title: Transcriptional response in human umbilical vein endothelial cells exposed to insulin

status: Public on May 26 2010

city: Padova

first: Tiziana

last: Sanavia

address: Gradenigo, 6/B

institute: University of Padova

summary:
Background: In diabetes chronic hyperinsulinemia is responsible for the instability of the atherosclerotic plaque and stimulates cellular proliferation through the activation of the MAP kinases, which in turn regulate cellular proliferation. However, it is not known whether insulin itself could increase the transcription of specific genes for cellular proliferation in the endothelium. Hence, the characterization of transcriptional modifications in endothelium is an important step for a better understanding of the mechanism of insulin action and the relationship between endothelial cell dysfunction and insulin resistance.

Methodology and principal findings: The transcriptional response of endothelial cells in the 440 minutes following insulin stimulation was monitored using microarrays and compared to a control condition. About 1700 genes were selected as differentially expressed based on their treated minus control profile, thus allowing the detection of even small but systematic changes in gene expression. Genes were clustered in 7 groups according to their time expression profile and classified into 15 functional categories that can support the biological effects of insulin, based on Gene Ontology enrichment analysis. In terms of endothelial function, the most prominent processes affected were NADH dehydrogenase activity, N-terminal myristoylation domain binding, nitric-oxide synthase regulator activity and growth factor binding. Pathway-based enrichment analysis revealed “Electron Transport Chain” significantly enriched.
Results were validated on genes belonging to “Electron Transport Chain” pathway, using quantitative RT-PCR.

Conclusions: As far as we know, this is the first systematic study in the literature monitoring transcriptional response to insulin in endothelial cells, in a time series microarray experiment. Since chronic hyperinsulinemia is responsible for the instability of the atherosclerotic plaque and stimulates cellular proliferation, some of the genes identified in the present work are potential novel candidates in diabetes complications related to endothelial dysfunction.

overall_design: Experiments were carried on human umbilical venous endothelial cells (HUVEC) to elucidate the regulatory aspects of insulin from dynamic gene expression data. HUVEC incubated with or without insulin were collected at times 0', 40', 100', 200', 340' and 440'. RNA was extracted and quantified for high-density oligonucleotide microarrays Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA).

first: Barbara

last: Di Camillo

first: Elisabetta

last: Iori

first: Enzo

last: Bronte

first: Enrica

last: Roncaglia

first: Alberto

last: Maran

first: Angelo

last: Avogaro

first: Gianna

last: Toffolo

first: Claudio

last: Cobelli


title: Expression data from purified human platelets

status: Public on Jun 05 2010

city: Lund

first: Christian

last: Lood

address: Sölvegatan 23

department: Laboratory Medicine

country: Sweden

institute: Lund University

summary: Patients with systemic lupus erythematosus (SLE) have a markedly increased risk to develop cardiovascular disease, and traditional cardiovascular risk factors fail to account for this increased risk. We used microarray to probe the platelet transcriptome in individuals with SLE and healthy controls, and the gene and protein expression of a subset of differentially expressed genes was further investigated and correlated to platelet activation status. Real-time PCR was used to confirm a type I interferon (IFN) gene signature in patients with SLE, and the IFN-regulated proteins PRKRA, IFITM1 and CD69 (p<0.0001) were found to be up-regulated in platelets from SLE patients as compared to healthy volunteers. Notably, patients with a history of vascular disease had increased expression of type I IFN-regulated proteins as well as more activated platelets as compared with patients without vascular disease. We suggest that interferogenic immune complexes stimulate production of IFNα which up-regulates the megakaryocytic type I IFN-regulated genes and proteins. This could affect platelet activation and contribute to development of vascular disease in SLE. In addition, platelets with type I IFN signature could be a novel marker for vascular disease in SLE.

overall_design: Platelets were purified from SLE patients (n=10) and age and sex-matched healthy volunteers (n=10). cDNA was generated for each individual. For the microarray analysis, cDNA from the 10 SLE patients were pooled, as well as the cDNA from the 10 healthy volunteers to represent a mean mRNA expression level from 10 individuals.

first: Stefan

last: Amisten

first: Birgitta

last: Gullstrand

first: Andreas

last: Jönsen

first: Maria

last: Allhorn

first: Lennart

last: Truedsson

first: Gunnar

last: Sturfelt

first: David

last: Erlinge

first: Anders

middle: A

last: Bengtsson


title: The Relationship between Virus Replication and Host Gene Expression in Lymphatic Tissue during HIV-1 Infection

status: Public on Jun 01 2010

city: Minneapolis

first: Anthony

middle: James

last: Smith

state: MN

address: 420 Delaware Street S.E.

department: Microbiology

country: USA

institute: University of Minnesota

summary: During HIV-1 infection, there is a massive perturbation of host gene expression, but as yet, genome-wide studies have not identified host genes affecting HIV-1 replication in lymphatic tissue, the primary site of virus-host interactions.  In this study, we isolated RNA from the inguinal lymph nodes of 22 HIV-1-infected individuals and utilized a microarray approach to identify host genes critically important for viral replication in lymphatic tissue by examining gene expression associated with viral load.  Strikingly, ~95% of the transcripts (558) in this data set (592 transcripts total) were negatively associated with HIV-1 replication.  Genes in this subset (1) inhibit cellular activation/proliferation (ex.: TCFL5, SOCS5 and SCOS7, KLF10), (2) promote heterochromatin formation (ex.: HIC2, CREBZF, ZNF148/ZBP-89), (3) increase collagen synthesis (ex.: PLOD2, POSTN, CRTAP), and (4) reduce cellular transcription and translation.  Potential anti-HIV-1 restriction factors were also identified (ex.: NR3C1, HNRNPU, PACT).  Only ~5% of the transcripts (34) were positively associated with HIV-1 replication.  Paradoxically, nearly all these genes function in innate and adaptive immunity, particularly highlighting a heightened interferon system.  The predominance of negative correlations as well as the disconnect between host defenses and viral load point to the importance of genes that regulate target cell activation and genes that code for potentially new restriction factors as determinants of viral load rather than conventional host defenses.

overall_design: Total RNA was isolated from the inguinal lymph nodes of 22 HIV-1-infected subjects at different clinical stages (and varying viral loads) and prepared for RNA extraction and hybridization on Affymetrix Human Genome U133 Plus 2.0 microarrays.  Replicate arrays were performed for lymph node samples to minimize assay noise and host genes critically important for viral replication in lymphatic tissue were identified by examining gene expression and its association with viral load. Replicates were not performed for samples WB91 and TS35 due to limited amounts of biomaterial.

middle: J

first: Qingsheng

last: Li

first: Steve

middle: W

last: Wietgrefe

first: Timothy

last: Schacker

first: Cavan

middle: S

last: Reilly

first: Ashley

middle: T

last: Haase


title: Gene Expression Profiles in Thermally Injured Human Skin: A Temporal Microarray Analysis

status: Public on May 23 2010

city: Nashville

first: Lillian

middle: B

last: Nanney

state: TN

department: Plastic Surgery

institute: Vanderbilt University

summary:
Thermal injury incites inflammatory responses that often transcend the local environment and lead to structural deficiencies in skin that give way to scar formation. We hypothesized that extensive perturbations within burned skin following thermal insult and during subsequent events of wound repair induce vast alterations in gene expression that likely serve as a wound and systemic healing deterrent. A high-throughput microarray experiment was designed to analyze genetic expression patterns and identify potential genes to target for therapeutic augmentation or silencing. The study compares gene expression from burn wound margins at various times following thermal injury to expression observed in normal skin. Utilizing this design, we report that the totality of gene expression alterations is indeed enormous. Further, we observed that the differential expression of many inflammatory and immune response genes appear to be continually up-regulated in burn wound margins seven days or more after initial thermal insult. As it is well established that the inflammatory process must abate for wound healing to proceed, the finding of ongoing local inflammation is cause for further investigation. To our knowledge, this is the first report of the gene expression alterations induced by thermal injury of human skin. As such, it provides a wealth of data to mine with the ultimate goal of better understanding the local pathophysiologic changes at the site of thermal injury that not only affect wound healing capacity, but may also contribute to systemic derangements within the burn patient.
Keywords: time course, disease state analysis

overall_design: The study compares gene expression from burn wound margins at various times following thermal injury to expression observed in normal skin. All skin specimens were obtained in the operating room within minutes of being removed from the patient. Burn specimens were taken from wound margins. Harvested tissue at the burn wound margin maximized the capture of viable cells from the multiple lineages important to the healing process and minimized the inclusion of non-viable cells destroyed by full-thickness injury. After isolation, RNA samples were pooled equally by mass as to contain RNA from 5 tissue specimens for each array replicate.

first: Joseph

last: Greco III

first: Alonda

last: Pollins

first: Braden

last: Boone

first: Lauren

last: Sims


title: Expression data from human renal allograft biopsies

status: Public on May 24 2010

city: Edmonton

first: Jeff

last: Reeve

state: Alberta

address: 250 HMRC University of Alberta

country: Canada

institute: University of Alberta

summary:
Kidney transplants that develop dysfunction or proteinuria after one year post transplant are at considerable risk for progression to renal failure. Identifying the molecules associated with graft failure could potentially lead to interventions that would slow the progression of organ failure.
We analyzed the relationship between gene expression in late biopsies for cause in human kidney transplants and subsequent graft loss, and assessed the predictive value of gene expression. We evaluated the performance of these genes in an independent , and in a population of early biopsies that have a very low risk of subsequent graft failure.

overall_design: All consenting renal transplant patients undergoing biopsies for cause as standard of care between 09/2004 and 10/2007 at the university of Alberta or between 11/2006 and 02/2007 at the University of Illinois were included in the analysis. In addition, biopsies obtained from Minnesota between 09/2006 and 09/2007 were used as an independent . In addition to the cores required for standard histopathology, we collected one core for gene expression studies. the relationship between gene expression in the biopsy and subsequent graft loss was analyzed.

first: Gunilla

last: Einecke

first: Philip

middle: F

last: Halloran


title: Gene expression changes upon treatment of T47D breast cancer cells with the Pan-PI3 kinase inhibitor GDC-0941

status: Public on May 25 2010

city: South San Francisco

first: Debraj

last: GuhaThakurta

state: CA

address: 1 DNA Way

department: Bioinformatics and Computational Biology

institute: Genentech Inc

summary: We sought to determine genes whose expression changed upon treatment with a selective inhibitor of class I PI3 kinase.

overall_design: Total of 6 samples: cells were treated with GDC-0941 at a concentration of 1mM for 6 hours (3 replicates) and control (3 replicates)

first: Mark

middle: R

last: Lackner


title: Gene expression analysis in non-failing and failing myocardium pre and post pulsatile and non-pulsatile VAD support

status: Public on May 20 2010

city: Bad Oeynhausen

first: Patrick

last: Schwientek

address: Georgstr. 11

department: Klinik f. Thorax- & Kardiovaskularchirurgie

country: Germany

institute: Herz- & Diabeteszentrum NRW

summary:
Mechanical unloading by ventricular assist devices (VAD) leads to significant gene-expression changes often summarized as reverse remodeling. However, little is known on individual transcriptome changes during VAD-support and its relationship to non-failing hearts (NF). In addition no data are available for the transcriptome regulation during non-pulsatile VAD-support. Therefore we analysed the gene-expression patterns of 30 paired samples from VAD-supported (including 8 non-pulsatile VADs) and 8 non-failing control hearts (NF) using the first total human genome-array available.
Transmural myocardial samples were collected for RNA-isolation. RNA was isolated by commercial methods and processed according to chip-manufacturer recommendations. cRNA were hybridized on Affymetrix HG-U133 Plus 2.0 arrays, providing coverage of the whole human genome Array. Data was analyzed using Microarray Analysis Suite 5.0 (Affymetrix) and clustered by Expressionist software (Genedata). 352  transcripts were differentially regulated between samples from VAD-implantation and NF, whereas 510 were significantly regulated between VAD-transplantation and NF (paired t-test p<0.001, fold change >=1.6). Remarkably, only a minor fraction of 111 transcripts was regulated in heart failure (HF) and during VAD-support. Unsupervised hierarchical clustering of paired VAD- and NF-samples revealed separation of HF- and NF- samples, however individual differentiation of VAD-implantation and VAD-transplantation was not accomplished. Clustering of pulsatile and non-pulsatile VAD did not lead to robust separation of gene expression patterns.
During VAD-support myocardial gene expression changes do not indicate reversal of the HF-phenotype, but reveal a distinct HF-related pattern. Transcriptome analysis of pulsatile and non-pulsatile VAD-supported hearts did not provide evidence for a pump-mode specific transcriptome pattern.

overall_design: Microarrays were used to elucidate the differences between non-failing control hearts and those, suffering from end-stage heart failure pre and post mechanical unloading.

first: Peter

last: Ellinghaus

first: Sonja

last: Steppan

first: Donatella

last: D’Urso

first: Michael

last: Seewald

first: Astrid

last: Kassner

first: Ramona

last: Cebulla

first: Sebastian

last: Schulte-Eistrup

first: Michiel

last: Morshuis

first: Daniela

last: Röfe

first: Aly

last: El Banayosy

first: Reiner

last: Körfer

first: Hendrik

last: Milting


title: Evolution of neuronal and endothelial transcriptomes in primates

city: Leipzig

first: Thomas

last: Giger

address: Deutscher Platz 6

department: Evolutionary Genetics

institute: Max-Planck-Institute of Evolutionary Anthropology

summary:
Neurons and endothelial cells were identified by immunohistochemistry in human brains, isolated by laser-capture-microdissection and used to find genes preferentially expressed in the two cell types.

Keywords: cell type comparison

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Laser capture microdissection was used to isolate approximately 1000 neurons and endothelial cells from 6 (for neurons) and 7 (for endothelial cells) human post mortem brain samples. RNA was isolated and amplified (3 linear amplifications) and genome wide expression was measured. This allowed the identification of genes that are differentially expressed between neurons and endothelial cells in the human brain.


title: Expression data from Snail over-expressing non-small cell lung cancer cell lines

status: Public on May 21 2010

city: Los Angeles

first: Jane

last: Yanagawa

department: Medicine

institute: UCLA

summary:
Snail is a zinc-finger transcription factor best known for its ability to down-regulate E-cadherin. Its established significance in embryology and organogenesis has been expanded to include a role in the tumor progression of a number of human cancers. In addition to E-cadherin, it has more recently been associated with the down-regulation and up-regulation of a number of other genes that affect important malignant phenotypes.
After establishing the presence of up-regulated Snail in human non-small cell lung cancer specimens, we used microarrays to detail the global programme of gene expression in non-small cell lung cancer cell lines stably transduced to over-express Snail as compared to vector control cell lines.

overall_design: Non-small cell lung cancer cell lines (H441, H292, H1437) were stably transduced with a retroviral vector to over-express Snail. Elevated Snail and a corresponding down-regulation of E-cadherin was verified in the Snail over-expressing cell lines as compared to vector control cell lines by Western analysis. RNA extraction was performed and samples submitted to the UCLA Clinical Microarray Core for hybridization to Affymetrix arrays.

first: Tonya

middle: C

last: Walser

first: Jie

last: Luo

first: Steven

middle: M

last: Dubinett


title: 786-O and 786-VHL in EMCV study

status: Public on Jun 10 2010

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary: 786-0 is a cell line derived from a clear cell renal carcinoma.  Previous studies have shown that the 786-O cell line harbors an inactivating mutation in the von-Hippel Lindau (VHL) gene.  Mutations  in the VHL gene occur in the majority of sporadic clear cell renal cell.  To determine how inactivation of the VHL affects cellular functions, we created a derivative of 786-0, which we call 786-VHL in which a functional allele of VHL has been introduced back into the 786-O cell line.

overall_design: The renal cell carcinoma cell line 786-0, which harbors a mutated allele of VHL, was compared to a cell line derived from 786-0, termed 786-VHL, that contains a functional allele of VHL.  Genes whose expression characteristics were dependent on functional VHL were identified.

last: Ohh


title: Effective Targeting of Quiescent Chronic Myelogenous Leukemia Stem Cells by Histone Deacetylase Inhibitors in Combination with Imatinib Mesylate

city: Duarte

first: Ravi

last: Bhatia

address: 1500 E Duarte Road

department: Hematopoietic Stem Cell and Leukemia Research

institute: City of Hope Beckman Research Institute

summary: We investigated the ability of HDAC inhibitors (HDACi) to target CML stem cells. Treatment with HDACi combined with IM effectively induced apoptosis in quiescent CML progenitors resistant to elimination by IM alone, and eliminated CML stem cells capable of engrafting immunodeficient mice. In vivo administration of HDACi with IM markedly diminished LSC in a transgenic mouse model of CML. The interaction of IM and HDACi inhibited genes regulating hematopoietic stem cell maintenance and survival. HDACi treatment represents a novel and effective strategy to target LSC in CML patients receiving tyrosine kinase inhibitors.

overall_design: CML CD34+CD38- cells were selected using flow cytometry sorting and treated with IM, LBH and the combination of IM and LBH or cultured without exposure to drugs (controls) for 24 hours (n=3 each). Total RNA from 5000 cells was extracted using the RNeasy kit (Qiagen), amplified and labeled using GeneChip Two-Cycle Target Labeling and Control Reagents (Affymetrix, Santa Clara, CA). 15 µg cRNA from each sample was hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays. Microarray data analyses were performed using R (version 2.9) with genomic analysis packages from Bioconductor (version 2.4). Expression data were normalized using the robust multiarray average (RMA) algorithm, with background adjustment, quantile normalization and median polish summarization. Probesets with low expression levels or low variability across samples were filtered. For genes with multiple probesets, the gene level expression was set to be the median of the probesets. Linear regression was used to model the gene expression with the consideration of 2x2 factorial design and matched samples. Differentially expressed genes were identified by calculating empirical Bayes moderated t-statistic, and p-values were adjusted by FDR using the “LIMMA” package.  Gene Set Enrichment Analyses (GSEA) was performed using GSEA software version 2.04 [http://www.broadinstitute.org/gsea/] to detect enrichment of predetermined gene sets using t-scores and gene sets  in C2 (curated gene sets) category from the Molecular Signature Database (MsigDB). Gene sets representing common functional categories were categorized and grouped. We also analyzed enrichment of gene sets with common transcription factor binding sites (586 sets) from MsigDB.

first: Sierra

last: Li

first: Keh-Dong

last: Shiang


title: Identification of EP4 as a Potential Target for the Treatment of Castration-Resistant Prostate Cancer Using a Novel Xenograft Model

status: Public on May 19 2010

city: Kyoto

first: Naoki

last: Terada

address: 54, Shogoinkawahara-cho, Sakyo-ku

department: Department of Urology

country: Japan

institute: Naoki Terada

summary: More effective therapeutic approaches for castration-resistant prostate cancer (CRPC) are urgently needed, thus reinforcing the need to understand how prostate tumors progress to castration resistance. We have established a novel mouse xenograft model of prostate cancer, KUCaP-2, which expresses the wild-type androgen receptor (AR) and which produces the prostate-specific antigen (PSA). In this model, tumors regress soon after castration, but then reproducibly restore their ability to proliferate after 1 to 2 months without AR mutation, mimicking the clinical behavior of CRPC. In the present study, we used this model to identify novel therapeutic targets for CRPC. Evaluating tumor tissues at various stages by gene expression profiling, we discovered that the prostaglandin E receptor EP4 subtype (EP4) was significantly upregulated during progression to castration resistance. Immunohistochemical results of human prostate cancer tissues confirmed that EP4 expression was higher in CRPC compared with hormone-naïve prostate cancer. Ectopic overexpression of EP4 in LNCaP cells (LNCaP-EP4 cells) drove proliferation and PSA production in the absence of androgen supplementation in vitro and in vivo. Androgen-independent proliferation of LNCaP-EP4 cells was suppressed when AR expression was attenuated by RNA interference. Treatment of LNCaP-EP4 cells with a specific EP4 antagonist, ONO-AE3-208, decreased intracellular cyclic AMP levels, suppressed PSA production in vitro, and inhibited castration-resistant growth of LNCaP-EP4 or KUCaP-2 tumors in vivo. Our findings reveal that EP4 overexpression, via AR activation, supports an important mechanism for castration-resistant progression of prostate cancer. Furthermore, they prompt further evaluation of EP4 antagonists as a novel therapeutic modality to treat CRPC.

overall_design: 4 samples in each group: androgen-dependent growth (AD), castration-induced regression nadir (ND), and castration-resistant regrowth (CR) stages

first: Yosuke

last: Shimizu

first: Tomomi

last: Kamba

first: Takahiro

last: Inoue

first: Atsushi

last: Maeno

first: Takashi

last: Kobayashi

first: Eijiro

last: Nakamura

first: Toshiyuki

last: Kamoto

first: Toshiya

last: Kanaji

first: Takayuki

last: Maruyama

first: Yoshiki

last: Mikami

first: Yoshinobu

last: Toda

last: Matsuoka

first: Yasushi

last: Okuno

first: Gozoh

last: Tsujimot

first: Shuh

last: Narumiya

first: Osamu

last: Ogawa


title: Interfering with Proximal TLR4 to NF-kappaB Signal Transduction in Human Monocytes

city: Bethesda

first: Jennifer

last: Barb

state: MD

address: 12 South Drive Bldg 12A Room 2001

department: DCB

institute: NIH

summary: Carbon monoxide (CO) is an endogenous messenger that suppresses inflammation, modulates apoptosis and promotes vascular remodeling. Here, microarrays were employed to globally characterize the CO (250 ppm) suppression of early (1 h) LPS-induced inflammation in human monocytic THP-1 cells. CO suppressed 79 of 101 immediate-early genes induced by LPS; 19% (15/79) were transcription factors and most others were cytokines, chemokines and immune response genes. The prototypic effects of CO on transcription and protein production occurred early but decreased rapidly. CO activated p38 MAPK, ERK1/2 and Akt and caused an early and transitory delay in LPS-induced JNK activation. However, selective inhibitors of these kinases failed to block CO suppression of LPS-induced IL-1beta, an inflammation marker. Of CO-suppressed genes, 81% (64/79) were found to have promoters with putative NF-kappaB binding sites. CO was subsequently shown to block LPS-induced phosphorylation and degradation of IkappaBalpha in human monocytes, thereby inhibiting NF-kappaB signal transduction. CO broadly suppresses the initial inflammatory response of human monocytes to LPS by reshaping proximal events in TLR4 signal transduction such as stress kinase responses and early NF-kappaB activation. These rapid, but transient effects of CO may have therapeutic applications in acute pulmonary and vascular injury.

overall_design: The microarrays were performed on THP-1 cells, a human monocytic cell line. Cells were treated with or without LPS (1 µg/ml) in presence or absence of carbon monoxide (250 ppm) for 1 h. Total RNA was isolated, reverse transcribed, labeled and hybridized to oligonucleotide microarrays.

first: Peter

last: Munson

first: Robert

middle: L

last: Danner

first: Maneesha

last: Chhikara

first: Gabriela

last: Ferreyra


title: A novel method of amplification of FFPET derived-RNA enables accurate disease classification with microarrays

status: Public on May 18 2010

city: Pleasanton

first: Rachel

last: Li

address: 4300 Hacienda Dr.

institute: Roche

summary:
A new method for amplification and labeling of RNA is assessed that permits gene expression microarray analysis of formalin-fixed paraffin embedded tissue (i.e. FFPET) samples.
Valid biological data was obtained using gene expression microarrays of diffuse large B-cell lymphoma (i.e. DLBCL) FFPET samples.

overall_design:
We examined 59 matched DLBCL patient samples, FFPET and fresh/frozen. The samples contained both prognostic subgroups of DLBCL: germinal center B-cell (i.e. GCB) and activated B-cell (ABC).
Fresh/frozen (i.e. FF) samples were amplified by both the traditional Eberwine oligo-dT method and a new method described herein. The matching FFPET samples were also amplified using the new method.
This study is a collaboration among Roche Molecular Diagnostics, British Columbia Cancer Agency, National Cancer Institute and Nugen Technologies (the maker of the WT-Ovation FFPET reagents).

first: Mickey

middle: P

last: Williams

first: Rui

first: Nathalie

last: Johnson

first: George

last: Wright

first: Joe-Don

last: Heath

first: Randy

middle: D

last: Gascoyne


title: The Polycomb Group Protein Bmi-1 is essential for the growth of Multiple Myeloma cells

city: Cambridge

first: Michael

last: Morrissey

state: MA

address: 250 Massachusetts Ave

department: Oncology

institute: Novartis Institutes for Biomedical Research

summary: The RPMI-8226 human multiple myeloma cell line was stably infected with either a validated shRNA against BMI1 or a control shRNA.  RNA was prepared from these lines, +/- doxycycline induction and at various time points post-induction.  Samples were hybridized on the Affymetrix U133plus2 human genome expression microarray.

first: Zainab

last: Jagani


title: Mitochondria regulate the unfolded protein response leading to cancer cell survival under glucose deprivation conditions

status: Public on May 14 2010

city: Tokyo

first: Naomi

last: Haga

address: 3-10-6 Ariake, Koto-ku

department: Cancer Chemotherapy Center

institute: Japanese Foundation for Cancer Research

summary:
Cancer cells consume large amounts of glucose because of their specific metabolic pathway. However, cancer cells exist in tumor tissue where glucose is insufficient. To survive, cancer cells likely have the mechanism to elude their glucose addiction. Here we show that functional mitochondria are essential if cancer cells are to avoid glucose addiction.
Cancer cells with dysfunctional mitochondria, such as mitochondrial DNA-deficient rho0 cells and electron transport chain blocker-treated cells, were highly sensitive to glucose deprivation. Our data demonstrated that this sensitization was caused by failure of the unfolded protein response (UPR), an adaptive response mediated by the endoplasmic reticulum (ER). This study suggests a link between mitochondria and the ER during the UPR under glucose deprivation conditions and that mitochondria govern cell fate, not only through ATP production and apoptosis regulation but also through modulating the UPR for cell survival.

overall_design:
Human cancer cell lines (HT-1080, HT-29, and mtDNA-deficient cells derived from these cell lines) were selected for RNA extraction and hybridization on Affymetrix microarrays. We examined the unfolded protein response (UPR), an adaptive response mediated by the endoplasmic reticulum (ER), of cancer cells under stress conditions.

Abbreviations List:
AA, antimycin A; Bu, buformin; Met, metformin; Phen, phenformin; Rot, rotenone; VST, versipelostatin; TM, tunicamycin; 2DG, 2-deoxyglucose; GS, glucose starvation. Capital S (_S) indicates the supernatant of sample including floating cells.

first: Sakae

last: Saito

first: Aki

last: Furuno

first: Takashi

last: Tsuruo

first: Akihiro

last: Tomida


title: Expression data from human HeLa cells exposed to interferon gamma for 2, 4, and 6 hours

status: Public on May 11 2010

city: Berlin

first: Elke

last: Krueger

address: Monbijoustr. 2

department: Institute of Biochemistry

institute: Charité Universitaetsmedizin Berlin

summary:
The ubiquitin proteasome system (UPS) is known to possess important regulatory functions in the immune response. To gain a better and first comprehensive insight into the mechanisms of remodelling of  UPS related gene expression inresponse to interferon-gamma, we undertook a comparative gene expression profiling during interferon-gamma stimulation at very early time points.

Keywords: time course

overall_design: Human HeLa cells were harvested at 3 different periods of time following stimulation with interferon-gamma for RNA extraction and hybridization on Affymetrix microarrays.

first: Ulrike

last: Seifert

last: Krüger


title: Human Insulin Resistance and Thiazolidinedione-Mediated Insulin Sensitization

status: Public on May 17 2010

city: La Jolla

first: Gene

last: Hsiao

address: 9500 Gilman Dr

institute: UCSD

summary:
Cellular and tissue defects associated with insulin resistance are coincident with transcriptional abnormalities and are improved after insulin sensitization with thiazolidinedione (TZD) PPARγ ligands.
We transcriptionally profiled 364 biopsies gathered from 72 human subjects harvested before and after hyperinsulinemic-euglycemic clamp, at baseline and after three-month TZD treatment. Subjects range from insulin-sensitive to insulin-resistant. Insulin resistant subjects responded to TZD treatment with varied improvements in insulin sensitivity, thus they were ranked by their degree of TZD response to define responder and non-responder subgroups.

overall_design:
Skeletal muscle biopsies were obtained from vastus lateralis before and after hyperinsulinemic-euglycemic clamp, at baseline and after three-month TZD treatment. Adipose tissue biopsies were obtained from abdominal subcutaneous before clamp, at baseline and after three-month TZD treatment.

*** CEL files not provided for 40 Samples. ***

first: Dorothy

last: Sears

first: Albert

first: Joseph

middle: G

last: Yu

first: C

middle: H

last: Courtney

first: Jachelle

last: Ofrecio

first: Justin

last: Chapman

first: Shankar

last: Subramaniam


title: Differential Expression of NF-kB target genes in MALT lymphoma with and without chromosome translocation: insights into molecular mechanism

status: Public on May 31 2010

city: London

first: Rifat

last: Hamoudi

address: 67-73 Riding House Street

department: Surgery

country: United Kingdom

institute: University College London

summary: MALT lymphoma is characterized by t(11;18)(q21;q21)/API2-MALT1, t(1;14)(p22;q32)/BCL10-IGH and t(14;18)(q32;q21)/IGH-MALT1, which commonly activate the NF-κB pathway. Gastric MALT lymphomas harboring such translocation do not respond to H. pylori eradication, while those without translocation can be cured by antibiotics. To understand the molecular mechanism of these different MALT lymphoma subgroups, we performed gene expression profiling analysis of 24 MALT lymphomas (15 translocation-positive, 9 translocation-negative). Gene set enrichment analysis (GSEA) of the NF-κB target genes and 4394 additional gene sets covering various cellular pathways, biological processes and molecular functions showed that translocation-positive MALT lymphomas are characterized by an enhanced expression of NF-κB target genes, particularly TLR6, CCR2, CD69 and BCL2, while translocation-negative cases were featured by active inflammatory and immune responses, such as IL8, CD86, CD28 and ICOS. Separate analyses of the genes differentially expressed between translocation-positive and negative cases and measurement of gene ontology term in these differentially expressed genes by hypergeometric test reinforced the above findings by GSEA. Finally, expression of TLR6, in the presence of TLR2, enhanced both API2-MALT1 and BCL10 mediated NF-κB activation in vitro. Our findings provide novel insights into the molecular mechanism of MALT lymphomas with and without translocation, potentially explaining their different clinical behaviors.

overall_design: This study compares MALT with other lymphomas namely follicular and mantle cell lymphomas, and investigates the molecular mechanisms of the lymphomagenesis between translocation positive versus negative MALT lymphoma cases in order to derive the pathways leading to MALT lymphoma pathogenesis using GSEA, GO, dynamic pathway analysis as well as other bioinformatics analysis. Samples were run on the Affymetrix HG-U133A and HG-U133 plus2 GeneChips.

first: Alex

last: Appert

first: Hongtao

last: Ye

first: Agnes

last: Ruskone-Fourmestraux

first: Berthold

last: Streubel

first: Andreas

last: Chott

first: Markus

last: Raderer

first: Liping

last: Gong

first: Iwona

last: Wlodarska

first: Christiane

last: De Wolf-Peeters

first: Kenneth

last: MacLennan

first: Laurence

last: de Leval

first: Peter

last: Isaacson

first: Ming

middle: Q

last: Du


title: Expression Data from Escherichia coli grown to mid-log growth phase.

status: Public on May 07 2010

city: Laurel

first: Isha

last: Patel

address: 8301 Muirkirk Rd,

department: Division of Molecular Biology

summary:
B-methylthiolation of the Escherichia coli Ribosomal Protein S12 Regulates Anaerobic Gene Expression.
B-methylthiolation is a unique post-translational modification (PTM) that maps to a conserved Asp 88 of the bacterial ribosomal protein S12.  This modification is phylogenetically conserved in several bacteria yet has not been identified on other proteins.

overall_design: We use microarrays to delineate the association of prokaryotic ribosomal protein PTM to the regulation of genes.

first: Christopher

middle: A

last: Elkins

first: Michael

last: Strader


title: CD62L expression identifies a unique subset of polyfunctional CD56dim NK cells: Groups 1-3

status: Public on May 12 2010

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

summary: Human Natural Killer (NK) cells comprise two main subsets, CD56bright and CD56dim cells, that differ in function, phenotype and tissue localization. To further dissect the heterogeneity of CD56dim cells, we have performed transcriptome analysis and functional ex vivo characterization of human NK cell subsets according to the expression of markers related to differentiation, migration or competence. Here, we show for the first time that the ability to respond to cytokines or to activating receptors is mutually exclusive in almost all NK cells with the exception of CD56dim CD62L+ cells. Indeed, only these cells combine the ability to produce interferon (IFN)-gamma after cytokines and proliferate in vivo during viral infection with the capacity to kill and produce cytokines upon engagement of activating receptors. Therefore, CD56dim CD62L+ cells represent a unique subset of polyfunctional NK cells. Ex vivo analysis of their function, phenotype, telomere length, frequencies during ageing as well as transfer experiments of NK cell subsets into immunodeficient mice suggest that CD56dim CD62L+ cells represent an intermediate stage of NK cell maturation, which after restimulation can accomplish multiple tasks and further develop into terminally differentiated effectors.

overall_design: Gene expression profiles of FACSAria sorted CD3- CD56bright CD62L+, CD3- CD56dim CD62L+ and CD3- CD56dim CD62L- NK cells from human peripheral blood of three donors were compared using Affymetrix GeneChip Human Genome HG-U133_Plus_2. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the three groups to the GeneChip arrays. Group1: CD3- CD56bright CD62L+,.Group2: CD3- CD56dim CD62L+, Group3: CD3- CD56dim CD62L-. Lists of differentially regulated genes were created using High Performance Chip Data Analysis (HPCDA) with Bioretis database (http://www.bioretis-analysis.de). Worldwide data sharing is possible via Bioretis, please ask the authors.

first: Kerstin

last: Juelke

first: Monica

last: Killig

first: Merlin

last: Luetke-Eversloh

first: Eliana

last: Parente

first: Joachim

last: Grün

first: Barbara

last: Morandi

first: Guido

last: Ferlazzo

last: Thiel

first: Isabela

last: Schmitt-Knosalla

first: Chiara

last: Romagnani


title: Expression data from undifferentiated human embryonic stem cells (hESC) and Day 3.5 mesodermal progenitor (CD326neg CD56+) population

status: Public on May 06 2010

first: Denis

last: Evseenko

address: 1450 Biggy St

department: Orthopaedic Surgery

institute: University of Southern  California

summary:
Our understanding of how mesodermal tissue is formed, has been limited by the absence of specific and reliable markers of early mesoderm commitment. We report that mesoderm commitment from human embryonic stem cells (hESC) is initiated by Epithelial to Mesenchymal transition (EMT) as shown by gene expression profiling and by reciprocal changes in expression of the cell surface proteins, EpCAM/CD326 and NCAM/CD56. Molecular and functional assays reveal that CD326negCD56+ cells, generated from hESC in the presence of activin A, BMP4, VEGF and FGF2, represent a novel, multi-potent mesoderm-committed progenitor population. CD326negCD56+ progenitors are unique in their ability to generate all mesodermal lineages including hematopoietic, endothelial, mesenchymal (bone, cartilage, fat, fibroblast), smooth muscle and cardiomyocytes, while lacking the pluripotency of hESC. CD326negCD56+ cells are the precursors of previously reported, more lineage-restricted mesodermal progenitors. These findings present a novel approach to study how germ layer specification is regulated, and offer a unique target for tissue engineering.
We used microarrays to compare gene expression profile of early mesodermal progenitors with undifferentiated hESC (H9 line).

overall_design: Mesoderm induction from hESC was initiatiated with combination of morphogens and growth factors including activin A, bone morphogenic protein 4, basic fibroblast growth factor and vascular endothelial growth factor. Proposed mesodermal progenitor population was isolated by FACS on day 3.5 of culture based on the presence of CD56 expression and the absenbce of CD326 expression.

first: Gay

last: Crooks


title: Expression data for early stage NSCLC

city: Rotterdam

first: Sjaak

last: Philipsen

address: Dr. Molewaterplein 50

department: Cell Biology

country: Netherlands

institute: Erasmus MC

summary: We identified a tumor signature of 5 genes that aggregates the 156 tumor and normal samples into the expected groups. We also identified a histology signature of 75 genes, which classifies the samples in the major histological subtypes of NSCLC. A prognostic signature of 17 genes showed the best association with post-surgery survival time. The performance of the signatures was validated using a patient cohort of similar size

overall_design: A genome-wide gene expression analysis was performed on a cohort of 91 patients. We used 91 tumor- and 65 adjacent normal lung tissue samples. We defined sets of predictor genes (probe sets) with the expression profiles. The power of predictor genes was evaluated using an independent cohort of 96 non-small cell lung cancer- and 6 normal lung samples


title: Expression data from 22 Pancreatic Cancer Cell Lines

status: Public on May 05 2010

city: grand rapids

first: brian

last: haab

address: 333 bostwick avenue NE

department: lab of cancer immunodiagnostics

institute: van andel institute

summary: We used microarrays to analyze the global expression patterns for 22 commercially available pancreatic cancer cell lines

overall_design: 22 pancreatic cancer cell lines were grown to 80% confluence in DMEM/FBS/PenStrep media and then harvested for total RNA

first: Emily

last: Euger

first: Jeremy

last: Miller

first: Kevin

last: Maupin

first: Craig

last: Webb


title: Hypoxia modulates EWS-FLI1 transcriptional signature and enhances malignant properties of Ewing’s tumor cells in vitro

status: Public on May 26 2010

city: Vienna

first: Maximilian

last: Kauer

address: Zimmermannplatz 10

department: Molecular Biology

country: Austria

institute: CCRI, St.Anna Children Cancer Research Institute

summary:
Hypoxia is an important condition in the tumor cell microenvironment and approximately 1-1.5% of the genome is transcriptionally responsive to hypoxia with hypoxia-inducible factor-1 (HIF-1) as a major mediator of transcriptional activation. Tumor hypoxia is associated with a more aggressive phenotype of many cancers in adults, but data on pediatric tumors are scarce. By immunohistochemical analysis, HIF-1α expression was readily detectable in 18/28 primary Ewing´s sarcoma family tumors (ESFT), a group of highly malignant bone-associated tumors in children and young adults, which encouraged us to study the effect of hypoxia on ESFT cell lines in vitro.
Many tumors are profoundly hypoxic and multiple studies have demonstrated that hypoxic tumors have a poorer prognosis than non-hypoxic tumors. The cellular adaptations of cancer cells to hypoxia have been shown to profoundly influence transcriptional regulation. Intriguingly, we found that EWS-FLI1 protein expression, which characterizes ESFT, is up-regulated by hypoxia in a HIF-1α-dependent manner. Hypoxia modulated the EWS-FLI1 transcriptional signature relative to normoxic conditions. Both synergistic as well as antagonistic transcriptional effects of EWS-FLI1 and of hypoxia were observed. Consistent with alterations in the expression of metastasis related genes, hypoxia stimulated the invasiveness and soft-agar colony formation of ESFT cells in vitro. Our data represents the first transcriptome analysis of hypoxic ESFT cells and identifies hypoxia as an important microenvironmental factor modulating EWS-FLI1 expression and target gene activity with far-reaching consequences for the malignant properties of ESFT.

Keywords: Consequences on gene expression of hypoxic condition created by exposure of cells to 1% oxygen in a hypoxia chamber.

overall_design: We analysed the consequences of hypoxia on gene expression in two ESFT cell lines (SK-N-MC, TC252) grown as multicellular spheroids and as adherent monolayers.

first: Dave

middle: N

last: Aryee

first: Stephan

last: Niedan

first: Raphaela

last: Schwentner

first: Idriss

last: Bennani-Baiti

first: Jozef

last: Ban

first: Michael

last: Kreppel

first: Karin

last: Muehlbacher

first: Chris

last: Poremba

first: Reinhard

last: Kofler

first: Heinrich

last: Kovar

first: Robert

last: Walker

first: Paul

last: Meltzer


title: A gene expression signature identifies two prognostic subgroups of basal breast cancer

city: Marseille

first: Pascal

last: FINETTI

state: BdR

address: 232 Bd Ste Marguerite

department: Centre de cancérologie de Marseille

country: France

institute: Institut Paoli-Calmettes

summary: Medullary breast cancers (MBC) display a basal profile, but a favorable prognosis. We hypothesized that a previously published 368-gene expression signature associated with MBC might serve to define a prognostic classifier in basal cancers. We collected public gene expression and histoclinical data of 2145 invasive early breast adenocarcinomas. We developed a Support Vector Machine (SVM) classifier based on this 368-gene list in a learning set, and tested its predictive performances in an independent validation set. Then, we assessed its prognostic value and that of six prognostic signatures for disease-free survival (DFS) in the remaining 2034 samples. The SVM model accurately classified all MBC samples in the learning and validation sets. A total of 466 cases were basal across other sets. The SVM classifier separated them into two subgroups, subgroup 1 (resembling MBC) and subgroup 2 (not resembling MBC). Subgroup 1 exhibited 71% 5-year DFS, whereas subgroup 2 exhibited 50% (p=9.93E-05). The classifier outperformed the classical prognostic variables in multivariate analysis, conferring lesser risk for relapse in subgroup 1 (HR=0.52, p=3.9E-04). This prognostic value was specific to the basal subtype, in which none of the other prognostic signatures was informative.

overall_design: The IPC series contained frozen tumor samples obtained from 266 early breast cancer patients who underwent initial surgery in our institution between 1992 and 2004. They included 227 cases previously reported {Finetti, 2008 #1758} and 39 additional cases, all similarly profiled using Affymetrix U133 Plus 2.0 human oligonucleotide microarrays as previously described {Finetti, 2008 #1758}. The study was approved by the IPC review board, and informed consent was available for each case. Gene expression data of 266 BCs  were quantified by using whole-genome DNA microarrays (HG-U133 plus 2.0, Affymetrix).

first: R

last: Sabatier

first: P

last: Finetti

first: N

last: Cervera

first: E

last: Lambaudie

first: B

last: Esterni

last: Mamessier

first: A

last: Tallet

first: C

last: Chabannon

first: JM

last: Extra

first: J

last: Jacquemier

last: Viens

first: D

last: Birnbaum

first: F

last: Bertucci


title: Array-based gene expression in neuroblastic tumors

city: Helsinki

first: Maija

middle: K

last: Wolf

address: Biomedicum Helsinki 2U, Tukholmankatu 8,

country: Finland

institute: Institute for Molecular Medicine Finland (FIMM)

summary:
Title: Array-based gene expression, CGH and tissue data define a 12q24 gain in neuroblastic tumors with prognostic implication.
Background: Neuroblastoma has successfully served as a model system for the identification of neuroectoderm-derived oncogenes. However, in spite of various efforts, only a few clinically useful prognostic markers have been found. Here, we present a framework, which integrates DNA, RNA and tissue data to identify and prioritize genetic events that represent clinically relevant new therapeutic targets and prognostic biomarkers for neuroblastoma.
Methods: A single-gene resolution aCGH profiling was integrated with microarray-based gene expression profiling data to distinguish genetic copy number alterations that were strongly associated with transcriptional changes in two neuroblastoma cell lines. FISH analysis using a hotspot tumour tissue microarray of 37 paraffin-embedded neuroblastoma samples and in silico data mining for gene expression information obtained from previously published studies including up to 445 healthy nervous system samples and 123 neuroblastoma samples were used to evaluate the clinical significance and transcriptional consequences of the detected alterations and to identify subsequently activated gene(s).
Results: In addition to the anticipated high-level amplification and subsequent overexpression of MYCN, MEIS1, CDK4 and MDM2 oncogenes, the aCGH analysis revealed numerous other genetic alterations, including microamplifications at 2p and 12q24.11. Most interestingly, we identified and investigated the clinical relevance of a previously poorly characterized amplicon at 12q24.31. FISH analysis showed low-level gain of 12q24.31 in 14 of 33 (42%) neuroblastomas. Patients with the low-level gain had an intermediate prognosis in comparison to patients with MYCN amplification (poor prognosis) and to those with no MYCN amplification or 12q24.31 gain (good prognosis) (P = 0.001). Using the in silico data mining approach, we identified elevated expression of five genes located at the 12q24.31 amplicon in neuroblastoma (DIABLO, ZCCHC8, RSRC2, KNTC1 and MPHOSPH9). Among these, DIABLO showed the strongest activation suggesting a putative role in neuroblastoma progression.
Conclusions: The presented systematic and rapid framework, which integrates aCGH, gene expression and tissue data to obtain novel targets and biomarkers for cancer, identified a low-level gain of the 12q24.31 as a potential new biomarker for neuroblastoma progression. Furthermore, results of in silico data mining suggest a new neuroblastoma target gene, DIABLO, within this region, whose functional and therapeutic role remains to be elucidated in follow-up studies.

overall_design:
High-resolution aCGH was utilized to identify novel genetic alterations in two neuroblastoma cell lines, NGP and IMR-32. Through the integration of gene copy number and gene expression data, the impact of copy number changes on expression levels was determined. Fluorescence in situ hybridization (FISH) on a tissue microarray (TMA) format was used to assess the clinical significance of the identified copy number increase at 12q24.31 in neuroblastoma patients. Finally, we used in silico data mining of publicly available transcriptomics data, to evaluate the transcriptional consequences of the detected 12q24.31 alteration and to identify subsequently activated gene(s).

Here, gene expression analysis of the NGP and IMR-32 cell lines was performed. A pooled sample of 16 cancer cell lines was used as reference.

first: Miikka

last: Korja

first: Ritva

last: Karhu

first: Henrik

last: Edgren

first: Sami

last: Kilpinen

first: Kalle

last: Ojala

first: Spyro

last: Mousses

first: Anne

last: Kallioniemi

first: Hannu

last: Haapasalo


title: Gene expression profiles of E10.5 ureteric trunk cells isolated from Hoxb7-GFP transgenic mice using FACS. (GUDMAP Series ID: 40)

status: Public on May 01 2010

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

institute: IGMM MRC Human Genetics Unit

summary: The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing kidney.  The central thesis is straightforward. The combination of fluorescent activated cell sorting (FACS) plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing kidney. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene in FACS isolated components of the developing kidney. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone.

overall_design: HoxB7-GFP transgenic mice were utilized to isolate the ureteric duct cells from E10.5 embryonic  kidneys.  The ureteric duct cells were isolated from embryos using microdissection, trypsin treatment and FACS.   The RNA was isolated from purified ureteric duct cells and the gene expression profiles were determined by microarrays.

first: Steve

last: Potter

first: Eric

last: Brunskill


title: Array-based gene expression, CGH and tissue data define a 12q24 gain in neuroblastic tumors with prognostic implication

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: The Effect of Hepatitis C Virus Infection on Host Gene Expression

first: Michael

middle: J

last: McGarvey

address: Norfolk Place

institute: Imperial College London

summary: Hepatitis C Virus is a leading cause of chronic liver disease. The identification and characterisation of key host cellular factors that play a role in the HCV replication cycle is important for the understanding of disease pathogenesis and the identification of novel anti-viral therapeutic targets. Gene expression profiling of HCV infected Huh7 cells by microarray analysis was performed to identify host cellular genes that are transcriptionally regulated by infection. The expression of host genes involved in cellular defence mechanisms (apoptosis, proliferation and anti-oxidant responses), cellular metabolism (lipid and protein metabolism) and intracellular transport (vesicle trafficking and cytoskeleton regulation) was significantly altered by HCV infection. The gene expression patterns identified provide insight into the potential mechanisms that contribute to HCV associated pathogenesis. These include an increase in pro-inflammatory and pro-apoptotic signalling and a decrease in the anti-oxidant response pathways of the infected cell.

overall_design: 5x105 Huh7 cells were seeded in 25cm2 culture flasks and infected in triplicate either with the genotype 2a HCV clone, JFH-1 at a multiplicity of infection (MOI) of 3 or mock infected with an equal volume of concentrated conditioned growth medium. At 6, 12, 18, 24 and 48 hours post-infection, cellular RNA was extracted using TRIzol reagent (Invitrogen). Trizol lysates were shipped to Expression Analysis (NC, USA) where RNA was purified, quality tested using the Agilent Bioanalyser and hybridised onto Human U133 Plus 2.0 Affymetrix microarray chips for fluorescence data acquisition. In summary, a total of 30 RNA samples were analysed including 3x mock infected samples taken at 6, 12, 18, 24 and 48 hours post-treatment and 3x JFH-1 infected samples taken at 6, 12, 18, 24 and 48 hours post-infection.  Two samples (Mock_6hrs_1 and JFH-1_6hrs_1) did not pass our data quality control measures and were therefore excluded from the statistical analysis.

first: Samantha

last: Blackham

first: Andrew

last: Baillie

first: Fadel

last: Al-Hababi

first: Katja

last: Remlinger

first: Shihyun

last: You

first: Robert

last: Hamatake


title: Expression data for serum stimulation of human primary fibroblasts

city: Baltimore

first: Karen

last: Zeller

address: 720 Rutland Ave

institute: Johns Hopkins School of Medicine

summary: We used microarrays to profile gene expression changes following growth factor stimulation of primary human fibroblasts.

overall_design: We serum starved (0.1% serum) fibroblasts for 48 hrs and restimulated with 10% serum for 0, 2, 4, 6 and 8 hrs.  Total RNA was extracted from 2 independent biological replicas for each time point and hybridized to expression arrays.

middle: I

first: Chi

middle: V

last: Dang


title: Transcriptomic analysis of pluripotent stem cells

city: Montpellier

first: John

last: De Vos

address: 80 av. Augustin Fliche

department: Institute for Research in Biotherapy

institute: University Hospital of Montpellier


title: ZMYM2/FGFR1, BCR/FGFR1 or BCR/ABL1 in human cord blood CD34+ cells reveals similar but distinct gene expression profiles

city: Lund

first: Helena

last: Ågerstam

address: Lund University Hospital

institute: Lund University

summary: The 8p11 myeloproliferative syndrome (EMS), also referred to as the stem cell leukemia/lymphoma syndrome, is a chronic myeloproliferative disorder that rapidly progresses into an acute leukemia. Molecularly, EMS is characterized by fusion of various partner genes to the FGFR1 gene, resulting in constitutive activation of the tyrosine kinase activity within FGFR1. The two most common fusion genes in human EMS are ZMYM2/FGFR1 (previously known as ZNF198/FGFR1) and BCR/FGFR1. To study the transcriptional programs becoming deregulated by the FGFR1 fusion genes, global gene expression analysis on human CD34+ cord blood cells expressing either of the fusion oncogenes ZMYM2/FGFR1 and BCR/FGFR1 was performed. As a reference gene we also included the more studied BCR/ABL1 fusion oncogene associated with chronic myeloid leukemia. We found that the 3 different fusion oncogenes had in common the upregulation of several genes involved in the JAK/STAT signalling pathway and also other sets of genes. However, the gene expression profiles were not identical, suggesting that both the tyrosine kinase containing gene and the partner gene would affect the transcription of downstream target genes.

overall_design: Bicistronic retroviral murine stem cell virus (MSCV) vectors expressing ZMYM2/FGFR1, BCR/FGFR1or P210 BCR/ABL1 and GFP were used. The MIG control vector expressed GFP only. Two days post transfection of human CD34+ umbilical cord blood cells, GFP-sorted cells were collected in three biological replicates and RNA was isolated immediately. RNA extraction and data analysis were performed as described (Ågerstam et al., submitted). In total, 12 samples were hybridized and scanned.

first: Marcus

last: Järås

first: Anna

last: Andersson

first: Petra

last: Johnels

first: Carin

last: Lassen

first: David

last: Gisselsson

first: Tor

last: Olofsson

first: Johan

last: Richter

first: Xiaolong

last: Fan

first: Mats

last: Ehinger

first: Thoas

last: Fioretos


title: Gene expression profiles of E10.5 ureteric tip cells isolated from Hoxb7-GFP transgenic mice using FACS. (GUDMAP Series ID: 39)

first: GUDMAP

last: Developers

overall_design: HoxB7-GFP transgenic mice were utilized to isolate the ureteric bud cells  from E10.5 embryonic kidneys.  The ureteric bud cells were isolated from embryos using microdissection, trypsin treatment and FACS.   The RNA was isolated from purified ureteric bud cells and the gene expression profiles were determined by microarrays.

first: Steve

last: Potter

first: Eric

last: Brunskill


title: Stat5-regulated gene expression in human prostate cancer cells

status: Public on Apr 30 2010

city: Philadelphia

first: Marja

last: Nevalainen

state: PA

department: Cancer Biology

institute: Thomas Jefferson University

summary:
Transcription factor Stat5 is constitutively active in human prostate cancer but not in normal prostate epithelium. Stat5 activation is associated with prostate cancer lesions of high histological grades, and is present in the majority of castration-resistant recurrent human prostate cancers. The molecular mechnisms underlying constitutive activation of Stat5 in primary and recurrent human prostate cancer are currently unclear.
We used microarrays to detail gene expression regulated by Stat5 in human prostate cancer cells.

overall_design: DU145 human prostate cancer cells were transfected with Stat5a/b siRNA or scramble siRNA as control. After 48 h, the cells were harvested and total RNA was prepared for Affymetrix microarrays.

first: Lei

last: Guo

first: Paraskevi

last: Vogiatzi

first: Martin

last: Puhr

first: Ayush

last: Dagvadorj

first: Jacqueline

last: Lutz

first: Amy

last: Ryder

first: Sanker

last: Addya

first: Paolo

last: Fortina

first: Carlton

last: Cooper

first: Benjamin

last: Leiby

first: Abhijit

last: Dasgupta

first: Terry

last: Hyslop

first: Lukas

last: Bubendorf

first: Kalle

last: Alanen

first: Tuomas

last: Mirtti

middle: T


title: Generation of pluripotent stem cells

first: John

last: De Vos

summary: Pluripotent stem cells, which are capable to generate any cell type of the human body, such as human embryonic stem cells (hESC) or human induced pluripotent stem cells (hiPS) are a very promising source of cells for regenerative medicine. However, the genesis, the in vitro amplification and the differentiation of these cells still need improvement before clinical use. This study aimed to improve our knowledge on these critical steps in pluripotent stem cell generation. We derived new hESC lines, generated hiPS and compared these cell types with human foreskin fibroblasts and partially reprogrammed fibroblasts.

overall_design:
We included in the overall study hESC, hiPS, human foreskin fibroblasts and partially reprogrammed fibroblasts. Here, hESC lines derived from embryos were hybridized on U133 Plus 2.0 GeneChips (Affymetrix). All samples were normalized using the MAS5 (GCOS 1.2) algorithm, using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.
Human pluripotent stem cells were compared with somatic samples and partially reprogrammed cells.

last: DE VOS

first: Said

last: ASSOU

first: Marilyne

last: DIJON

first: Cécile

last: MONZO

first: Laure

last: NADAL

first: Véronique

last: PANTESCO

first: Samir

last: HAMAMAH


title: Dys and Eureprogramming

summary: Pluripotent stem cells have the potential to differentiate in vitro in many, if not all, functional cell types. Induced pluripotent stem cells (iPS) have recently emerged as a reproducible model of pluripotent stem cells that can be generated from post-natal tissues. To understand this process at the transcriptome level, we generated iPS cell lines, partially reprogrammed cell lines and compared their transcriptome with that of the partental human foreskin fibroblasts and human embryonic stem cell lines.

overall_design: Four categories of samples, comprising human foreskin fibroblasts, fully reprogrammed iPS cell lines, partially reprogrammed iPS cell lines and human embryonic stem cell lines were compared using Significance Analysis of Microarrays (SAM). These data were also compared to a compendium of differentiated human samples and a pluripotency classifier was computed.

last: Dijon-Grinand

first: Aude

last: Couturier

last: Assou

last: Hamamah


title: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: IGF2BP data

status: Public on Apr 29 2010

city: New York

first: Markus

last: Hafner

state: NY

address: 1230 York Ave, Box 186

department: Laboratory of RNA Molecular Biology

institute: The Rockefeller University

summary: To test the influence of IGF2BPs on the stability of their interacting mRNAs, as reported previously for some targets (Yisraeli, 2005), we simultaneously depleted all three IGF2BP family members using siRNAs and compared the cellular RNA from knockdown and mock-transfected cells on microarrays. The levels of transcripts identified by PAR-CLIP decreased in IGF2BP-depleted cells, indicating that IGF2BP proteins stabilize their target mRNAs. Moreover, transcripts that yielded clusters with the highest T to C mutation frequency were most destabilized (Figure 4G of PMID 20371350), indicating that the ranking criterion that we derived based on the analysis of PUM2 and QKI data generalizes to other RNA-binding proteins (RBPs).

overall_design: The RBPs IGF2BP1-3 were depleted by siRNAs and the expression level was compared to mock-transfected HEK 293 cells.

first: Thomas

last: Tuschl


title: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: miRNA inhibition data

summary: To obtain evidence that Argonaute (AGO) crosslink-centered regions (CCRs) indeed contain functional miRNA-binding sites, we blocked 25 of the most abundant miRNAs in HEK 293 cells (Figure 5C of PMID 20371350) by transfection of a cocktail of 2'-O-methyl-modified antisense oligoribonucleotides and monitored the changes in mRNA stability by microarrays (Figure 7A of PMID 20371350). Consistent with previous studies of individual miRNAs (Grimson et al., 2007), the magnitude of the destabilization effects of transcripts containing at least one CCR depended on the length of the seed-complementary region and dropped from 9-mer to 8-mer to 7-mer to 6-mer matches (Figure 7B of PMID 20371350). We did not find evidence for significant destabilization of transcripts that only contained imperfectly paired seed regions.

overall_design: The top 25 expressed miRNAs expressed in HEK 293 cells were inhibited by transfection of a cocktail of 25 antisense 2'-O-Me oligoribonucleotides and the gene expression was compared to mock-transfected cells.


title: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: QKI data

summary: To assess whether the transcripts identified by PAR-CLIP are regulated by the RNA-binding protein (RBP) Quaking (QKI), we analyzed the mRNA levels of mock-transfected and QKI-specific siRNA-transfected cells with microarrays. Transcripts crosslinked to QKI were significantly upregulated upon siRNA transfection, indicating that QKI negatively regulates bound mRNAs (Figure 3H of PMID 20371350), consistent with previous reports of QKI being a repressor.

overall_design: The RBP QKI was depleted by siRNAs and the expression level was compared to mock-transfected HEK 293 cells.


title: Frizzled 4 regulates stemness and invasiveness of migrating glioma cells established by serial in vivo intracranial transplantation

city: Seoul

first: Woong Yang

last: Park

address: 28 Yongondong, Chongnogu

department: Biochemistry and Molecular Biology

country: South Korea

institute: Seoul National University

summary: One of the most detrimental hallmarks of glioblastoma multiforme (GBM) is cellular invasiveness, considered a potential cause of tumor recurrence. Infiltrated GBM cells are difficult to completely eradicate surgically and with local therapeutic modalities. Although much effort has focused on understanding the various mechanisms controlling GBM invasiveness, the nature of the invasiveness remains poorly characterized. Here, we established a highly invasive glioma cell line (U87MGR2/R3 cells) and a non-invasive cell line (U87MGL2/L3 cells) from U87MG glioma cells following four rounds of serial in vivo intracranial transplantation. Compared to U87MGL2/L3 cells, U87MGR2/R3 cells were highly invasive and had glioma stem cell-like properties. Microarray analysis showed that apoptosis-inducing genes (caspase3 and PDCD4) were downregulated, whereas several cancer stem cell-relevant genes (Wnt10A, Frizzled 4, and CD44) were upregulated in U87MGR2/R3 cells compared to U87MGL2/L3 cells. U87MGR2/R3 cells were resistant to anticancer drug-induced cell death, which was partially due to downregulation of caspase3 and PDCD4. U87MGR2/R3 cells retained activated Wnt/β-catenin signaling through Frizzled 4, which was sufficient to control neurosphere formation. In addition, Frizzled 4 promoted expression of the epithelial to mesenchymal transition regulator, SNAI1, and acquisition of a mesenchymal phenotype. Taken together, our results indicate that Frizzled 4 may be a member of the Wnt signaling family that governs both stemness and invasiveness of glioma stem cells, and may be a major cause of GBM recurrence and poor prognosis.

overall_design: We established a highly invasive glioma cell line (U87MGR2/R3 cells) and a non-invasive cell line (U87MGL2/L3 cells) from U87MG glioma cells following four rounds of serial in vivo intracranial transplantation to characterize the mRNA expression profile of highly invasive glioma cells compared to non-invasive/parental glioma cell lines.

first: Woong-Yang

first: Do-Hyun

last: Nam

first: Hyunggee

last: Kim


title: Nascent mRNA profiling of LPS-stimulated mouse macrophages

status: Public on Apr 25 2010

city: Erlangen

first: Roland

last: Lang

address: Wasserturmstr. 3-5

institute: University Hospital Erlangen

summary:
To identify transcriptionally regulated genes in primary mouse macrophages stimulated with LPS with high sensitivity, we isolated nascent RNA following metabolic labelling with 4-thiouridine during the last 35 min before cell harvest, as recently described (Dolken et al. 2008 RNA 14:1959-72). Microarray analyses of nascent RNA identified substantially more probe sets as up-regulated after 45 min of LPS stimulation than parallel analyses of total cellular RNA. In contrast, 4.5 h after stimulation, up-regulated genes in total and nascent RNA largely overlapped. This approach therefore allowed a much more sensitive detection of early changes in transcription, and the respective genes are likely to be direct targets of LPS-regulated transcription factors.

Keywords: Effect of LPS stimulation; comparison of changes in expression of total versus nascent RNA; timecourse

overall_design: Two completely independent experiments were performed. Macrophages were stimulated with 100 ng/ml LPS for 45 or 270 minutes. Thiouridine pulsing was done in last 35 minutes before harvest. Total RNA was isolated. Nascent RNA was subsequently purified.

first: Katja

last: Frühauf

first: Lars

last: Dölken


title: B-Cell Gene Signature with Massive Intrahepatic Production of Antibodies to Hepatitis B Core Antigen in HBV-Associated Acute Liver Failure

status: Public on Apr 26 2010

city: Bethesda

first: Patrizia

last: Farci

address: 50 South Drive

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

summary: Hepatitis B virus (HBV)-associated acute liver failure (ALF) is a dramatic clinical syndrome due to a sudden loss of hepatic cells leading to multiorgan failure. The mechanisms whereby HBV induces ALF are unknown. We used gene expression profiling to establish a molecular definition of hepatitis B virus (HBV)-associated ALF. Two patients who underwent liver transplantation for HBV-associated ALF were studied. Gene expression profiling was performed on 8 liver specimens obtained from the two patients with ALF (4 samples per liver) and individual liver specimens from 8 liver donors and normal livers from 11 patients who underwent resection for angioma. Statistical analyses were used to identify the signature genes of HBV-associated ALF. Multivariate permutation analysis identified 1,368 transcripts that were differentially expressed in ALF; 709 were up-regulated and 659 down-regulated. The most represented up-regulated transcripts were those involved in the immune response, whereas the most abundant down-regulated transcripts were those involved in metabolism and hepatic synthesis. ALF was characterized by overriding B-cell signature comprising genes related to mature B cells and plasma cells with abundant polyclonal expression of immunoglobulin genes.  By contrast, there was a limited T-cell signature and up-regulation of several inhibitors of T-cell activation. Immunohistochemical analysis confirmed the prominent B-cell signature showing diffuse liver infiltration by plasma blasts and plasma cells with strong cytoplasmic staining for IgM and IgG, associated with a significant deposition of complement factors. Using phage display technology, we demonstrated that the molecular target of the massive intrahepatic antibody response is the hepatitis B core antigen (HBcAg). These data suggest that the humoral immunity may exert a primary role in the pathogenesis of HBV-associated ALF.

overall_design: Liver samples were obtained from explanted livers of two patients with HBV-associated ALF (4 samples per liver), 8 normal liver donors and 11 patients who underwent resection for angioma. Gene expression profiling was used to establish a molecular definition of ALF.

first: Giacomo

last: Diaz

first: Zhaochun

last: Chen

first: Sugantha

last: Govindarajan

first: Ashley

last: Tice

first: Liane

last: Agulto

first: Stefania

last: Pittaluga

first: Denali

last: Boon

first: Claro

last: Yu

first: Ronald

middle: E

last: Engle

first: Mark

last: Haas

first: Richard

last: Simon

first: Robert

last: Purcell

first: Fausto

last: Zamboni


title: Expression analysis of Reh cells after transfection with shRNA targeting CBFA2T3 and/or constitutively active IKKβ(EE)

status: Public on Apr 23 2010

city: Berlin

first: Karl

last: Koechert

address: Robert-Roessle-Str. 10

institute: Max-Delbrueck-Centre for Molecular Medicine

summary: Genome-wide gene expression analysis of Reh cells following transfection with shRNA targeting CBFA2T3, constitutively active IKKβ(EE), or both in combination.

overall_design: Affymetrix U133 Plus 2.0 oligonucleotide arrays were hybridized to determine the gene expression profile of acute lymphoblastic leukemia-derived Reh cells following transfection with i) control shRNA construct, ii) shRNA construct targeting CBFA2T3, iii) a constitutively active variant of the IkB kinase β (IKKβ(EE)), or iv) shRNA targeting CBFA2T3 in combination with IKKβ(EE). All hybridizations were done in biological duplicates.

first: Björn

last: Lamprecht

first: Stephan

last: Mathas

first: Martin

last: Janz

last: Köchert

first: Michael

last: Hummel


title: Gene expression pattern in CXCR4+ and CXCR4- subpopulation of breast cancer cells

status: Public on Apr 20 2010

city: Indianapolis

first: Harikrishna

last: Nakshatri

state: IN

address: 980 W. Walnut St. R3C218C

department: General Surgery

institute: Indiana University School of Medicine

summary: The goal of this study was to identify signaling molecules downstream of CXCR4 in breast cancer cells. For this purpose, we sorted CXCR4-positive and CXCR4-negative cells from MDA-MB-231 breast cancer cell line by flow cytometry and performed microarrays analysis.

overall_design: Three sets of samples, each in quadrupicate, were analyzed. These include CXCR4-positive subpopulation, CXCR4-positive subpopulation treated with SDF-1 (ligand for CXCR4, also called CXCL12) for one hour and CXCR4-negative subpopulation.


title: Transcriptome Analysis and Molecular Signature of Human Retinal Pigment Epithelium

status: Public on Apr 15 2010

first: Jennifer

last: Barb

address: 12 South Drive Bldg 12A Room 2001

department: DCB

institute: NIH

summary: The retinal pigment epithelium (RPE) is a polarized cell layer that is critical for photoreceptor function and survival. It’s unique relationship to the photoreceptors and its specific physiology makes the RPE a critical determinant of human vision.  Therefore we performed global expression profiling of native and cultured human fetal and adult RPE and determined a unique set of highly-expressed genes (called the “signature” set) by comparing the observed RPE gene profiles to the Novartis expression database (SymAtlas: http://wombat.gnf.org/index.html) of 78 tissues.

overall_design: A comparative analysis of transcriptomes from human fetal and adult RPE, primary cultures and commonly-used cell lines was performed. Using selection criteria of at least 10-fold higher expression in each of three RPE preparations, we identified 154 RPE signature genes, which were validated by qRT-PCR analysis in RPE and in an independent set of 11 tissues.

first: Natalia

last: Strunnikova

first: Peter

last: Munson

first: Sheldon

last: Miller


title: Human embryonic stem cells with biological and epigenetic characteristics similar to those of mouse ESCs

status: Public on Apr 22 2010

city: Cambridge

first: Albert

middle: W

last: Cheng

address: Room 453, 9 Cambridge Center

institute: Whitehead Institute

summary: Human and mouse embryonic stem cells (ESCs) are derived from blastocyst stage embryos but have very different biological properties, and molecular analyses suggest that the pluripotent state of human ESCs isolated so far corresponds to that of mouse derived epiblast stem cells (EpiSCs). Here we rewire the identity of conventional human ESCs into a more immature state that extensively shares defining features with pluripotent mouse ESCs. This was achieved by exogenous induction of Oct4, Klf4 and Klf2 factors combined with LIF and inhibitors of glycogen synthase kinase 3 (GSK3) and mitogen-activated protein kinase (ERK) pathway.  Forskolin, a protein kinase A pathway agonist that induces Klf4 and Klf2 expression, can transiently substitute for the requirement for ectopib transgene expression. In contrast to conventional human ESCs, these epigenetically converted cells have growth properties, an X chromosome activation state (XaXa), a gene expression profile, and signaling pathway dependence that are highly similar to that of mouse ESCs. Finally, the same growth conditions allow the derivation of human induced pluripotent stem (iPS) cells with similar properties as mouse iPS cells. The generation of “naïve” human ESCs will allow the molecular dissection of a previously undefined pluripotent state in humans, and may open up new opportunities for patient-specific, disease-relevant research.

overall_design: RNA of different naive and primed hESCs and hiPSCs cell lines were hybridized to get a genome-wide gene expression profile of these cells

first: Jacob

last: Hanna

first: Krishanu

last: Saha

first: Jongpil

last: Kim

first: Frank

last: Soldner

first: John

last: Cassady

first: Christopher

last: Lengner

first: Bryce

last: Carey

first: Rudolf

last: Jaenisch


title: Expression data from RECK-overexpressing HT1080 fibrosarcoma cells

status: Public on Apr 14 2010

city: wako

first: Satoshi

last: Takagi

state: Saitama

department: ASI

institute: RIKEN

summary: RECK, a glycosylphosphatidylinositol-anchored glycoprotein, inhibits the enzymatic activities of some matrix metalloproteinases (MMP), thereby suppressing tumor cell metastasis; however, the detailed mechanism is still obscure. In this study, we compared the gene expression profiles between mock- and RECK-transfected HT1080 cells.

overall_design: Three established cell lines were selected for RNA extraction and hybridization on Affymetrix microarrays: (1) mock-transfected HT1080 cells, designated as HT1080-Zeo, (2) RECK-overexpressing HT1080 cells, designated as HT1080-RECK, and (3) RECK/4NQ-overexpressing HT1080 cells (in which four N-glycosylation asparagine residues of RECK (Asn86, Asn200, Asn297, and Asn352) were replaced with glutamine residues), designated as HT1080-RECK/4NQ.


title: Effects of sidA and AHL on EHEC virulence

status: Public on Apr 09 2010

first: David

last: Rasko

address: 801 W. Baltimore Street, Room 619

department: Istitute for Genome Sciences/Microbiology and Immunology

institute: University of Maryland School of Medicine

summary: A study on the effects of an sdiA mutant and the AHL molecule on the virulence of EHEC

overall_design: Comparison of wild type E. coli 8624 with and without AHL to and E. coli 8624 sdiA mutant with and without AHL to determine the effects of each factor on gene expression

last: Hughes

first: Vanessa

last: Sperandio


city: Jerusalem

first: Uri

last: Ben-David

address: Givat-Ram

department: Genetics

country: Israel

institute: Hebrew University

summary: Due to their somatic cell origin, human induced pluripotent stem cells (HiPSCs) are assumed to carry a normal diploid genome, and adaptive chromosomal aberrations have not been fully evaluated. Here, we analyzed the chromosomal integrity of 66 HiPSC and 38 human embryonic stem cell (HESC) samples from 18 different studies by global gene expression meta-analysis. We report identification of a substantial number of cell lines carrying full and partial chromosomal aberrations, half of which were validated at the DNA level. Several aberrations resulted from culture adaptation, and others are suspected to originate from the parent somatic cell. Our classification revealed a third type of aneuploidy already evident in early passage HiPSCs, suggesting considerable selective pressure during the reprogramming process. The analysis indicated high incidence of chromosome 12 duplications, resulting in significant enrichment for cell cycle related genes. Such aneuploidy may limit the differentiation capacity and increase the tumorigenicity of HiPSCs.

overall_design:
Expression data from undifferentiated human induced pluripotent stem cells
total RNA was isolated from undifferentiated induced pluripotent stem cells grown in standard HESC growth conditions on mouse embryonic fibroblast feeder layer.

first: Yoav

last: Mayshar

first: Juan-Carlos

last: Biancotti

first: William

last: Lowry

first: Nissim

last: Benvenisty


title: Inhibition of transglutaminase 2 mitigates transcriptional dysregulation in models of Huntington disease

status: Public on Apr 08 2010

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: Huntington Disease (HD) is a dominantly inherited, relentlessly progressive neurodegenerative disease. Caused by a polyglutamine expansion in the mutant huntingtin protein (mhtt), HD pathogenesis impairs function in the cerebral cortex and in medium spiny neurons of the striatum  and involves transcriptional dysregulation of a number of genes. Of these genes, silencing of  genes related to mitochondrial function is believed to explain metabolic dysfunction in rodent  models of HD. Here we show that transglutaminase 2 (TG2), which is upregulated in HD,  exacerbates transcriptional dysregulation by acting as a selective corepressor of nuclear genes.  TG2 inhibition by RNA knockdown, genetic deletion, or administration of a novel irreversible,  peptide-based TG2 inhibitor (ZDON) de-repressed two established regulators of mitochondrial  function, PGC-1α and cytochrome c in a cell model of HD. TG2 must localize to non-coding or  coding regions of these mitochondrial metabolic genes to silence their transcription. As expected,  TG2 inhibition reversed the increased susceptibility of HD mouse cells and human HD  myoblasts to the mitochondrial toxin, 3-nitroproprionic acid (3-NP); however, protection  mediated by TG2 inhibition was not associated with improved mitochondrial bioenergetics.  Indeed, an unbiased array analysis indicated that TG2 inhibition leads to normalization of not  only mitochondrial genes but of nearly 40% of genes that are dysregulated in HD mouse striatal  neurons, including chaperone and histone genes. Indeed, TG2 interacts directly with Histone 3 in  the nucleus. Moreover, TG2 inhibition significantly attenuated photoreceptor degeneration in a  Drosophila model of HD and protected mouse HD striatal neurons (YAC128) from NMDA-  induced toxicity. Altogether these findings demonstrate that TG2 mediates its deleterious effects  in HD by contributing to broad transcriptional dysregulation of genes representing many cellular  functions. These studies define a novel HDAC-independent epigenetic strategy for treating  neurodegeneration.

overall_design: To evaluate the effect of TG2 inhibition (treatment with ZDON, Boc-DON, CystamineA, and Control) in striatal cell lines from a transgenic model of Huntington disease (Q111) vs. control (Q7). One sample (WT.boc.3, 4068264015_G) failed the QC test and was excluded from further analyses.

first: Stephen

last: McConoughey

first: Manuela

last: Basso

first: Zoya

last: Niatsetskaya

first: Sama

middle: F

last: Sleiman

first: Natalia

last: Smirnova

first: Brett

middle: C

last: Langley

first: Arthur

last: Cooper

first: Marc

last: Antonyak

first: Rick

last: Cerione

first: Bo

last: Li

first: Anatoly

last: Starkov

first: Rajnish

last: Chaturvedi

first: M

last: Beal

first: Daniel

last: Geschwind

first: Hoon

last: Ryu

first: Xia

first: Siiri

last: Lismaa

first: Judit

last: Pallos

first: Ralf

last: Pasternack

first: Martin

last: Hils

first: Jing

last: Fan

first: Lynn

last: Raymond

first: J

last: Marsh

first: Leslie

last: Thompson

first: Rajiv

middle: R

last: Ratan


title: Differential gene expression in mouse retina related to regional differences in vulnerability to hyperoxia

city: Canberra

first: Yuan

last: Zhu

state: ACT

address: Bldg 46, RSBS, ANU

department: Research School of Biology

country: Australia

institute: Australian National University

summary: Purpose: In the C57BL/6J mouse retina, hyperoxia-induced degeneration of photoreceptors shows strong regional variation, beginning at a locus ~0.5mm inferior to the optic disc. To identify gene expression differences that might underlie this variability in vulnerability, we have used microarray techniques to describe regional (superior-inferior) variations in gene expression in the retina.

overall_design: Methods: Young adult C57BL/6J mice raised in dim cyclic illumination (12h 5lux, 12h darkness) were exposed to hyperoxia (75% oxygen for 2w). Retinas were collected from hyperoxia-exposed and control animals without fixation, and divided into superior and inferior halves. RNA was extracted from each sample, purified and hybridised to mouse 1.0 ST arrays (Affymetrix). The consistency of the microarray results was assessed with quantitative PCR for selected genes. Expression data were analysed to identify genes and ncRNAs whose differential expression between superior and inferior retina could be associated with relative vulnerability to hyperoxia.

first: Kaiman

last: Peng

first: Stephen

last: Ohms


title: Genes regulated by YAP in normal breast cell line and breast cancer cell lines

city: london

first: Subham

last: Basu

address: Charterhouse Square

department: Molecular Oncology Unit

institute: Cancer Research UK

summary:
Frequent loss of heterozygosity (LOH) at 11q22-23 in breast cancer strongly suggests that this region contains a tumor suppressor gene, yet to be identified. We and others have shown Yes-associated protein (YAP), which is located at 11q22.2, transactivates the p53 family member p73 upon DNA damage, suggesting a tumor suppressive function for YAP. Our analysis of breast tumor tissues by immunohistochemistry (IHC) showed loss of YAP protein expression in great portion of breast cancers.
We used microarray to look at the targte genes regulated by YAP in normal breast luminal cell and breast cancer cell lines.
Keywords: gene knock down

overall_design: We generated stable cell lines by introducing control vector(pRS-IRES-GFP/pmig) or YAP shRNA(pRS-IRES-GFP-YAP/pmig-YAP) in a normal breast luminal cell line 1089 luminal and breast cancer cell lines MDA MB231. RAN was extracted and hybridized on Affymetrix microarrays.We looked for new target genes regulated by YAP in normal breast luminal cell and breast cancer cell lines.

first: Ming

last: Yuan

first: Deborah

last: Holliday

first: Claude

last: Chelala

first: Tomohiko

last: Harada

first: Rathi

last: Gangeswaran

first: Safia

last: Ali

first: Charles

last: Mein

first: Nick

last: Lemoine

first: Louise

last: Jones


title: cdr2 siRNA knockdown during passage through mitosis: HeLa cells, Rat1 wild type and c-myc null cells

status: Public on Apr 07 2010

first: Kevin

last: O'Donovan

address: 1230 York Avenue

institute: Rockefeller Univeristy

summary:
[Hela cells]: We performed cdr2 knockdown with a pool of 4 cdr2-specific siRNAs to test whether cdr2 may regulate c-myc target genes as cells passage through mitosis.

[Rat1a wild type and myc null cells]: We performed cdr2 knockdown using a pool of 4 cdr2-specific siRNAs  to test whether cdr2 may regulate c-myc target genes as cells passage through mitosis.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design:
[HeLa cells]: Cells were transfected with control or cdr2 siRNAs and then cells were synchronized in mitosis using a sequential thymidine/nocodazole block.  Cells were subsequently released from nocodazole block and after 3 hours RNA was harvested for microarray analysis
[Rat-1 wild type (TGR) and c-myc null (15.19) cells]: Cells were transfected with control or cdr2 siRNAs and then cells were synchronized in mitosis using a sequential thymidine/nocodazole block.  Cells were then subsequently released from nocodazole block and after 3 hours RNA was harvested for microarray analysis

first: Robert

middle: B

last: Darnell


title: Expression data from undifferentiated and induced human pluripotent stem cells

first: Uri

last: Ben-David

summary:
Due to their somatic cell origin, human induced pluripotent stem cells (HiPSCs) are assumed to carry a normal diploid genome, and adaptive chromosomal aberrations have not been fully evaluated. Here, we analyzed the chromosomal integrity of 66 HiPSC and 38 human embryonic stem cell (HESC) samples from 18 different studies by global gene expression meta-analysis. We report identification of a substantial number of cell lines carrying full and partial chromosomal aberrations, half of which were validated at the DNA level. Several aberrations resulted from culture adaptation, and others are suspected to originate from the parent somatic cell. Our classification revealed a third type of aneuploidy already evident in early passage HiPSCs, suggesting considerable selective pressure during the reprogramming process. The analysis indicated high incidence of chromosome 12 duplications, resulting in significant enrichment for cell cycle related genes. Such aneuploidy may limit the differentiation capacity and increase the tumorigenicity of HiPSCs.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Mechanism of biphasic effects of alcohol on gene expression

status: Public on Apr 05 2010

city: New Orleans

first: guoshon

last: wang

state: LA

address: 533 Bolivar St.

department: Gene Therapy

institute: LSUHSC

summary: the molecular mechanisms for the biphasic effect of alcohol are not fully understood. The goal of the study is to identify genes that are differentially expressed following alcohol exposure of 50mM and 100mM ethanol for 24 hours.

overall_design: Primary human bronchial airway epithelia (NHBE) cells were obtained from a commercial source and cultured on millicel-pcf membrane insert at air liquid interface.  Cells were allowed to differentiate for a specified time, and treated with different concentrations (0, 50mM, 100mM) of ethanol for 24 hours. The cells are derived from three different lots. Total RNA was extracted using the RNeasy Mini Kit, quantified by NanoDrop and evaluated by the Bioanalyzer. Samples with RIN value of 9.8 were used for analysis using the human U133 plus 2.0 chips. Three replicates were used for each condition. Cel files were imported into GeneSrping GX 7.3 and preprocessed using the RMA method and per gene normalization was applied using the median values of the untreated, control samples (0 Ethanol). Genes were filtered using the volcano plot set at p<= 0.01 and 2-fold or greater, by comparing the untreated to 50 mM ethanol and untreated to 100 mM ethanol.

first: Guoshun

last: Wang

first: Marla

last: Gomez-Perez

first: Anand

last: Viswanathan

first: Sammeta

last: Raju

first: Richard

last: Painter

first: Patrick

last: Byrne

first: Doan

last: Nguyen

first: Gregory

last: Bagby

first: Steve

last: Nelson


title: Expression profiling analysis of mouse E10.5 Magoh mutant brain cortices

status: Public on Apr 04 2010

first: Christopher

last: Pan

address: Rm 5228, Bldg 50, South Dr.

department: NHGRI

summary:
Human brain structure and size requires regulated division of neural stem cells (NSCs).  NSCs undergo precise divisions to self-renew and to produce intermediate neural progenitors (INPs) and neurons. The factors that regulate NSC divisions remain poorly understood, as do mechanistic explanations of how aberrant NSC division causes reduced brain size, as seen in microcephaly. Here we demonstrate that Magoh, a component of the core exon junction complex (EJC) that binds spliced RNA, controls cerebral cortical size by regulating NSC division. Magoh haploinsufficiency causes microcephaly due to INP depletion, neuronal apoptosis, and improper mitotic spindle orientation. Defective mitosis underlies these phenotypes as depletion of EJC components disrupts mitotic spindle integrity, chromosome number and genomic stability. We show that an essential function of Magoh is to regulate expression of the human microcephaly protein, LIS1, and that Lis1 addition rescues neurogenesis defects caused by Magoh knockdown, thus providing a genetic explanation for the microcephaly. This study uncovers new requirements for the EJC in brain development, NSC maintenance, mitosis and chromosome stability, thus implicating this complex in the pathogenesis of microcephaly.
Mouse embryonic cortices were used for expression analysis

overall_design: 5 biological replicates each of control (C57BL/6) and Magoh mutant brains were analyzed

first: Debra

middle: L

last: Silver

first: Dawn

last: Watkins-Chow

first: Karisa

last: Schreck

first: Tarran

last: Pierfelice

first: Denise

middle: M

last: Larson

first: Anthony

last: Burnetti

first: Hung-Jiun

last: Liaw

first: Kyungjae

last: Myung

last: Walsh

first: Nicholas

last: Gaiano

first: William

last: Pavan


title: NRG1/ERBB3 signaling in melanocyte Melan-Ink4a cells

summary: Neuregulin (NRG) signaling through the receptor tyrosine kinase, ERBB3, is required for embryonic development, and dysregulated signaling has been associated with cancer progression. Here, we show that NRG1/ERBB3 signaling inhibits melanocyte (MC) maturation and promotes undifferentiated, migratory and proliferative cellular characteristics. Embryonic analyses demonstrated that initial MC specification and distribution were not dependent on ERBB3 signaling. However NRG1/ERBB3 signaling was both necessary and sufficient to inhibit differentiation of later stages of MC development in culture. Analysis of tissue arrays of human melanoma samples suggests that ERBB3 signaling may also contribute to metastatic progression of melanoma as ERBB3 was phosphorylated in primary tumors compared with nevi or metastatic lesions. Neuregulin 1-treated MCs demonstrated increased proliferation and invasion and altered morphology concomitant with decreased levels of differentiation genes, increased levels of proliferation genes and altered levels of melanoma progression and metastases genes. ERBB3 activation in primary melanomas suggests that NRG1/ERBB3 signaling may contribute to the progression of melanoma from benign nevi to malignancies. We propose that targeting ERBB3 activation and downstream genes identified in this study may provide novel therapeutic interventions for malignant melanoma.

overall_design: Gene expression changes are compared between Melan-Ink4a cells stimulated with NRG1-b1 (NRG1) for 21 days and NRG1 untreated Melan-INK4a cells in triplicate using Affymetrix Mouse GeneChip 1.0 ST chip .

first: Kristina

last: Buac

first: Mai

last: Xu

first: Julie

last: Cronin

first: Ashani

last: Weeraratna

first: Stephen

last: Hewitt


title: The role of qseE, qseF and qseG in the regulation of EHEC virulence

city: Baltimore

first: David

last: Rasko

summary: Escherichia coli 8624 and the isogenic mutants in qseE, qseF and qseG are compared to determine the role that each of the genes play in regulation of the transcriptome.  These results are verified by qRT-PCR and reveal the important role of this three-component signaling system.

overall_design: Escherichia coli 8624 and the isogenic mutants in qseE, qseF and qseG are compared to determine the role that each of the genes play in regulation of the transcriptome. Single Affymetrix E. coli 2.0 Arrays are used as a starting point for this study and these results are further verified by qRT-PCR.

first: Nicola

last: Reading

first: Vanessa

last: Sperandio


title: role of miR-146a on Jurkat T cells

status: Public on Apr 03 2010

city: Chongqing

first: jingyi

last: li

address: Gao Tan Yan

department: institute of immunology

country: China

institute: the third millitary medical university

summary: screenning the differentially expressed genes of Jurkat-FF3, Jurkat-miR146a, Jurkat-miR146a-sponge cell lines.

overall_design: To investigate the role of  miR-146a on Jurkat T cells, we screened the differentially expressed genes of Jurkat-FF3 (as control), Jurkat-miR146a (as miR-146a overexpression cell line), Jurkat-miR146a-sponge (as miR-146a knock down cell line).


title: Expression data from human adipose stem cells expanded in allogeneic human serum and fetal bovine serum

status: Public on Apr 01 2010

city: Tampere

first: Kaisa-Leena

last: Aho

address: Korkeakoulunkatu 10

department: Department of Signal Processing

institute: Tampere University of Technology

summary:
Human adipose stem cells (ASCs) have been shown, in pre-clinical studies, to have therapeutic applicability in diverse fields, but a standard expansion method for clinical applications remains yet to be established. Isolated ASCs are typically expanded in medium containing fetal bovine serum (FBS). However, sera and other animal-derived culture reagents stage numerous safety issues in clinical therapy, including possible infections and severe immune reactions. By expanding the ASCs in medium containing human serum (HS), the problem can be eliminated.
To define how allogeneic HS performs in ASC expansion compared to FBS, we used microarrays to explore differences in gene expression between human adipose stem cells expanded in allogeneic human serum and fetal bovine serum.

overall_design: Adipose stem cells from 5 human donors were cultured in two media containing either 1) 10 % fetal bovine serum or 2) 15 % allogeneic human serum, and collected for RNA extraction and hybridization to 10 Affymetrix arrays. This experiment represents a paired design since cells of each donor were cultured in both conditions.

first: Bettina

last: Lindroos

first: Hannu

last: Kuokkanen

first: Sari

last: Raty

first: Heini

last: Huhtala

first: Riina

last: Lemponen

first: Olli

last: Yli-Harja

first: Riitta

last: Suuronen

first: Susanna

last: Miettinen