title: Location of indigenous human HSCs reveals functional properties of HSCs that are dictated by anatomic and cellular architecture of bone marrow I

summary: Demonstration of hematopoietic stem cells (HSCs) was first shown in the mouse and was dependent on recipient bone marrow (BM) to support in vivo multilineage hematopoietic reconstitution, thereby illustrating non-cell-autonomous requirements for HSC functions. Murine studies have defined microanatomic compartments in the BM comprised of osteoblasts, mesenchymal cells, subsets of vasculature, and innervating neural cells functioning as an HSC-supportive niche. Despite the potential clinical applications, analyses of putative HSCs in the BM of humans has not been examined. Here, using human bone biopsies, we provide evidence of HSC propensity to endosteal regions of Trabecular Bone Area (TBA). Independent of phenotypic definitions based on prospective isolation, functional studies indicate that human HSCs residing in the TBA of human and transplanted recipients had superior regenerative and self-renewal capacity and are molecularly distinct to those repopulating the Long Bone Area (LBA). Consistent with the non-cell-autonomous nature of HSC function, osteoblasts in the TBA possess unique characteristics and expressed a key network of factors including those involving Notch activity which could regulate TBA vs. LBA location of human HSCs in vivo. Our study illustrates that human-mouse xenografts provide a surrogate to indigenous human HSC in the BM, and demonstrates that BM architecture plays a critical role in defining functional properties of human HSCs.

overall_design: Lin- MNCs from human Umbilical Cord blood (CB) were injected via tail vein into sublethally irradiated NOD/SCID adult mice. After 10 weeks post-transplantation, engrafted-CB cells were sorted based on the co-expression of CD45 and CD34, and absence or presence of CD38 using a FACSAria II (BD). Total RNA from purified populations was extracted and amplified as described previously (Shojaei et al., 2005). Amplified-labeled RNA was hybridized to HG-U133Plus v2.0 chip.

first: Borhane

last: Guezguez

first: Clinton

middle: V

last: Campbell

first: Allison

middle: L

last: Boyd

first: Francis

last: Karanu

first: Fanny

last: Casado

first: Christine

last: Di Cresce

first: Tony

last: Collins

first: Zoya

last: Shapovalova

first: Anargyros

last: Xenocostas


title: Aerobic training modulation of the host systemic milieu directly alters breast cancer cell phenotype in vitro.

status: Public on Aug 01 2013

city: Durham

first: Jeff

last: Jasper

state: NC

department: Pharmacology and Cancer Biology

country: USA

institute: Duke University

summary: Aberrant production and/or function of multiple host systemic factors (e.g., metabolic and immune-inflammatory mediators) act in concert to promote a ‘tumorigenic’ host milieu that directly promotes an aggressive malignant phenotype as well as drug resistance. Hence, strategies with the capacity to simultaneously act across multiple host systemic pathways may be required to optimize therapeutic outcomes in solid tumors.  We hypothesized that chronic aerobic training, a pleiotropic whole-body intervention, modulates multiple systemic host pathways that, in turn, effectively alters cancer cell phenotype in vitro. Plasma samples from patients with solid tumors exposed to chronic aerobic training or sedentary control were comprehensively characterized for changes in immune, inflammatory, and metabolic pathways. Compared with sedentary control, aerobic training caused significant reductions in interleukin (IL)-4, macrophage inflammatory protein-1 beta (MIP1-β), vascular endothelial growth factor (VEGF), tumor necrosis factor-alpha (TNF-α), and hepatocyte growth factor (HGF). There were no significant changes in leukocyte phenotype or any plasma metabolite signatures. Exposure of estrogen receptor (ER) distinct human breast cancer cell lines (MCF-7 and MDA-MB-231) to post-intervention serum from breast cancer patients exposed to aerobic training caused marked increases in proliferation, migration, and apoptosis, compared to control patient serum. Only the combination of cytokines significantly reduced in plasma following aerobic training recapitulated the phenotype observed with patient serum in MCF-7 cells whereas only the single addition of MIP-1β or HGF significantly increased apoptosis in MDA-MB-231 cells. Co-culturing of MDA-MB-231 cells with patient exercise serum and a HGF neutralizing antibody increased proliferation and completely abrogated exercise serum-induced apoptosis. Finally, whole-genome microarray of MDA-MB-231 cells exposed to exercise or control patient serum revealed differential modulation of 310 genes including PTEN, CDK3, and IGFBP1. Our findings indicate the widespread potential of chronic aerobic training to modulate host immune-inflammatory systemic factors in patients with solid tumors. Modulation of such pathways directly alters breast cancer phenotypes providing novel insight into the molecular pathways by which exercise may inhibit malignant progression.

overall_design: MDA-MB-231 cells were plated at 250,000 cells/well in triplicate with 10% FBS in 6-well plates and left overnight to adhere. Media was suctioned off and replaced with serum free media. Patient serum was then added to the wells at a 10% final concentration and RNA was harvested using Qiagen RNeasy kit after 4 days.

first: Oliver

middle: K

last: Glass

first: Brant

middle: A

last: Inman

first: Gloria

last: Broadwater

first: Neil

last: Spector

first: Kerry

middle: S

last: Courneya

first: John

middle: R

last: Mackey

first: Erik

last: Nelson

first: Zachary

middle: C

last: Hartman

first: Catherine

middle: J

last: Field

first: Susan

last: Goruk

first: Matthew

middle: D

last: Hirschey

first: Lee

middle: W

last: Jones


title: Expression profiling of PBMC from patients with hepatocellular carcinoma

status: Public on Aug 03 2013

city: Singapore

first: Kam

last: Hui

address: 11 Hospital Drive

country: Singapore

institute: National Cancer Centre Singapore

summary: Aberrant gene expression analysis between peripheral blood mononuclear cell (PBMC) samples from healthy individuals and patients with pancreatic carcinoma, gastric carcinoma and hepatocellular carcinoma (HCC) were identified using Affymetrix gene arrays.

overall_design: Peripheral blood mononuclear cell (PBMC) from healthy individuals, patients with pancreatic carcinoma, gastric carcinoma and HCC were isolated and total RNA was extracted for Affymetrix gene microarray analysis.

middle: M


title: Expression data from homozygous deletion of the Lgi1 gene in murine neural precursor-like cells

city: Augusta

first: Mingqiang

last: Ren

state: GA

address: 1120 15th Street

department: Cancer Center

institute: Georgia Regents University

summary:
The hypercellularity in the outer layers of the cortex in Lgi1 null mice suggested that Lgi1 possibly plays a role in controlling cell migration dynamics. To investigate this hypothesis, we first generated and immortalized neural precursor-like cells (NPC), isolated from Lgi1 null and wild type mice at E13.5 stage using Large-T antigen. Subsequently, we compared gene expression patterns between the immortalized NPC-like cells with the two different Lgi1 genotypes using Affymetrix GeneChip Mouse Gene 1.0 ST Array.
Our studies suggest that Lgi1 has a role in regulating neuronal migration and their synapse formation and that its absence/dysregulation can result in seizure despite a histologically subtle cortical dysplastic phenotype.

overall_design: RNAs were extracted from the null and wild type NPC cells, respectively. The samples were biologically triplicated. RNA samples were hybridized to Mouse Gene 1.0 ST Array.

first: Silva

last: Jeane

first: Cowell

last: John


title: BET Bromodomains Mediate Transcriptional Pause Release in Heart Failure [Mouse Heart Expression]

status: Public on Aug 06 2013

city: Boston

first: James

last: Bradner

state: MA

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Heart failure (HF) is driven via interplay between master regulatory transcription factors and dynamic alterations in chromatin structure. While pathologic gene transactivation in this context is known to be associated with recruitment of histone acetyl-transferases and local chromatin hyperacetylation, the role of epigenetic reader proteins in cardiac biology is unknown. We therefore undertook a first study of acetyl-lysine reader proteins, or bromodomains, in HF. Using a chemical genetic approach, we establish a central role for BET-family bromodomain proteins in gene control during HF pathogenesis. BET inhibition potently suppresses cardiomyocyte hypertrophy in vitro and pathologic cardiac remodeling in vivo. Integrative transcriptional and epigenomic analyses reveal that BET proteins function mechanistically as pause-release factors critical to activation of canonical master regulators and effectors that are central to HF pathogenesis and relevant to the pathobiology of failing human hearts. This study implicates epigenetic readers in cardiac biology and identifies BET co-activator proteins as therapeutic targets in HF.

overall_design: Gene expression analysis of mouse hearts subjected to either trans aortic constriction (TAC) or sham surgeries followed by treamtent with dmso vehicle or the BET bromodomain inhibitor JQ1

first: Priti

last: Anand

first: Jonathan

last: Brown

first: Charles

middle: Y

last: Lin

first: Jun

last: Qi

first: Madeleine

last: Lemieux

first: Saptarsi

last: Haldar


title: Expression data from Control, Uninfected and BRAF infected cells

city: Glasgow

first: Peter

middle: D.

last: Adams

address: Switchback Rd, Bearsden

country: United Kingdom

institute: University of Glasgow, Beatson Institute for Cancer Research

summary:
Melanocytes within benign human nevi are the paradigm for tumor suppressive senescent cells in a pre-malignant neoplasm. These cells typically contain mutations in either the BRAF or N-RAS oncogene and express markers of senescence, including p16. However, a nevus can contain 10s to 100s of thousands of clonal melanocytes and approximately 20-30% of melanoma are thought to arise in association with a pre-existing nevus. Neither observation is indicative of fail-safe senescence-associated proliferation arrest and tumor suppression. We set out to better understand the status of nevus melanocytes. Proliferation-promoting Wnt target genes, such as cyclin D1 and c-myc, were repressed in oncogene-induced senescent melanocytes in vitro, and repression of Wnt signaling in these cells induced a senescent-like state. In contrast, cyclin D1 and c-myc were expressed in many melanocytes of human benign nevi. Specifically, activated Wnt signalling in nevi correlated inversely with nevus maturation, an established dermatopathological correlate of clinical benignancy. Single cell analyses of lone epidermal melanocytes and nevus melanocytes showed that expression of proliferation-promoting Wnt targets correlates with prior proliferative expansion of p16-expressing nevus melanocytes. In a mouse model, activation of Wnt signaling delayed, but did not bypass, senescence of oncogene-expressing melanocytes, leading to massive accumulation of proliferation-arrested, p16-positive non-malignant melanocytes. We conclude that clonal hyperproliferation of oncogene-expressing melanocytes to form a nevus is facilitated by transient delay of senescence due to activated Wnt signaling. The observation that activation of Wnt signaling correlates inversely with nevus maturation, an indicator of clinical benignancy, supports the notion that persistent destabilization of senescence by Wnt signaling contributes to the malignant potential of nevi.
We used microarrays to detail the global programme of gene expression after lentiviral infection of BRAF in 3 replicates.

overall_design: Primary human melanocytes were infected/uninfected with lentivirus containing either an Empty Vector or activated BRAFV600E mutant in three biological replicates

first: Jeff

last: Pawlikowski

first: Tony

last: McBryan


title: Expression data from H295R cells in basal conditions/overexpressing SF-1

city: Valbonne

first: Enzo

last: LALLI

address: 660 route des Lucioles

department: CNRS UMR 7275

country: France

institute: IPMC

summary:
SF-1 is a nuclear receptor transcription factor playing a key role in adrenogonadal development and in adrenocortical tumorigenesis when overexpressed.
We studied gene expression profiles using Affymetrix microarrays in the H295R/TR SF-1 adrenocortical cancer cell line, where SF-1 expression can be increased in a doxycycline-dependent manner (Mol. Endocrinol. 21: 2968–2987, 2007)

overall_design: H295R/TR SF-1 cells were cultured either in basal conditions or with doxycycline (Dox) added to the culture medium for 72 hours. RNA was extracted and hybridized to HG-U133 Plus 2.0 Affymetrix microarrays.

last: Lalli


title: 27-Hydroxycholesterol links cholesterol and breast cancer pathophysiology.

last: Jasper

summary:
The cholesterol metabolite and SERM, 27HC, is the signaling molecule that links cholesterol to breast cancer pathophysiology
Hypercholesterolemia is a risk factor for breast cancer, and patients taking statins demonstrate lower breast cancer incidence and decreased breast cancer recurrence, data that highlights the potential importance of the recent finding that 27-Hydroxycholesterol (27HC), a primary metabolite of cholesterol, acts as a selective estrogen receptor modulator (SERM). The goal of this study was to evaluate the impact of 27HC on breast cancer pathophysiology. Elevation of 27HC in murine models increased tumor growth in an estrogen receptor dependent manner. Importantly, a high cholesterol diet decreased the time to tumor onset and increased tumor growth, and this response required presence of CYP27A1. Within human breast cancer samples, CYP27A1 expression increasesd with grade, in addition to being highly expressed in tumor associated macrophages. Finally 27HC increases metastasis to the lung. The findings herein strongly support a role for 27HC in breast cancer pathophysiology, providing support for the exploration of potential chemopreventative benefits of lower cholesterol diets, and pharmacological inhibitors of HMG-CoA reductase or CYP27A1.

overall_design: MCF-7 cells were treated as indicated in the presence of E2 or vehicle; RNA was isolated and used for preparation of label for 3' expression analysis.

first: Erik

last: Nelson

first: Suzanne

middle: E

last: Wardell

first: Donald

middle: P

last: McDonnell


title: Expression data from the reproductive tracts of WT, Hoxa9,10,11, and Hoxd9,10,11 mutant mice

city: Cincinnati

first: Steve

last: Potter

state: OH

address: 3333 Burnet Ave.

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

summary: Hox genes are key regulators of development. In mammals, the study of these genes is greatly confounded by their large number, overlapping functions, and their interspersed shared enhancers. In this report, we describe a novel recombineering strategy that was used to introduce simultaneous frameshift mutations into the flanking Hoxa9, Hoxa10, and Hoxa11 genes, as well as their paralogs on the HoxD cluster. The resulting mutant mice displayed dramatic homeotic transformations of the reproductive tracts, with uterus anteriorized towards oviduct and the vas deferens anteriorized towards epididymis. The Hoxa9,10,11 mutant mice provided a sensitized genetic background that allowed the discovery of Hoxd9,10,11 reproductive tract patterning function. Both shared and distinct Hox functions were defined. The HoxD genes played a crucial role in the regulation of the uterine immune function. Non-coding nonpolyadenylated RNAs were among the key Hox targets. In addition, we observed a surprising anti-dogmatic posteriorization of the uterine epithelium.

overall_design: Reproductive tracts were collected from WT and Hox mutant mice (n=3/genotype) aged 3-7 months in order to characterize the molecular changes caused by mutation of Hoxa9,10,11 and Hoxd9,10,11. Female mice were staged and collected in diestrus.

first: Anna

last: Raines

first: Mike

last: Adam

first: Bliss

last: Magella

first: Sara

last: Meyer

first: H

last: Grimes

first: Sudhansu

last: Dey

first: S


title: Expression profiling of human medulloblastoma cell line ONS76 upon siRNA-mediated knockdown of KDM5A/LSD1

city: Essen

first: Alexander

last: Schramm

address: Hufelandstr. 55

department: Childrens Hospital

country: Germany

institute: University Hospital Essen

summary: KDM5A/LSD1 is an important epigenetic regulator in medulloblastoma, the most frequent brain tumor of childhood. Here, the response of ONS76 medulloblastoma cells upon siRNA-mediated knockdown of KDM5A is analysed.

overall_design: The expression profile of ONS76 cells upon KDM5A knockdown was compared to mock control. Both conditions were run in triplicate.

first: Kristian

last: Pajtler


title: Combinatorial treatment of DNMT inhibitor and LSD1 inhibitor results in cell growth inhibition and reexpression of epigenetically silenced genes (methylation)

city: Los Angeles

first: Xiaojing

last: Yang

state: CA

address: 1441 Eastlake Ave, Room 7336

institute: USC/Norris Comprehensive Cancer Center

summary: A combinatorial treatment consisting of a DNMTi and a LSD1i shows synergistic effects in reactivating aberrantly silenced genes by enriching H3K4me2 and H3K4me.

overall_design: Bisulphite converted DNA from the 8 samples were hybridised to the Illumina Infinium HM450 Human Methylation Beadchip

first: Han

last: Han


title: Identification of a core cross-regulatory neurogenic network regulated by the transcription factor Pax6 interacting with Brg1-containing SWI/SNF chromatin remodeling complex

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary:
The molecular mechanisms of neurogenic fate determination are of particular importance in light of the need to regenerate neurons. However the molecular logic of neurogenic fate determination is still ill understood, even though some key transcription factors have been implicated. Here we describe how one of these, the transcription factor Pax6, regulates adult neurogenesis by initiating a cross-regulatory network of 3 transcription factors executing neuronal fate and regulating genes required for neuronal differentiation. This network is initiated and driven to sufficiently high expression levels by the transcription factor Pax6 in close interaction with Brg1-containing SWI/SNF chromatin remodeling factors.
Genetic deletion of either Pax6 or Brg1, the ATPase unit of the SWI/SNF complex, in neural stem cells of the adult mouse subependymal zone results in a fate conversion to distinct glial subtypes most pronounced when neuroblasts leave the neurogenic niche. Consistent with the phenocopy in vivo virtually all genes down-regulated by Brg1 deletion have Pax6-binding motifs. Amongst the few down-stream transcription factors are Sox11, Nfib and Brn4 that crossregulate each other and rescue neurogenesis also in direct reprogramming in the absence of Brg1 (or Pax6). Thus the function of Pax6-SWI/SNF is necessary and sufficient for neuronal fate maintenance and initiates a cross-regulatory effector network required for neuronal fate execution and maintenance to counteract glial differentiation in the adult brain. This identifies a novel role highly specific role of a chromatin-remodelling complex in stabilizing fate decisions in normal and forced neurogenesis.

overall_design: We performed gene expression microarray analysis on tissue derived from the SEZ or from the core region of the olfactory bulb from Brg1 cKO and control mice

first: Jovica

last: Ninkovic

first: Martin

last: Irmler

first: Magdalena

last: Goetz


title: Genes regulated by SDC1

first: George

last: Yip

address: 4 Medical Drive, Block MD10

institute: National University of Singapore

summary: We used Affymetrix HG U133 Plus 2.0 GeneChips to compare the transcriptome of MDA-MB-231 cells transfected with SDC1-siRNA against negative control siRNA-transfected cells.

overall_design: MDA-MB-231 cells were transfected with SDC1-siRNA or negative control siRNA. Subsequently, total RNA was collected and processed for analysis using Affymetrix microarrays. Three independent replicates were prepared for each comparison group.

first: G

first: M

last: Götte


title: Combinatorial treatment of DNMT inhibitor and LSD1 inhibitor results in cell growth inhibition and reexpression of epigenetically silenced genes

type:
Expression profiling by array
Methylation profiling by array

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

overall_design: Refer to individual Series


title: RB pathway deregulation promotes invasion and disease progression in a mouse model of MYC-overexpressing mammary tumorigenesis

city: PHILADELPHIA

first: Adam

last: Ertel

state: PA

address: 233 S 10TH ST

department: Cancer Biology

institute: Thomas Jefferson University

summary: Breast cancer is a highly heterogeneous disease that is categorized into distinct tumor subtypes based on specific molecular attributes, which ultimately influence therapeutic options. Unlike ER+ and/or HER2+ cancers that are subject to specific targeted therapies, triple negative breast cancers (TNBCs) do not express these receptors, which leaves patients with limited treatment options. Thus, significant focus has been placed on identifying molecular attributes of basal-like disease that could be used to develop and/or direct novel treatment regimens. Activation of MYC signaling and inactivation of the RB-pathway are frequent events in many types of human cancers. These pathways influence many biological processes, such as cell proliferation, that contribute to the aggressiveness and therapeutic response of tumors. The current study examines the interaction of the MYC and RB pathways in mammary epithelial cell tumorigenesis.

overall_design: Mouse mammary epithelial cells were isolated and sub-cultured. Adenoviral expression of Cre-recombinase was used to delete the RB and/or p53 genes, and retrovirus was used to achieve MYC overexpression (OE). Proliferating cells were harvested for each condition, and RNA was isolated for analyses.

first: A

last: McClendon

first: Justine

last: Yu

first: Jeffry

last: Dean

first: Dayana

middle: B

last: Rivadeneira

first: Erik

last: Knudsen


title: IDENTIFICATION OF BIOMARKERS OF RESPONSE TO IFNG DURING ENDOTOXIN TOLERANCE: APPLICATION TO SEPTIC SHOCK

status: Public on Jul 31 2013

city: Lyon

first: Florence

last: Frager

address: 5 place d'arsonval

department: LCR HCL-biomérieux

institute: biomerieux

summary: The rapid development in septic patients of features of marked immunosuppression associated with increased risk of nosocomial infections and mortality represents the rational for the initiation of immune targeted treatments in sepsis. However, as there is no clinical sign of immune dysfunctions, the current challenge is to develop biomarkers that will help clinicians identify the patients that would benefit from immunotherapy and monitor its efficacy.  Using an in vitro model of endotoxin tolerance (ET), a pivotal feature of sepsis-induced immunosuppression in monocytes, we identified using gene expression profiling by microarray a panel of transcripts associated with the development of ET which expression was restored after immunostimulation with interferon-gamma (IFN-γ). These results were confirmed by qRT-PCR. Importantly, this short-list of markers was further evaluated in patients. Of these transcripts, six (TNFAIP6, FCN1, CXCL10, GBP1, CXCL5 and PID1) were differentially expressed in septic shock patients’ blood compared to healthy blood upon ex vivo LPS stimulation and were restored by IFN-γ.   In this study, by combining a microarray approach in an in vitro model and a validation in clinical samples, we identified a panel of six transcripts that could be used for the identification of septic patients eligible for IFNg therapy. The potential value of these markers should now be evaluated in a larger cohort of patients. Upon favorable results, they could serve as stratification tools prior to immunostimulatory treatment and to monitor drug efficacy.

overall_design: PBMCs from 6 healthy donor were left unstimulated (medium) or with 1 shot of LPS (LPS unprimed), 2 shots of LPS (LPS primed) or 2 shots of LPS and Interferon gamma (LPS primed + IFNg).

last: Allantaz-Frager

first: Fanny

last: Turrel-Davin

first: Fabienne

last: Venet

first: Cécile

last: Monnin

first: Amélie

last: De Saint Jean

first: Véronique

last: Barbalat

first: Elisabeth

last: Cerrato

first: Alexandre

last: Pachot

first: Alain

last: Lepape

first: Guillaume

last: Monneret


title: Affymetrix microarray and qRT-PCR expression profile of HEK293 cells stably transfected with PRL-1 (PTP4A1) or empty pcDNA4 vector (control)

status: Public on Jul 30 2013

city: Indianapolis

first: Carmen

middle: M.

last: Dumaual

state: IN

address: 723 West Michigan St., Room SL306

department: Biology

institute: Indiana University-Purdue University Indianapolis

type:
Expression profiling by array
Expression profiling by RT-PCR


title: Gene expression on in vitro activated DCs

first: Francisco

last: Quintana

address: 77 Ave Louis Pasteur

department: Center for Neurological Diseases

institute: Harvard Medical Institute

summary:
We have analyzed the effects of IL-27 signaling in dendritic cells (DCs) in the activation and polarization of effector and regulatory T cells, and the development of experimental autoimmune encephalomyelitis, an experimental model of multiple sclerosis.
In this dataset, we include the results of treating DCs with IL-27.

overall_design: Primary splenic C57BL/6 DCs were isolated, cultured in vitro +/- IL-27 and RNA was prepared.

first: Ivan

last: Mascanfroni

first: Bonny

last: Patel


title: Expression profile of HEK293 cells stably transfected with PRL-1 (PTP4A1) or empty pcDNA4 vector (control)

summary:
The multifunctional protein tyrosine phosphatase PRL-1 (Gene Symbol:  PTP4A1) has been identified as an important oncogene with roles in promoting cell proliferation, survival, migration, invasion, and metastasis.  However, little is currently known about the signaling pathways through which it mediates its effects.
We used Affymetrix Human Genome U133 Plus 2.0 arrays to examine the global molecular changes of gene expression occurring in response to stable PRL-1 overexpression in human embryonic kidney 293 (HEK293) cells.

overall_design: Total RNA was extracted from triplicate cultures of HEK293 cells stably overexpressing PRL-1 (HEK293-PRL-1) and HEK293 cells stably transfected with empty pcDNA4 vector (HEK293-Vector).  Samples were hybridized to Affymetrix HG U133 Plus 2.0 microarrays (1 array per sample for a total of 6 arrays).  One of the arrays hybridized with a PRL-1 transfected sample was excluded after qRT-PCR demonstrated that this sample did not exhibit increased PRL-1 expression over the level of the empty vector controls.  The remaining 2 HEK293-PRL-1 samples both expressed PRL-1 at least 2-fold higher than any of the 3 empty vector controls.

first: Boyd

last: Steere


title: Genes regulated by AGR2 in pancreatic cancer cell lines FA6 and MiaPaCa2

status: Public on Jul 28 2013

city: London

first: Hannah

last: Whiteman

address: Charterhouse Square

institute: QMUL

summary:
We and others have shown that AGR2 is frequently upregulated during the development of pancreatic cancer.
We used microarray to look at the target genes regulated by AGR2 in pancreatic cancer cell lines FA6 and MiaPaCa2.

Keywords: gene knock-down, overexpression

overall_design:
We transiently down-regulated AGR2 expression in FA6 pancreatic cancer cells using INTERFERin transfection reagent and either AGR2 siRNA or non-targeting control siRNA for 48 hours. RNA was extracted and hybridized on Affymetrix microarrays. We looked for new target genes regulated by AGR2.

We generated stable cell lines by introducing control vector pCEP4 or AGR2 overexpressing vector pCEP4-AGR2 into the pancreatic cancer cell line MiaPaCa2, single cell clones were then isolated. RNA was extracted and hybridized on Affymetrix microarrays.We looked for new target genes regulated by AGR2.

first: Teresa

last: Brentnall

first: Claude

last: Chelala

first: Mary

last: Bronner

first: Mark

last: Weeks

first: Roger

last: Feakins

first: Deepak

last: Hariharan

first: Nicholas

last: Lemoine

first: John

middle: F

last: Timms

first: Tatjana

last: Crnogorac-Jurcevic


title: Expression data from Klf4 KD cells in the presence and absence of TGFβ in NMuMG cells

status: Public on Jul 24 2013

city: Basel

first: Neha

last: Tiwari

address: Mattenstrasse 28

country: Switzerland

institute: University of Basel

summary: Expression profiling after Klf4 KD during EMT in NMuMG reveals a significant number of genes that are transcriptionally deregulated

overall_design: Gene expression profiling is performed in Klf4 ablated (siKlf4) NMuMG cells. Cells transfected with siControl is used as a control. The cells were either treated with TGFβ (2ng/ml) or not.


title: Expression data for knockdown of H2ac in E2-treated MCF-7 cell lines

city: Taipei

first: CH

last: Su

address: Li-Long

country: Taiwan

institute: YMGC

summary: Estrogens(E2) are important steroid hormones that regulate differentiation, proliferation, and apoptosis in hormone-dependent breast cancer.In order to detect the E2-dependent transcription program associated with the observed cell cycle response, we analyzed the effect of H2ac knockdown on MCF-7 gene expression using microarray. Interestingly, we noticed that 51% of the E2-upregulated genes are down-regulated by depletion of H2ac. The data also show that H2ac regulated E2-dependent genes through E2-induction signaling pathway.

overall_design: MCF-7 cell line was transfected with scrambled or H2ac siRNA in the absence or persence of E2.

first: Chia-Hsin

first: Ching

last: Cheng

first: Ming-Ta

last: Hsu


title: Gene expression profile of mutated and wild-type PMF CD34+ cells

status: Public on Jul 23 2013

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

summary:
Primary mielofibrosis (PMF) is a rare chronic myeloproliferative disorder characterized by the accumulation of abnormal megakaryocytes (Mks) in the bone marrow (BM), variable degrees of BM fibrosis, osteosclerosis and angiogenesis, immature myeloid and erythroid cells, and tear-drop erythrocytes in the peripheral blood (PB), and extramedullary hematopoiesis. The identification of the JAK2V617F mutation represented a seminal discovery in the field of Philadelphia-chromosome–negative chronic myeloproliferative neoplasms (MPNs), providing clues to the pathogenesis, prompting a revision of the diagnostic criteria, and culminating in the development of clinical trials with JAK2 (and JAK1) inhibitors. The JAK2V617F mutation occurs in almost all patients with polycythemia vera (PV) and in 50%-70% of those with essential thrombocythemia (ET) and primary myelofibrosis (PMF). Soon after the identification of the JAK2V617F mutation, mutations in JAK2 exon 12 were described in rare patients with JAK2V617F-negative PV and mutations in MPL were reported in 5%-10% of ET or PMF subjects. The complexity of the molecular pathogenesis of MPNs is reinforced by discovery of additional mutations in TET2, ASXL1, CBL, IDH1/IDH2, EZH2 and IKZF1. These mutations are detected in a minority of patients at different phases of the disorder, including leukemic transformation, and are variably associated each other and with JAK2 or MPL mutations.
In order to better characterize biological differences between mutated and wild-type PMF cell populations we performed a gene expression profiling on 9 samples carrying at least one mutation in ASXL1, SRSF2 or EZH2 genes and 11 wild-type samples using the Affymetrix GeneChip technology. After data preprocessing and filtering a supervised analysis approach was used to define a gene expression signature for mutated samples. PMF samples carrying at least one mutation in ASXL1, SRSF2 or EZH2 genes exhibit a specific molecular signature as compared with WT samples.

overall_design: Gene expression profile (GEP) of CD34+ cells from 20 PMF patients (1 replicate for each sample). In particular, GEP was performed on 9 samples carrying at least one mutation in ASXL1, SRSF2 or EZH2 genes and 11 wild-type  samples.

first: Paola

last: Guglielmelli

first: Flavia

last: Biamonte

first: Ambra

last: Spolverini

first: Alessandro

last: Pancrazzi

first: Lisa

last: Pieri

first: Tiziana

last: Fanelli

first: Paoli

last: Chiara

first: Costanza

last: Bogani

first: Alberto

last: Bosi

first: Roberta

last: Zini

first: Enrico

last: Tagliafico

first: Daniela

last: Pietra

first: Elisa

last: Rumi

first: Gianni

last: Barosi

first: Mario

last: Cazzola

last: Vannucchi


title: NRSF/REST knockdown, and SF-1 overexpression and knockdown

first: Enzo

last: LALLI


title: Microarray characterization of gene expression changes in blood during acute ethanol exposure

status: Public on Jul 25 2013

city: Oklahoma City

first: Dennis

last: Burian

state: OK

address: 6500 S. MacArthur Blvd., AAM610

department: Aviation Medicine

institute: Federal Aviation Administration

summary: As part of the civil aviation safety program to define the adverse effects of ethanol on flying performance, we present results of our DNA microarray analysis of samples from a timecourse study of individuals given ethanol orally, and then evaluated by breathalyzer to monitor blood alcohol content (BAC). At five blood alcohol levels, T1-T5, blood was drawn such that the samples represented 0%, 0.04%, 0.08% BAC, and return to 0.04%, and 0.02% BAC. Microarray analysis showed that changes in gene expression could be detected across the time-course. We verified these expression changes by quantitative polymerase chain reaction (qPCR). Candidate target genes identified from the microarray analysis were clustered by expression change pattern, examined for shared functions and functional network membership. Five coordinately expressed groups were revealed and functional analysis showed shared transcription factor binding sites and functions for members of the clusters. These functions include protein synthesis and modification, expected for changes in gene expression, hematological and immune functions, expected for a blood sample, and pancreatic and hepatic function, expected as response to ethanol. The results provide a first look at changing gene expression patterns in blood during acute increase of ethanol concentration and its depletion due to metabolism or excretion and demonstrate that it is possible to detect significant changes in gene expression using total RNA isolated from whole blood. The analysis approach for this study can be utilized as part of a workflow to identify target genes by timecourse changes in gene expression that may affect pilot performance.

overall_design: Blood samples were collected from six male subjects given a mixture of orange and vodka such that their BAC would reach a maximum level of 0.08%. Five blood samples, T1-5, were taken from each subject, 0% prior to drinking alcohol, 0.04% and 0.08% as their BAC increased and 0.04% and 0.02% BAC as the alcohol concentration declined. Blood samples were taken from a control set of five male subjects drinking only orange juice. Five sample collections at times averaged from the ethanol blood draws were performed. Total RNA was isolated from all samples. All samples were hybridized to microarrays to examine gene expression changes over the timed exposure to ethanol. One experimental sample failed. The remaining samples for Subject 18, T1-3, T5 were included in the study. There are 29 arrays for the experimental samples and 25 arrays for the control set of samples. There are separate RMA files for the experimental series and for the control series.

first: D

last: Kupfer


title: Transcriptome comparison of murine wild-type and dumbo retinas at P15

city: SION

first: Arnaud

last: Boulling

address: Avenue de Grand-Champsec 64

institute: Institute for Research in Ophthalmology

summary: Hmx1 is a transcription factor expressed in the developing eye and ear and in some other parts of the nervous system. Dumbo mice are carrying the Hmx1 p.Q64X loss-of-function mutation (Munroe et al., 2009. BMC Developmental Biology). Transcriptomic analyses of this mouse model allows to decipher biological pathways under the control of Hmx1. In our study, we used it to better understand the role of Hmx1 in the retina and to identify several of its target genes.

overall_design: Wild-type and dumbo mice were maintained in a 12-hours light/12-hours dark cycle with free access to food and water. Animals were sacrified at P15 for retina isolation and RNA extraction.

first: Daniel

last: Schorderet


title: Expression data from G9a knockdown ovarian cancer cell

status: Public on Jul 18 2013

first: kuo-tai

last: hua

address: No.2, Xu-Zhou Road

institute: National Taiwan University

summary:
G9a depleted SKCO3 cells were used to identify genes regulated by G9a-dependent epigenetic regulations
We used microarrays to detail the global programme of gene expression underlying paritoneal dissemination and identified distinct classes of G9a-regulated genes during this process.

overall_design: SKOV3 cells receiving G9a-specific shRNAs were analyzed compare to cells receiving control shRNA

first: Kuo-Tai

last: Hua

first: Min-Liang

last: Kuo

first: Men-Luh

last: Yen


title: Dietary heme modulates microbiota and mucosa of mouse colon without significant host-microbe cross talk

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Previously, we showed that dietary heme injured the colonic surface epithelium and induced hyperproliferation by changing the surface to crypt signaling. In this study we investigated whether bacteria play a role in this changed signaling. Dietary heme increased the Bacteroidetes and decreased the Firmicutes in colonic content. This shift was caused by a selective susceptibility of Gram-positive bacteria to the heme cytotoxic fecal waters, which is not observed for Gram-negative bacteria allowing expansion of the Gram-negative community. The increased amount of Gram-negative bacteria increased LPS exposure to colonocytes, however, there is no appreciable immune response detected in the heme-fed mice. There were no signs of sensing of the bacteria by the mucosa, as changes in TLR signaling were not present. This lack of microbe-host cross talk indicated that the changes in microbiota do not play a causal role in the heme-induced hyperproliferation.

overall_design: Mice received control or heme diet for 14 days, whereafter pooled colon samples were analysed on microarrays.

first: Noortje

last: IJssennagger

first: Anneke

last: Rijnierse

first: Michael

last: Muller

first: Roelof

middle: v

last: Meer


title: Expression data from human NHL cell lines treated with agonistic antibodies

city: Penzberg

first: Helmut

last: Burtscher

address: Nonnenwald 2

institute: Roche Pharma

summary:
CD20 is a clinically validated target for Non-Hodgkin’s lymphomas and autoimmune diseases. Interactions of CD20 with the B cell receptor (BCR) and components of the BCR signaling cascade have been reported. In this study we show that antibodies against CD20 or activation of the BCR by specific antibodies induce very similar expression patterns of up- or down-regulated genes in NHL cell lines indicating that CD20 may play a role in BCR signaling and vice versa.
We used microarray data to show that antibodies against CD20 or activation of the BCR by specific antibodies induce very similar expression patterns of up- or down-regulated genes in NHL cell lines indicating that CD20 may play a role in BCR signaling and vice versa.

overall_design: Four different cell lines were treated with various antibodies for 4h (3 replicates per treatment), all in all 96 arrays were analysed for 32 samples. Changes were calculated relative to control/reference experiments. Expression patterns of each treatment were compared to determine overlaps.

first: Andreas

last: Franke

first: Christian

last: Klein

first: Gerhard

last: Niederfellner


title: MGMT-STP27 methylation status as Predictive Marker for Response to PCV in Anaplastic Oligodendrogliomas and Oligoastrocytomas. A report from EORTC study 26951

status: Public on Aug 26 2013

city: Rotterdam

first: Pim

last: French

address: Dr Molewaterplein 50

department: Neurology

institute: Erasmus MC

first: Martin

last: van den Bent

first: Lale

last: Erdem-Eraslan

first: Ahmed

last: Idbaih

first: Johan

last: de Rooi

first: Paul

middle: H

last: Eilers

first: Wim

middle: G

last: Spliet

first: Wilfred

last: den Dunnen

first: Cees

last: Tijssen

first: Pieter

last: Wesseling

first: Peter

last: Sillevis Smitt

last: Kros

first: Thierry

last: Gorlia


title: Expression analysis of mock- or RAD21-transduced Kasumi1 cells

status: Public on Jul 16 2013

city: Tokyo

first: Ayana

last: Kon

address: Hongo 7-3-1, Bunkyo-ku

department: Cancer Genomics Project

country: Japan

institute: The University of Tokyo

summary:
We recently identified recurrent mutations of cohesin complex in myeloid neoplasms through whole-exome sequencing analysis. RAD21 is one of the main components of the cohesin complex.
In this study, to investigate the biological impact of wild-type RAD21 on Kasumi1 cells harboring RAD21 mutation, Kasumi1 cells were retrovirally transduced with either mock or wild-type RAD21, and expression array was performed.

overall_design: Expression analysis was performed for mock- or wild-type RAD21-transduced Kasumi-1 cells in triplicate. The experiment was performed twice independently.

first: Masashi

last: Sanada

first: Aiko

last: Sato-Otsubo

first: Kenichi

last: Yoshida

first: Yasunobu

last: Nagata

first: Yusuke

last: Sato

first: Seishi

last: Ogawa


title: Novel insights into DNA methylation features in spermatozoa: stability and peculiatities

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

type: Methylation profiling by genome tiling array

summary: Data about the entire sperm DNA methylome are limited to two sperm donors whereas studies dealing with a greater number of subjects focused only on a few genes or were based on low resolution arrays. This implies that information about what we can consider as a normal sperm DNA methylome and whether it is stable among different normozoospermic individuals is still missing. The definition of the DNA methylation profile of normozoospermic men, the entity of inter-individual variability and the epigenetic characterization of quality-fractioned sperm subpopulations in the same subject (intra-individual variability) are relevant for a better understanding of pathological conditions. We addressed these questions by using the high resolution Infinium 450K methylation array and compared normal sperm DNA methylomes against somatic cells. Our study, based on the largest number of subjects (n = 8) ever considered for such a large number of CpGs (n = 487,517), provided clear evidence for i) a highly conserved DNA methylation profile among normozoospermic subjects; ii) a stable sperm DNA methylation pattern in different quality-fractioned sperm populations of the same individual. The latter finding is particularly relevant if we consider that different quality fractioned sperm subpopulations show differences in their structural features, metabolic and genomic profiles. We demonstrate, for the first time, that DNA methylation in normozoospermic men remains highly uniform regardless the quality of sperm subpopulations. In addition, our analysis provided both confirmatory and novel data concerning the sperm DNA methylome, including its peculiar features in respect to somatic and cancer cells. Our description about a highly polarized sperm DNA methylation profile, the clearly distinct genomic and functional organization of hypo- versus hypermethylated loci as well as the association of histone-enriched hypomethylated loci with embryonic development, which we now extended also to hypomethylated piRNAs-linked genes, provides solid basis for future basic and clinical research.

overall_design: Bisulphite converted DNA from the 26 normal sperm and 2 somatic cell samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.2

first: Csilla

last: Krausz

first: Juan

last: Sandoval


title: Gene expression profiling of LT-HSCs and ST-HSCs conditionally expressing MLL-ENL

status: Public on Jul 17 2013

city: Tsu

first: Tetsuya

last: Nosaka

address: 2-174 Edobashi

department: Department of Microbiology and Molecular Genetics

institute: Mie University Graduate School of Medicine

summary: We have developed a new conditional transgenic mouse showing that MLL-ENL, at an endogenous-like expression level, induces leukemic transformation selectively in LT-HSCs. To investigate the molecular mechanism of leukemic transformation in LT-HSCs conditionally expressing MLL-ENL, we preliminarily performed comprehensive gene expression profiling of CreER-transduced LT-HSCs and ST-HSCs using cDNA microarray analysis.

overall_design: For initial screening of candidate genes invloved in the leukemic transformation, total RNA was extracted from colony-forming cells derived from LT-HSCs and ST-HSCs transduced with CreER or mock. Four samples were analyzed, and CreER-transduced LT/ST-HSC-derived cells were compared with mock-transduced LT/ST-HSC-derived cells, while CreER/mock-transduced LT-HSC-derived cells were compared with CreER/mock-transduced ST-HSC-derived cells.

first: Ryoichi

last: Ono


title: Evaluating cross-hybridization of murine cDNA to the Affymetrix Human Genome U133 Plus 2.0 chipset

city: Frederick

first: Luke

middle: Hunter

last: Stockwin

state: MD

address: Ft. Detrick

department: DTP

institute: NCI Frederick

summary: Transcriptomic studies of human tumor xenografts are complicated by the presence of murine cellular mRNA. As such, it is useful to know the extent to which mouse mRNA cross-hybridizes to any given array platform. In this study, murine cDNA samples from diverse sources were hybridized to Affymetrix Human Genome U133 Plus 2.0 Arrays. In this regard it is possible to identify specific probes that are potential targets of cross-species interference.

sample_organism:
Homo sapiens
Mus musculus

overall_design: Array data was generated for 5 different mouse cDNAs and 5 different human cDNAs hybridized to human Affymetrix U133 Plus 2 arrays [3 replicates for each biological sample]. Samples included A) mouse and B) human universal RNA (Strategene, La Jolla, CA), C) B16F10 murine melanoma tumor and D) skin from same model [C57BL/6 mice] E) COLON-26 murine tumor xenograft and F) skin from same model [Balb/C mice] G) NCI-H522 human lung carcinoma xenograft and H) skin from same model (nude mice) I) LOX-IMVI human melanoma xenograft and J) skin from same model (nude mice).

first: Melinda

last: Hollingshead

first: Sergio

last: Alcoser

first: Dianne

middle: L

last: Newton

first: Benjamin

last: Orsburn

first: Carrie

middle: A

last: Bonomi

first: Suzanne

last: Borgel

first: Raymond

last: Divelbiss

first: Kelly

last: Dougherty

first: Elizabeth

last: Hager

first: Susan

last: Holbeck

first: Gurmeet

last: Kaur

first: David

last: Kimmel

first: Mark

last: Kunkel

first: Angelena

last: Millione

first: Michael

last: Mullendore

first: Howard

last: Stotler

first: Jerry

last: Collins


title: Fibrillar collagen implicated in pregnancy-induced protection of mammary cancer

city: Salt Lake City

first: Aik Choon

last: Tan

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: Huntsman Cancer Institute

summary: A suggested role for fibrillr collagen topology in the pregnancy-induced protection and invasive phenotype.

overall_design: Two conditions: RNA was isolated from murine mammary D2.OR cells cultured in fibrillar collagen I and non-fibrillar collagen I in 3D cell culture

first: Aik

middle: C

first: Maller

last: Ori

first: Doan

last: An

first: Schedin

last: Pepper


title: Expression data from PML4 overexpressing and control K562 cells

status: Public on Jul 13 2013

city: Beijing

first: xiang

last: Lv

address: No.5 Dongdansantiao

country: China

institute: PUMC&CAMS

summary:
PML functions as a platform for the interaction of transcription factors and coactivators. Role of PML in erythroid clone formation has been reported but the detail mechanism is unclear.
We used microarrays to identify downstream-regulated genes of PML4.

overall_design: We transfected K562 cells with retrovirus overexpressing PML4 and control vector pMSCV for RNA extraction and hybridization on Affymetrix microarrays.

first: Jie

last: Wu

first: Li-Quan

last: Zhou

first: De-Pei

last: Liu

first: Xiang


title: In Vivo Endothelial Cell Heterogeneity

status: Public on Jul 15 2013

city: New York

first: Daniel

middle: J

last: Nolan

state: NY

address: 1300 York Ave

department: Genetic Medicine

institute: Weill Cornell Medical College

summary:
Endothelial cells from nine steady state tissues and two regenerating tissues (bone marrow and liver) were intravitally labeld, isolated via flow sorting, and immediately processed for RNA extraction.
When of sufficient quality, the RNA was amplified and hybridized.  For comparison, Human Emybryonic Stem Cell-derived Endothelial cells (hESC-ECs) were differentiated and isolated based on similarities to the adult mouse counterparts.

platform_organism:
Homo sapiens
Mus musculus

overall_design: Endothelial cells were labeled via intravitally labeling of the vascular bed 8 minutes prior to sacrifice with minimally three markers to identify endothelial cells followed by flow sorting.

first: Shahin

last: Rafii


title: Comparison of gene expression profile in RAG2+ B lineage cells from the small intestinal lamina propria and RAG2+ B lineage cells from the bone marrow

status: Public on Jul 12 2013

city: Boston

first: Frederick

last: Alt

address: 1 Blackfan Circle

department: Program in Cellular and Molecular Medicine

institute: Boston Children's Hospital

summary:
We used a RAG2-GFP reporter mouse to show that RAG+ B lineage cells can be found in the small intestinal lamina proria in normally-housed mice at weaning age. We used microarry expression analysis to compare the RAG2+ population in the gut to the RAG2+ B lineage population in the bone marrow.
Microarray was used to compare RAG2+ lamina propria B cells to RAG2+ bone marrow B cells.

overall_design: For each experiment, RAG2-GFP+ cells from 8-12 post-natal day 17-25 RAG2-GFP reporter mice were sorted from small intestinal lamina propria lymphocyte preparations and bone marrow. RNA extracted from trizol was used for the analysis. 3 independent replicates were performed.

first: Duane

middle: R

last: Wesemann

first: Andrew

last: Portuguese

first: Robin

last: Meyers

last: Gallagher

first: Kendra

last: Cluff-Jones

first: Jennifer

first: Rohit

last: Panchakshari

first: Scott

last: Rodig

first: Thomas

last: Kepler

middle: W


title: Meta-analysis of IDH-mutant cancers identifies EBF1 as an interaction partner for TET2

city: Toronto

first: Paul

last: Guilhamon

state: ON

address: 686 Bay Street

country: Canada

institute: SickKids

summary: Illumina Infinium 450k Human DNA Methylation BeadChip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in 51 central chondrosarcoma.

overall_design: Bisulphite converted DNA from each sample was hybridised to the Illumina Infinium 450k Human Methylation BeadChip.


title: Transcriptional analysis of pre and post excision human induced pluripotent stem cells

city: Los Angeles

first: James

last: Byrne

address: 610 Charles E. Young Drive East

department: Department of Molecular and Medical Pharmacology

institute: University of California, Los Angeles

summary: Transcriptional analysis was performed on pre and post excision human induced pluripotent stem cells, the donor human dermal fibroblasts (HDFs) they were derived from and control human embryonic stem cells

overall_design: We isolated total RNA from pre and post excision human induced pluripotent stem cells, the donor human dermal fibroblasts (HDFs) they were derived from and control human embryonic stem cells and analyzed via Affymetrix microarray analysis.

first: J


title: Expression data from WT and ELK-1 overexpressing stem cells

city: Jerusalem

first: Tal

last: Bruck

address: Givat Ram

department: Genetics

country: Israel

institute: Hebrew University of Jerusalem

summary:
Two ELK-1 overexpressing cells were generated from CSES7 cell line and compared to WT CSES7.
We used microarrays to study the gene expression profiles of the ELK-1 overexpressing cells in order to identify ELK-1 target genes that might be involve in the processes of apoptosis and differentiation

overall_design: CSES7 cells were transfected with the ELK-1 vector.

first: Ofra

last: Yanuka

first: Nissim

last: Benvenisty


title: Vav proteins orchestrate a keratinocyte auto/paracrine program critical for skin tumorigenesis.

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

institute: CIEMAT

summary: Cutaneous squamous tumors rely on autocrine/paracrine loops for proper fitness.  Targeting this Achilles’ heel is therefore considered a potential avenue for patient treatment.  However, the mechanisms that engage and sustain such programs during tumor ontogeny are poorly understood.  Here, we show that two Rho/Rac activators, the exchange factors Vav2 and Vav3, control the expression of an epithelial autocrine/paracrine program that regulates keratinocyte survival and proliferation as well as the creation of an inflammatory microenvironment.  Vav proteins are also critically involved in some of the subsequent autocrine signaling loops activated in keratinocytes.  The genetic inactivation of both Vav proteins reduces tumor multiplicity without hampering skin homeostasis, thus suggesting that pan-specific Vav therapies may be useful in skin tumor prevention and treatment.

overall_design: The dorsal skin of WT and DKO mice (Vav2-/-;Vav3-/-) were treated with either one or four applications of phorbol ester 12-O-tetradecanoylphorbol-13 acetate (TPA) (6.8 nmol in 200 μl acetone) two days after shaving.  As control, we applied 200 μl of acetone. Animals were euthanized 24 hours after treatment.

first: Mauricio

last: Menacho-Márquez

first: Ramón

last: García-Escudero

first: Antonio

last: Abad

first: Pilar

last: Delgado

first: Clotilde

last: Costa

first: Sergio

last: Ruiz

first: Balbino

last: Alarcón

first: Jesús

middle: M

last: Paramio

first: Xosé

last: Bustelo


title: Gene expression from Escherichia coli.

city: Leuven

first: Kristof

last: Engelen

address: Kasteelpark Arenberg 20

country: Belgium

institute: KULeuven

summary: Gene expression from Escherichia coli.

overall_design: Escherichia coli (4 biological replicates).


title: Gene expression and methylation profile of breast cancer cells.

city: Baltimore

first: Francescopaolo

last: Di Cello

address: 1650 Orleans Street

institute: The Johns Hopkin University School of Medicine

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

overall_design: Refer to individual Series


title: Expression data from osteoblastic lineage cells isolated from normal and leukemic mice

status: Public on Jul 11 2013

city: San Francisco

first: Emmanuelle

last: Passegué

state: California

address: 35 Medical Center Way, RMB-1017 Pod B, box 0667

department: Medicine

institute: University of California San Francisco

summary:
Multipotent stromal cells (MSC) and their osteoblastic lineage cell (OBC) derivatives are part of the bone marrow (BM) niche and contribute to hematopoietic stem cell (HSC) maintenance. During myeloproliferative neoplasm (MPN) development, MSCs are stimulated to overproduce functtionally altered OBCs, which accumulate in the BM cavity as myelofibrotic cells. These MPN-expanded OBCs, in turn, impair the maintenance of normal HSCs but not of leukemic stem cells.
We used microarrays to detail the global gene expression changes in OBCs during BCR/ABL-induced MPN development, and understand the molecular deregulations contributing to their functional changes.

overall_design: OBCs were isolated from diseased Scl-tTA::TRE-BCR/ABL (BA) mice and age-match controls around 5-6 weeks post-doxycycline withdrawal. Five independent biological replicate corresponding to single mice were used for each population. RNA was extracted, amplified and hybridized on Affymetrix Gene ST 1.0 microarrays.

first: Schepers

last: Koen

first: Pietras

last: Eric

first: Passegué

last: Emmanuelle


title: Role and function of MYC in BCR-ABL1 driven pre-B cells

first: Markus

last: Müschen

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

institute: University of Southern California

summary: In order to investigate the function of MYC in ALL, we isolated bone marrow cells from conditional MYC knockout mice and transformed them with BCR-ABL1. In a second transduction the BCR-ABL1 driven pre-B cells were transformed either with CRE or empty vector control.

overall_design: Three days post transduction, total RNA of GFP positive sorted cells were extracted and subjected to gene expression analysis.

first: Carina

last: Ng


title: Gene methylation profile of breast cancer cells.

summary: We compared the gene methylation profile of 26 breast cancer cell lines to identify variations associated with different phenotypes and molecular subtype. The panel includes 13 estrogen receptor negative (ER-) and 13 ER+ cell lines. Four of the ER- cell lines and 5 of the ER+ cell lines are HER2 positive.

overall_design: Bisulphite converted DNA from the 26 samples was hybridised to the Illumina Infinium Human Methylation450 Beadchip.

first: Cynthia

last: Zahnow

first: Huili

last: Li


title: Effects of pre-B Cell Receptor in BCR-ABL1 driven pre-B cells

summary: In order to investigate the function of pre-B cell receptor in ALL, we isolated bone marrow cells from Ighm KO mice and transformed them with BCR-ABL1. In a second transduction the BCR-ABL1 driven pre-B cells were transformed either with uchain-CD8 or empty vector control (CD8) and subjected to gene expression analysis.

overall_design: Five days post transduction, total RNA of CD8 positive sorted cells were extracted and subjected to gene expression analysis.

first: Rahul

last: Nahar


title: Recurrent mutations of multiple components of cohesin complex in myeloid neoplasms

first: Ayana

last: Kon

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


title: Role and function of PAX5 in BCR-ABL1 driven pre-B cells

summary: In order to investigate the function of PAX5 in ALL, we isolated bone marrow cells from C57Bl6 mice and transformed them with BCR-ABL1. In a second transduction the BCR-ABL1 driven pre-B cells were transformed either with PAX5-GFP or empty vector control (GFP) and subjected to gene expression analysis.

first: Parham

last: Ramezani-Rad


title: Role and function of Bach2 in BCR-ABL1 driven pre-B ALL

summary: In order to investigate the function of Bach2 in pre-B ALL, we isolated bone marrow cells from wildtype and Bach2 knockout mice of C57Bl6 background and transformed them with BCR-ABL1.

overall_design: We compared the gene expression profiles of Bach2 wildtype and knockout pre-B ALL cells, both with and without imatinib treatment (2uM for 16h).

first: Srividya

last: Swaminathan


title: Identification of C/EBPβ Target Genes in ALK+ Anaplastic Large Cell Lymphoma (ALCL) by Gene Expression Profiling and Chromatin Immunoprecipitation

status: Public on Jul 10 2013

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary: C/EBPβ (CCAAT enhancer binding protein) is a transcription factor that plays a crucial role in survival and transformation of ALK+ anaplastic large cell lymphoma (ALCL). The aim of this study was to identify the downstream targets of C/EBPβ responsible for ALK-mediated oncogenesis. C/EBPβ was knocked down in ALK+ ALCL cell lines with a C/EBPβ-shRNA, followed by gene expression profiling (GEP). GEP analysis revealed a reproducible signature of genes that were significantly regulated by C/EBPβ. Classification into biological categories revealed overrepresentation of genes involved in the immune response, apoptosis and cell proliferation. Transcriptional regulation by C/EBPβ was found in 6 of 11 (BCL2A1, G0S2, TRIB1, S100A9, DDX21 and DDIT4) genes investigated by chromatin immunoprecipitation. We demonstrated that BCL2A1, G0S2 and DDX21 play a crucial role in survival and proliferation of ALK+ ALCL cells. DDX21, a gene involved in rRNA biogenesis, was found differentially overexpressed in primary ALK+ ALCL cases. All three candidate genes were validated in primary ALCL cases by either immunohistochemistry or RT-qPCR. In conclusion, we identified and validated several key C/EBPβ-regulated genes with major impact on survival and cell growth in ALK+ ALCL, supporting the central role of C/EBPβ in ALK-mediated oncogenesis.

overall_design: Kijk and SUDHL1 cell lines transfected with shRNA for C/EBPbeta were compared to control cells (3 biological replicates per group) and untreated cells (1 biological replicate)

first: Irina

last: Bonzheim

first: Martin

last: Irmler

first: Leticia

last: Quintanilla-Martinez


title: Genome-wide DNA methylation in murine ascitic leukemia cells (P388)

status: Public on Jul 09 2013

city: Chapel Hill

first: Daria

middle: Y

last: Alakhova

address: 120 Mason Farm rd GMB 1098

department: MOPH

institute: UNC

type: Methylation profiling by high throughput sequencing

summary: We report the effect of long-term treatment with doxorubicin alone or in combination with amphiphilic block copolymers in mice bearing P388 ascitic leukemia tumors on DNA methylation status in cancer cells. Purpose: Pluronic block copolymers are potent sensitizers of multidrug resistant cancers. SP1049C, a Pluronic-based micellar formulation of doxorubicin (Dox) has completed Phase II clinical trial and demonstrated safety and efficacy in patients with advanced adenocarcinoma of the esophagus and gastroesophageal junction. This study elucidates the ability of SP1049C to deplete cancer stem cells (CSC) and decrease tumorigenicity of cancer cells in vivo.   Experimental design. P388 murine leukemia ascitic tumor was grown in BDF1 mice. The animals were treated with: (a) saline, (b) Pluronics alone, (c) Dox or (d) SP1049C. The ascitic cancer cells were isolated at different passages and examined for 1) in vitro colony formation potential, 2) in vivo tumorigenicity and aggressiveness, 3) development of drug resistance and Wnt signaling activation 4) global DNA methylation profiles, and 5) expression of CSC markers.  Results: SP1049C treatment reduced tumor aggressiveness, in vivo tumor formation frequency and in vitro clonogenic potential of the ascitic cells compared to drug, saline and polymer controls. SP1049C also prevented overexpression of BCRP and activation of Wnt-β-catenin signaling observed with Dox alone. Moreover SP1049C significantly altered the DNA methylation profiles of the cells. Finally, SP1049C decreased CD133+ P388 cells populations, which displayed CSC-like properties and were more tumorigenic compared to CD133- cells.  Conclusions: SP1049C therapy effectively suppresses the tumorigenicity and aggressiveness of P388 cells in a mouse model. This may be due to enhanced activity of SP1049C against CSC and/or altered epigenetic regulation restricting appearance of malignant cancer cell phenotype.

overall_design:
DNA methylation was analysed in P388 parental cells as control and in isolated ascitic cells from four treamtnet groups ((a) saline, (b) Pluronics alone, (c) Dox or (d) SP1049C) in the beginning and at the end of serial passaging - in Passage 1 and Passage 4
*** The original raw data files are not available.

first: Yi

last: Zhao

first: Alexander

last: Kabanov

first: David

last: Klinkebiel


title: Expression data from murine intestinal tissue upon depletion of regulatory T cells

city: Zurich

first: Stefan

last: Zoller

address: Universitatstrasse 16

department: Genetic Diversity Centre

institute: ETH Zurich

summary:
Regulatory T cells (Treg) play a pivotal role in modulating immune responses and were shown to decrease atherosclerosis in murine models. How this effect is brought about remains elusive.
We used microarrays to detail the global programme of gene expression in intestinal tissue from chimeric DEREG x Ldlr-/- mice +/- diphteria toxin enabling selective depletion of Treg.

overall_design: Chimeric DEREG x Ldlr-/- mice were kept on a high fat diet for 8 weeks and treated with DT  or PBS  i.p. for 8 weeks. Upon harvest, intestinal tissue was ascertained from animals from both groups and a gene array was performed.

first: Roland

last: Klingenberg


title: Maternal obesity affects fetal neurodevelopmental and metabolic gene expression

status: Public on Jul 04 2013

city: Medford

first: Heather

last: Wick

address: 161 College Ave

department: Department of Computer Science

institute: Tufts University

summary:
To investigate fetal gene expression in obese compared to lean women in the second trimester, by performing global gene expression analysis of amniotic fluid (AF) cell-free RNA
Analysis of paired data from obese cases and lean controls revealed differential expression of 205 genes. Functional analysis of differentially expressed genes suggested down-regulation of apoptosis in fetuses of obese women, particularly within nervous system pathways involving the cerebral cortex, and activation of pro-estrogenic, pro-inflammatory transcriptional regulators.

overall_design: Prospective whole transcriptome microarray study analyzing cell-free RNA in AF from obese cases and lean controls in the second trimester. Significantly differentially-regulated genes in fetuses of obese cases (N= 8) vs. matched lean controls (N = 8) were identified and functional analyses were performed. Tissue-specific differential gene expression in fetuses of obese women was also examined.

first: Andrea

last: Edlow

first: Neeta

last: Vora

first: Lisa

last: Hui

first: Janet

last: Cowan

first: Diana

last: Bianchi


title: INTESTINAL FILTER FOR USE IN OESOPHAGEAL CANCER RESEARCH

status: Public on Jul 07 2013

city: Dublin

first: Shane

last: Duggan

address: TCD Health Sciences Building, St James Hospital,

department: Clinical Medicine

country: Ireland

institute: Institute of Molecular Medicine

summary: This study utilise the examination of normal gastro-intestinal tissues to determine a tissue specific signal for use in deriving the intestinal signature of intestinal metaplasias of the oesophagus. Normal oesophageal, colonic and duodenal tissue biopsies were taken after informed consent and RNA was extracted following histological examination of adjacent tissues for normal aperaing mucosa.

overall_design: Three of each tissue type

first: Murat

last: Kirca


title: Expression data of A224 cell with ectopic overexpression of FGF18 and RFP

status: Public on Jul 08 2013

first: Michael

last: Birrer

address: 70 Blossom Street

institute: MGH

summary:
We have identified the overexpression of FGF18 as an independent predictive marker for poor clinical outcome in patients with advanced stage, high-grade serous ovarian cancer. Functional studies have demonstrated that FGF18 promotes migration, invasion and tumorigenicity of ovarian cancer cells in vitro and in vivo.
To identify the FGF18 responsive genes contributing its biologic effects on ovarian tumorigenesis, we performed gene expression profiling in ovarian cancer cell line A224 with ectopic overexpression of FGF18 or RFP (as control).

overall_design: Microarrays were completed using total genomic DNA free RNA extracted from three independent paired cultures of A224 cells overexpressing FGF18 or RFP.

first: Wei

last: Wei


title: Pre-leukemic Cebpa mutant myeloid progenitors

city: Copenhagen N

first: Anne-Katrine

last: Frank

address: Ole Maaløesvej 5

department: Porse Group

country: Denmark

institute: Finsenlaboratoriet

summary: In this study, we use pre-malignant cells from different Cebpa mutant acute myeloid leukemia (AML) models. We have used conditional KO models (CreLoxP) and isolated hematopoietic cells shortly after induction of recombination, in order to look at pre-leukemic cells, which have acquired the first hit, but not yet undergone full malignant transformation.

overall_design: We have sorted granulocyte-macrophage progenitors (GMPs) and the more immature population pre-granulocyte-macrophages (preGMs) from pre-leukemic mice. We analyzed gene-expression profiles in order to find deregulated genes, which make the cells more prone to undergo transformation.

first: Mikkel

last: Schuster

first: Anne

middle: K

first: Frederik

middle: O

last: Bagger

first: Nicolas

last: Rapin

first: Jonas

last: Vikesaa

first: Bo

middle: T

last: Porse


title: Expression data from well-differentiated human bronchial epithelial cells infected with H1N1 Influenza isolates

status: Public on Jul 03 2013

city: Louisville

first: Rachael

last: Gerlach

state: KY

address: 505 S Hancock, CTR 626

department: Microbiology and Immunology

country: USA

institute: University of Louisville

summary: We used microarrays to compare the  gene expression profiles of different H1N1 isolates (seasonal and pandemic) in lung epithelial cells in vitro.

overall_design: Well-differentiated primary human lung, bronchial epithelial cells (wd-NHBE) were infected with two pandemic and one seasaonl H1N1 influenza viruses at a multiplicity of infection of 3.0. The cells were then collected, in triplicate, at 36 hours after infection. This timepoint was selected as we saw significant differences in soluble cytokine and chemokine protein levels at this time point in the supernatant.


title: Genome-wide analysis of mRNA expression alterations in human primary hepatocytes compared with cAMP treated and non-treated human embryonic stem cell (hESC) derived hepatic populations

first: carl

last: virtanen

state: Ontario

address: 101 College St

department: Princess Margaret Genomics Centre

institute: University Health Network

summary: Microarrays were used to examine gene expression differences between primary human hepatocytes and hESC derived hepatoblast cultures treated or non-treated with cAMP. hESC's were differentiated with a hepatic cell lineage specific protocol that included the use of a 3-dimensional cell aggregation culturing technique. Followed by cAMP signaling, this promoted the maturation of hepatoblasts into a more hepatocyte-like population. Importantly, key enzymes related to liver function show that cAMP induced populations have a gene expression profile that is similar to primary human hepatocytes.

overall_design: Total RNA obtained from cultured primary hepatocytes and hESC derived hepatic populations.

first: Shinichiro

last: Ogawa

first: Carl

last: Virtanen

first: Gordon

last: Keller


title: Microarray analysis of xenograft models in use at the Developmental Therapeutics Program of the National Cancer Institute (DTP-NCI)

status: Public on Jul 01 2013

city: Frederick

first: Luke

last: Stockwin

address: Ft. Detrick

department: DTP

institute: NCI Frederick

summary: Xenograft models remain a cornerstone technology in the development of anti-cancer agents. The ability of immunocompromised rodents to support the growth of human tumors provides an invaluable transition between in vitro testing and clinical trials. Therefore, approaches to improve model selection are required. In this study, cDNA microarray data was generated for a collection of xenograft models at in vivo passages 1, 4 and 10 (P1, P4 and P10) along with originating cell lines (P0). These data can be mined to determine transcript expression 1) relative to other models 2) with successive in vivo passage and 3) during the in vitro (P0) to in vivo (P1) transition.

overall_design: For originating cell lines (P0) and xenograft fragments at P1, P4 and P10, RNA was isolated, cDNA transcribed and hybridized to Affymetrix HG-U133 Plus 2.0 arrays. P0 samples have 2-3 replicates, whereas P1, P4 and P10 samples have 5 replicates. This dataset comprises a total of 823 array files.

first: Melinda

last: Hollingshead

first: Sergio

last: Alcoser

first: Dianne

last: Newton

first: Benjamin

last: Orsburn

first: Carrie

last: Bonomi

first: Suzanne

middle: D

last: Borgel

first: Raymond

last: Divelbiss

first: Kelly

last: Dougherty

first: Elizabeth

last: Hager

first: Susan

last: Holbeck

first: Gurmeet

last: Kaur

first: David

last: Kimmel

first: Mark

last: Kunkel

first: Angelena

last: Millione

middle: E

last: Mullendore

first: Howard

last: Stotler

first: Jerry

last: Collins


title: HCV Replication: permissive and non-permissive cells

city: Dallas

first: Qiuyue

last: Chen

state: TX

address: 5323 Harry Hines Blvd.

department: Molecular Genetics

institute: UT Southwestern Medical Center

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


title: Identification of Nrf2-regulated genes in A549 lung cancer cells by oligonucleotide microarray

city: Worcester

first: George

last: Acquaah-Mensah

address: 19 Foster Street

institute: MASS COLLEGE OF PHARM HEALTH SCIENCES

summary: To elucidate the mechanisms by which Nrf2 regulates cell growth, we performed global gene expression profiling of A549 lung cancer cells with knockdown of Nrf2. Gene networks associated with carbohydrate metabolism and drug metabolism were significantly downregulated in Nrf2-depleted A549 cells. Gene Set Enrichment Analysis revealed significant enrichment of genes associated with carbohydrate catabolic processes, positive regulation of metabolic processes, PPP, and arachidonic acid metabolism. In summary, this analysis revealed that Nrf2 positively regulates transcription of genes that play key roles in central carbon metabolism.

overall_design: A549 cells were transfected with non targeting NS siRNA or siRNA targeting Nrf2. Mock transfected A549 cells were treated with transfection reagent alone. We had 3 biological replicates for each of the 3 groups. Ninty six hours post transfection, cells were lysed and total RNA was isolated.

first: Anju

last: Singh

first: Shyam

last: Biswal


title: Expression data from Ribonuclease Inhibitor (RI/Rnh1) deficient  E9.5 yolksac

city: EPALINGES

first: ramanjaneyulu

last: allam

state: Vaud

address: Chemin des Boveresses 155

department: Biochemistry

institute: University of lausanne

summary:
Ribonuclease Inhibitor (RI also known as Rnh1) is a 50 kDa, ubiquitously expressed leucine-rich repeat (LRR) protein. It is localized in cytosol and binds to pancreatic-type ribonucleases and inhibit their function. However the entire biological role for Rnh1 is unknown. We generated Rnh1 knock out mice by homologous recombination. Here we studied differential gene expression from wild type (Rnh1 +/+), Heterozygous (Rnh1+/-) and Knock out (Rnh1-/-) yolk sacs isolated from embryonic day 9.5 (E9.5).
We used microarrays to study global gene expression regulated by Rnh1 in yolk sacs.

overall_design: Total RNA was isolated from E9.5 yolk sacs of Rnh1 Wild type, heterozygous and knock out.

first: Ramanjaneyulu

last: Allam


title: MX1 is Silenced in Permissive HRP4 Cells Supporting HCV Replication

summary: MX1 is a well-characterized interferon-induced antiviral gene. MX1 is activated by viral infection due to interferon production in cells. We treated non-permissive Huh7 cells and permissive HRP4 cells with interferon. We compared the expression of genes induced by interferon to determine host factors affecting HCV replication.

overall_design: Huh7 cells and HRP4 cells were treated with 40U/ml interferon-α for 6h. RNA was extracted and hybridized on Affymetrix microarrays


title: GENE EXPRESSION PROFILE REGULATED BY THE HPV16-E7 ONCOPROTEIN AND ESTRADIOL IN CERVICAL TISSUE

city: Mexico

first: Sandra

middle: Lorena

last: Romero-Cordoba

state: Mexico

address: Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan. México, D.F.

department: Cancer Genomics

country: Mexico

institute: National Instute of Genomic Medicine

summary: The HPV16-E7 oncoprotein and 17β-estradiol are import factors for the induction of premalignant lesions and cervical cancer. The study of these factors is crucial for a better understanding of cervical tumorigenesis. In this study, we performed a microarray analysis to obtain a global gene expression profile induced by both, HPV16-E7 and 17β-estradiol in cervical tissue of K14E7 transgenic mice. We found that 17β-estradiol is the main cause of the up-regulation of a large number of cellular genes involved in the immune response whereas E7 oncoprotein mainly affects the cellular metabolism. Our microarray data also shows some novel differentially expressed genes that were not previously reported in cervical cancer. The identification of these genes, regulated by E7 and 17β-estradiol, provides the basis for further studies on their role in cervical carcinogenesis.

overall_design: 15 Mouse Gene 1.0 ST Affymetrix microarrays were used to analyze gene expression of cervical tissue from K14E7 hemizygote and nontransgenic FvB control virgin female untreated and treated mice. Briefly, one-month virgin female transgenic and nontransgenic mice were implanted in the dorsal skin with continuous release pellets delivering 0.05 mg of17-β estradiol over 60 days. As control samples we used K14E7 and FvB untreated mice. For the microarray analysis we used triplicates for each group (3 treated K14E7 mice, 3 treated FvB mice, 3 untreated K14E7 mice, 3 untreated FvB mice).

first: Enoc

last: Cortés-Malagón

first: José

last: Bonilla-Delgado

last: Díaz-Chavéz

first: Alfredo

last: Hidalgo-Miranda

first: Aykut

last: Üren

first: Haydar

last: Celik

first: Matthew

last: McCormick

first: Jóse

last: Munguía-Moreno

first: Eloisa

last: Ibarra-Sierrai

first: Jaime

last: Escobar-Herrera

first: Paul

middle: F

last: Lambert

first: Patricio

last: Gariglio


title: Gene expression analysis for CD56- T, NK, CD56+ T cells, and iNKT cells

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary:
A small subset of T cells also expresses kiler-cell immunoglobulin-like receptors (KIRs). We find that KIR+ T cells primarily reside in the CD56+ T population. However, little is known on how these cells are different from the conventional CD56- T, NK, and iNKT cells.
We used microarray profiling to compare and determine the distinctive differences of CD56+ T cell and its KIR subsets when compared to the conventional CD56- T, NK and iNKT cells.

overall_design: Lymphocyte subsets were sorted from human peripheral blood mononuclear cells with FACSAriaII (BD Biosciences, San Jose, CA) using anti-CD3, anti-CD56, anti-CD14, anti-KIR2DL1, anti-KIR2DL2/3, anti-KIR3DL1 and anti-TCRValpha24 antibodies. The purity of CD3+CD56- T cells, CD3-CD56+ NK cells, CD3+CD56+ T cells, KIR-CD3+CD56+ T cells, and KIR+CD3+CD56+ T cells were more than 98% in all experiments. The purities of iNKT cells for TCRValpha24 and CD1d-tetramer were >95% and >90%, respectively. RNA pre-amplification, labeling and hybridization on Human Genome U133Plus 2.0 GeneChip array were performed in the St. Jude Hartwell Center for Bioinformatics & Biotechnology microarray core facility according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA).

first: Wing

last: Chan

last: Leung


title: Role of Dec1 transcription factor in naive CD4+ T cell activation transcriptome

city: London

first: MARC

last: MARTINEZ-LLORDELLA

address: 3rd Floor Cheyne Wing, Denmark Hill

department: Liver Science Department

country: United Kingdom

institute: King's College London

summary: We used microarrays to detail the global gene transcription effect of Dec1 underlying T cells activation during the first 24 hours after stimulation.

overall_design: CD4+CD62LhiCD25- T cells were sorted and cultured with different stimulatory conditions (anti-CD3 and anti-CD3 plus anti-CD28) for 24 hours. 4 replicates for each condition were analyzed.


title: Human naive CD4+ T cell activation transcriptome

summary: We used microarrays to detail the global gene transcription underlying T cells activation during the first 24 hours after stimulation.

overall_design: CD4+CD45RA+ T cells were sorted and cultured with different stimulatory conditions (Non-stimulated, anti-CD3 and anti-CD3 plus anti-CD28) for different times (0 hours, 4 hours and 24 hours). 3 replicates for each condition were analyzed.


title: Microarray-based gene expression data from BPLER tumor explants.

status: Public on Jul 02 2013

city: Miami

first: Tan

last: Ince

state: FL

address: 1501 NW 10th Avenue, Suite 913

department: Department of Pathology

institute: Interdisciplinary Stem Cell Institute and Braman Family Breast Cancer Institute, Miller School of Medicine, University of Miami

summary:
The gene expression of 6 different mouse xenografts initiated by BPLER cells analyzed by microarray.

Basal-like triple negative breast cancers (TNBC) have poor prognosis. To study the basal-like transcriptional profile of tumors transformed by defined genetic elements, the human breast epithelial cell line BPLER was injected into NOD/SCID mice. The resulting tumors were excised for expression analysis. Keywords: breast cancer, BPLER, metastasis, tumor stem cells, tumor initiating cells, breast adenocarcinoma

overall_design: BPLER cells were derived from human primary breast epithelial cells propagated in WIT medium (Ince et al, Cancer Cell, 2007). These cells were transformed with hTERT, SV40 early region and hRASV12 by retroviral transduction. BPLER have a TNBC-like phenotype in vitro and are highly enriched for tumor-initiating cells. To define the phenotype of BPLER-derived tumors in vivo, BPLER cells were injected in the mammary fat-pad of 6 NOD/SCID mice. Once tumors were palpable, mice were sacrificed and tumors excised. Total RNA was extracted using Trizol. The gene expression profile of each tumor was assessed by mRNA microarray analysis. Based on histology and principal component analysis of microarray data, BPLER tumors were remarkably similar to human primary TNBC encountered in the clinic (Petrocca et al, Cancer Cell, 2013).

first: T


title: MLLT10 gene recombinations in pediatric T-Acute Lymphoblastic Leukemia

city: Padova

first: Andrea

last: Zangrando

address: Via Giustiniani, 3

department: Woman and Child's Health

institute: University of Padova

summary: MLLT10, a 24 exons gene at 10p12, is known in leukemogenesis as partner of MLL or PICALM and recently NAP1L1. We identified HNRNPH1 and DDX3X, genes involved in RNA processing, as new MLLT10 partners in 2 cases of pediatric NOTCH1 positive T-ALL. HNRNPH1/5q35 encodes for a member of the ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) subfamily of RNA binding protein. DDX3X/Xp11.3, belongs to the big family of RNA helicases with a DEAD box domain.

overall_design:
Whole genome analysis by SNPs and Combined Interphase FISH (CI-FISH) identified different co-operating lesions in the two cases. Fusion isoforms were found in both cases: interestingly all fusions retained the OM-LZ domain of MLLT10 that is needed to induce Acute Myeloid Leukemia in mice. Gene expression profiling (GEP) of the two new MLLT10 fusions was similar to PICALM-MLLT10 positive but differed from other HOXA positive T-ALL, suggesting MLLT10 fusions share a common leukemogenic pathway. Clinical data indicate relative good prognosis in T-ALL with MLLT10 variants.

This submission represents the gene expression component of the study [For privacy reasons, SNP data will not be deposited].

first: Marco

last: Giordan


title: Effect of Bach2 overexpression in BCL6+/+ and -/- BCR-ABL1 transformed pre-B cells

city: Los Angeles

first: Markus

last: Müschen

state: CA

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

institute: University of Southern California

summary: The aim was to investigate how BCL6 genotype affects Bach2 dependent gene expression changes.

overall_design: We compared gene expression profiles of BCL6+/+ and BCL6-/- BCR-ABL1 transformed pre-B cells after inducible overexpression of Bach2.

first: Srividya

last: Swaminathan

first: Christian

last: Hurtz


title: Naive CD4+ T cell activation transcriptome

overall_design: Refer to individual Series


title: Enterohemorrhagic Escherichia coli (EHEC) 8624 double deletions of kdpe and cra grown in DMEM

first: Jacqueline

last: Njoroge

state: Tx

address: 5323 Harry hines

institute: UTSW

summary: Analysis of effect of deletion of the two transcriptional factors KdpE and Cra on gene expression of EHEC 8624

overall_design: A double mutant of kdpE and cra in the EHEC 8624 was grown  to OD600=1.0 in DMEM then processed according to manufacturer's specifications: http//www.affymetrix.com/support/technical/manual/expression_manual.affx

first: Vanessa

last: Sperandio


title: Kinetic analysis of the response to anti-CD3 in conventional and regulatory CD4+ T cells, in mice and in vitro.

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Several clinical trials have shown anti-CD3 treatment to be a promising therapy for autoimmune diabetes, but its mechanism of action remains unclear. Foxp3+ regulatory T (Treg) cells are likely to be involved, and we have shown a strong effect of anti-CD3 on homeostatic control of CD4+ FoxP3+ regulatory T (Treg) cells. To analyze the early consequences of anti-CD3 treatment, we sorted and profiled Treg and conventional CD4+ T (Tconv) cells in the first hours and days after anti-CD3 treatment of NOD mice. In practice, NOD mice carrying the Foxp3-GFP reporter were treated with anti-CD3 mAb KT3 (50 ug iv) and CD4+ T cells were sorted from pooled spleen and lymph nodes after 2, 8, 24 and 72 hrs, separating Treg and Tconv cells on the basis of GFP expression. Anti-CD3 treatment led to a transient transcriptional response, terminating faster than most antigen-induced responses. Most transcripts were similarly induced in Treg and Tconv cells, but several were differential, in particular those encoding the IL7 receptor (IL7R) and transcription factors Id2/3 and Gfi1, upregulated in Treg but repressed in Tconv cells. In parallel experiments, we tested the effect of soluble anti-CD3 added to cultures of fresh splenocytes, sorting Treg and Tconv cells at the same time points. Many of the anti-CD3 elicited changes, and of the differential response observed in vivo, were also observed in vitro. Two independent replicate series; Treg and Tconv samples abbreviated TR and TC, respectively.    Keywords: Transcriptional activation, TCR

overall_design: All gene expression profiles were obtained from highly purified T cell populations sorted by flow cytometry. RNA from 5 x 104 cells was amplified, labeled, and hybridized to Affymetrix ST1.0 Gene arrays. Raw data were preprocessed with the RMA algorithm in GenePattern, and averaged expression values were used for analysis.

first: J

last: Nishio

first: L

last: Li

first: D

last: Mathis

first: C

last: Benoist


title: A Genetic-to-Epigenetic Crosstalk Plays a Pivotal Role in the Promotion of KrasG12D-Induced Senescence and PanIN formation

city: Quebec

first: Ezequiel

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

institute: CRCHUL

summary: Nupr1 is a chromatin protein which cooperates with KrasG12D to induce PanIN formation in mice, though the molecular mechanisms underlying this effect remain to be fully characterized. In the current study, we find that Nupr1 acts as a gene modifier of the effect of KrasG12D-induced senescence by regulating Dnmt1 expression, changing the genome-wide levels of DNA methylation and activating the growth regulatory FoxO3a-Skp2-p27Kip1-pRb-E2F pathway. Congruently, 5-aza-2'-deoxycytydine, a general inhibitor of DNA methylation, reverses the KrasG12D-induced PanIN development through an effect on oncogene-induced senescence. Therefore, mechanistically this data reveals that epigenetic events modulate the functional outcome of genetic mutations during the progression of pancreatic cancer. The fact that small drug inhibitors of these epigenetic pathways reverse the effects triggered by genetic changes lends significant biomedical relevance to this knowledge for the future design of novel therapies aimed at controlling the progression of pancreatic cancer.

overall_design: The pancreatic gene expression profile of Nupr1 (+/+) Kras-G12D mouse was compared to the Nupr1 (-/-) Kras-G12D mouse.

first: Daniel

last: Grasso

first: Maria

middle: N

last: Garcia

first: Tewfik

last: Hamidi

first: Carla

last: Cano

first: Gwen

last: Lomberk

first: Raul

last: Urrutia

first: Juan

last: Iovanna


title: Radiation-induced epigenetic DNA methylation modification of radiation-response pathways

city: Detroit

first: Steven

middle: P

last: Zielske

state: MI

address: 540 E. Canfield

department: Department of Radiation Oncology

institute: Wayne State University

summary: Treatment of tumors with ionizing radiation for cancer therapy induces biological responses that include changes in cell cycle, activation of DNA repair mechanisms, and induction of apoptosis or senescence programs.  What is not known is whether ionizing radiation induces an epigenetic DNA methylation response or whether epigenetic changes occur in genes in pathways classically associated with the radiation response.  We exposed breast cancer cells to 0, 2, or 6 Gy and determined global DNA methylation at 1, 2, 4, 8, 24, 48, and 72 hours post-irradiation.  We found that radiation treatment resulted in a DNA methylation response and that cell cycle, DNA  repair, and apoptosis pathways were enriched in genes are were differentially-methylated.

overall_design: DNA methylation profiling of ionizing radiation treated cells using the Infinium HumanMethylation450 BeadChip.

last: Antwih

first: K

last: Gabbara

first: W

last: Lancaster

last: Ruden

first: S


title: PRC2 is required for acute myeloid leukemias initiated by MLL-AF9

city: Cold Spring Harbor

first: Junwei

last: Shi

address: 1 Bungtown Rd

institute: cold spring harbor lab

summary: The transcriptional activating and repressive functions performed by Trithorax and Polycomb group complexes, respectively, are critical for to maintain cellular fates in ontogeny and in cancer. Here we report that leukemias initiated by a Trithorax-related oncogene, MLL-AF9, depend upon the Polycomb Repressive Complex 2 (PRC2) to sustain a transformed cellular state. RNAi mediated suppression of PRC2 subunits is sufficient to inhibit proliferation of MLL-AF9 leukemias, with little impact on growth of non-transformed cells. This requirement is partly due to PRC2-mediated transcriptional repression of several anti-self-renewal regulators, including Cdkn2a. These results suggest that, unlike the classical antagonism generally observed between Polycomb and Trithorax group proteins during development, the activities of these two pathways can cooperate to promote myeloid neoplasia.

overall_design: In order to understand downstream targets of PRC2 complex in MLL-AF9 leukemia, we performed array in murine MLL-AF9/NrasG12D cell line under the condition that two subunits of PRC2(Eed and Suz12) were suppressed by using shRNAs.

first: Eric

last: Wang

first: Johannes

last: Zuber

first: Christopher

last: Johns

first: Scott

last: Lowe

last: Vakoc


title: Epigenome analysis of U937, U937 treated with 5mM azacytidine for 24 and 72 hours and its azacytidine-resistant derivative

city: Tokyo

first: Satoshi

last: Imanishi

address: nishi-shinnjuku 6-7-1

institute: Tokyo medical univ

summary: Genome-wide DNA methylation profiling of U937 and its azacytidine-resistant derivative R-U937.

overall_design: Bisulphite-converted DNA from the samples were hybridised to Illumina HumanMethylation450 BeadChips.

first: Tomohiro

last: Umezu

first: Junko

last: Ohyashiki

first: Kazuma

first: Chiaki

last: Kobayashi


title: CD47 Inhibits Self-renewal and Reprogramming by Regulating c-Myc and Other Stem Cell Transcription Factors

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

summary: Signaling through the thrombospondin-1 receptor CD47 broadly limits cell and tissue survival of stress, but the molecular mechanisms are incompletely understood. We now show that loss of CD47 permits sustained proliferation of primary murine endothelial cells and enables these cells to spontaneously reprogram to form multipotent embryoid bodies.  c-Myc, Klf4, Oct4, and Sox2 expression is elevated in CD47-null endothelial cells, in several tissues of CD47- or thrombospondin-1-null mice, and in a human T cell line lacking CD47. CD47 knockdown acutely increases mRNA levels of c-Myc and other stem cell transcription factors in cells and in vivo, whereas CD47 ligation by thrombospondin-1 suppresses c-Myc expression. The inhibitory effects of increasing CD47 levels can be overcome by maintaining c-Myc expression and are absent in cells with dysregulated c-Myc. Thus, CD47 antagonists enable cell self-renewal and reprogramming by overcoming negative regulation of c-Myc and other stem cell transcription factors.

overall_design: To identify gene expression changes associated with CD47 null cells, we compared the gene expression profile of these cells with WT endothelial cell, CD47 null Embryoid bodies cells and an established Embryonic Stem cell line.

first: Sukhbir

last: Kaur

first: Abdel

first: David

last: Roberts

first: Weiwei

last: Wu


title: Gene expression of human isogenic trisomy 21 induced pluripotent stem cells and derived neurons

city: Madsion

first: Anita

last: Bhattacharyya

state: WI

address: 1500 Highland Avenue

department: Waisman Center

institute: University of Wisconsin

summary: Down syndrome (trisomy 21) is the most common genetic cause of intellectual disability, but the precise molecular mechanisms underlying impaired cognition remain unclear. Elucidation of these mechanisms has been hindered by the lack of a model system that contains full trisomy of chromosome 21 (Ts21) in a human genome that enables normal gene regulation. To overcome this limitation,we created Ts21-induced pluripotent stem cells (iPSCs) from two sets of Ts21 human fibroblasts. One of the fibroblast lines had low level mosaicism for Ts21 and yielded Ts21 iPSCs and an isogenic control that is disomic for human chromosome 21 (HSA21). Differentiation of all Ts21 iPSCs yielded similar numbers of neurons expressingmarkers characteristic of dorsal forebrain neurons that were functionally similar to controls. Expression profiling of Ts21 iPSCs and their neuronal derivatives revealed changes in HSA21 genes consistent with the presence of 50% more genetic material as well as changes in non- HSA21 genes that suggested compensatory responses to oxidative stress. Ts21 neurons displayed reduced synaptic activity, affecting excitatory and inhibitory synapses equally. Thus, Ts21 iPSCs and neurons display unique developmental defects that are consistent with cognitive deficits in individuals with Down syndrome and may enable discovery of the underlying causes of and treatments for this disorder.

overall_design:
Three independent RNA samples were collected from Down syndrome (DS) and control iPSCs between passages 24 and 48.
Three independent RNA samples were collected from 30 day old neurons differentiated from Down syndrome (DS) and control iPSCs.

first: Jason

last: Weick

first: Su-Chun

last: Zhang

first: Dustie

middle: L

last: Held

first: George

last: Bonadurer III

first: Yingnan

last: Yin

first: Jianfeng

last: Lu

first: Xiaoqing