed to obtain CPM+ cells for comparison.

overall_design: We extracted total RNA from hiPSCs-derived AFECs, VAFECs, EPCAM+CPM+ and EPCAM+CPM- VAFECs and CPM+ VAFECs and hybridized them to Affymetrix microarrays.

first: Isao

last: Ito


title: Expression data in MDA-MB-231 cells treated with siATM, sip53 or control (SiNC) siRNA

status: Public on Aug 18 2014

city: Austin

first: Wei-Ta

last: Chen

state: TX

address: 2506 Speedway Stop A5000

department: Molecular Biosciences

institute: The University of Texas at Austin

summary:
Ataxia-telangiectasia mutated (ATM) protein kinase regulates the DNA damage response and is associated with cancer suppression.
Here, we used microarray to study global transcriptomic expression to identify tumor-promoting functions of ATM.

overall_design: Human breast cancer MDA-MB-231 cells were transfected with siATM, sip53 or control siRNA followed by RNA extraction and hybridization on Affymetrix GeneChip Human Gene 2.0 ST array.

first: Nancy

last: Ebelt

first: Blerta

last: Xhemalce

first: Carla

last: Van Den Berg

first: Kyle

last: Miller


title: Peripheral blood mononuclear cell in patients with type 1 diabetes compared with normal controls

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

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Endogenous Intrahepatic Interferons and Association with IFN-free HCV Treatment Outcome

status: Public on Aug 15 2014

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: Hepatitis C virus (HCV) chronically infects 170 million people worldwide and is a leading cause of liver-related mortality due to hepatocellular carcinoma and cirrhosis1.  Standard-of-care treatment is shifting from interferon-alpha (IFNα)-based to IFNα-free directly acting antiviral (DAA) regimens, which demonstrate improved efficacy and tolerability in clinical trials2,3. Virologic relapse after completion of DAA therapy is a common cause of treatment failure, although mechanisms are unclear2,3. We conducted a clinical trial using the DAA sofosbuvir with ribavirin (SOF/RBV)4, and report here detailed mRNA expression analysis of pre- and end-of-treatment (EOT) liver biopsies and blood samples.  On-treatment viral clearance was accompanied by rapid down-regulation of interferon-stimulated genes (ISGs) in liver and blood.  Analysis of paired liver biopsies from patients who achieved a sustained virologic response (SVR) revealed that viral clearance was accompanied by decreased expression of ISGs, IFNG, and IFNLs, but increased expression of IFNA2.  Patients who achieved SVR had higher expression of a hepatic type-I interferon gene signature in unpaired EOT liver biopsies than patients who later relapsed.  Together, these results support a model whereby restoration of type-I intrahepatic interferon signaling at the EOT is associated with sustained hepatic HCV suppression and prevention of relapse upon withdrawal of SOF/RBV.

overall_design: Sustained Virologic Response for Chronic Hepatitis C Patients Treated with Sofosbuvir and Ribavirin

first: E

last: Meissner

first: D

last: Wu

first: A

last: Osinusi

last: Bon

first: K

last: Virtaneva

first: S

last: Porcella

first: H

last: Wang

last: Herrmann

first: J

last: McHutchison

last: Hewitt

last: Prokunina-Olsson

last: Masur

last: Kottilil

last: Fauci


title: Expression data from heterotopically grafted mouse small intestinal epithelium and the normal colonic epithelium

city: Bunkyo-ku

first: Tetsuya

last: Nakamura

state: Tokyo

address: 1-5-45 Yushima

department: Department of Advanced Therapeutics for GI Diseases

institute: Tokyo Medical and Dental University

summary:
Epithelia of small and large intestines differ in their structures and functions. Such heterogeneity between these two epithelial tissues might be controlled by both epithelium-intrinsic and -extrinsic programs. By employing the cell transplantation technique developed in our laboratory, we investigated how adult SI epithelial cells behave when heterotopically transplanted onto colon. Then the gene expression profiles of small intestinal epithelium heterotopically transplanted onto colon and control colonic epithelium were compared.
We used  laser capture microdissection and microarray analysis to compare the global gene expression profiles of small intestinal epithelium in the heterotopically grafted tissues and control colonic epithelium.

overall_design: Dissected epithelia obtained from serial sections (~ 30 sections) of each specimen were combined and then total RNA extraction was performed. After calculating RNA Integrity Number (RIN), we subjected one graft sample and one control colon sample, which showed the highest RIN value, for the following gene expression analysis.


title: Expression Profiles of Responders versus Non-Responders with AML or MDS to the Novel Mitochondrial Inhibitor CPI-613

status: Public on Aug 13 2014

city: Winston-Salem

first: Jeff

last: Chou

state: NC

address: Medical Center Blvd

institute: Atrium Health Wake Forest Baptist

summary: To determine if there are differences in the gene expression profile of peripheral blood mononuclear cells in patients with Acute Myeloid Leukemia (AML) or Myelodysplastic Syndrome (MDS) who responded to CPI-613 when compared to those patients who did not respond we generated gene expression profiles from four responding patients and compared them to four non-responders. None of the gene expression profiles have been previously published. Here we describe the origins and provide associated clinical annotations with the hope that other investigators will be able to utilize this data in their own research.

overall_design: Peripheral blood mononuclear cells were isolated from 4 patients (3 MDS, 1 AML) who responded to treatment with CPI-613 and four patients (all with AML) who did not respond. Total RNA was isolated and gene expression levels were profiled on the Affymetrix Gene Atlas U219 array strips.

first: Timothy

last: Pardee

first: Lance

last: Miller

middle: W

first: Kristin

last: Stadelman

first: Robin

last: Harrleson


title: Culture-expanded mouse lymph node-derived fibroblastic reticular cells

status: Public on Aug 14 2014

city: Boston

first: Jillian

last: Astarita

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: Lymph node stromal cells were isolated from young C57Bl6/J mice and ex-vivo expanded and purified for gene expression analysis. The aim was to assess gene expression patterns for cultured FRCs.

overall_design: Two replicate samples of untreated young (4-6 weeks old) C57BL6/J mice

first: Anne

last: Fletcher


title: Gene Expression of Malignant Pleural Mesothelioma Tumor and paired Normal Lung tissue

city: Houston

first: Milind

middle: Bhalchandra

last: Suraokar

address: 1515 Holcombe Blvd.

institute: Univ. of Texas M. D Anderson Cancer Center

summary: In order to discover critical pathways /networks or therapeutic targets in pleural mesothelioma we profiled 55 tumors along with paired normal tissue (for 41 tumors) using Affymetrix U133 plus 2.0 chips

overall_design: RNA isolated from frozen resected tumor and normal tissues was hybridized to Affymetrix U133 plus 2.0 chips to discover genes upregulated/downregulated in mesothelioma tumors compared to paired normal non-tumor adjacent tissue as well as find differences between the different tumors

first: Ignacio

last: Wistuba


title: Expression data from the rituximab-resistant lymphoma cell lines and the parental cell lines

city: Nanning

first: Fang

middle: Mei

last: Pan

state: Guangxi

address: No.71, Hedi Road

department: Chemotherapy

institute: Tumor Hospital of Guangxi Medical University

summary: Rituximab, a monoclonal antibody against CD20, has achieved great success in the treatment of B cell lymphoma, but many patients have shown resistance to it and led to disease progression eventually. At present, the mechanism of resistance is still not clear, but we consider that it may involve the multiple genes and multiple signaling pathways. Therefore, our study aimed at searching differentially expressed genes of rituximab resistant cell lines (RRCL) by cDNA microarray, and exploring the resistant mechanism of RRCL by using the subsequent bioinformatics methods. In this study, we successfully identified seventy up-regulated genes and forty-two down-regulated genes in both two RRCL. We also isolated the MAPK signaling pathway, which was the significantly enriched pathway in resistant mechanism, through KEGG pathway analysis. Moreover, we discovered the biological behaviors of RRCL that mainly inhibit apoptosis, promote cellular proliferation, transcription and angiogenesis through Gene Ontology (GO) terms analysis. In conclusion, our results suggested that the most closely related pathway to rituximab resistance was MAPK signaling pathway, which may partly be related to its inhibiting the apoptosis of cells and promoting the proliferation of cells and vascular development.

overall_design: We utilized human mantle cell lymphoma cell line Jeko-1 and human Burkitt lymphoma cell line Raji to establish rituximab resistant Jeko-1/R and Raji/R cell lines. And then, in order to explore rituximab resistant mechanism, we looked for the different gene expression profile of rituximab resistant cell lines compared with the parental cell lines by cDNA microarray and carried out subsequent KEGG pathway and GO terms analysis.

first: Hong

last: Cen

first: Meifang


title: Expression data from Eµ-Myc B-cell lymphoma

city: Los Angeles

first: Colin

last: Flinders

address: 2250 Alcazar St. CSC-140

department: Biological Chemistry

institute: University of California, Los Angeles

summary:
We used microarrays to understand gene expression changes in response to DNA crosslinking agent mafosfamide over a 48 hour period.
We also created resistant cell lines (R100, R500, R1000, R2000, R4000) via dose escalation and used microarrays to probe expression changes between the parental and resistant cell lines.

overall_design: Eµ-Myc B-cells were co-cultured in vitro with 750nM mafosfamide for 48 hours.  Samples were collected at 0, 6, 12, 24, and 48 hours. Additionally, resistant lines were either treated or untreated with 750nM for 24 hours.

first: Flinders

last: Colin

first: Lam

last: Larry


title: Role of Yes-Associated Protein 1 (YAP1) in rhabdomyosarcoma

status: Public on Aug 12 2014

first: Annie

last: Tremblay

address: 1 Blackfan Circle

department: Hematology/Oncology and Stem Cell program

institute: Boston Childrens Hospital

summary:
Doxycycline-inducible YAP1 S127A-driven rhabdomyosarcoma (RMS) tumors, control skeletal muscle and regressed tumors following YAP1 normalization by doxycycline withdrawal were compared to determine the YAP1-regulated gene expression profile relevant to RMS formation.
To characterize the role of YAP1 in embryonal RMS at the molecular level and identify a gene signature for YAP1 activity readout, we compared the gene expression profiles of our YAP1-driven ERMS with control donor skeletal muscle (SKM) and doxycycline-withdrawn regressing tumors by microarray (doxycycline withdrawal for 3 or 6 days; OFF3 and OFF6, respectively). We next extracted a list of genes regulated by YAP1 in our YAP1-driven ERMS tumors (TUM) versus the 3 other conditions: skeletal muscle control (SKM), Doxycycline-withdrawn 3 days (OFF3) and 6 days (OFF6). The overlap between the 3 lists identified a subset of 633 common upregulated genes, named the YAP1-ERMS_UP signature, as well as 249 common downregulated genes, termed the YAP1-ERMS_DOWN signature. Proliferative pathways and transcriptional targets of E2F factors were highlighted in the YAP1-ERMS_UP genes, while muscle differentiation and trancriptional targets of myogenic factors Myod1 and Mef2 were highlighted in the YAP1-ERMS_DOWN genes.

overall_design: Tumor regression conditions (OFF3 days; OFF6 days) as well as control muscle (CTL) were compared with tumors at day 0 of doxycycline withdrawal (TUM). 3 samples for each conditions were used.

first: Fernando

last: Camargo


title: eIF3a in Urinary Bladder Cancer – in vivo and in vitro insights

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

summary:
The eukaryotic translation initiation factor (eIF) 3a is described in various tumor entities as potential tumor marker involved in development and progression of cancer. eIF3a is the largest subunit of the eIF3 complex, a key functional entity in 80S establishment and translation initiation. We hypothesize that eIF3a is more a specific than global translation initiator and involved in signalling pathways that are frequently targeted in UBC therapy.

Methods: In FFPE samples of UBC patients eIF3a expression was analysed together with overall survival. In cell culture we investigated proliferation, migration, clonogenicity and tumorgenicity of UBC cell lines with and without knockdown of eIF3a and compared the cytotoxicity of eIF3a knockdown with other translational inhibitors, including the chemotherapeutic Rapamycine. Detailed information on changed gene expression and global translation initiation were gathered by mRNA expresssion and polysomal profiling.

Results: and Conclusion eIF3a is upregulated in UBC and high expression of eIF3a corresponds with longer overall survival in low grade tumors. Knockdown of eIF3a in UBC cell lines reduces their malignant phenotype, including reduced tumor growth in xenotransplanted mice. eIF3a regulates DNA damage response (ATM, ATR, CDC25A) on a translational level and we show that reduction in eIF3a expression does not hamper global translation initiation.

overall_design:
The knockdown of eIF3a strongly influences proliferation of UBC cell lines without dramatically disturbing general translation as depicted in polysomal profiles. We therefore analysed potential changes on the mRNA level in eIF3a knockdown  compared to control HT1197 cells.
Differential expression of genes between eIF3a knock-down and control samples was assessed with the moderated t-test (Bioconductor's limma package). Raw p-values were adjusted for multiple hypothesis testing using the method from Benjamini and Hochberg for a strong control of the false discovery rate.

first: Rita

last: Spilka

first: Christina

last: Ernst

first: Helmut

last: Bergler

first: Susanne

last: Flechsig

first: Alexander

last: Vogetseder

first: Stephan

last: Geley

first: Robert

last: Schneider

first: Andreas

last: Eger

last: Haybaeck

first: Peter

last: Obrist


title: Gene expression of the colonic epithelial cells in CRB mice fed with HFD and LFD

status: Public on Aug 11 2014

city: Tsuruoka

first: Shinji

last: Fukuda

state: Yamagata

address: 246-2 Mizukami, Kakuganji

department: Institute for Advanced Biosciences

institute: Keio University

summary: To elucidate the mechamisms of colonic Treg cell induction by microbial metabolite(s), chroloform-resistant bacteria (CRB)-associated mice was developed and given low-fiber diet (LFD) and high-fiber diet (HFD). The colonic epithelial cells were isolated and gene expression profiles were analyzed by GeneChip.

overall_design: Clonic epithelial cells in CRB mice fed with HFD and LFD were isolated for RNA extraction and hybridization on Affymetrix microarrays.

first: Koji

last: Hase

first: Hiroshi

last: Ohno


title: Gene expression of colonic epithelial cells in starved and re-fed mice

summary: Oral food intake maintains gastrointestinal cell turnover and impacts the morphology and function of intestinal epithelial cells. However, the underlying mechanism is not fully elucidated, especially in the large intestine. Therefore, we analyzed the colonic epithelial cell turnover in starved and re-fed mice.

overall_design: EpCAM+CD45- colonic epithelial cells (ECs) in re-fed mice treated with or without antibiotics were isolated and sorted by FACS for RNA extraction and hybridization on Affymetrix microarrays.

first: Toshiki

last: Okada

first: Taeko

last: Dohi


title: Expression data from control and GAPLINC knockdown human gastric cancer cell lines

city: Shanghai

first: Ye

last: Hu

address: 145 Middle Shandong Rd

institute: Division of Gastroenterology and Hepatology, Shanghai Jiao-Tong University School of Medicine Renji Hospital

summary: Transcriptional profiling of comparing control and GAPLINC knocking-down human gastric cancer cell lines. Goal was to determine the different gene expression between control and GAPLINC knocking-down human gastric cancer cell lines.

overall_design: Control and GAPLINC knocking-down human gastric cancer cell lines were prepared for RNA extraction and hybridization on Affymetrix microarrays.

first: Y

first: J

last: Xu

last: Fang


title: UCSD GBM Data Set

status: Public on Aug 08 2014

city: San Diego

first: Clark

last: Chen

state: CA

address: 3855 Health Sciences Drive, Room 5345, Bay 5M

department: Neurosurgery

institute: UC San Diego

summary: Total RNA microarray data from Fresh-Frozen Glioblastoma tumor samples.

overall_design: Untreated, newly diagnosed patients.

first: Zachary

last: Taich


title: Gene expression profiles of human Ad5- and CMV-specific CD4 T cells

status: Public on Aug 07 2014

city: Silver Spring

first: Haitao

state: MD

address: 503 Robert Grant Ave

department: US Military HIV Research Program

institute: Walter Reed Army Institute of Research

summary:
Analysis of global gene expression profiles of FACS-sorted, human Ad5- and CMV-specific CD4 T cells from the same PBMC sample of healthy donros, using affymetrix Human Gene 2.0ST Gene-Chips;
The analysis show that Ad5- and CMV-specific CD4 T cells demonstrate differential gene expression profiles even though the cells are from the same PBMC

overall_design: PBMC from healthy donors (n=3) were CFSE-labeled, then equally divided and stimulated with Ad5 and CMV antigens; On day 6 post stimulation, Ag-specific CD4 T cells were sorted by flow based on CFSE-low.


title: Role of Ror2 in primordial germ cell migration

city: San Francisco

first: Diana

middle: J.

last: Laird

address: 35 Medical Center Way

department: ObGyn

institute: UCSF

summary:
Primordial germ cells (PGCs), the embryonic precursors of eggs and sperm, are a unique model for identifying and studying regulatory mechanisms in singly migrating cells. From their time of specification to eventual colonization of the gonad, mouse PGCs traverse through and interact with many different cell types, including epithelial cells and mesenchymal tissues. Work in drosophila and zebrafish have identified many genes and signaling pathways involved in PGC migration, but little is known about this process in mammals.
We have generated a point mutation in the Ror2 gene that we know disrupts primordial germ cell migration in the developing mouse embryo. We used microarray analysis to determine if this defect is mediated through genome-wide or pathway-specific transcriptional changes.

overall_design: We analyzed primordial germ cells (PGCs) from 4 wild-type (WT) and 4 Ror2Y324C/Y324C mutant embryos using Oct4-DPE-EGFP. PGCs were collected during their active migratory state at embryonic day 9.5 (somite range 20-25).

first: Andrea

last: Cantu


title: Gene-expression profiles of BMP signaling-affected SK-OV-3 cells

first: Jin

last: Peng

address: 54 Shogoin Kawaharacho, Sakyo-ku

department: Department of Gynecology and Obstetrics

institute: Kyoto University Graduate School of Medicine

summary:
Bone morphogenetic proteins (BMPs) are extracellular signaling molecules that belong to the transforming growth factor beta (TGF-β) superfamily. By regulating target gene transcription, BMPs control various cellular processes, such as proliferation, differentiation, apoptosis and migration.
In addition, rBMP2 was used to observe BMP signaling in treatment of ovarian cancer cell line SK-OV-3. We attempted to address the possible roles of BMP signaling by inhibiting a wide-range of downstream pathways using a small molecule inhibitor of type I BMPRs, dorsomorphin. The potential utility of this molecule as a molecular inhibitor of BMP signaling in treatment of ovarian cancer cell line SK-OV-3 was also evaluated.

overall_design: SK-OV-3 cells were incubated in 12 separate culture dishes, 3 dishes with PBS, 3 dishes with recombinant BMP2 (rBMP2) (100 ng/ml), 3 dishes with DM (5 μM) and 3 dishes with recombinant BMP2 (rBMP2) (100 ng/ml) plus DM (5 μM) in the culture medium for 24 hours prior to the analysis.

first: Masaki

last: Mandai


title: Expression data from PTEN-deficient regulatory T cells

status: Public on Aug 05 2014

first: Laurence

last: Turka

institute: Harvard Medical School and Massachusetts General Hospital

summary: We used microarrays to assess transcriptional changes in regulatory T cells upon deletion of PTEN.

overall_design: Foxp3+ CD25+ or Foxp3+ CD25- cells were double-sorted from 3 individual healthy 7 week old mice to over 99% purity.

first: Alexandria

last: Huynh


title: Gene expression profiling of Follicular Lymphoma (FL) cultured in the presence or absence  of the Follicular Dendritic Cell (FDC) line  HK

status: Public on Aug 04 2014

city: Bethesda

first: Patricia

last: Perez-Galan

address: 10 center drive

department: Hematology Branch

institute: NHLBI-NIH

summary:
Cells from 2 FL patients and 1 FL cell line were cultured for up to 48h, with no stroma or on top of HK cells pre-establised layers. RNA from FL cells was isolated after 24 and 48h of culture
The aim of this study was to uncover the molecular mechanisms underlying the FL-FDC crosstalk

overall_design: Global RNA expression in FL cells that have been in contact or not with the FDC cell line HK

first: Alba

last: Matas Céspedes

last: Pérez Galán


title: Novel Immunotherapy-Induced Tertiary Lymphoid Aggregates Accumulate as Intratumoral Nodal Structures of Immune Regulation in Pancreatic Cancer

city: Baltimore

first: Lei

last: Zheng

address: 1650 Orleans Street, CRB1 Rm 488

institute: Johns Hopkins University School of Medicine

summary: Immunotherapy provides an alternative approach for cancer treatment.  However, in-depth analyses of the effects of immunotherapy on the tumor microenvironment (TME) have not been conducted in non-melanoma tumors. Here we describe changes in the pancreatic ductal adenocarcinoma (PDAC) TME following immunotherapy treatment, and show for the first time that vaccine-based immunotherapy directly alters the TME, inducing neogenesis of tertiary lymphoid structures that convert immunologically quiescent tumors into immunologically active tumors.  Alterations in five pathways important for immune modulation and lymphoid structure development (TH17/Treg, NFkB, Ubiquitin-proteasome, Chemokines/chemokine receptors, and Integrins/adhesion molecules) in vaccine-induced intratumoral lymphoid aggregates were associated with improved post-vaccination responses.   Additional studies in other cancers and patients treated with other forms of immunotherapy are warranted to further develop signatures defined in intratumoral lymphoid structures into biomarkers that predict effective anti-tumor immune responses.  These signatures may also expose therapeutic targets for promoting more robust antitumor immune responses in the TME.

overall_design: Between July 2008 and September 2012, 59 patients were enrolled into an ongoing study of an irradiated, allogeneic GM-CSF-secreting pancreatic tumor vaccine (GVAX) administered intradermally either alone or in combination with immune modulatory doses of cyclophophamide (Cy) as neoadjuvant and adjuvant treatment for patients with resectable pancreatic ductal adenocarcinoma (PDAC). Patients were randomized 1:1:1 to 3 treatment arms.  In Arm A, patients received GVAX alone; in Arm B, patients received GVAX plus a single intravenous dose of Cy at 200 mg/m2 1 day prior to each vaccination; in Arm C, patients received GVAX plus oral Cy at 100 mg once daily for 1 week on and 1 week off.  Up to 6 GVAX treatments were administered and all of the patients remained in their initial treatment arms throughout the duration of the study.  All 59 of the patients received the 1st GVAX treatment 2 weeks +/-4 days prior to surgery. Formalin-fixed paraffin-embedded (FFPE) tissue blocks of surgically resected PDAC were obtained from the pathology archive. FFPE tissue blocks from each subject were stained by H&E immediately before the vaccine therapy-induced lymphoid aggregates were microdissected .  To better understand the functional status of these vaccine therapy induced lymphoid aggregate structures, gene microarray analysis on RNA isolated from microdissected lymphoid aggregates was performed.  Gene expression was compared among samples grouped according to patient overall survival, post-vaccination induction of enhanced mesothelin-specific T cell responses in peripheral blood lymphocytes (PBL), and the intratumoral CD8+ T effector to FoxP3+ Treg ratio. Post-vaccination induction of enhanced mesothelin-specific T cell responses has been reported to correlate with longer survival in patients treated with Panc GVAX.

first: Eric

middle: R

last: Lutz

first: Annie

last: Wu

first: Elaine

last: Bigelow

first: Rajni

last: Sharma

first: Guanglan

last: Mo

first: Kevin

last: Soares

first: Sara

last: Solt

first: Alvin

last: Dorman

first: Anthony

last: Wamwea

first: Allison

last: Yager

first: Daniel

last: Laheru

first: Christopher

last: Wolfgang

first: Jiang

last: Wang

first: Ralph

middle: H

last: Hruban

first: Robert

last: Anders

first: Elizabeth

last: Jaffee


title: Molecular profiling of contact dermatitis skin identifies allergen-dependent differences in immune response

status: Public on Aug 02 2014

city: New York

first: Joel

last: Correa da Rosa

state: New York

address: 1230 York Avenue

department: CTSA

institute: Rockefeller University

summary: Different allergens induce different immune responses

overall_design: genomic profiling of specific allergen obtained after patched tests in skin

last: da Rosa

first: Nikhil

last: Dighra


title: TSLP effects on primary human blood dendritic cells

status: Public on Aug 01 2014

city: London

first: Raphael

last: Zollinger

state: London

address: Charterhouse Square

country: United Kingdom

institute: Barts Cancer Institute (QMUL)

summary:
The ontogeny of human Langerhans cells (LCs) remains poorly characterized, in particular the nature of LC precursors and the factors that may drive LC differentiation. Through a systematic transcriptomic analysis of TSLP-activated dendritic cells (DCs), we unexpectedly identified markers that have been associated with a skin-homing potential as well as with a LC phenotype. We performed transcriptomic analysis of TSLP-activated blood DCs, as compared to freshly purified, Medium-, and TNF-activated DCs. Among TSLP up-regulated genes, we identified molecules associated with skin homing, LC phenotype, and LC function, as determined by a literature-based survey. Conversely, genes not expressed in LCs were not found among TSLP-induced genes. Further experiments showed that TGF-β synergized with TSLP leading to the differentiation of blood BDCA-1+ DCs into bona fide Birbeck granule-positive LCs.
The ontogeny of human Langerhans cells (LCs) remains poorly characterized, in particular the nature of LC precursors and the factors that may drive LC differentiation. Through a systematic transcriptomic analysis of TSLP-activated dendritic cells (DCs), we unexpectedly identified markers that have been associated with a skin-homing potential as well as with a LC phenotype. We performed transcriptomic analysis of TSLP-activated blood DCs, as compared to freshly purified, Medium-, and TNF-activated DCs. Among TSLP up-regulated genes, we identified molecules associated with skin homing, LC phenotype, and LC function, as determined by a literature-based survey. Conversely, genes not expressed in LCs were not found among TSLP-induced genes. Further experiments showed that TGF-β synergized with TSLP leading to the differentiation of blood BDCA-1+ DCs into bona fide Birbeck granule-positive LCs.

overall_design: Dendritic cells (DC) were purified from the blood of healthy human donors. Each replicate comes from a different donor. There are 6 freshly purified samples (Control_0h),  4  DC samples cultured during 6h with no additional stimulus than the medium (Control_6h), 5 samples cultured during 6h with recombinant TSLP (Thymic Stromal Lymphopoietin at 20 ng/uL) (TSLP_6h) and 3 samples cultured during 6h with recombinant TNF (Tumor necrosis factor at 20 ng/mL) (TNF_6h).

first: Carolina

last: Martínez Cingolani

first: Vassili

last: Soumelis


title: Critical role of transient activation of human endogenous retroviruses during reprogramming toward pluripotency

city: Kyoto

first: Kazutoshi

last: Takahashi

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

department: Center for iPS Cell Research and Application

institute: Kyoto University

type:
Expression profiling by array
Methylation profiling by array

summary: We recently showed that some human induced pluripotent stem cell (iPSC) clones were defective in neural differentiation and were marked with the activation of long term repeats (LTRs) of human endogenous retroviruses (HERVs). We herein demonstrated that these LTRs were transiently overexpressed during the generation of iPSCs and contributed to reprogramming. When the generation of iPSCs was completed, LTRs were re-suppressed to levels similar to those in human ES cells. However, differentiation-defective iPSC clones maintained high LTR expression levels, which indicated that these clones failed to complete reprogramming. lincRNA-RoR, a long intergenic non-coding RNA (lincRNA) that was previously shown to support the induction and maintenance of pluripotency, was detected among the LTR-driven transcripts. Short hairpin RNAs against the conserved sequence in LTRs or lincRNA-RoR markedly reduced the efficiency of iPSC generation. Reprogramming factors including OCT3/4, SOX2, and KLF4 bound to most LTRs. The expression of KLF4 was low in normal iPSC clones, but remained high in differentiation-defective clones. The forced expression of KLF4 in human embryonic stem cells led to the activation of LTRs and defects in neural differentiation. These results demonstrated that the transient overexpression of KLF4/LTR/lincRNA-RoR played crucial roles in reprogramming toward pluripotency in humans, whereas a failure in its re-silence resulted in differentiation defects.

overall_design: Four human induced pluripotent stem cell lines were subcloned into 55 separate lines. Bisulfite converted genomic DNA lysates from fibroblast, induced pluripotent stem cell, intermediate reprogrammed cell and embryonic stem cell lines were hybridized to Illumina HumanMethylation450 BeadChip.

first: Mari

last: Ohnuki

first: Shinya

last: Yamanaka


title: Repeated gestational exposure of mice to chlorpyrifos oxon is associated with paraoxonase 1 (PON1)-modulated effects in maternal and fetal tissues

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: Chlorpyrifos oxon (CPO), the toxic metabolite of the organophosphorus (OP) insecticide chlorpyrifos, causes developmental neurotoxicity in humans and rodents. CPO is hydrolyzed by paraoxonase-1 (PON1), with protection determined by PON1 levels and the human Q192R polymorphism. To examine how the Q192R polymorphism influences fetal toxicity associated with gestational CPO exposure, we measured biomarker inhibition and fetal-brain gene expression in wild-type (PON1+/+), PON1-knockout (PON1-/-), and tgHuPON1R192 and tgHuPON1Q192 transgenic mice. Pregnant mice exposed dermally to 0, 0.50, 0.75 or 0.85 mg/kg/d CPO from gestational days (GD) 6 through 17 were sacrificed on GD18. Biomarkers of CPO exposure inhibited in maternal tissues included brain acetylcholinesterase (AChE), RBC acylpeptide hydrolase (APH), plasma butyrylcholinesterase (BChE) and carboxylesterase (CES). Fetal plasma BChE was inhibited in PON1-/- and tgHuPON1Q192, but not PON1+/+ or tgHuPON1R192 mice. Fetal brain AChE and plasma CES were inhibited in PON1-/- mice, but not in other genotypes.

overall_design:
Pregnant mice (wild type (WT), PON1-knockout (KO), tgHuPON1R192 (R-tg) and tgHuPON1Q192 (Q-tg)) were exposed to various amounts of CPO (0, 0.5, 0.75 and 0.85 mg/kg/d) for 12 days (gestational days 6-17). On gestational day 18, dams were sacrificed and fetal brains were collected.

A total of 264 fetal brains from 80 dams were processed to extract total RNA using TRIZOL and the QIAamp Tissue kit from QIAGEN. Microarray analysis was performed using the fetuses of 5 dams per experimental group (total RNA was pooled from individual fetal brains from each dam). The dams used for fetal-brain microarray analysis were selected using a random-number generator, after first eliminating dams with brain AChE activities > 1.5 SD compared to the mean for their treatment group. RNA samples isolated from individual fetal brains from each dam were combined, then labeled and hybridized to Affymetrix Mouse Gene 1.0 ST  microarrays.

first: Toby

middle: B

last: Cole

first: Wan-Fen

last: Li

first: Aila

last: Co

first: Theo

last: Bammler

first: Federico

last: Farin

first: Lucio

last: Costa

first: Clement

last: Furlong


title: Gene expression profiles of Siglec-14/THP-1 and Siglec-5/THP cell lines, with or without NTHi stimulation

city: Taipei

first: Takashi

last: Angata

address: 128, Section 2, Academia Road, Nangang District

department: Institute of Biological Chemistry

country: Taiwan

institute: Academia Sinica

summary:
Acquisition of a new strain of non-typeable Haemophilus influenzae (NTHi) is often associated with exacerbation of chronic obstructive pulmonary disease (COPD). We have previously reported that COPD patients who are homozygous null for SIGLEC14 gene is less susceptible to COPD exacerbation than those who have wild-type allele with functional SIGLEC14 gene.
In order to gain insight into the mechanism behind the COPD exacerbation, and to find new clues that may lead to the discovery of objective biomarker of COPD exacerbation, Siglec-14/THP-1 and Siglec-5/THP-1 cell lines, which mimic monocytes from homozygous wild-type and homozygous SIGLEC14-null person, respectively, were incubated with or without NTHi, and their gene expression profiles were compared by using Affymetrix Human Genome U133 Plus 2.0 Array.

overall_design: Four samples (2 cell lines x 2 conditions) were analyzed. No replicates were made.


title: Effect of fbw7 deletion in mouse pancreatic ducts

first: Rocio

last: Sancho

address: 44 Lincoln's inn fileds

department: Mammalian Genetics

institute: London Research Institute - CRUK

summary:
The adult pancreas is capable of limited regeneration after injury, but has no defined stem cell population. The cell types and molecular signals that govern the production of new pancreatic tissue are not well understood. Here we show that inactivation of the SCF-type E3 ubiquitin ligase substrate recognition component Fbw7 induces pancreatic ductal cells to reprogram into β-cells. The induced β-cells resemble islet β-cells in morphology and histology, express genes essential for β-cell function, and release insulin upon glucose challenge. Thus, loss of Fbw7 appears to reawaken an endocrine developmental differentiation program in adult pancreatic ductal cells. Our study highlights the plasticity of seemingly differentiated adult cells, identifies Fbw7 as a master regulator of cell fate decisions in the pancreas, and reveals adult pancreatic duct cells as a latent multipotent cell type.
We used microarray to compare adult mouse fbw7 knock out ductal cells with bonafide beta cells

overall_design: In order to isolate fbw7 ko, fbw7 wt ductal cells and beta cells we used adult mice with the following genotypes: MIP-GFP (beta cells are constitutively labelled with GFP), Ck19-CreERT; R26-LSL-YFP; Fbw7 +/+ (ductal cells are labelled with YFP upon tamoxifen injection) and Ck19-CreERT; R26-LSL-YFP; Fbw7 F/F mice (ductal cells are labelled with YFP upon tamoxifen injection). 30000 GFP+ cells were isolated by FACS-sorting. RNA was extracted and amplified using NuGEN kit.

first: Axel

last: Behrens


title: Identification of lncRNA-NTT regulated genes using small interference RNA knockdown for cDNA microarray

city: Taichung

first: Shih-Ya

last: Hung

address: 2 Yude Road

institute: China Medical University

summary:
We used microarrays to detail the global programme of gene expression underlying lncRNA-NTT knockdown
We employed small interference RNA (siRNA) and microarray techniques to investigate the effect of NTT silencing on gene expression in HepG2 cells.

overall_design: HepG2 cells were transfected with NTT siRNA (siNTT) or control siRNA (siCon) for 120 h, and then RNA extraction and cDNA synthesis for hybridization on Affymetrix microarrays. We collect siRNA-transfection HepG2 cells and test knockdown efficiency. After comparison of the siCon group then we choose the best three sample for microarray.


title: Expression data from human fetal lung normal diploid fibroblasts

city: Tokyo

first: Ryo

last: Otomo

address: 5-1-1 Tsukiji, Chuo-ku

department: Division of Refractory Cancer Research

institute: National Cancer Center Research Institute

summary:
The interaction between cancer and stroma plays a key role in tumor progression. Inactivation of p53 is often observed in stromal cells surrounding in cancer, suggesting that p53 in fibroblasts is involved in tumor progression.
To elucidate the mechanism by which p53 loss in fibroblasts effect on proliferation and invasiveness of cancer cells, we performed comprehensive expression profiling analyses between p53 knockdown and control fibroblasts using GeneChip Human Genome U133 plus 2.0 arrays.

overall_design: Intact human fetal lung normal diploid fibroblasts TIG-7 cells and TIG-7 cells infected with lentiviruses for the expression of shRNA against p53 were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Hitoshi

last: Ichikawa

first: Masato

last: Enari


title: Effect of increased FOXA1 on gene expression in bladder cancer cells

city: Sheffield

middle: WF

last: Catto

address: Beech Hill Road

department: School of Medicine

institute: University of Sheffield

summary: Urothelial cell carcinoma of the bladder (UCC) is a common disease characterized by FGFR3 mutation. Whilst upregulation of this oncogene occurs most frequently in low-grade non-invasive tumors, recent data reveal increased FGFR3 expression characterizes a common sub-type of invasive UCC sharing genetic similarities with lobular breast cancer. These similarities include upregulation of the FOXA1 transcription factor and reduced expression of microRNAs-99a/100. We have previously identified direct regulation of FGFR3 by these two microRNAs and now search for further targets. Using a microarray meta-database we find potential FOXA1 regulation by microRNAs-99a/100. We confirm direct targeting of the FOXA1 3’UTR by microRNAs-99a/100 and also potential indirect regulation through microRNA-485-5p/SOX5/JUN-D/FOXL1 and microRNA-486/FOXO1a. In 292 benign and malignant urothelial samples, we find an inverse correlation between the expression of FOXA1 and microRNAs-99a/100 (r=-0.33 to -0.43, p<0.05). As for FGFR3 in UCC, tumors with high FOXA1 expression have lower rates of progression than those with low expression (Log rank p=0.009). Using global gene expression and CpG methylation profiling we find genotypic consequences of FOXA1 upregulation in UCC. These are associated with regional hypomethylation and near FOXA1 binding sites, and mirror patterns previously reported in FGFR3 mutant UCC. These include gene silencing through aberrant hypermethylation (e.g. IGFBP3) and affect genes that characterize lobular breast cancer (e.g. ERBB2, XBP1). In conclusion, we have identified microRNAs-99a/100 mediate a direct relationship between FGFR3 and FOXA1, and potentially facilitate cross talk between these pathways in UCC.

overall_design: Gene expression profiling of EJ Bladder cancer cells transfected with FOXA1 construct or with empty pUC19 vector.

first: Ross

last: Drayton

first: Helen

last: Bryant


title: Direct genesis of functional rodent and human Schwann cells from skin mesenchymal precursors

city: Toronto

first: Freda

last: Miller

state: ON

address: 555 University Avenue

institute: Hospital for Sick Children

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

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: Refer to individual Series


title: DNA methylation modifications associated with Chronic Fatigue Syndrome

first: Patrick

last: McGowan

state: Ontario

address: 1265 Military Trail

department: Biological Sciences

institute: University of Toronto Scarborough

summary: Chronic Fatigue Syndrome (CFS), also known as myalgic encephalomyelitis, is a complex multifactorial disease that is characterized by the persistent presence of fatigue and other particular symptoms for a minimum of 6 months. Symptoms fail to dissipate after sufficient rest and have major effects on the daily functioning of CFS sufferers. CFS is a multi-system disease with a heterogeneous patient population showing a wide variety of functional disabilities and its biological basis remains poorly understood. Stable alterations in gene function in the immune system have been reported in several studies of CFS. Epigenetic modifications have been implicated in long-term effects on gene function, however, to our knowledge, genome-wide epigenetic modifications associated with CFS have not been explored. We examined the DNA methylome in peripheral blood mononuclear cells isolated from CFS patients and healthy controls using the Illumina HumanMethylation450 BeadChip array, controlling for invariant probes and probes overlapping polymorphic sequences.

overall_design: Genomic DNA from 24 peripheral blood mononuclear cells (PBMC) samples (12 CFS, 12 controls) were bisulfite-converted and hybridised to the Illumina Infinium HumanMethylation450 BeadChip. GenomeStudio files were generated and the data was analyzed using the Illumina Methylation Analyzer R package.

first: Wilfred

middle: C

last: de Vega

first: Suzanne

middle: D

last: Vernon

middle: O


title: Expression data from Epstein-Barr virus infection of immortalized normal oral keratinocytes

city: Shreveport

first: Rona

middle: S.

last: Scott

state: LA

address: 1501 Kings Highway

department: Microbiology and Immunology

institute: Louisiana State University Health Sciences Center-Shreveport

summary:
The oral cavity is the persistent reservoir for EBV with lifelong infection of resident epithelial and B cells. Infection of these cell types results in distinct EBV gene expression patterns that are regulated by epigenetic modifications involving DNA methylation and chromatin structure. Such regulation of EBV gene expression relies on viral manipulation of the host epigenetic machinery that may inadvertently result in long-lasting, oncogenic host epigenetic reprogramming. To test this hypothesis in the context of EBV infection of epithelial cells, we established a transient infection model to identify the epigenetic consequences after EBV infection of immortalized normal oral keratinocytes and subsequent viral loss.
With mounting evidence that EBV can induce epigenetic alterations, we developed a transient infection model where a clonal derivative (designated cl1) from a human telomerase immortalized normal oral keratinocyte (NOK) cell line was infected with a recombinant Akata EBV carrying neomycin resistance and GfP cassette in place of the BXLF1 open reading frame. Infected cells were passaged ten times, and then selection pressure was removed for an additional ten passages to allow for viral loss. Three transiently-infected EBV-negative clones were identified by single cell cloning (designated cl1, cl3, cl4). Uninfected parental clone and cells transfected with PTRUF5 plasmid were passaged alongside the transiently-infected clones. The transcription profiles were analyzed using Affymetrix microarray U133Plus2.0 arrays in  duplicate.

overall_design: NOK cells were single cell cloned (designated as cl1) and EBV infected by co-culture with a recombinant Akata EBV strain carrying neomcycin resistance and GFP expression cassette in place of EBV BXLF1.  Cells were selected with 350 ug/ml G418.  As a selection control, cells were transfected a plasmid carrying a neomycin resistance cassette.  Cells were passaged 10 times with G418, followed by removal of selection pressure.  After an additional 10 passages, cells were single cell cloned and the presence of EBV was determined by various methods.  Three clones were identified as being EBV negative and said to be transiently infected.  Uninfected parental and vector transfected cells were passaged in the same manner and also single cell cloned.


title: Expression data from Burkitt's Lymphoma cell line BL2 transiently transfected with Epstein-Barr Virus miRNA mimics BART 18-5p, 10, 14*

city: boston

first: Thorley-Lawson

last: David

state: MA

address: 150 harrison ave

institute: Tufts University

summary:
Cellular targets for most of EBV miRNAs are not known. In our study, we aimed at identifying genes that are regulated by individual EBV mature miRNA, particularly BART 18-5p
We used microarrays to explore the global gene expression (particularly the downregulated genes) targeted by EBV miRNA mimics.

overall_design: Burkitt's lymphoma cell lines, BL2 and BJAB, were transfected with miRNA mimic control (MC) and EBV miRNA mimics BART 18-5p, 10 and 14* for 24 hour prior to RNA extraction and hybridization on Affymetrix human HGU133 plus 2.0 microarrays.

first: Jin

last: Qiu

first: David

last: Thorley-Lawson


title: MicroRNA-150 Contributes to the Proficiency of B-Cell Receptor Signaling in Chronic Lymphocytic Leukemia by Regulating Expression of GAB1 and FOXP1 Genes

city: Brno

first: Marek

last: Mraz

address: Kamenice 5

country: Czech Republic

institute: Masaryk University and University Hospital Brno

summary: We examined the microRNAs (miRNAs) expressed in chronic lymphocytic leukemia (CLL) and identified miR-150 as the most abundant, but with leukemia-cell-expression levels that varied among patients. CLL cells that expressed ZAP-70 or that used unmutated IGHV each had a median expression-level of miR-150 that was significantly lower than that of ZAP-70-negative CLL cells or those that used mutated IGHV. In samples stratified for expression of miR-150, CLL cells with low-level miR-150 expressed relatively higher levels of forkhead box P1 (FOXP1) and GRB2-associated binding protein 1 (GAB1), genes with 3’ UTRs having evolutionary-conserved binding sites for miR-150. High-level expression of miR-150 could repress expression of these genes, which encode proteins that may enhance B-cell receptor (BCR) signaling, a putative CLL-growth/survival signal. Also, high-level expression of miR-150 levels was a significant independent predictor of longer treatment-free-survival (TFS) or overall survival (OS), whereas an inverse association was observed for high-level expression of GAB1 or FOXP1 for OS. This study demonstrates that expression of miR-150 can influence the relative expression of GAB1 and FOXP1 and the signaling potential of the B-cell receptor (BCR), thereby possibly accounting for the noted association of expression of miR-150 and disease outcome.

overall_design: We performed gene expression analysis on isolated leukemia cells from 100 CLL patients using the Affymetrix HG-U133 Plus 2 platform. Array data was processed by dChip software (http://www.dchip.org). No techinical replicates were performed.

first: Liguang

last: Chen

first: Laura

middle: Z

last: Rassenti

first: Emanuela

middle: M

last: Ghia

first: Hongying

last: Li

first: Kristen

last: Jepsen

first: Erin

middle: N

last: Smith

first: Karen

last: Messer

first: Kelly

middle: A

last: Frazer

first: Thomas

middle: J

last: Kipps


title: Human mesenchymal stromal cell expansion in a 3D scaffold-based system under direct perfusion

city: Basel

first: Sophie

last: Brachat

address: Novartis Campus

department: Muskuloskeletal

institute: Novartis Institutes For Biomedical Research

summary: Development of systems allowing the maintenance of native properties of mesenchymal stromal cells (MSC) is a critical challenge for studying physiological functions of skeletal progenitors, as well as towards cellular therapy and regenerative medicine applications. Conventional stem cell culture in monolayer on plastic dishes (2D) is associated with progressive loss of functionality, likely due to the absence of a biomimetic microenvironment and the selection of adherent populations. Here we demonstrate that 2D MSC expansion can be entirely bypassed by culturing freshly isolated bone marrow cells within the pores of 3D scaffolds in a perfusion-based bioreactor system, followed by enzymatic digestion for cell retrieval. The 3D-perfusion system supported MSC growth while maintaining cells of the hematopoietic lineage, and thus generated a cellular environment mimicking some features of the bone marrow stroma. As compared to 2D-expansion, sorted CD45- cells derived from 3D-perfusion culture after the same time (3 weeks) or a similar extent of proliferation (7-8 doublings) maintained a 4.3-fold higher clonogenicity and exhibited a superior differentiation capacity towards all typical mesenchymal lineages, with similar immunomodulatory function in vitro.  Transcriptomic analysis performed on MSC from 5 donors validated the robustness of the process and indicated a reduced inter-donor variability as well as a significant upregulation of multipotency-related gene clusters following 3D-perfusion as compared to 2D expansion. The described system offers a model to study how factors of a 3D engineered niche may regulate MSC function and, by streamlining conventional labor-intensive processes, is prone to automation and scalability within closed bioreactor systems.

overall_design: Nucleated cells were isolated from 5 fresh human bone marrow aspirates by means of red blood cells lyses buffer and then were seeded into a 3D perfusion bioreactor system using a pure hydroxyapatite 3D scaffold and in conventional Petri dishes (2D). After culture for 19 days, cells from both systems were enzymatically retrieved and sorted using anti-CD45-coated magnetic beads. Total RNA was extracted from CD45- cells, QCed and hybridized to Affymetrix microarrays.

first: Adam

last: Papadimitropoulos

first: Elia

last: Piccini

first: Alessandra

last: Braccini

first: Carsten

last: Jacobi

first: Ivan

last: Martin


title: Expression data from primary human hepatic stellate cells treated with coated and uncoated ZnO nanoparticles, or ZnSO4

city: North Ryde

first: Megan

last: Osmond-McLeod

address: 11 Julius Avenue

country: Australia

institute: CSIRO

summary:
ZnO nanoparticles can elicit a range of perturbed cell responses in vitro. The liver is a target for ZnO nanoparticle-, or Zn2+ released from ZnO nanoparticles-induced accumulation and/or impact in vitro and in vivo. The response of human hepatic stellate cells to ZnO nanoparticles has not yet been assessed.
We aimed to determine whether the presence of surface coatings could protect human hepatic stellate cells from ZnO nanoparticle-induced cytotoxicity.

overall_design: Primary human hepatic stellate cells were treated with one of two types of uncoated ZnO nanoparticles (Z-COTE or Nanosun), two types of coated ZnO nanoparticles (HP1, MAX), a mass equivalent of ZnSO4, or were left untreated. After 24 h, RNA was isolated and processed for whole genome transcriptional profiling, comparing the expresson profiles of treated cells to the untreated controls. Each treatment was prepared in duplicate.

last: Osmond

first: Yalchin

last: Oytam

first: Fariborz

last: Sobhanmanesh


title: Sporadic early-onset colorectal carcinoma is a distinct clinicopathological and molecular entity

city: Paris

first: Nabila

last: Elarouci

address: 14 rue Corvisart

department: Recherche

institute: Ligue Nationale contre le Cancer

summary: Sporadic early onset colorectal carcinoma (EOCRC) is a growing problem that remains poorly understood. Clinical specificities and mechanisms of tumorigenesis might be relevant to both diagnosis and treatment. In this prospective study, clinicopathological features, genomic and gene expression profiles of sporadic EOCRC were compared to other well defined groups of CRC.

overall_design: Seventy selected patients were divided into 4 groups according to age (< 45 or > 60 years) and mismatch repair status. Mutations of key genes involved in colorectal carcinogenesis (P53, KRAS, BRAF, PIK3CA) were detected and the methylator phenotype (CIMP) established. Gene expression profiles (GEP) were obtained using pangenomic Affymetrix GeneChip.

first: S

last: Kirzin

first: L

last: Marisa

first: R

last: Guimbaud

first: A

last: De Reynies

first: MP

last: Gaub

first: P

last: Cordelier

first: B

last: Pradère

first: D

last: Bonnet

first: F

last: Meggetto

first: G

last: Portier

last: Brousset

first: J

last: Selves


title: RNAi off-target analysis in Trp53-/- mouse embryonic fibroblasts transduced with miRNA-based shRNAs targeting Trp53.

city: Cold Spring Harbor

first: Christof

last: Fellmann

state: NY

address: 1 Bungtown Road

institute: Mirimus Inc

summary:
We analyzed miRNA-based shRNA off-target effects by transducing Trp53-/- MEFs at single- and high-copy with six well-characterized, potent and weak Trp53 shRNAs.
To advance RNAi therapy for KRAS-mutant cancer, we developed a functionally validated library of siRNAs against RAS pathway genes that minimize off-target effects and enable combination gene silencing at low dose. We developed an in vivo model for real-time tracking of nanoparticle-based siRNA delivery and offer proof-of-principle that siRNA-mediated inhibition of a single gene (KRAS) or combinations of genes (A/B/C-RAF or KRAS+PIK3C-A/B) can impair the growth of KRAS-mutant colorectal cancer xenografts.

overall_design: Trp53-/- MEFs were transduced with LMP expressing Trp53 shRNAs at single copy (11-21% infection efficiency) and high copy (>98% infection efficiency), selected on puromycin and grown in absence of the selection agent before harvest. Uninfected Trp53-/- MEFs and Trp53-/- MEFs infected with an empty vector control served as “no shRNA” reference.

first: Vishal

last: Thapar

first: Johannes

last: Zuber

first: Scott

middle: W

last: Lowe


title: Gene expression profile of MM1S under normoxic and hypoxic conditions

city: Boston

first: Patricia

last: Maiso

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: MM1S cells have been cultured under normoxic and hypoxic conditions, and gene expression profiling has been performed using the Affymetrix Human Genome U133 Plus 2.0 array.

overall_design: We used microarrays to dissect the possible changes occurring at the mRNA level in normoxic cells versus hypoxic cells.

first: Irene

last: Ghobrial


title: Infiltrating monocyte-derived macrophages and resident kupffer cells display different ontogeny and functions in acute liver injury

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

institute: Tel Aviv University

summary:
Molecular profiling of infiltrating monocyte-derived macrophages versus resident kupffer cells following acute liver injury
The liver has a remarkable capacity to regenerate after injury; yet, the role of macrophages (MF) in this process remains controversial mainly due to difficulties in distinguishing between different MF-subsets. Here, we utilized a murine model of acute liver injury caused by overdose of acetaminophen (APAP) and defined three distinct MF subsets that populate the liver following injury. Accordingly, resident Kupffer cells (KC) were significantly reduced upon APAP-challenge and started recovering by self-renewal at resolution phase without contribution of circulating Ly6Chi monocytes. The latter were recruited in a CCR2 and M-CSF mediated pathway at the necro-inflammatory phase and differentiated into ephemeral Ly6Clo MF subset at resolution phase. Moreover, their inducible ablation resulted in impaired recovery. Microarray based molecular profiling uncovered high similarity between steady state KC and those recovered at the resolution phase. In contrast, KC and monocyte-derived MF displayed distinct pro-restorative genetic signature at the resolution phase. Finally, we show that infiltrating monocytes acquire a pro-restorative polarization manifested by unique expression of pro-angiogenesis mediators and genes involved with inhibition of neutrophil activity and recruitment and promotion of their clearance. Collectively, our results present a novel phenotypic, ontogenic and molecular definition of liver-MF compartment following acute injury.

overall_design: 11 Samples (arrays) were performed. We generated pairwise comparison between all the different macrophages stages, using Partek Genomics Suite. Genes with p≤5%[FDR] and a fold-change difference of  ≥2 or <-2 were selected.

first: Chen

last: Varol

first: Ehud

last: Zigmond

first: Shany

last: Samia-Grinberg

first: Eli

last: Brazowski

first: Oren

last: Shibolet

first: Zamir

last: Halpern


title: Gene Body Methylation Directly Increases Gene Expression and is a Therapeutic Target for Genes Upregulated in Cancer

city: Los Angeles

first: Xiaojing

last: Yang

address: 1441 Eastlake Ave, Room 7336

institute: USC/Norris Comprehensive Cancer Center


title: Combined multiphoton live-cell imaging and molecular systems approaches reveal mosaic contribution of dynamic transiently signaling INPs to the adult Dentate Gyrus NSC niche

first: James

last: MacDonald

address: 4225 Roosevelt Way NE

institute: University of Washington

summary: Here we directly compare for the first time how the longstanding static model of mouse Dentate Gyrus (DG) development compares with a comprehensive high-resolution live-cell multiphoton (live-MPM) imaging approach. We took advantage of multiple fluorescent protein-based cell-type specific reporters to identify Neural Stem Cells (NSC), Intermediate Neurogenic Progenitors (INPs), and Granule Neurons (GNs) to generate live 4D cellular datasets across embryonic, postnatal and adult ages. Live-MPM revealed that INPs and NSCs migrated long distances along multiple routes to seed the SGZ from multiple directions, and from mosaic progenitor zones along the septo-temporal axis of the hippocampus. We found that dynamic INPs processes and interactions contributed to the architecture of both transient and permanent NSC niches during embryonic development, and that INP cellular plasticity is maintained in the adult SGZ NSC niche. We also used a Molecular Systems (MS) approach to determine the basis for maintained INP cellular plasticity that revealed an overlapping signaling network infrastructure based largely on Rho-family mediated regulation of cytoskeletal dynamics. Our combined strategies revealed that dynamic INPs are a major molecular signaling transition state in the adult SGZ, and that Tbr2 expression defines the initial stage of GN commitment. Our novel findings reveal fundamental new insight into one of the most well studied brain regions key for normal cognitive function, and the importance of analyzing the development of live stem cell niches in vivo.

overall_design: In concert with live-cell imaging, we used microarray analysis to identify genes that may be involved in the development of the Dentate Gyrus NSC niche.

first: Branden

last: Nelson

first: Rebecca

last: Hodge

first: Sengkeo

last: Srinouanprachanh

first: Theo

middle: K

last: Bammler

first: Dustin

last: Chernick

first: Sebastian

last: Arnold

first: Matthias

last: Groszer

first: Gary

last: Westbrook

first: Robert

middle: F

last: Hevner


title: Gene Body Methylation Directly Increases Gene Expression and is a Therapeutic Target for Genes Upregulated in Cancer (methylation)

summary: Demethylation treatment reduce gene body methylation as well as gene expression

overall_design: Bisulphite converted DNA from the 22 samples were hybridised to the Illumina Infinium HM450 Human Methylation Beadchip

first: Han

last: Han