title: Kupffer cells promote hepatic steatosis via interleukin-1beta-dependent suppression of peroxisome proliferator-activated receptor alpha activity.

status: Public on Oct 18 2011

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: Kupffer cells have been implicated in the pathogenesis of various liver diseases. However, their involvement in metabolic disorders of the liver, including fatty liver disease, remains unclear. The present study sought to determine the impact of Kupffer cells on hepatic triglyceride storage and to explore the possible mechanisms involved. To that end, C57Bl/6 mice rendered obese and steatotic by chronic high-fat feeding were treated for 1 week with clodronate liposomes, which cause depletion of Kupffer cells. Loss of expression of marker genes Cd68, F4/80, and Clec4f, and loss of Cd68 immunostaining verified almost complete removal of Kupffer cells from the liver. Also, expression of complement components C1, the chemokine (C-C motif) ligand 6 (Ccl6), and cytokines interleukin-15 (IL-15) and IL-1beta were markedly reduced. Importantly, Kupffer cell depletion significantly decreased liver triglyceride and glucosylceramide levels concurrent with increased expression of genes involved in fatty acid oxidation including peroxisome proliferator-activated receptor alpha (PPARalpha), carnitine palmitoyltransferase 1A (Cpt1alpha), and fatty acid transport protein 2 (Fatp2). Treatment of mice with IL-1beta decreased expression of PPARalpha and its target genes, which was confirmed in primary hepatocytes. Consistent with these data, IL-1beta suppressed human and mouse PPARalpha promoter activity. Suppression of PPARalpha promoter activity was recapitulated by overexpression of nuclear factor kappaB (NF-kappaB) subunit p50 and p65, and was abolished upon deletion of putative NF-kappaB binding sites. Finally, IL-1beta and NF-kappaB interfered with the ability of PPARalpha to activate gene transcription. CONCLUSION: Our data point toward important cross-talk between Kupffer cells and hepatocytes in the regulation of hepatic triglyceride storage. The effect of Kupffer cells on liver triglycerides are at least partially mediated by IL-1beta, which suppresses PPARalpha expression and activity.

overall_design: Expression profiling of livers from mice fed control, low-fat diet diet or high-fat diet for 20weeks with or without knockdown of Kupffer cells.

first: Rinke

last: Stienstra

first: Fredy

last: Saudale

first: Caroline

last: Duval

first: Shohreh

last: Keshtkar

first: Johanna

middle: E

last: Groener

first: Nico

last: van Rooijen

first: Bart

last: Staels

first: Sander

last: Kersten

last: Müller


title: MicroRNA-29 in Aortic Dilation: Implications for Aneurysm Formation

status: Public on Oct 13 2011

city: Amsterdam

first: Reinier

last: Boon

address: De Boelelaan 1117

country: Netherlands

institute: Amsterdam UMC

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

summary: We compared the aorta of 6-weeks-old mice (young) with 18-months-old mice (old). Using the publicly available tools Sylamer and DIANA-mirExTra, we identified an enrichment for miR-29 binding sites in the 3'UTR of genes downregulated in the aged aortas. We subsequently showed that inhibition of miR-29 in aged mice prevented dilation of the aorta.

overall_design: aortas of 6 week old and 18 month old mice

first: Stefanie

last: Dimmeler


title: MicroRNA expression and regulation in human, chimpanzee, and macaque brain

city: shanghai

first: Song

last: Guo

address: 320 Yue Yang Road

country: China

institute: PICB

type: Non-coding RNA profiling by high throughput sequencing

summary: Among other factors, changes in gene expression on the human evolutionary lineage have been suggested to play an important role in the establishment of human-specific phenotypes. However, the molecular mechanisms underlying these expression changes are largely unknown. Here, we have explored the role of microRNA (miRNA) in the regulation of gene expression divergence between adult humans, chimpanzees and rhesus macaques, in two brain regions: prefrontal cortex and cerebellum. Using combination of high-throughput sequencing, miRNA microarrays and Q-PCR, we have shown that up to 11% of the 325 expressed miRNA diverged significantly between humans and chimpanzees and up to 31% - between humans and macaques. Measuring mRNA and protein expression in human and chimpanzee brains, we found a significant inverse relationship between the miRNA and the target genes expression divergence, explaining 2-4% of mRNA and 4-6% of protein expression differences. Notably, miRNA showing human-specific expression localize in neurons and target genes that are involved in neural functions. Enrichment in neural functions, as well as miRNA-driven regulation on the human evolutionary lineage, were further confirmed by experimental validation of predicted miRNA targets in two neuroblastoma cell lines. Finally, we identified a signature of positive selection in the upstream region of one of the five miRNA with human-specific expression, miR-34c-5p. This suggests that miR-34c-5p expression change took place after the split of the human and the Neanderthal lineages and had adaptive significance. Taken together these results indicate that changes in miRNA expression might have contributed to evolution of human cognitive functions.

sample_organism:
Macaca mulatta
Pan troglodytes
Homo sapiens

overall_design:
Human, chimpanzee, and rhesus: mRNA, microRNA, and microRNA sequencing.

Neuroblastoma cell lines: miRNA transfection experiments were conducted on two human-derived neuroblastoma cell lines (SH-SY5Y and SK-N-SH). Briefly, cells were plated in 0.5ml of growth medium, without antibiotics, 24h prior to transfection. miRNA mimics-Lipofectamine 2000 (Invitrogen) complexes were prepared freshly before transfection according to the manufacturer's protocol. SH-SY5Y and SK-N-SH cells were transfected in six-well plates using miRNA mimics-Lipofectamine 2000 with a final oligonucleotide concentration of 10nmol/L. In parallel, negative control transfections with mock oligonucleotides were conducted according to the manufacturer's protocol. For each cell line, transfections with negative control oligonucleotides were carried out in two independent replicates. Cells were harvested after 24h, total RNA were extracted with Trizol reagent (Invitrogen) and further processed and hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays following the manufacturer's instructions. The gene expression levels were determined using rma in the R Affy package.

first: Haiyang

last: Hu

first: Zheng

last: Yan

first: Philipp

last: Khaitovich


title: Highly efficient derivation of ventricular cardiomyocytes from induced pluripotent stem cells with a distinct epigenetic signature

status: Public on Oct 05 2011

city: Boston

first: Kenneth

last: Chien

state: MA

address: Richard B. Simches Research Center, CPZN 3208, 185 Cambridge Street

department: Cardiovascular Research Center

country: USA

institute: Masschusetts General Hospital

summary: The generation of sufficient numbers of mature ventricular myocytes for effective cell-based therapy is a central barrier for cardiac regenerative medicine. Here we demonstrate that induced pluripotent stem cells (iPSCs) can be derived from murine ventricular myocytes, and consistent with other reports of iPSCs derived from various somatic cell types, ventricular myocyte derived iPSCs (ViPSCs) exhibit a markedly higher propensity to differentiate into beating cardiomyocytes as compared to genetically-matched embryonic stem cells (ESCs) or iPSCs derived from tail-tip fibroblasts. Strikingly, ViPSC-derived cardiomyocytes form up to 99% ventricular myocytes suggesting that ventricular myocyte-derived iPSCs may be a viable strategy to generate specific cardiomyocyte subtypes for cell-based therapies. The enhanced ventricular myogenesis in ViPSCs is mediated via increased numbers of cardiovascular progenitors at early stages of differentiation. In order to investigate the mechanism of enhanced ventricular myogenesis from ViPSCs, we performed global gene expression and DNA methylation analysis, which revealed a distinct epigenetic signature that may be involved in specifying the ventricular myocyte fate in pluripotent stem cells.

overall_design: Total RNA was extracted from mouse ES cells,  tail tip fibroblasts (TTFs), ventricular myocytes (VMs), TTF-derived induced pluripotent stem cells (TiPSCs) and VM-derived induced pluripotent stem cells (ViPSCs).  Global gene expression profiling was performed using affymetrix mouse 430 2.0 gene arrays.

first: Huansheng

last: Xu

first: Alex

last: Yi

first: Hao

last: Wu


title: Alterations in gene expression in lacrimal and salivary glands of male NOD mice  due to LTBR-Ig treatment relative to control antibody

status: Public on Oct 07 2011

city: Cambridge

first: Jadwiga

last: Bienkowska

address: 45 Fayette Str Apt 3

institute: BiogenIdec

summary: NOD mice were injected once a week with LTBR-Ig to block the LTBR-pathway, or with control monoclonal antibody MOPC from age 8 to 16 weeks old.  Extraorbital  lacrimal glands or submaxillary glands were dissected and total mRNA prepared.    Each sample was either the combined lacrimals (2) from each mouse or individual  salivary glands.  There were 4 mice in each treatment group. Total mRNA was isolated  and the quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies,  Palo Alto, CA).  Reverse transcription to prepare cDNA was performed using Invitrogen  M-MLV system. The purpose was to determine changes in gene expression in glands  due to blockade of the LTBR-pathway.

overall_design: Differential Gene Expression in NOD mouse lacrimal and salivary glands after LTBR-Ig treatment

first: Roy

last: Fava

first: Jeff

last: Browning


title: Dietary heme stimulates epithelial cell turnover by downregulating feedback inhibitors of proliferation in murine colon (part 2)

status: Public on Oct 02 2011

first: Guido

last: Hooiveld

summary: The risk for colon cancer is associated with nutrition, especially high fat and low calcium diets high in red meat. Red meat contains the iron porphyrin pigment heme, which induces cytotoxicity of the colon contents and epithelial hyperproliferation. Using a mouse model, we showed that heme caused damage to the colonic surface epithelium and induced compensatory hyperproliferation. Expression levels of heme- and stress-related genes show that heme affects surface cells and not directly crypt cells. Therefore, injured surface cells should signal to crypt TA cells to induce compensatory hyperproliferation. Surface-specific downregulated inhibitors of proliferation were Wnt inhibitory factor 1, Indian Hedgehog, Bone morphogenic protein 2 and possibly Interleukin-15.  Heme also upregulated Amphiregulin, Epiregulin and Cyclooxygenase-2 mRNA in the surface cells, however, their protein/metabolite levels were not increased as heme induced surface-specific translation repression by increasing 4E-BP1. Therefore, we conclude that heme induced colonic hyperproliferation and hyperplasia by repressing feedback inhibition of proliferation.

overall_design: C57BL/6 mice received a Westernized high fat and low calcium diet with or without heme (the polyporphyrin pigment of red meat). Mice received control or heme diet for 14 days. After 14 days, mice were sacrificed and colons were taken out. RNA was isolated from colon scrapings and subjected to gene expression profiling (n=7 control mice and n=9 heme-fed mice).

first: Noortje

last: IJssennagger

first: Anneke

last: Rijnierse

first: Michael

first: Roelof

last: van der Meer


title: Post-mortem cardiac tissue maintains gene expression profile even after late harvesting.

status: Public on Oct 01 2011

city: Baltimore

first: Dan

middle: E.

last: Arking

state: Maryland

address: 733 N. Broadway

department: McKusick-Nathans Institute of Genetic Medicine

institute: Johns Hopkins University School of Medicine

summary:
Gene expression studies are used to help identify disease-associated genes, by comparing the levels of expressed transcripts between cases and controls, and to identify functional genetic variants known as expression quantitative loci (eQTLs). While many of these studies are performed in blood or lymphoblastoid cell lines due to tissue accessibility, the relevance of expression differences in tissues that are not the primary site of disease is unclear.  Further, many eQTLs are tissue specific. Thus, there is a clear and compelling need to conduct gene expression studies in tissues that are specifically relevant to the disease of interest. One major technical concern about using autopsy-derived tissue is how representative it is of physiologic conditions, given the effect of postmortem interval on tissue degradation.
In this study, we monitored the gene expression of 13 tissue samples harvested from a rapid autopsy heart (non-failed heart) and 7 from a cardiac explant (failed heart) through 24 hours of autolysis. The 24 hour autopsy simulation design reflects a typical autopsy scenario where a body may begin cooling to ambient temperature for ~12 hours, before transportation and storage in a refrigerated room in a morgue. In addition, we also simulated a scenario wherein the body was left at room temperature for up to 24 hours before being found.

overall_design: RNA from the 20 samples and triplicate from the HeLa cell line were run on the Affymetrix Exon arrays according to the manufacturer's protocol. The expression profiles of 7 cardiac tissue samples from the cardiac transplant operation (explant/failed heart) and 13 from a rapid-autopsy program (autopsy/non-failed heart) were harvested under the cold- and warm-24 hour autolysis conditions. The 7 explant samples include - 2 biological replicates at 0 hr, 1 at 6 hrs, 1 at 12 hrs, 2 biological replicates at 18 hr cold-autolysis condition and 1 at 18 hr warm-autolysis condition.  The 13 autopsy samples include - 3 biological replicates at 0 hr (2 from the left and 1 from the right ventricle), 1 at 6 hrs, 2 biological replicates at 12 hrs (1 from the left and 1 from the right ventricle), 3 biological replicates at 18 hr cold-autolysis condition (2 from the left and 1 from the right ventricle), 2 biological replicates at 18 hr warm-autolysis condition ( 1 from the left and 1 from the right ventricle), 1 at 24 hr cold-autolysis condition and 1 at 24 hr warm-autolysis condition.  Gene expression profiles of triplicate liver and heart exon array data obtained from Affymetrix were also used as reference .

first: Simone

last: Gupta

first: Marc

middle: K

last: Halushka

first: Gina

middle: M

last: Hilton


title: Expression data from mouse testis cells

status: Public on Oct 06 2011

first: Katrin

last: Arnold

address: 185 Cambridge Street

department: Cancer Center

institute: MGH

summary: Our testis transplantation data demonstrate that only Sox2-GFP+c-kit- cells contain testis-repopulating potential and we wondered whether a molecular comparison of the Sox2-GFP+c-kit+ and Sox2-GFP+c-kit- spermatogonial cells would uncover genes that could explain the exclusive repopulation potential of the latter cell population. To this end, we sorted individual testis cell populations and subjected extracted and amplified RNA to array analysis.

overall_design: Mouse testes of 2-week old Sox2GFP mice were isolated, and dissociated with collagenase. Single cell suspensions were generated and stained with FACS antibody for ckit. FACS analysis was done based on internal GFP signal and ckit antibody signal. PI was used to exclude dead cells. Sox2GFP+ckit- and Sox2GFP+ckit+ populations were sorted into Trizol and sent to ExpressionAnalysisR for processing and profiling. 20 testis were pooled into one sample, two biological replicates were analyzed.

first: Konrad

last: Hochedlinger


title: Comparative transcriptomics and metabolomic analysis of fenofibrate and fish oil treatments in mice

status: Public on Oct 08 2011

summary: Elevated circulating triglycerides, which are considered a risk factor for cardiovascular disease, can be targeted by treatment with fenofibrate or fish oil. To gain insight into underlying mechanisms, we carried out a comparative transcriptomics and metabolomics analysis of the effect of 2 week treatment withfenofibrate and fish oil in mice. Plasma triglycerides were significantly decreased byfenofibrate (-49.1%) and fish oil (-21.8%), whereas plasma cholesterol was increased by fenofibrate (+29.9%) and decreased by fish oil (-32.8%). Levels of various phospholipid species were specifically decreased by fish oil, while levels of Krebs cycle intermediates were increased specifically by fenofibrate. Plasma levels of many amino acids were altered by fenofibrate and to a lesser extent by fish oil. Both fenofibrate and fish oil upregulated genes involved in fatty acid metabolism, and downregulated genes involved in blood coagulation and fibrinolysis. Significant overlap in gene regulation by fenofibrate and fish oil was observed, reflecting their property as high or low affinity agonist for PPARα, respectively. Fenofibrate specifically downregulated genes involved in complement cascade and inflammatory response. Fish oil specifically downregulated genes involved in cholesterol and fatty acid biosynthesis, and upregulated genes involved in amino acid and arachidonic acid metabolism. Taken together, the data indicate that despite being similarly potent towards modulating plasma free fatty acids, cholesterol and triglyceride levels, fish oil causes modest changes in gene expression likely via activation of multiple mechanistic pathways, whereas fenofibrate causes pronounced gene expression changes via a single pathway, reflecting the key difference between nutritional and pharmacological intervention.

overall_design: Expression profiling of liver from mice fed control diet, fish oil or fenofibrate for 2 weeks.

first: Yingchang

last: Lu

first: Mark

middle: V

last: Boekschoten

first: Suzan

last: Wopereis

last: Müller

first: Sander

last: Kersten


title: Expression data from adult telogen hair cycle

city: Irvine

first: William

last: Gordon

state: CA

address: 839 Health sciences way

department: Medicine

institute: University of CA Irvine

summary: Telogen is not simply a quiescent part of the hair cycle

overall_design: Mid and late timepoints were selected during adult telogen

first: Mikhail

last: Geyfman


title: Defective K-Ras Oncoproteins Initiate Cancer In Vivo and Evolve to Overcome Impaired Effector Binding

city: San Francisco

first: Ashley

middle: Flynn

last: Ward

address: 505 Parnassus Ave, M649

institute: UCSF

summary: The oncogenic proteins expressed in human cancer cells are exceedingly difficult targets for drug discovery due to intrinsic properties of the Ras GTPase switch. As a result, recent efforts have largely focused on inhibiting Ras-regulated kinase effector cascades, particularly the Raf/MEK/ERK and PI3 kinase/Akt/mTOR pathways. We constructed murine stem cell leukemia virus (MSCV) vectors encoding oncogenic K-RasD12 with additional “second site” amino acid substitutions that that impair PI3 kinase/Akt or Raf/MEK/ERK activation and performed bone marrow transduction/transplantation experiments in mice. In spite of attenuated signaling properties, defective K-Ras oncoproteins induced aggressive clonal T lineage acute lymphoblastic leukemia (T-ALL). These leukemias exhibited a high frequency of somatic Notch1 mutations, which is also true of human T-ALL. Multiple independent T-ALLs restored full oncogenic Ras activity by acquiring “third site” mutations within the viral KrasD12 transgenes. Other leukemias with undetectable PTEN and elevated phosphoryated Akt levels showed a similar gene expression profile to human early T progenitor (ETP) T-ALL.  Expressing oncoproteins that are defective for specific functions is a general strategy for assessing requirements for tumor maintenance and uncovering potential mechanisms of drug resistance in vivo. In addition, our observation that defective Kras oncogenes regain potent cancer initiating activity strongly supports simultaneously targeting distinct components of Ras signaling networks in the substantial fraction of cancers with RAS mutations.

overall_design: WT Balb/c mice were lethally irradiated and transplanted with WT Balb/c bone marrow cells transduced with MSCV-IRES-Kras mutant-GFP vectors.  Mice developed T-cell lymphoproliferative disease.

first: Shieh

last: Angell

first: Ward

last: Ashley

first: Harding-Theobald

last: Emily

first: Mullighan

last: Charles

first: Zhang

last: Chao

first: Chen

last: Shann-Ching

first: Su

last: Xiaoping

first: Downing

last: James

first: Bollag

last: Gideon

first: Shannon

last: Kevin


title: Expression profiling of Noto-GFP+ notochord progenitor cells sorted from E8.5 mouse embryos

city: Madison

first: Owen

middle: James

last: Tamplin

state: WI

address: 1111 Highland Ave

department: Cell and Regenerative Biology

institute: University of Wisconsin-Madison

summary:
Using a combination of cell sorting and microarray analysis, we identified almost 200 genes as having a high level of expression in the notochord.
After whole mount in situ hybridization screening, we confirmed approximately one third of these as having a novel notochord expression pattern.

Keywords: cell type comparison - embryonic Noto-GFP+ notochord progenitors versus surrounding GFP- comparator cells

overall_design: 3 biological replicates - each replicate includes an experiment cell population (Noto-GFP positive cell sort) and a comparator population (GFP negative cell sort)

middle: J

first: Brian

last: Cox

first: Janet

last: Rossant


title: Expression data from primary mouse embryonic fibroblasts from wild-type and Cry double-knockout embryos

city: Rotterdam

first: Eugin

last: Destici

address: Dr. Molewaterplein 50

department: Genetics

institute: Erasmus MC

summary: By gating cell cycle progression to specific times of the day, the intracellular circadian clock is thought to reduce the exposure of replicating cells to potentially hazardous environmental and endogenous genotoxic compounds. Although core clock gene defects that eradicate circadian rhythmicity can cause an altered in vivo genotoxic stress response and aberrant proliferation rate, it remains to be determined to what extent these cell-cycle-related phenotypes are due to a cell-autonomous lack of circadian oscillations. We investigated the DNA damage sensitivity and proliferative capacity of cultured primary Cry1-/-|Cry2-/- fibroblasts. Contrasting previous in vivo studies, we show that the absence of CRY proteins does not affect the cell-autonomous DNA damage response upon exposure of primary cells in vitro to genotoxic agents, but causes cells to proliferate faster. By comparing primary wild type, Cry1-/-|Cry2-/-, Cry1+/-|Cry2-/- and Cry1-/-|Cry2+/- fibroblasts, we provide evidence that CRY proteins influence cell cycle progression in a cell-autonomous, but circadian clock-independent manner and that the accelerated cell cycle progression of Cry-deficient cells is caused by global dysregulation of Bmal1-dependent gene expression. These results suggest that the inconsistency between in vivo and in vitro observations might be attributed to systemic circadian control rather than a direct cell-autonomous control.

overall_design: Asynchronous proliferating MEFs grown under low (3%) oxygen tension and lysed in Trizol. Four independent cell lines were used for each genotype (WT, Cry DKO).

first: Malgorzata

last: Oklejewicz

first: Gijsbertus

middle: T

last: van der Horst


title: Mammary Tissue: Wild type mammary glands vs IGF-IR induced mammary tumors vs IGF-IR independent tumors

city: Guelph

first: Roger

middle: A

last: Moorehead

state: Ontario

address: 50 Stone Rd East

department: Department of Biomedical Sciences

country: Canada

institute: University of Guelph

summary: Molecular profiling was used to classify mammary tumors that develop in MTB-IGFIR transgenic mice. It was determined that the primary mammary tumors (PMT), which develop due to elevated expression of the type I insulin-like growth factor receptor (IGF-IR) in mammary epithelial cells, most closely resemble murine tumors with basal-like or mixed gene expression profiles and with human basal-like breast cancers. Downregulation of IGF-IR transgene in MTB-IGFIR tumor-bearing mice leads to the regression of most of the tumors followed by tumor re-appearance in some of the mice. These tumors that re-appear following IGF-IR transgene downregulation do not express the IGF-IR transgene and cluster with murine mammary tumors that express a mesenchymal gene expression profile and with human claudin-low breast cancers. Therefore, IGF-IR overexpression in murine mammary epithelial cells induces mammary tumors with primarily basal-like characteristics while tumors that develop following IGF-IR downregulation express a gene signature that most closely resembles human claudin-low breast tumors.

overall_design: Three conditions: 8 wild type (WT) mammary glands, 11 primary mammary tumor (PMT) samples, 9 recurrent spindle tumor (RST) samples, each sample was hybridized against a universal mouse reference RNA

first: Julie

last: Livingstone


title: Transcriptional profiling of MKK4-depleted cells

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary:
Mitogen-activated protein kinase kinase 4 (MKK4) is a dual-specificity kinase activated by environmental stress, cytokines, and peptide growth factors that reportedly can promote or inhibit tumor cell growth and metastasis. Somatic mutations in the gene encoding MKK4 (MAP2K4) have been identified in various human cancers, but the consequences of these mutations on MKK4 function and the biology of tumor cells that have them have not been elucidated. Here we report that, of the eleven mutations within the MAP2K kinase domain described thus far, one had gain-of-function (Q142L) and six had loss-of-function. Three of the loss-of-function mutations are nonsense mutations that produced C-terminally-truncated proteins (I295fs*23, R304*, and W310*) that were highly ubiqitinated and rapidly degraded when introduced into cells, and three are missense mutations in the ATP-binding pocket (N234I), activation loop (S251N), or C-lobe (P326L). We modeled the consequences of MAP2K4 loss-of-function mutations on cells by introducing MKK4 short-hairpin RNA constructs and found that MKK4 depletion enhanced the ability of a weakly tumorigenic murine cancer cell to metastasize when injected into syngeneic mice but had no effect on primary tumor formation. MKK4-depleted cells exhibited an increased capacity to migrate across PET filters and to invade through matrigel but no change in anchorage-dependent or -independent proliferation. Transcriptional profiling of these cells revealed gene expression changes that promote epithelial-to-mesenchymal transition and angiogenesis. We conclude that MKK4 inactivation promoted metastasis but not primary tumor formation. Collectively, these findings implicate loss-of-function MAP2K4 somatic mutations in tumor metastasis and provide one of the few examples of a somatic mutation in cancer cells that exerts a metastasis-specific effect.

Keywords: Two-group comparison.

overall_design: 393P cells were infected with retroviruses expressing a MKK4-specific shRNA construct (shZ) or scrambled control (scr). 393P-shZ and 393P-scr were transcriptionally profiled in triplicate cultures.

first: Jon

last: Kurie

first: Young-Ho

last: Ahn

first: Don

last: Gibbons

first: Wei

last: Lin


title: MicroRNA array analysis of platelets in premature coronary artery disease

first: Brigitte

last: Sondermeijer

address: Meibergdreef 9

institute: Academic Medical Center

summary:
Coronary artery disease (CAD) is the leading cause of human morbidity and mortality worldwide, underscoring the need to improve diagnostic strategies. Platelets play a major role, not only in the process of acute thrombosis during plaque rupture, but also in the formation of atherosclerosis itself. MicroRNAs are endogenous small non-coding RNAs that control gene expression and are expressed in a tissue and disease-specific manner. Therefore they have been proposed to be useful biomarkers. It remains unknown whether differences in miRNA expression levels in platelets can be found between patients with premature CAD and healthy controls.
Methodology/Principal Findings In this case-control study we measured relative expression levels of platelet miRNAs using microarrays from 12 patients with premature CAD and 12 age- and sex-matched healthy controls. Six platelet microRNAs were significantly upregulated (miR340*, miR451, miR454*, miR545:9.1. miR615-5p and miR624*) and one miRNA (miR1280) was significantly downregulated in patients with CAD as compared to healthy controls. To validate these results, we measured the expression levels of these candidate miRNAs by qRT-PCR in platelets of individuals from two independent cohorts; validation cohort I consisted of 40 patients with premature CAD and 40 healthy controls and validation cohort II consisted of 27 patients with artery disease and 40 healthy relatives. MiR340* and miR624* were confirmed to be upregulated in patients with CAD as compared to healthy controls in both validation cohorts.
Conclusion/Significance Two miRNAs in platelets are significantly upregulated in patients with CAD as compared to healthy controls.

overall_design: miRNA array analysis of isolated platelets from subjects with premature coronary artery disease compared to healthy control subjects.

first: Sara

last: Pinto-Sietsma

first: Esther

last: Creemers


title: Expression data from differentiating ES cells expressing Snail during Wnt inhibition

status: Public on Sep 22 2011

city: Saint Louis

first: Jennifer

last: Gill

state: MO

address: 660 South Euclid Ave.

department: Pathology/Immunology

institute: Washington University School of Medicine

summary:
ES cells differentiated in the presence of the Wnt inhibitor DKK1 fail to express the transcription factor Snail and undergo EMT.  We generated an ES cell line, A2.snail, that induced Snail expression upon addition of doxycycline addition.
Microarrays were used to gain a global picture of ES cell differentiation at early timepoints after Snail was expressed during Wnt inhibition.

overall_design: A2.snail ES cells, which express Snail upon addition of doxycycline, were differentiated as embryoid bodies in differentiation media and DKK1.  Total RNA was harvested from control (no doxycycline) and Snail-induced (doxycycline at day 2) cultures at 6, 12, and 24 hours after doxycycline addition (corresponding to days 2.25, 2.5, and 3 of differentiation).

middle: G

first: Ellen

last: Langer

first: Robert

middle: C

last: Lindsley

first: Mi

last: Cai

first: Theresa

middle: L

last: Murphy

first: Michael

last: Kyba

first: Kenneth


title: Macrophage response to serum in culture medium

status: Public on Sep 23 2011

first: Douglas

last: Hayden

address: 50 Staniford St, Suite 560

institute: Mass General Hospital

summary: Most cell culture experiments utilize media containing fetal calf serum.  Results are often interpreted regarding importance to human pathways.  We studied gene expression in mouse macrophages grown in the absence of serum, and in fetal calf serum, mouse serum, and human serum using genome wide expression systems in resting conditions and after stimulation with lipopolysaccharide.

overall_design: We cultured mouse bone marrow derived macrophages in media containing no serum, or 5% fetal calf, or mouse or human serum.  The experiment was performed in conditions without or with stimulation by LPS.  We harvested the cells at 4 hours after stimulation and analyzed whole genome mRNA expression by microarray as a proxy for transcriptional responses.  Three replicate experiments were performed.

first: H

middle: S

last: Warren


title: IL-17-induced NF-kB activation via CIKS/Act1: Physiologic significance and signaling mechanisms

status: Public on Oct 19 2011

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary:
Interleukin-17 (IL-17) is essential in host defense against extracellular bacteria and fungi, especially at mucosal sites, but it also contributes significantly to inflammatory and autoimmune disease pathologies. Binding of IL-17 to its receptor leads to recruitment of the adaptor protein CIKS/Act1 via heterotypic association of their respective SEFIR domains and to activation of the transcription factor NF-kB; it is not known whether CIKS and/or NF-kB are required for all gene induction events. Here we report that CIKS is essential for all IL-17 induced immediate-early genes in primary mouse embryo fibroblasts, while NF-kB is profoundly involved.  We also identify a novel sub-domain in the N-terminus of CIKS that is essential for IL-17-mediated NF-kB activation. This domain is both necessary and sufficient for the interaction between CIKS and TRAF6, an adaptor required for NF-kB activation.  The ability of decoy peptides to block this interaction may provide a new therapeutic strategy for intervention in IL-17-driven autoimmune and inflammatory diseases.

Keywords: strain comparisons

overall_design: strain comparisons

first: Søren

middle: U

last: Sønder

first: Sun

last: Saret

first: Wanhu

last: Tang

first: Stephen

middle: F

last: Porcella

first: Ulrich

last: Siebenlist


title: Expression data from differentiating ES cells expressing miR-200c and miR-141

summary:
ES cells express the miR-200 family which becomes down-regulated during the course of differentiation in serum.  We generated an ES cell line which expresses miR-200c and miR-141 upon addition of doxycycline.
Microarrays were used to gain a global picture of differentiation when miR-200c and miR-141 expression were maintained throughout differentiation through the addition of doxycycline.

overall_design: A2.miR200c ES cells, which express miR-200c/miR-141 upon addition of doxycycline, were differentiated as embryoid bodies in six petri dishes.  Half of the samples were treated with doxycycline on both days 2 and 4 of differentiation, and RNA was collected from all samples on days 3, 4, and 5.


title: Expression profiling FSHD vs. control myoblasts and myotubes

status: Public on Sep 29 2011

city: Rensselaer

first: Sridar

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary:
The gene expression pathways leading to muscle pathology in facioscapulohumeral dystrophy (FSHD) remain to be elucidated. This muscular dystrophy is caused by a contraction of an array of tandem 3.3-kb repeats (D4Z4) at 4q35.2. We compared expression of control and FSHD myoblasts and myotubes (three preparations each) on exon microarrays (Affymetrix Human Exon 1.0 ST) and validated FSHD-specific differences for representative genes by qRT-PCR on additional myoblast cell strains. The FSHD and control myoblasts used for these experiments were shown to grow and differentiate into myotubes equally efficiently as control myoblasts. There were no significant FSHD-control differences in RNA levels for MYOD1 and MYOG at the myoblast and myotube stages and for MYF5 and MYF6 at the myoblast stage. In contrast, 295 other genes were dysregulated at least 2-fold in FSHD vs. control myoblasts (p <0.01, adjusted for multiple comparisons).
Remarkably, only 10% of the FSHD-associated gene dysregulation at the myoblast stage was downregulation. At the myotube stage, about ten times as many genes exhibited FSHD-associated downregulated as at the myoblast stage and twice as many genes displayed FSHD-associated upregulation. The FSHD-related changes in RNA levels appear to be due to posttranscriptional as well as transcriptional alterations. Among the prominently dysregulated pathways were signaling and oxidative stress pathways. By comparing expression profiles of control myoblasts and myotubes to each other and to 19 non-muscle cell types profiled identically, our study also revealed many new myogenesis associations for genes not previously annotated as muscle-specific.

Keywords: Disease state analysis and time course for differentiation

overall_design: For the microarray, two normal-control myoblast-myotube sample pairs and one disease-control pair (sporadic inclusion body myositis; IBM), which are  previously described samples GSM443914_CM33j_ Undiff_06042009_, GSM443913_CM33j_Diff_06042009_, GSM443916_CM01154_002_Undiff,  GSM443915_CM01154_002_Diff_06012009, GSM443918_CM01201_001_Undiff_06012009, GSM443917_CM01201_001_Diff_06012009, were compared to three myoblast-myotube sample pairs generated from moderately affected skeletal muscle from patients with molecularly confirmed FSHD. Myoblasts were harvested at about 70% confluency, and myotubes were harvested at maximal myotube formation, 5 or 7 days of differentiation. The control myoblast and myotube biological replicates 1-3 were from a normal-control 23 year-old male (quadriceps biopsy), a normal-control 27 year-old female (quadriceps biopsy), and a 74 year-old female (deltoid biopsy), respectively. The FSHD myoblast biological replicates 1-3 were from a 45 year-old female (quadriceps biopsy), 22 year-old female (orthopedic scapular fixation rhomboid tissue), and 13 year-old male (quadriceps biopsy) and contained six, five, and three copies of the D4Z4 repeat unit in their disease-linked arrays, respectively. The FSHD myotube biological replicates 1-3 were from the same batch of cells as for the FSHD myoblasts with the exception of biological replicate 3, which was from a 14 year-old female (deltoid biopsy, 2 copies of the disease-linked D4Z4 repeat unit). For qRT-PCR validation, 4 - 8 FSHD myoblast or myotube samples from different patients with a molecularly confirmed diagnosis were compared to 4 - 8 analogous control samples from different unaffected individuals. Most of these were from quadriceps biopsies, and all but one had not been used on the microarray. Methods for generation of myoblast cell strains, propagation of myoblasts, and induction of differentiation by serum limitation were previously described (http://genome.ucsc.edu/ENCODE/protocols/cell/human/HSMM_HSMMtube_Crawford_protocol.pdf). Each batch of myoblasts and myotubes was checked by immunocytochemical staining for the quality of the cell preparation. The myoblast preparations for the microarray or qRT-PCR validation had >85% desmin-positive cells as determined with an antibody preparation confirmed to have selectivity for myogenic cells (Labvision/Thermo Scientific) using DAPI counterstaining. The myotube preparations had >70% of the nuclei in desmin-positive cells containing more than 2 nuclei per cell. Five of the six preparations for the microarray analysis (all but FM1795) were also immunostained with a monoclonal antibody to myosin heavy chain (MF20, a gift of Stephen D. Hauschka) and had >70% of the nuclei in multinucleated myosin heavy chain-positive cells.

first: Melanie

last: Ehrlich

first: Koji

last: Tsumagari


title: Expression data from naive and memory CD8 T cells cultured in presence or absence of IL-4

status: Public on Sep 28 2011

city: Lyon

first: erwan

last: ventre

address: 21, avenue Tony Garnier

country: France

institute: INSERM U851

summary:
Effects of IL-4 on CD8 T cells functions are largely unknown. IL-4 induces survival and proliferation of CD8 T cells, but several studies suggest that IL-4 could also affect several functions of CD8 T cells such as cytotoxicity. Our team has shown that IL-4 repress the expression of Ccl5 in vitro.
To define more precisely the impact of IL-4 on CD8 T cells, we performed a whole genome expression microarray analysis of naive and memory CD8 T cells cultured in presence or absence of IL-4. This approach allowed us to define the IL4-gene-expression signature on CD8 T cells.

overall_design:
18 samples were processed. Two populations of F5 naive CD8 T cells were FACS-sorted: samples from each population were incubated 20 hours with IL-7 in presence or absence of IL-4. Thus, a total of 6 “Naive” samples were processed.
In addition, 4 populations of F5 TIM memory CD8 T cells were FACS-sorted: samples from 2 of these populations were incubated 20 hours in presence of IL-7 and/or IL-4, or in medium alone. Thus, 12 “Memory” samples were processed.

first: Erwan

last: Ventre

first: Lilia

last: Brinza

first: Stéphane

last: Schicklin

first: Charles-Antoine

last: Coupet

first: Jacqueline

last: Marvel


title: Discovery of genes differentially-expressed in the endothelium of lymph nodes draining metastatic versus non-metastatic tumors

city: Clayton

first: Rae

last: Farnsworth

state: VIC

address: Wellington Rd

country: Australia

institute: Monash University

summary:
Metastasis to lymph nodes is an early and prognostically important event in the progression of many human cancers, and is associated with expression of vascular endothelial growth factor-D (VEGF-D). Changes to lymph node vasculature occur during metastasis, and may establish a metastatic niche capable of attracting and supporting tumor cells.
We used microarrays to characterise the molecular profiles of endothelial cells from lymph nodes draining metastatic (VEGF-D-overexpressing) and non-metastatic tumors, and to identify differentially-expressed genes that might have therapeutic or prognostic potential.

overall_design: Draining lymph nodes of metastatic (VEGF-D-overexpressing) or non-metastatic tumors were pooled from 1-5 mice and enzymatically digested. Lymph nodes draining metastatic tumors were included for the analysis only if macroscopically enlarged, indicating the presence of metastatic cells. After digestion, tumor cells and leukocytes were depleted via immunomagnetic selection, and the resulting lymph node stromal cells were cultured briefly. Podoplanin was then used as a positive immunomagnetic selection marker to enrich for lymphatic and other endothelial cells in the lymph node. RNA was isolated from biological duplicate lymph node endothelial cell (LN EC) preparations and analysed by microarray.

middle: H

first: Steven

last: Stacker


title: Specific modulation of mucosal immune response, tolerance and proliferation in mice colonized with A. muciniphila

status: Public on Sep 21 2011

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

institute: Wageningen University

summary:
Epithelial cells of the mammalian intestine are covered with a mucus layer that prevents direct contact with intestinal microbes but also constitutes a substrate for mucus-degrading bacteria. To study the effect of mucus degradation on the host response, germ-free mice were colonized with Akkermansia muciniphila. This anaerobic bacterium belonging to the Verrucomicrobia is specialized in the degradation of mucin, the glycoprotein present in mucus, and found in high numbers in the intestinal tract of human and other mammalian species. Efficient colonization of A. muciniphila was observed with highest numbers in the cecum, where most mucin is produced. In contrast, following colonization by Lactobacillus plantarum, a facultative anaerobe belonging to the Firmicutes that ferments carbohydrates, similar cell-numbers were found at all intestinal sites. Whereas A. muciniphila was located closely associated with the intestinal cells, L. plantarum was exclusively found in the lumen. The global transcriptional host response was determined in intestinal biopsies and revealed a consistent, site-specific, and unique modulation of about 750 genes in mice colonized by A. muciniphila and over 1500 genes after colonization by L. plantarum. Pathway reconstructions showed that colonization by A. muciniphila altered mucosal gene expression profiles toward increased expression of genes involved in immune responses and cell fate determination, while colonization by L. plantarum led to up-regulation of lipid metabolism. These indicate that the colonizers induce host responses that are specific per intestinal location. In conclusion, we propose that A. muciniphila modulates pathways involved in establishing homeostasis for basal metabolism and immune tolerance toward commensal microbiota.

Keywords: Analysis of target gene regulation by using microarrays

overall_design: Adult germ-free female NMRI-KI mice (45 – 65 days) were used for bacterial mono-association. Two bacterial strains were used in this study, A. muciniphila MucT (ATTC BAA-835) and L. plantarum WCFS1 (NCIMB 8826). A. muciniphila was grown anaerobically in a basal mucin based medium and L. plantarum was grown anaerobically at 37°C in Man-Rogosa-Sharpe broth (MRS; Le Pont de Claix, France). After 7 days of colonization, mice were killed by cervical dislocation and terminal ileum, cecum and ascending colon specimens were sampled.

first: Muriel

last: Derrien

first: Peter

last: van Baarlen

first: Elisabeth

last: Norin

first: Michael

last: Müller

first: Willem

last: de Vos


title: Either Kras activation or Pten loss similarly enhance the dominant-stable CTNNB1-induced genetic program to promote granulosa cell tumor development in ovary and testis

status: Public on Sep 20 2011

first: JoAnne

last: Richards

address: One Baylor Plaza

department: Molecular and Cellular Biology

summary: Stable activation of the WNT signaling effector beta-catenin (CTNNB1(ex3) in ovarian granulosa cells results in the formation of premalignant lesions that develop into granulosa cell tumors (GCTs) spontaneously later in life. Loss of the tumor suppressor gene Pten accelerates GCT formation in the CTNNB1 strain.  Conversely, expression of oncogenic KRASG12D causes the dramatic arrest of proliferation, differentiation and apoptosis in granulosa cells, and consequently, small abnormal follicle-like structures devoid of oocytes accumulate in the ovary. Because of the potent anti-proliferative effects of KRASG12D in granulosa cells, we sought to determine if KRASG12D would block precancerous lesion and tumor formation in follicles of the CTNNB1 mutant mice.  Unexpectedly, transgenic Ctnnb1;Kras mutant mice developed early-onset GCTs leading to premature death in a manner similar to theCtnnb1;Pten mutant mice.  Moreover, the GCTs in the Ctnnb1;Kras mutant mice exhibited increased GC proliferation, decreased apoptosis and impaired differentiation. Microarray and RT-PCR analyses revealed that ovaries from mice expressing dominant-stable CTNNB1 with either Pten loss or KRAS activation were unpredictably similar.  Specifically, gene regulatory processes induced by CTNNB1 were mostly enhanced by either KRAS activation or Pten loss in remarkably similar patterns and degree.  Furthermore, the concomitant activation of CTNNB1 and KRAS in Sertoli cells resulted in the development of granulosa cell tumors of the testis.  RT-PCR studies showed a partial overlap in gene regulatory processes associated with tumor development in the ovary and testis.  Together, these results suggest that KRAS activation and Pten loss induce GCT development from premalignant lesions via highly similar molecular mechanisms.

overall_design: four samples: average of two wild type samples (previously submitted as GSM403220 and GSM403221), beta-Catenin constitutively active mutant, beta-Catenin;Pten double mutant, and beta-Catenin;Kras(G12D) double mutant

first: Heng-Yu

last: Fan

first: Zhilin

last: Liu

first: Lisa

last: Mullany

first: Marie-Noëlle

last: Laguë

first: Alexandre

last: Boyer

first: Derek

last: Boerboom


title: Gene expression from human B-lymphocytes (P493-6)

status: Public on Sep 19 2011

first: Hongkai

last: Ji

state: MD

address: 615 North Wolfe Street, Rm E3638

department: Department of Biostatistics

institute: Johns Hopkins Bloomberg School of Public Health

summary: P493-6 contain a tet repressible MYC contruct.  In the presense of tetracycline, MYC levels are great reduced and the cells cease to cycle.  Gene expression was compared between high and low MYC expressing cells

overall_design: P493-6 cells were grown in both the presence and absence of tetracycline.  RNA was extracted and gene expression analysis was performed using exon arrays

first: Karen

last: Zeller

first: Chi

last: Dang


title: Cell-type independent MYC target genes reveal a primordial signature involved in biomass accumulation

type: Genome binding/occupancy profiling by genome tiling array

summary:
The functions of key oncogenic transcription factors independent of context have not been fully delineated despite our richer understanding of the genetic alterations in human cancers. The MYC oncogene, which produces the Myc transcription factor, is frequently altered in human cancer and is a major regulatory hub for many cancers.  In this regard, we sought to unravel the primordial signature of Myc function by using high-throughput genomic approaches to identify the cell-type independent core Myc target gene signature.  Using a model of human B lymphoma cells bearing inducible MYC, we identified a stringent set of direct Myc target genes via chromatin immunoprecipitation (ChIP), global nuclear run-on assay, and changes in mRNA levels. We also identified direct Myc targets in human embryonic stem cells (ESCs).  We further document that a Myc core signature (MCS) set of target genes is shared in mouse and human ESCs as well as in four other human cancer cell types. Remarkably, the expression of the MCS correlates with MYC expression in a cell-type independent manner across 8,129 microarray samples, which include 312 cell and tissue types.  Furthermore, the expression of the MCS is elevated in vivo in Em-Myc transgenic murine lymphoma cells as compared with premalignant or normal B lymphocytes.  Expression of the MCS in human B cell lymphomas, acute leukemia, lung cancers or Ewing sarcomas has the highest correlation with MYC expression.  Annotation of this gene signature reveals Myc's primordial function in RNA processing, ribosome biogenesis and biomass accumulation as its key roles in cancer and stem cells.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Global gene expression response to BET inhibition in two cancer cell lines

first: Barbara

last: Bryant

address: 215 First Street

institute: Constellation Pharmaceuticals

summary: The MYC transcription factor is a master regulator of diverse cancer pathways and somatic cell reprogramming. MYC is a compelling therapeutic target that exhibits cancer-specific cellular effects. Pharmacologic inhibition of MYC function has proven challenging due to its numerous modes of forced expression and the difficulty of disrupting protein-DNA interactions. Here we demonstrate the rapid and potent abrogation of MYC gene transcription by representative small molecule bromodomain inhibitors of the BET family of chromatin adaptors. This transcriptional suppression of MYC was observed in the context of the natural, chromosomally translocated, and amplified gene locus. Inhibition of BET bromodomain-promoter interactions and subsequent reduction of MYC transcript and protein levels resulted in G1 arrest and extensive apoptosis in a variety of leukemia and lymphoma cell lines. Exogenous expression of MYC from an artificial promoter that is resistant to BET regulation significantly protected cells from growth suppression by BET inhibitors and revealed that MYC exerts a direct and tight control of key pro-growth and anti-apoptotic target genes. Transcriptional profiling of two cells after 4 and 8 hours of treatment with BET inhibitor shows that both MYC and its targets are strongly down-regulated.  We thus demonstrate that pharmacologic inhibition of MYC is achievable through targeting BET bromodomains, and suggest that such inhibitors may have broad clinical applicability given the widespread pathogenetic role of MYC in cancer.

overall_design: LP-1, a multiple myeloma cell line, and Raji, a Burkitt lymphoma cell line, were treated with BET inhibitor and an inactive enantiomer for 4 or 8 hours.  Two biological replicates of each sample were profiled on exon arrays.

first: Jennifer

last: Mertz

first: Andrew

middle: R

last: Conery

first: Robert

last: Sims

first: Srividya

last: Balasubramanian

first: Louise

last: Bergeron

first: Deanna

last: Mele

last: Sandy


title: Arsenate Sub-chronic Drinking Water Study

status: Public on Sep 15 2011

city: RTP

first: Harvey

last: Clewell

state: NC

address: 6 Davis Drive

institute: The Hamner Institutes for Health Sciences

summary:
Concentration- and time-dependent genomic changes in the mouse urinary bladder following exposure to arsenate in drinking water for up to twelve weeks.

Inorganic arsenic (Asi) is a known human bladder carcinogen.  The objective of this study was to examine the concentration dependence of the genomic response to Asi in the urinary bladders of mice.  C57BL/6J mice were exposed for 1 or 12 weeks to arsenate in drinking water at concentrations of 0.5, 2, 10, and 50 mg As/L.  Urinary bladders were analyzed using gene expression microarrays.   A consistent reversal was observed in the direction of gene expression change: from predominantly decreased expression at 1 week to predominantly increased expression at 12 weeks.  These results are consistent with evidence from in vitro studies of an acute adaptive response that is suppressed on longer exposure due to down-regulation of Fos.  Pathways with the highest enrichment in gene expression changes were associated with epithelial-to-mesenchymal transition, inflammation, and proliferation.  Benchmark dose (BMD) analysis determined that the lowest median BMD values for pathways were above 5 mg As/L, despite the fact that pathway enrichment was observed at the 0.5 mg As/L exposure concentration.  This disparity may result from the non-monotonic nature of the concentration-responses for the expression changes of a number of genes, as evidenced by the much fewer gene expression changes at 2 mg As/L compared to lower or higher concentrations.  Pathway categories with concentration-related gene expression changes included cellular morphogenesis, inflammation, apoptosis/survival, cell cycle control, and DNA damage response. The results of this study provide evidence of a concentration-dependent transition in the mode of action for the subchronic effects of Asi in mouse bladder cells in the vicinity of 2 mg Asi/L.

overall_design: Female C57Bl/J mice will be exposed to COLD Arsenate in drinking water.  One week interium sac on 7/18/06.  100 samples including liver, lung, kidney and bladder.  Bladder will be analyzed with microarrays, 24 samples.  Twelve week terminal sac on 10/05/06.  75 total samples including lung, kidney, and bladder.  Bladdler will be analyzed by microarray, 25 samples. Drinking water containing As will be prepared weekly with monitoring to determine amount used by mice.  Following tissues will be available for genomic study:  Bladder, liver, lung, and kidney.

first: H

first: R

last: Thomas

first: E

last: Kenyon

first: M

last: Hughes

first: B

last: Adair

first: P

last: Gentry

first: J

middle: W

last: Yager


title: Smad3 regulates the miR-200 family in gastric cancer

city: incheon

first: DeokHoon

last: Kim

address: 7-45 songdo-dong yeonsu-ku

country: South Korea

institute: Lee Gil Ya cancer and diabets institute

summary: To find potential microRNA links between Smad3 and E-cadherin, we characterized the microRNA profiles of two gastric cancer cell lines: SNU484-LPCX, which does not express Smad3, and SNU484-Smad3, in which Smad3 is overexpressed. We found that miR-200 families, among other differentially expressed miRNAs, are overexpressed in SNU484-Smad3. Through subsequent studies, including silencing of Smad3 in SNU484-Smad3 and expression profiling of epithelial-mesenchymal markers and ZEB1/2, known repressors of E-cadherin, we found that Smad3 regulates miR-200 families at the transcriptional level, which regulate ZEB 1/2, known transcriptional repressors of E-cadherin, at the post-transcriptional level. This represents an important link between the TGF-beta signaling pathway and post-transcriptional regulation by miRNAs.

overall_design: Examination of small RNA expression in 2 different cell lines (SNU484-LPCX, SNU484-Smad3).

first: Deokhoon

first: Sung-Min

last: Ahn


title: Expression data from lung tumors of KrasTgfbr2 -/- mouse model

city: New York

first: Charles

last: Powell

address: One Gustave Levy Place, Box 1232

department: MEDICINE/PULMONARY

institute: Mount Sinai School of Medicine

summary:
Recent data suggests that repression of the Type II TGF-B Receptor (Tgfr2) repression in human lung adenocarcinoma is important for progression from noninvasive to invasive adenocarcinoma. To test this hypothesis in a animal model of non-invasive lung cancer, we generated an inducible, lung specific Tgfbr2 knockout model in the oncogenic Kras mouse.
LSL-KrasG12D positive mice were simultaneously backcrossed to C57/Bl6 mice and to the Tgfbr2 flox/flox mice. To induce tumors, 100 _l of saline containing 3x10e10 particles of an adenovirus containing the Cre recombinase (Ad.Cre) was administered to each LSL-KrasG12D mouse intra-nasally.

overall_design: Mice were sacrificed at 7 weeks after administration of Adeno-Cre.  We used laser capture microdissection to acquire tumor cells from KrasTgfbr2-/-  and KrasTgfbr2 wt mouse tumors.

first: Alain

last: Borczuk


title: Expression data from fibroblasts, iPSCs and neurons with four copies of SNCA, and equivalent cell lines from an unaffected first degree relative

city: Edinburgh

first: Tilo

last: Kunath

address: 5 LIttle France Drive

department: Centre for Regenerative Medicine

country: United Kingdom

institute: University of Edinburgh

summary:
A major barrier to research on Parkinson’s disease (PD) is inaccessibility of diseased tissue for study. One solution is to derive induced pluripotent stem cells (iPSCs) from patients with PD and differentiate them into neurons affected by disease. We created an iPSC model of PD caused by triplication of SNCA encoding α-synuclein. α-Synuclein dysfunction is common to all forms of PD, and SNCA triplication leads to fully penetrant familial PD with accelerated pathogenesis. After differentiation of iPSCs into neurons enriched for midbrain dopaminergic subtypes, those from the patient contain double α-synuclein protein compared to those from an unaffected relative, precisely recapitulating the cause of PD in these individuals. A measurable biomarker makes this model ideal for drug screening for compounds that reduce levels of α-synuclein, and for mechanistic experiments to study PD pathogenesis.
This gene expression microarray study was carried out as part of the validation process for demonstrating that the generated iPSC lines are pluripotent.

overall_design: 15 samples were analysed: the two parent fibroblast lines (AST denoting alpha-synuclein triplication and NAS denoting normal alpha-synuclein), two iPSC lines from each parent fibroblast line (four in total), a human embryonic stem cell line (SHEF4) and eight neuronal samples (each iPSC line differentiated into a neuronal population enriched for dopaminergic neurons, at two different time points).

first: Michael

last: Devine

first: Mina

last: Ryten

first: Petr

last: Vodicka

first: Alison

last: Thomson

first: Henry

last: Houlden

first: Tom

last: Burdon

first: Fatima

last: Cavaleri

first: Nicola

last: Drummond

first: Masumi

last: Nagano

first: Jan-Willem

last: Taanman

first: Anthony

last: Schapira

first: Katrina

last: Gwinn

first: Johm

last: Hardy

first: Patrick

last: Lewis


title: Expression data from lung tumor and stromal cells of KrasTgfbr2 -/- mouse model

first: Charles

last: Powell

summary:
Recent data suggests that repression of the Type II TGF-B Receptor (Tgfr2) repression in human lung adenocarcinoma is important for progression from noninvasive to invasive adenocarcinoma. To test this hypothesis in a animal model of non-invasive lung cancer, we generated an inducible, lung specific Tgfbr2 knockout model in the oncogenic Kras mouse.
LSL-KrasG12D positive mice were simultaneously backcrossed to C57/Bl6 mice and to the Tgfbr2 flox/flox mice. To induce tumors, 100 ul of saline containing 3x10e10 particles of an adenovirus containing the Cre recombinase (Ad.Cre) was administered to each LSL-KrasG12D mouse intra-nasally.

overall_design: We evaluated the tumor microenvironment response to Tgfbr2 deficient tumor cells.  We compared lung tumor cell and stromal cell transcriptional profiles from five-week KrasTgfbr2 -/-  and nine-week KrasTgfbr2 WT mice. We used mice at these time points to allow comparison of the stromal compartment of similarly advanced tumors.


title: Genome-wide microarray analysis of immortalized human fibroblasts in response to alpha-particle radiation and the radiation induced bystander effect

status: Public on Sep 14 2011

city: Oslo

first: Erta

last: kalanxhi

address: Montebello 0310

country: Norway

institute: Oslo University Hospital

summary: The bystander effect from ionizing radiation consists of cellular responses generated from unirradiated cells to the irradiation of their neighbors. The bystander effect can lead to DNA damage and genomic instability in the affected cells. This non-targeted effect of radiation has received attention due to its potential implications for cancer therapy and radiation protection. Although studied extensively, a complete understanding of its molecular mechanism is the subject of ongoing research. While many studies have targeted specific factors which are suggested to be involved in the bystander effect, few have looked at whole genome gene expression in bystander cells. Furthermore, even fewer studies have looked at the expression in noncancerous human cell lines. In this study we have used a genome-wide microarray approach to investigate transcriptional responses in irradiated and bystander immortalized human fibroblasts following 0.1 Gy α-particle irradiation.

overall_design: Total RNA was isolated from F11hTERT fibroblasts irradiated with 0.1 Gy α-particles and bystander fibroblasts receiving medium from control (sham irradiated) and irradiated cells (0.1 Gy). RNA was isolated 4, 8 and 26 h after irradiation.

last: Kalanxhi

first: Jostein

last: Dahle


title: Cerebellar gene expression analysis of Gb5-deficient mice

status: Public on Sep 13 2011

city: Bethesda

first: WeiPing

last: Chen

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: Gb5 is a divergent, evolutionarily-conserved, member of the heterotrimeric G protein b subunit family that is expressed principally in brain and neuronal tissue.  Among Gb isoforms, Gb5 is unique in its ability to heterodimerize with members of the R7 subfamily of the regulator of G protein signaling (RGS) proteins that contain G protein-g like (GGL) domains.  Previous studies employing Gb5 knockout mice have shown that Gb5 is an essential stabilizer of GGL domain-containing RGS proteins and regulates the deactivation of retinal phototransduction and the proper functioning of retinal bipolar cells.  The purpose of this study is to better understand the functions of Gb5 in the brain outside the visual system by employing molecular biology, immunohistochemistry and confocal imaging technologies.  We show here that mice lacking Gb5 have a markedly abnormal neurologic phenotype that includes neurobehavioral developmental delay, wide-based gait, motor learning and coordination deficiencies, and hyperactivity.  Using immunohistochemical analysis and a green fluorescent reporter of Purkinje cell maturation we show that the phenotype of Gb5-deficient mice includes, in part, delayed development of the cerebellar cortex, an abnormality that likely contributes to the neurobehavioral phenotype.  Multiple neuronally-expressed genes are dysregulated in cerebellum of Gb5 KO mice.

overall_design: Brain tissues from WT and KO with three biological replications of mice were collected, frozen in liquid nitrogen, and stored at -70 °C

first: Jian-Hua

last: Zhang

first: Mritunjay

last: Pandey

first: Erica

last: Seigneur

first: Leelamma

last: Panicker

first: Lily

last: Koo

first: Weiping

first: Ching-Kang

first: William

last: Simonds


title: Differential gene expression profiles during embryonic heart development in diabetic mice pregnancy

city: Singapore

first: Srinivasan

last: Dinesh Kumar

address: 50 Nanyang Drive, Research Techno Plaza

department: Lee Kong Chian School of Medicine

country: Singapore

institute: Nanyang Technological University

summary: Congenital heart defects (CHD) are one of the most common defects in offspring of diabetic mothers. There is a clear association between maternal diabetes and CHD; however the underlying molecular mechanism remains unknown. We hypothesized that maternal diabetes affects with the expression of early developmental genes that regulate the essential developmental processes of the heart, thereby resulting in the pathogenesis of CHD. We analyzed genome-wide expression profiling in the developing heart of embryos from diabetic and control mice by using the oligonucleotide microarray. Microarray analysis revealed that a total of 878 genes exhibited more than 1.5 fold changes in expression level in the hearts of experimental embryos in either E13.5 or E15.5 compared with their respective controls. Expression pattern of genes that is differentially expressed in the developing heart was further examined by the real-time reverse transcriptase-polymerase chain reaction. Several genes involved in a number of molecular signaling pathways such as apoptosis, proliferation, migration and differentiation in the developing heart were differentially expressed in embryos of diabetic pregnancy. It is concluded that altered expression of several genes involved in heart development may contribute to CHD in offspring of diabetic mothers.

overall_design: Embryos with heart malformations from diabetic mice were used as the experimental samples. At least three or four embryos each from three or four different litters of diabetic or control groups were used for each microarray experiment (n = 3). Total RNA was extracted from the pooled embryonic heart tissues at E13.5 and E15.5 of diabetic and control groups using RNeasy micro kit (Qiagen, CA, USA). RNA was quantified by Nanodrop 1000 (Thermo Scientific, MA, USA) and its quality was determined using a Bioanalyzer (Agilent, CA, USA). For each sample, 100 ng of total RNA was used for the 3’ IVT Express assay according to Origen Labs SOP (Origen Labs, Singapore). The extracted total RNA was transcribed into cDNA, which was then used as a template to synthesize biotin-labeled aRNA (amplified RNA). The aRNA was then fragmented and hybridized to Affymetrix Mouse Genome 430 2.0 array(Affymetrix, CA, USA) for 16 hours at 45ºC with rotation at 60 rpm. Arrays were then washed and stained using the FS450_0004 fluidics protocol on 3 fluidics stations and scanned using an Affymetrix 3000 7G scanner (Affymetrix, CA, USA). The scanned images were inspected for hybridization efficiency. The raw data (CEL) files generated from GCOS (GeneChip Operating Software, Affymetrix, CA, USA) were imported into Expression Console (EC) 1.1 (Affymetrix, CA, USA) to perform the Mas5 normalization and generate the quality control (QC) metrics.

first: S

middle: D

last: Kumar

last: Tay


title: Mesenchymal stem cells and neural crest stem cells from adult bone marrow: characterization of their surprising similarities and differences

city: Liège

first: sabine

last: wislet

address: 1 avenue de l'hopital

department: GIGA-Neurosciences

country: Belgium

institute: university of Liège

summary: The generation of neuronal cells from stem cells obtained from adult bone marrow is of significant clinical interest in order to design new cell therapy protocols for several neurological disorders.  The recent identification in adult bone marrow of stem cells derived from the neural crests (NCSCs) might explain the neuronal phenotypic plasticity shown by bone marrow cells.  However, little information is available about the nature of these cells compared to mesenchymal stem cells (MSCs), their similarities and differences.  In this paper, using transcriptomic as well as proteomic technologies, we have compared NCSC to MSC and stromal nestin-positive cells, all of them isolated from adult bone marrow.  We demonstrated that the nestin-positive cell population, which was the first to be described as able to differentiate into functional neurons, was a mixed population of NCSC and MSC.  More interestingly, we demonstrated that MSC share with NCSC the same ability to truly differentiate into Tuj1-positive cells when co-cultivated with paraformaldehyde-fixed cerebellar granule neurons.  Altogether, those results suggest that both NCSCs and MSCs can be considered as important tools for cellular therapies in order to replace neurons in various neurological diseases.

overall_design:
Two sets of samples (NCSC and MSC), three biological replicates.

This submission represents the gene expression component of the study.

first: Sabine

last: Wislet-Gendebien

first: Emerence

last: Laudet

first: Virgini

last: Neirinckx

first: Pierre

last: Leprince

first: Aneta

last: Glejzer

first: Christophe

last: Poulet

first: Benoit

last: Hennuy

first: Lukas

last: Sommer

first: Olga

last: Shakova

first: Bernard

last: Rogister


title: Gene expression analysis of non-cerebellar portion of Gb5-deficient mice brain

first: WeiPing

last: Chen

summary: Gb5 is a divergent, evolutionarily-conserved, member of the heterotrimeric G protein b subunit family that is expressed principally in brain and neuronal tissue.  Among Gb isoforms, Gb5 is unique in its ability to heterodimerize with members of the R7 subfamily of the regulator of G protein signaling (RGS) proteins that contain G protein-g like (GGL) domains.  Previous studies employing Gb5 knockout mice have shown that Gb5 is an essential stabilizer of GGL domain-containing RGS proteins and regulates the deactivation of retinal phototransduction and the proper functioning of retinal bipolar cells.  The purpose of this study is to better understand the functions of Gb5 in the brain outside the visual system by employing molecular biology, immunohistochemistry and confocal imaging technologies.  We show here that mice lacking Gb5 have a markedly abnormal neurologic phenotype that includes neurobehavioral developmental delay, wide-based gait, motor learning and coordination deficiencies, and hyperactivity.  Using immunohistochemical analysis and a green fluorescent reporter of Purkinje cell maturation we show that the phenotype of Gb5-deficient mice includes, in part, delayed development of the cerebellar cortex, an abnormality that likely contributes to the neurobehavioral phenotype.  Multiple neuronally-expressed genes are dysregulated in non-cerebellar portion of Gb5 KO mice.

overall_design: Brain tissues(non-cerebellar portion of brain) from WT and KO with three biological replications of mice were collected, frozen in liquid nitrogen, and stored at -70 °C

first: Jian-Hua

last: Zhang

first: Mritunjay

last: Pandey

first: Erica

middle: M

last: Seigneur

first: Leelamma

last: Panicker

first: Lily


title: Knockout of heterotrimeric signaling G protein beta5 impaires brain development and causes severe neurologic dysfunction in mice

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

last: Koo

first: Weiping

first: Ching-Kang

first: William

last: Simonds


title: Expression and SNP data from fibroblasts, iPSCs and neurons with four copies of SNCA, and equivalent cell lines from an unaffected first degree relative

first: Tilo

last: Kunath

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

overall_design: Refer to individual Series from fibroblasts, iPSCs and neurons with four copies of SNCA, and equivalent cell lines from an unaffected first degree relative


title: Expression changes after loss of Dot1l in murine MLL-AF9 leukemia cells

city: Boston

first: Amit

last: Sinha

address: 44 Binney St

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary: MLL-fusions may induce leukemogenic gene expression programs by recruiting the histone H3K79 methyltransferase to MLL-target promoters. We evaluated gene expression changes after cre-mediated loss of Dot1l in leukemia cells obtained from mice injected with MLL-9 transformed lineage negative bone marrow cells.

overall_design: MLL-AF9 murine leukemia cells carrying two conditional Dot1l alleles were retrovirally transduced with Cre or empty control vector, and gene expression changes were monitored on day 3, 5, and 7 after transduction.

first: Kathrin

last: Bernt

first: Scott

last: Armstrong


title: Analysis of Gsk-3-Deficient Embryonic Stem Cells Reveals Large-Scale Alterations in Gene Expression

city: Columbus

first: Christopher

last: Phiel

state: OH

address: 700 Children's Drive W432

institute: The Research Institute at Nationwide Children's Hospital

summary: The two vertebrate Gsk-3 isoforms, Gsk-3a and Gsk-3b, are encoded by distinct genetic loci and exhibit mostly redundant function in murine embryonic stem cells (ESCs). Here we report that deletion of both Gsk-3a and Gsk-3b in mouse ESCs results in significant changes in gene expression. In contrast, deletion of either Gsk-3a or Gsk-3b individually had little effect on gene expression. These data support the notion that Gsk-3 isoforms are functionally redundant in embryonic stem cells. In addition, we did not find the expected upregulation of known Wnt target genes. Our data suggests that Gsk-3-meidated regulation of gene expression in embryonic stem cells is complex, and likely involves affects on numerous signaling pathways.

overall_design: The study was designed to examine the changes in gene expression between wild-type, Gsk-3a-/-, Gsk-3b-/-, and Gsk-3a-/-;Gsk-3b-/- mouse embryonic stem cells.

first: Anthony

middle: P

last: Popkie

first: Yulei

last: Wang

first: David

middle: E

last: Newsom

first: Joanna

last: Groden

first: Peter

last: White

first: Caifu

first: Bruce

last: Aronow


title: RNA-sequencing of left and right atrial

status: Public on Sep 10 2011

city: Cleveland

first: Jeff

last: Hsu

address: 9500 Euclid Ave

department: Cellular and Molecular Medicine

institute: Cleveland Clinic Lerner Research Institute

type: Expression profiling by high throughput sequencing

summary: The right and left atria have different susceptibilities towards developing arrhythmias, with left atrial arrhythmias more commonly observed.  To study potential underlying causes of this difference between the two upper chambers of the heart, four human left-right atrial pairs were subjected to whole-genome expression analyses via next generation sequencing of small RNAs, including microRNAs (miRNAs), and polyA enriched mRNAs.  Using a paired sample design, significant differences in gene expression were found between the left and right atria in both the poly-A and small RNA fractions.  Hsa-miR-143 was the most highly expressed miRNA in the atria as quantified by RNA-seq.  Gene expression differences established during development are retained into adulthood including that of PITX2 and BMP10.  In addition ten novel non-coding RNAs were found to be differentially expressed between the left and right atrias .

overall_design: Examination of mRNA and miRNA expression differences between the left and right atria from matched patient samples.  The title pattern is as follows (mRNA/miRNA)_tissue_patient.

first: Jonathan

last: Smith


title: Transcriptome of the Nxnl2-/- mouse retina

status: Public on Sep 12 2011

city: Illkirch/Strasbourg

first: Wolfgang

last: Raffelsberger

address: 1 rue Laurent Fries

department: DBGS

institute: IGBMC

summary:
A nxnl2 knockout mouse model was created and the transcriptome used to demonstrate that the retina is compromised by the absence of nxnl2.
For the mouse lacking Nxnl2, the gene encoding RdCVF2, the progressive decline of the visual performance of the cones in parallel with their degeneration arises due to loss of trophic support from RdCVF2

Keywords: genetic modification, transcription-profile, retina

overall_design: In total 6 samples were analyzed, they represent the genotypes wt/wt and ko/ko that were tested in triplicate each.

first: Céline

last: Jaillard

first: Aurélie

last: Mouret

first: Marie-Laure

last: Niepon

first: Lee-Rivera

last: Irene

first: Clerin

last: Emanuelle

first: Najate

last: Aït-Ali

first: Géraldine

last: Millet-Puel

first: Tina

last: Sedmak

first: Ying

last: Yang

first: Bernard

last: Kinzel

first: Alain

last: Trembleau

first: Olivier

last: Poch

first: Jean

last: Bennett

first: Uwe

last: Wolfrum

first: Marie-Pierre

last: Lledo

first: Jose-Alain

last: Sahel

first: Thierry

last: Leveillard


title: Brain BRCA1 conditional knockout

status: Public on Sep 08 2011

city: La Jolla

first: Gerald

last: Pao

address: 10010 North Torrey Pines

department: Laboratory of Genetics

institute: Salk Institute

summary:
BRCA1 nestin CRE conditional knockout cortrices of P7 animals were compared to wildtype littermates to characterize the mutant phenotype.
Keywords: expression

overall_design: BRCA1 conditional knockouts using nestin CRE and a null allele with an inverted  neo cassette at the 5' end of the exon 11 of BRCA1 on one floxed allele  flanking exons 5-13. Cortices of 3 wildtype animals were compred to 3 BRCA cKO at postnatal day 7.

first: Inder

last: Verma

first: Ling

last: Ouyang

first: Quan

last: Zhu


title: Necdin, a Negative Growth Regulator, is a Novel STAT3 Target Gene Down-Regulated in Human Cancer

status: Public on Sep 09 2011

city: Tampa

first: Steven

last: Eschrich

state: FL

address: 12902 Magnolia Drive

department: Biostatistics & Bioinformatics

institute: Moffitt Cancer Center

summary:
We took a broad approach to identify novel STAT3 regulated genes by examining changes in the genome-wide gene expression profile by microarray, using cells expressing constitutively-activated STAT3.  Using computational analysis, we were able to define the gene expression profiles of cells containing activated STAT3 and identify candidate target genes with a wide range of biological functions.
We demonstrated that STAT3 has an important role in regulating, both positively and negatively, a diverse array of cellular processes, including cell adhesion, cytoskeletal remodeling, nucleotide, lipid and protein metabolism, as well as signal transduction.  This suggest that STAT3 coordinates expression of genes involved in multiple metabolic and biosynthetic pathways, integrating signals that lead to global transcriptional changes and oncogenesis.

overall_design: Balb/c-3T3 mouse fibroblasts, v-Src 3T3 cells and STAT3-C 3T3 cells were grown in DMEM/10% bovine calf serum supplemented with 1% penicillin and streptomycin.  At each of 3 passages, cells from the five dishes were pooled and total RNA was extracted.

first: Rachel

last: Haviland

first: Gregory

last: Bloom

first: Yihong

last: Ma

first: Susan

last: Minton

first: Doug

last: Cress

first: Richard

last: Jove


title: Expression data from sorted epithelial CD34+ expressing cells from DMBA/TPA induced skin tumors

status: Public on Sep 07 2011

city: Brussels

first: Benjamin

last: Beck

address: Route de Lennik 808

department: IRIBHM

institute: ULB

summary: Transcriptional profile of control and VEGF overexpressing FACS-isolated CD34+ Cancer stem cells from DMBA/TPA induced skin tumours

overall_design: Tumours  were digested in collagenase I (Sigma) for 2 hours at 37°C on a rocking plate. Collagenase I activity was blocked by addition of EDTA (5mM) and then rinced in PBS supplemented with 2%FCS. After tumour digestion, cells were first incubated in PBS complemented with 30% FCS to block Fc receptors for 15 min at room temperature. Immunostaining was performed using biotin-conjugated anti-CD34 (clone RAM34; BD Pharmingen), FITC-conjugated anti-α6-integrin (clone GoH3; BD Pharmingen), PE-conjugated anti-CD45 (clone 30F11, eBiosciences), PE-conjugated anti CD31 (clone MEC13.3; BD Pharmingen), PE-conjugated anti-CD140a (clone APA5; eBiosciences), APC-Cy7-conjugated anti-Epcam (clone G8.8; Biolegend) by incubation for 30min on ice. Cells were washed and stained using APC-conjugated Streptavidin (BD Pharmingen) for 20min on ice. Living tumour cells were selected by forward scatter, side scatter and by Hoechst dye exclusion. Fluorescence-activated cell sorting analysis was performed using FACSAria and FACSDiva software (BD Biosciences). Sorted cells were collected in the lysis buffer provided by the manufacturer (Microprep kit, RNeasy, Stratagene) and RNA extraction was performed according to the manufacturer's protocol. Total RNA was analysed using Mouse whole genome 430 2.0 array from Affymetrix at the VIB microarray facility (KU – Leuven, Belgium).  We analyzed CD34+ TECs isolated by FACS from a K14CreER:Rosa-VEGF-164 and control mice. Analysis of the microarray was perfored by the VIB microarray facility (KU – Leuven, Belgium).

last: Driessens

first: Cedric

last: Blanpain


title: Genome-wide maps of histone modifications unwind in vivo chromatin states of the hair follicle lineage

status: Public on Sep 02 2011

first: Wen-Hui

last: Lien

address: 1230 York Ave Box#300

department: Mammalian cell biology and development

institute: The Rockefeller Unoversity

summary: Mouse hair follicles (HFs) undergo synchronized cycles. Cyclical regeneration and hair growth is fueled by stem cells (SCs). During the rest phase, the HF-SCs remain quiescent due to extrinsic inhibitory signals within the niche. As activating cues accumulate, HF-SCs become activated, proliferate, and grow downward to form transient-amplifying matrix progenitor cells. We used microarrays to detect the relative levels of global gene expression underlying the states of hair follicle stem cells and their transient-amplifying progeny before differentiation.

overall_design: Quiescent hair follicle stem cells (qHF-SCs), activated hair follicle stem cells (aHF-SCs) and transient-amplifying matrix cells (HF-TACs) were FACS-purified for RNA extraction and hybridization on Affymetrix microarrays. To obtain homogeneous populations of expression profiles, we applied the FACS technique to purify SC and TACs according to their cell surface markers.

first: Elaine

last: Fuchs


title: Genome-wide activity-dependent MeCP2 phosphorylation regulates nervous system development and function [cultured cortical neurons]

city: Brookline

first: Harrison

middle: Wren

last: Gabel

address: 7 Linden St Apt 3

department: Neurobiology

institute: Harvard Medical School

summary:
To examine potential differences in activity-dependent gene expression, we analyzed mRNA expression in cultured neurons isolated from Wild-type vs MeCP2 S421A mice at 0 (unstimulated), 1 or 6 hours after membrane depolarization by exposure to high extracellular KCl (55mM)
All mice were male littermates from one of three litters.

overall_design: We isolated RNA from dissociated cortical cultures (E16+7DIV) isolated from  Wild-Type or MeCP2 S421A knock-in mice littermates. Cells were either left unstimulated or depolarized for 1 or 6 hours by addition of 55mM KCl to the media.  mRNA expression was analyzed using the Affymetrix GeneChip Mouse Expression Set 430 2.0 microarray platform.

first: Sonia

last: Cohen

first: Martin

last: Hemberg

first: Ashley

middle: N

last: Hutchinson

first: L

last: Sadacca

first: Daniel

last: Ebert

first: David

last: Harmin

last: Greenberg

first: Zhaolan

last: Zhou

first: William

last: Wetsel

first: Anne

last: West

first: Michael


title: Expression data from quadriceps muscle of WT and ERRgamma transgenic mice

first: Ruth

middle: T

last: Yu

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

summary:
We show that the orphan nuclear receptor ERRg is expressed at high levels in type I muscle and when transgenically expressed in anaerobic type II muscles (ERRGO mice) or cultured cells, powerfully regulates VEGF expression, angiogenesis and vascular supply in absence of exercise.  ERRGO mice show increased expression of genes promoting fat metabolism, mitochondrial respiration and type I fiber specification.  In parallel, the type II muscle in ERRGO mice display an activated angiogenic program marked by myofibrillar induction and secretion of pro-angiogenic factors, frank neo-vascularization and a 100% increase in running endurance.  Surprisingly, the induction of VEGF and type I muscle properties by ERRg does not involve the transcriptional co-activator PGC1a.  Instead, ERRg genetically activates the energy sensor AMPK which is typically inactive in absence of exercise.  Therefore, ERRg and AMPK, known regulators of mitochondrial function and metabolism, together control a novel angiogenic pathway that anatomically synchronizes vascular arborization to oxidative metabolism revealing an exercise-independent mechanism for matching supply and demand.

Keywords: ERRgamma overexpression compared to wild-type

overall_design: Comparison of gene expression from quadriceps muscles isolated from wild type and alpha-skeletal actin-ERRgamma-transgenic mice.

first: Vihang

last: Narkar

first: Ronald

last: Evans


title: Expression data from Bmi1 mutant versus wild-type lung cells

first: Carla

last: Kim

address: 300 Longwood Ave

department: Hem/Onc, Stem Cell Program

institute: Children's Hospital Boston

summary:
Bmi1 is an important stem cell regulator in multiple tissues, including the lung.
We used microarrays to analyze the dysregulation of gene expression in the absence of Bmi1 in the lung, to identify pathways important in Bmi1-dependent lung stem cell regulation

overall_design: Primary lung cells (CD31-negative, CD45-negative) were FACS-isolated from Bmi1 wild-type or mutant mice; RNA was then extracted, amplified, and analyzed using Affymetrix Mouse Genome 430 2.0 Arrays.

first: Kim

last: Carla

first: Zacharek

last: Sima


title: Establishment of Enhancer Repertoires that Orchestrate the Myeloid and Lymphoid Cell Fates (gene expression dataset 1)

status: Public on Sep 01 2011

first: Yin

middle: Chun

last: Lin

address: 9500 Gilman Drive

department: Division of Biological Sciences

institute: UCSD

summary: Recent studies have documented genome-wide binding patterns of transcriptional regulators and their associated epigenetic marks in hematopoietic cell lineages. In order to determine how epigenetic marks are established and maintained during developmental progression, we have generated long-term cultures of hematopoietic progenitors by enforcing the expression of the E-protein antagonist Id2. Hematopoietic progenitors that express Id2 are multipotent and readily differentiate upon withdrawal of Id2 expression into committed B lineage cells, thus indicating a causative role for E2A in promoting the B cell fate. Genome-wide analyses revealed that a substantial fraction of lymphoid and myeloid enhancers are pre-marked by H3K4me1 in multipotent progenitors. However, H3K4me1 levels at a subset of enhancers are elevated during developmental progression, resulting in evolving enhancer repertoires that we propose orchestrate the myeloid and B cell fates.

overall_design:
ChIP-Seq and gene expression profiling were performed in an inducible hematopoietic pluripotent cell line that can be differentiated into multiple lymphoid lineages. This submission contains gene expression profiling data.

To characterize Id2-HPCs, we performed microarray analysis using RNA derived from cultured E2A-deficient cells, EBF-deficient cells and Id2-HPCs. Id2-HPC cells were cultured in IMDM medium supplemented with 10% FCS/2% PSG/β-me and IL7, Flt3-ligand, and SCF cytokines on S17 feeder cells in a humidified incubator at 37 degrees C with 5% CO2. Id2-HPC expanded cells were depleted of small (<1-5%) numbers of CD19-, CD25- and CD11b-positive cells by auto-MACS. E2A -/- and EBF -/- cells were cultured in IMDM supplemented with 10% FCS/2% PSG/β-me on S17 feeder cells in the presence of IL-7, Flt3-ligand, and SCF cytokines in a humidified incubator at 37 degree C with 5% CO2.

first: Elinore

last: Mercer

first: Christopher

last: Benner

first: Suchit

last: Jhunjhunwala

first: Janusz

last: Dutkowski

first: Martha

last: Flores

first: Mikael

last: Sigvardsson

first: Trey

last: Ideker

middle: K

last: Glass

first: Cornelis

last: Murre


title: Ciliary neurotrophic factor induces genes associated with inflammatory response and gliosis in the retina: A gene profiling study of flow-sorted, Muller (glial) cells

city: Rockville

first: Radu

last: Cojocaru

address: 5635 Fishers Lane, Suite 510

institute: Elsevier

summary: Our data suggest that CNTF remodels the transcription profile of Müller (glial) cells leading to induction of networks associated with transcription, cell cycle regulation and inflammatory response. CNTF also appears to function as an inducer of gliosis in the retina. These studies provide new insights into the biological functions of cytokines in the retina.

overall_design: Muller glial cells treated with CNTF for 1 and 3 days

first: Wei

last: Xue

middle: I

first: Joseph

middle: V

last: Dudley

first: Matthew

last: Brooks

first: Anand

last: Swaroop

first: Vijay

last: Sarthy


title: Pten deficiency cooperates with KrasG12D to activate NFkB pathway promoting the development of malignant pancreatic ductal adenocarcinoma

first: Haoqiang

last: Ying

address: 44 Binney St.

department: Medical Oncology

summary: Almost all human pancreatic ductal adenocarcinomas (PDACs) are driven by oncogenic Kras and the progression of the disease is characterized by the serial appearance of certain genetic lesions. Mouse models have convincingly shown that Kras mutation induces classical PanIN lesions that can progress to PDAC in the appropriate tumor suppressor background. However, the cooperative mechanism between mutant Kras-dependent signaling surrogates and other oncogenic pathways remains to be fully elucidated in order to devise better therapeutic strategy. Mounting evidence PTEN/PI3K perturbation on PDAC tumorigenesis, we observed frequent PTEN inactivation at both genomic and histopathological levels in primary human PDAC samples. The importance of PTEN/PI3K pathway during the development of PDAC was further supported by genetic studies demonstrating that Pten deficiency in cooperation with Kras activation accelerated the formation of invasive PDAC. Mechanistically, combined Kras mutation and Pten inactivation leads to NFkB activation and subsequent induction of cytokine pathways, accompanied with strong stromal activation and immune cell infiltration. Therefore, PTEN/PI3K pathway dictates the activity of NFkB network and serves as a major surrogate during Kras-mediated pancreatic tumorigenesis.

overall_design: Primary pancreatic ductal epithelial cell cultures were established from 6 week old Pdx1-Cre;LSL-KrasG12D L/+ (n=3) or  Pdx1-Cre;LSL-KrasG12D L/+;Pten L/+ (n=5) mice. Total RNA was collected from early passage cells.


title: Differential Gene and Transcript Expression Analysis with TopHat and Cufflinks

city: Cambridge

first: Cole

last: Trapnell

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary: This submission includes the sample data for a protocol covering differential expression analysis with TopHat and Cufflinks.  The protocol also covers several accessory tools and utilities that aid in managing data, including CummeRbund, a tool for visualizing RNA-Seq analysis results. While the procedure assumes basic informatics skills, these tools assume little to no background with RNA-Seq analysis and are meant for novices and experts alike. The protocol begins with raw sequencing reads and produces a transcriptome assembly, lists of differentially expressed and regulated genes and transcripts, and publication-quality visualizations of analysis results.

overall_design: The example data was generated in silico to closely resemble a real experiment in Drosophila melanogaster. First, expression values in cultured S2 cells were calculated for FlyBase 5.2 transcripts. These values were used to generate 3 sequencing replicates for condition "C1", with underlying variability in expression across replicates simulated by fitting a negative binomial model through the real S2 read count data. A second simulated condition "C2" was generated by perturbing expression for 300 randomly selected genes.  Genes were perturbed by selecting the most highly expressed isoform and increasing its relative expression by three fold.  Three replicates of this condtion were sequenced as above.  Simulated sequencing was performed by picking a transcript from the FlyBase transcriptome with equal to its abundance, choosing a fragment length from a normal distribution with mean = 180bp and standard deviation = 20bp, and then choosing a start point for the fragment within the transcript uniformly at random.  Total sequencing yield for each replicate was chosen to match that of the real S2 data. Each replicate was mapped to the fly genome with TopHat v 1.3.1 seperately.  The replicates were assembled seperately with Cufflinks v 1.1.0. The replicate assemblies were merged with Cuffmerge.  This merged assembly was then analysed for differentially expressed and regulated genes with Cuffdiff.

first: Adam

last: Roberts

first: Loyal

last: Goff

first: Geo

last: Pertea

first: Daehwan

last: Kim

first: David

last: Kelley

first: Harold

last: Pimentel

first: Steven

middle: L

last: Salzberg

first: John

last: Rinn

first: Lior

last: Pachter


title: The Role of microRNAs in Neural Stem Cell-supported Endothelial Morphogenesis

city: Albuquerque

first: Tamara

last: Roitbak

state: NM

address: 2212 Lomas NE

department: Neurosurgery

institute: UNM

summary: MicroRNA microarrays and RNA expression arrays were used to identify  functional signaling between neural stem cell progenitor cells (NSPC) and brain endothelial cells (EC) that are critical during embryonic development and tissue repair following brain injury.

platform_organism:
Mus musculus
synthetic construct

overall_design: Mouse neural stem /progenitor cells (NSPC) and brain endothelial cells (EC) were co-cultured to identify changes in gene and miRNA profiles induced in ECs under the influence of NSPCs

first: Olga

last: Bragina

first: Jamie

last: Padilla

first: Gavin

middle: G

last: Pickett


title: Expression data from 57 patients with oral cancer and 22 normal persons

city: Taoyuan

first: Chien-Hua

last: Peng

address: No. 5, Fu-Hsing ST.

country: Taiwan

institute: Chang Gung Memorial Hospital

summary:
In order to aid the development of patient-tailored diagnostics and therapeutics, we attempted to identify a genetic signature associated with disease prognosis in OSCC.  A genome-wide analysis of transcription with the Affymetrix GeneChip Human Gene 1.0 ST Array was conducted.
In this dataset, we include the expression data obtained from 57 specimens from patients with OSCC and 22 oral tissues from normal persons.

overall_design: 79 samples were analyzed. We compared gene expression levels between patients with and without OSCC. In addition, among 57 patients with OSCC, we also compared the expression levels between patients with and without amplicons scattered in chromosome 8q22.2~24.3.

first: Chun-Ta

last: Liao

first: Yin-Ju

last: Chen

first: Ann-Joy

last: Cheng

first: Jyh-Lyh

last: Juang

first: Chi-Ying

last: Tsai

first: Wen-Ping

last: Hsieh

first: Tzu-Chen

last: Yen


title: Global expression profiling of peripheral Qa-1 class Ib-restricted CD8aa+TCRab+ regulatory T Cells reveals innate-like features: implications for immune regulatory repertoire

first: Radu

last: Cojocaru

summary: To better understand the function of CD8aa Tregs, we have recently characterized several CD8aa+TCRab+ T cell clones and lines that are physiologically primed and are involved in recovery and protection from EAE (REF). In this report, we present a comparison of global gene expression patterns in CD8aa Tregs versus OT-1 CD8aa+TCRab+ T cells. The results of microarray data analysis are confirmed by real-time PCR and flow cytometry for better accuracy and phenotype expression. Our study reveals a unique gene signature in the CD8aa Tregs, including enhanced expression of several inhibitory molecules associated with the maintenance of peripheral T cell homeostasis. The identification of differentially expressed molecules by CD8aa Tregs should facilitate future functional studies in this area.

first: Shaohsuan

middle: S

last: Fanchiang

first: Mohammad

last: Othman

first: Ritu

last: Khanna

first: Matthew

middle: J

last: Brooks

first: Trevor

last: Smith

first: Xiaolei

last: Tang

first: Igor

last: Maricic

first: Anand

last: Swaroop

first: Vipin

last: Kumar


title: Expression data from GNMT knockout mice cerebral cortex

city: Taipei

first: Yi-Ming

middle: Arthur

state: Taiwan

address: 155, Li-Noun St., Sec. 2

department: AIDS Prevention and Research Center

institute: National Yang-Ming University

summary:
We report that Gnmt-/- mice have abnormal behavior including spontaneous locomotion activity, PPI, TST and FST. Microarray analysis showed that genes expression profiles  in male Gnmt -/- mice

Keywords: Gnmt knockout

overall_design: Cerebral cortex tissues from wild-type or Gnmt knockout mice were used for RNA extraction and hybridization on Affymetrix microarrays. For 4 weeks old mice, total RNA were mixed in equal proportion from 3 mice.

middle: A

first: Ching-Ping

last: Yang

first: Chia-Lang

last: Hsu

first: Ueng-Cheng