title: Increased Risk of Genetic and Epigenetic Instability in Human Embryonic Stem Cells Associated with Specific Culture Conditions I

city: La Jolla

first: Francesca

last: Boscolo

address: 9500 Gilman Drive

department: Reproductive Medicine

institute: UCSD

summary: The self-renewal and differentiation capacities of human pluripotent stem cells (hPSCs) make them good sources of cells for cell transplantation therapy, drug development, and studies of cellular differentiation and development. However, the large numbers of cells necessary for many of these applications require extensive expansion of hPSC cultures, a process that has been associated with applications require extensive expansion of hPSC cultures, a process that has been associated with genetic and epigenetic alterations. We have performed a systematic study over more than 100continuous passages to identify characteristics of culture conditions (including passage method, substrate, and media type) that influence the genetic and epigenetic stability and the phenotypic characteristics of hPSCs. The predominant effects we observed were increased genetic instability with enzymatic passage, higher cell proliferation with feeder-free substrate, and variations among cultures in global gene expression and DNA methylation with time in culture. We observed recurrent duplications in two genomic regions that have been noted in earlier studies to be hotspots for duplication in hPSCs, as well as a previously unreported recurrent deletion of the tumor suppressor gene TP53 in all but one of the long-term culture conditions; the exception was the condition using mechanical passaging on feeder layers. The deletion of TP53 is associated with decreased mRNA expression of TP53, as well as alterations in the expression of several other genes in the TP53 pathway, which taken together indicate a decrease in the function of the TP53 pathway. Our results highlight the need for careful assessment of effects of culture conditions on cells intended for clinical therapies.

overall_design: Total RNA extracted at different passages from Human Embryonic Stem Cells in different culture conditions. Total DNA extracted at different passages from Human Embryonic Stem Cells in different culture conditions.

first: Ibon

last: Garitaonandia

middle: S

first: Gerald

last: Wambua

first: Heather

last: Schultheiz

first: Shannon

last: Waltz

first: Yu-Chieh

last: Wang

first: Ha

last: Tran

first: Trevor

last: Leonardo

first: Kristopher

last: Nazor

first: Ileana

last: Slavin

first: Candace

last: Lynch

first: Yingchun

last: Li

first: Ronald

last: Coleman

first: Jordan

last: Seldeen

first: Irene

last: Gallego-Romero

first: Gulsah

last: Altun

first: Mana

last: Parast

first: Jeanne

last: Loring

first: Louise

last: Laurent


title: Inhibitor of apoptosis proteins as promising therapeutic targets in chronic lymphocytic leukemia

status: Public on Mar 31 2015

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

country: Germany

institute: Charité

summary: Inhibitor of apoptosis (IAP) proteins are expressed at high levels in CLL cells and may contribute to evasion of cell death leading to poor therapeutic outcome. Of note, prognostic unfavourable cases with e.g. non-mutated VH-status and TP53 mutation responded significantly better to BV6 than samples with unknown or favourable prognosis e.g. 13q deletion. The majority of cases with 17p deletion (10/12) and Fludarabine refractory cases were sensitive to BV6, indicating that BV6 acts independently of the p53 pathway. Importantly, BV6 dose-dependently induced cell death in 28 of 51 (54%) investigated patient samples while B cells from healthy donors were largely unaffected. BV6 also triggered cell death under survival conditions mimicking the microenvironment e.g. by adding CD40 ligand or in conditioned medium. Gene expression profiling identified cell death- and NF-kB-signaling among the top pathways regulated by BV6. This was confirmed by data showing that BV6 causes degradation of cIAP1 and cIAP2 and NF-kB pathway activation. BV6 induced cell death depended on production of reactive oxygen species, since addition of ROS scavengers significantly rescued BV6-triggerd cell death. In contrast, BV6 induced cell death independently of caspase activity, RIP1 activity or TNF-alpha, since zVAD.fmk, necrostatin-1 or TNF-alpha-blocking antibody Enbrel failed to protect against cell death. Of note, transcripts of ROS regulatory proteins were modulated by BV6. Thus, these data have important implications for developing new therapeutic strategies to overcome cell death resistance in CLL especially in poor prognostic subgroups.

overall_design: Gene expression was profiled in 12 CLL samples [n=3 CLL cases for 4 hours and 20 hours with either DMSO or BV6].

first: Daniela

last: Opel

first: Simone

last: Fulda


title: Anti-miR-21 Suppresses Hepatocellular Carcinoma Growth via Broad Transcriptional Network De-regulation

status: Public on Mar 24 2015

city: Cambridge

first: Dmitri

last: Wiederschain

state: MA

address: 640 Memorial Drive

department: Oncology

country: USA

institute: Sanofi

summary: Hepatocellular carcinoma (HCC) remains a significant clinical challenge with few therapeutic options available to cancer patients. MicroRNA 21-5p (miR-21) has been shown to be upregulated in HCC, but the contribution of this oncomiR to the maintenance of tumorigenic phenotype in liver cancer remains poorly understood. We have developed potent and specific single-stranded oligonucleotide inhibitors of miR-21 (anti-miRs) and used them to interrogate dependency on miR-21 in a panel of liver cancer cell lines. Treatment with anti-miR-21, but not with a mismatch control anti-miR, resulted in significant de-repression of direct targets of miR-21 and led to loss of viability in the majority of HCC cell lines tested. Robust induction of caspase activity, apoptosis and necrosis was noted in anti-miR-21 treated HCC cells. Furthermore, ablation of miR-21 activity resulted in inhibition of HCC cell migration and suppression of clonogenic growth. To better understand the consequences of miR-21

overall_design: SK-Hep1 cells are either treated with mock (PBS) compound or anti-mir21 compound.  Sixteen hours after treatment, total RNA were isolated for mRNA profiling.  Three biological replicates were used in each treatment group.

first: Timothy

middle: R

last: Wagenaar

first: Sonya

last: Zabludoff

first: Sung-Min

last: Ahn

first: Charles

last: Allerson

first: Heike

last: Arlt

first: Raffaele

last: Baffa

first: Hui

last: Cao

first: Scott

last: Davis

first: Carlos

last: Garcia-Echeverria

first: Rajula

last: Gaur

first: Shih-Min

middle: A

last: Huang

first: Lan

last: Jiang

first: Deokhoon

last: Kim

first: Christiane

last: Metz-Weidmann

first: Adam

last: Pavlicek

first: Jack

last: Pollard

first: Jason

last: Reeves

first: Jennifer

middle: L

last: Rocnik

first: Sabine

last: Scheidler

first: Chaomei

last: Shi

first: Fangxian

last: Sun

first: Tatiana

last: Tolstykh

first: William

last: Weber

first: Christopher

last: Winter

first: Eunsil

last: Yu

first: Qunyan

first: Gang

last: Zheng


title: Increased Risk of Genetic and Epigenetic Instability in Human Embryonic Stem Cells Associated with Specific Culture Conditions

status: Public on Mar 29 2015

first: Francesca

last: Boscolo

state: CA

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: DNA Methyltransferase Inhibitor Zebularine Induces Human Cholangiocarcinoma Cell Death through Alteration of DNA Methylation Status

city: Setagaya

first: Kazuhiko

last: Nakabayashi

state: Tokyo

department: Department of Maternal-Fetal Biology

country: Japan

institute: National Research Institute for Child Health and Development

summary: Cholangiocarcinoma (CCA) is a cancer arising from the neoplastic transformation of cholangiocytes. During tumorigenesis, tumor suppressor and cancer-related genes are commonly silenced by aberrant DNA methylation in their promoter regions. Zebularine (1-(β-D-ribofuranosyl)-1,2-dihydropyrimidin-2-one) acts as an inhibitor of DNA methylation and exhibits chemical stability and minimal cytotoxicity both in vitro and in vivo. In this study, we explore the effect and possible mechanism of action of zebularine on CCA cells. We demonstrate that zebularine exerts an antitumor effect on CCA cells. Zebularine treatment decreased the concentrations of DNA methyltransferase (DNMT) proteins, and DNMT1 knockdown led to apoptotic cell death in the CCA cell lines TFK-1 and HuCCT1. DNA methylation analysis demonstrated that zebularine induced DNA demethylation, and the GO Biological Process terms “hemophilic cell adhesion”, “regulation of transcription, DNAdependent” and “Wnt signaling pathway” were found to be significantly enriched in association with demethylated genes. Furthermore, we observed that zebularine treatment decreased β-catenin protein levels in TFK-1 and HuCCT1 cells. These results suggest that zebularine alters DNA methylation status, and that some aspect of DNA demethylation by zebularine induces suppression of the Wnt signaling pathway, which leads to apoptotic cell death in CCA. We previously reported a novel mechanism of zebularine-induced cell growth arrest and apoptosis in hepatocellular carcinoma via a DNA methylation-independent pathway. Together, our present and previous studies indicate that zebularine could function as both a DNMT inhibitor and a non-DNMT inhibitor reagent, and that, while the optimal usage of zebularine may depend on cancer type, zebularine may be useful for chemotherapy against cancer.

overall_design: DNA methylation profiles of cholangiocarcinoma-derived cell lines, TFK1 and HuCCT1, treated with or without zebularine were obtained in triplicate using Infinium HumanMethylation450 BeadChips (Illumina).

first: Kazuaki

last: Nakamura


title: The IDH2 mutation cooperates with the NPM1 mutation to activate Hoxa9/Meis1 and hypoxia pathways in acute myeloid leukemia (expression)

status: Public on Mar 25 2015

city: Cho-ku

first: yoko

last: ogawara

address: 5-1-1, Tsukiji

institute: National Cancer Center Research Institute

summary: Mutations in IDH1 and IDH2 are frequently observed in various cancers, including acute myeloid leukemia (AML). Mutant IDHs convert α-ketoglutarate (α-KG) to 2-hydroxyglutarate (2-HG), which dysregulates a set ofα-KG-dependent dioxygenases. To determine whether mutant IDHs are valid targets for cancer therapy, we established a mouse AML model harboring an IDH2 mutation by transplanting mice with nucleophosmin1 (NPM1)+/- mouse hematopoietic stem/progenitor cells that had been co-transduced with four mutant genes (NPMc, IDH2/R140Q, DNMT3A/R882H and FLT3/ITD) that frequently occur simultaneously in human AML patients. IDH2/R140Q is necessary for the engraftment or survival of NPMc+ cells in vivo.　Gene-expression analysis indicated that NPMc increased the expression of Hoxa9, and that IDH2/R140Q increased the level of Meis1 and activated the hypoxia pathway in AML cells.　Conditional deletion of IDH2/R140Q blocked 2-HG production and maintenance of leukemia stem cells, resulting in survival of the AML mice. IDH2/R140Q reversibly decreased the levels of 5hmC modification and gene expression at some differentiation inducing genes (Ebf1, Pax5 and Spib). These results indicate that the IDH2 mutation is critical for the development and maintenance of AML stem cells, and that mutant IDHs are promising targets for anticancer therapy.

overall_design: RNA were isolated from BM cells, and hybridized on Affymetrix microarrays. Two or three biological replicates for each cell types were  used in this study.

first: Yoko

last: Ogawara

first: Issay

last: Kitabayashi


title: Formalin-fixed, paraffin-embedded (FFPE) tissue epigenomics using Infinium HumanMethylation450 BeadChip assays (HM 450K).

city: maastricht

first: Tim

middle: C.

last: de Ruijter

address: universiteitssingel 40

department: Medical Oncololgy

country: Netherlands

institute: Maastricht University

summary: Comparative analysis of reproducibility of Fresh Frozen (FF) derived DNA, FFPE derived DNA and FFPE derived DNA restored using the Infinium FFPE DNA Restoration solution (FFPEr) when used on the Infinium HumanMethylation450 BeadChip assay.

overall_design: 9 normal colon samples and 11 breast tumour samples were analysed using 66 HM 450K analyses at varying DNA input amounts including technical duplicates and matched FF/FFPE/FFPEr biological duplicates. Reproducibility between technical and biological duplicates was assesed. Also, candidate gene discovery in FFPEr DNA was analysed by comparing methylation patterns between colon an breast samples and validating differentially methylated genes.

middle: C

first: Joep

middle: P

last: de Hoon

first: Jeroen

last: Slaats

first: Bart

last: de Vries

first: Marjolein

middle: J

last: Janssen

first: Tom

last: van Wezel

first: Maureen

last: Aarts

first: Manon

last: van Engeland

first: Vivianne

last: Tjan-Heijnen

first: Leander

last: Van Neste

first: Jürgen

last: Veeck


title: Expression data from epidermal samples

status: Public on Mar 23 2015

city: Baltimore

first: Andrew

last: Feinberg

state: Maryland

address: 855 N. Wolfe St

institute: Johns Hopkins University School of Medicine

summary: Gene expression profiling of epidermal samples obtained from sun-exposed and sun-protected body sites from younger (<35 years old) and older (>60 years old) individuals. The Affymetrix U133A plus 2.0 array  was used to obtain gene expression data. Samples included 4 younger sun exposed epidermal samples, 4 older sun exposed epidermal samples, 3 younger sun protected epidermal samples, 5 older sun protected epidermal samples.

overall_design: To determine how gene expression relates to identified methylation changes with aging and sun-exposure, RNA was extracted from dispase separated epidermal samples and analyzed using Affymetrix U133A plus 2.0 arrays.

first: Amy

last: Vandiver


title: Epigenome analysis of squamous cell carcinoma samples

summary: Genome wide DNA methylation profiling of squamous cell carcinoma and location matched normal samples

overall_design: Bisulphite converted DNA from the 13 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip.


title: Immortalization of T-cells is accompanied by gradual changes in CpG methylation resulting in a profile resembling a subset of T-cell leukemias

city: Umeå

first: Sofie

last: Degerman

state: Sweden

address: NUS, Blg 6M, 2nd floor

department: Medical Biosciensces

country: Sweden

institute: Umeå University


title: Expression data from islets of non-pregnant and pregnant PRLR+/+ and PRLR-/- mice

city: Leuven

first: Leentje

last: Van Lommel

address: Herestraat 49 bus 901

department: Molecular cell biology

country: Belgium

institute: KULeuven

summary: ABSTRACT:Pregnancy requires a higher functional beta cell mass and this is associated with profound changes in the gene expression profile of pancreatic islets. Taking Tph1 as a sensitive marker for pregnancy-related islet mRNA expression in female mice, we previously identified prolactin receptors and placental lactogen as key signalling molecules. Since beta cells from male mice also express prolactin receptors, the question arose whether male and female islets have the same phenotypic resilience at the mRNA level during pregnancy. We addressed this question in vitro, by using islet tissue culture with placental lactogen and in vivo, by transplanting male or female islets into female acceptor mice.  Additionally, the islet mRNA expression of pregnant prolactin receptor deficient mice was compared with that of their pregnant wild-type littermates. When cultured with placental lactogen, or transplanted in female recipients that became pregnant (day 12.5), male islets induced the ‘islet pregnancy gene signature’, which we defined as the 12 highest induced genes in non-transplanted female islets at day 12.5 of pregnancy. In addition, serotonin immunoreactivity was also induced in these male transplanted islets at day 12.5 of pregnancy. In order to investigate the importance of prolactin receptors in these mRNA changes we used a prolactin receptor deficient mouse model. For the 12 genes of the signature, which are highly induced in control pregnant mice, no significant induction of mRNA transcripts was found at day 9.5 of pregnancy. Together, our results support the key role of placental lactogen as a circulating factor that can trigger the pregnancy mRNA profile in male and female beta cells.

overall_design: Islets were isolated from non-prengant (NP) and pregnant (day 9.5) PRLR+/+ and PRLR-/- mice for RNA extraction and hybridization on Affymetrix microarrays. For every condition 3 biological replicates were used.

first: Anica

last: Schraenen

first: Katleen

last: Lemaire

first: Frans

last: Schuit

first: Ingrid

last: Arijs

first: Nadine

last: Binart


title: Regulation of gene expression by loss-of-YAP/TAZ in MDA-MB-231 breast cancer cells

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

summary: YAP1 (Yes-associated protein 1) and TAZ (transcriptional coactivator with PDZ-binding motif, or WWTR1) are nucleo-cytoplasmic shuttling proteins that can function in the nucleus as transcriptional coactivators. Their role in regulating gene transcription has been so far mainly investigated by overexpressing YAP1 or TAZ, while here we sought to determine which genes are regulated by endogenous levels of YAP/TAZ. To this end, we compared MCF10A cells transfected with a control non-targeting siRNA to cells transfected with two independent mixes of siRNA targeting both YAP and TAZ.

overall_design: MDA-MB-231 cells growing at low confluence in standard growth conditions were transfected with the indicated siRNAs (Dupont et al., Nature 2011). The following day, growth medium was renewed and cells were incubated for 24 more hours, and then harvested for total RNA extraction. 4 independent biological replicates were plated, transfected ans harvested in parallel for each siRNA.

first: Sirio

last: Dupont


title: Regulation of gene expression by loss-of-YAP/TAZ in MCF10A mammary epithelial cells

overall_design: MCF10A cells growing at low confluence in standard growth conditions were transfected with the indicated siRNAs (Dupont et al., Nature 2011). The following day, growth medium was renewed and cells were incubated for 24 more hours, and then harvested for total RNA extraction. 4 independent biological replicates were plated, transfected ans harvested in parallel for each siRNA.


title: Immortalization of T-cells is accompanied by gradual changes in CpG methylation resulting in a profile resembling a subset of T-cell leukemias [methylation]

summary: We have previously described gene expression changes during spontaneous immortalization of T cells, thereby identifying cellular processes important for cell growth crisis escape and long term proliferation. Here we analyze the same model to investigate the role of genome-wide methylation in the immortalization process at different time points pre- and post- crisis using high-resolution arrays. We show that over time in culture there is an overall accumulation of methylation alterations, with  preferential increased methylation close to transcription start sites, island and shore regions.  Interestingly, the pattern of CpG site methylation observed in post-crisis T-cell cultures was similar to clinical T-cell acute lymphoblastic leukemia (T-ALL) samples classified as CpG island methylator phenotype positive (CIMP+). These sites were highly overrepresented by polycomb target genes and involved in developmental, cell adhesion and cell signaling processes. The presence of nonrandom methylation events in in vitro immortalized T-cell cultures and diagnostic T-ALL samples indicates altered methylation of CpG sites with a possible role in malignant hematopoiesis.

overall_design: Bisulphite converted DNA from the Cell culture and leukemia samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Mattias

last: Landfors

first: Jan

middle: K

last: Siwicki

first: John

last: Revie

first: Magnus

last: Borssén

first: Emma

last: Evelönn

first: Erik

last: Forestier

first: Krystyna

middle: H

last: Chrzanowska

first: Patrik

last: Rydén

first: W

middle: N

last: Keith

first: Göran

last: Roos


title: Control of YAP/TAZ by glucose metabolism


title: Identification of targets for rational pharmacological therapy in childhood craniopharyngioma

status: Public on Apr 18 2015

city: Aurora

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

type:
Expression profiling by array
Third-party reanalysis

summary:
Introduction: Pediatric adamantinomatous craniopharyngioma (ACP) is a histologically benign but clinically aggressive brain tumor that arises from the sellar/suprasellar region. Despite a high survival rate with current surgical and radiation therapy (75-95% at 10 years), ACP is associated with debilitating visual, endocrine, neurocognitive and psychological morbidity, resulting in exceptionally poor quality of life for survivors. Identification of an effective pharmacological therapy would drastically decrease morbidity and improve long term outcomes for children with ACP.

Results: Using microarray analysis of 15 ACP patient samples, we have found several pharmaceutical targets that are significantly and consistently overexpressed in our panel of ACP relative to other pediatric brain tumors, pituitary tumors, normal pituitary and normal brain tissue. Among the most highly expressed are several targets of the kinase inhibitor dasatinib -- LCK, EPHA2 and SRC; EGFR pathway targets -- AREG, EGFR and ERBB3; and other potentially actionable cancer targets -- SHH, MMP9 and MMP12. We confirm by Western blot that a subset of these targets is highly expressed in ACP primary tumor samples.

Discussion: We report here the first microarray gene expression analysis for ACP and the identification of targets for rational therapy. Experimental drugs targeting each of these gene products are currently being tested clinically and pre-clinically for the treatment of other tumor types. This study provides a rationale for further pre-clinical and clinical studies of novel pharmacological treatments for ACP. Development of pre-clinical mouse and cell culture models for ACP will further enable the translation of these targets from the lab to the clinic.

overall_design:
Gene expression profiles were generated from surgical tumor and normal brain samples (n=210) using Affymetrix HG-U133 Plus 2.0 chips.
Gene expression profiles of adamantinomatous craniopharyngioma (ACP) were compared to a cohort of other tumor samples and normal brain tissues, and analyzed via gene set enrichment (GSEA analysis) and hierarchical clustering analysis to identify high expression of potential drug targets.

The sample metadata and processed data for the complete dataset, which includes reanalysis of 23 Samples from GSE26966, 33 Samples from GSE35493, and 42 Samples from GSE50385, are linked below as supplementary files.


title: Regulation of gene expression by glucose metabolism in mammary cell lines

summary: Reprogramming of cancer cell metabolism toward aerobic glycolysis, i.e. the Warburg effect, is a hallmark of cancer; according to current views, the rationale for selecting such energy-inefficient metabolism is the need to increase cellular biomass to sustain production of daughter cells and proliferation. In this view, metabolic reprogramming is considered as a simple phenotypic endpoint that occurs as a consequence of signal transduction mechanisms, including oncogene-driven nutrient uptake and metabolic rewiring. A newly emerging paradigm is instead that transcriptional networks and oncogenic signaling can also be regulated downstream of metabolic pathways, that assume causative roles in controlling cancer cell behavior, above and beyond their core biochemical function. To explore possible links between glucose metabolism and nuclear gene transcription we compared immortalized mammary epithelial cells (MCF10A) and metastatic breast cancer cells (MDA-MB-231) growing in high glucose or in the presence of a widely used inhibitor of glucose uptake / glucose metabolism, 2-deoxy-glucose (2DG).

overall_design: MCF10A or MDA-MB-231 cells growing at low confluence in standard growth conditions were compared to cells incubated for 24 hours with 2-deoxy-glucose (2DG, 50mM) to inhibit glucose metabolism, and then harvested for total RNA extraction. 4 independent biological replicates were performed in parallel for each cell line and experimental condition.


title: Gene expression analysis in EGFR-mutant NSCLC cells treated with erlotinib versus DMSO

status: Public on Mar 19 2015

first: Joshua

last: Korn

address: 250 Mass Ave

institute: Novartis

summary: This experiment is designed to detect genes differentially expressed in 2uM erlotinib treatment versus DMSO treatment and to identify differential gene set enrichments.

overall_design: PC9 or HCC827 cells were seeded in 150cm2 flasks and treated for 8 days with DMSO or 2uM Erlotinib.

first: Alexandra

middle: B

last: Lantermann

first: Kaitlin

last: McCutcheon

first: Sreenath

middle: V

last: Sharma


title: Gene expression profile in the heart of wild type and Adenosine Receptor A2a over expressing mice

status: Public on Mar 22 2015

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

summary:
Adenosine binds to 4 G protein-coupled receptors located on the cardiomyocyte (A1-R, A2a-R, A2b-R and A3-R) and modulates cardiac function during both ischemia and load-induced stress. While the role of adenosine receptor-subtypes has been well defined in the setting of ischemia-reperfusion, far less is known regarding their roles in protecting the heart during other forms of cardiac stress.
We characterized the gene expression profiles of heart from A2a-R over-expressing mice subjected to transverse aortic constriction to study the potential of A2a-R activation to protect from pressure-induced heart failure.

overall_design: Transgenic mice were generated by over-expression of Adenosine Receptor 2A in a cardiac-specific and inducible manner. 8-week-old male wild-type FVB mice (N=3) and A2a-R TG littermates (N=3) underwent transverse aortic constriction (TAC). Hearts were harvested after 14 weeks. Affymetrix Mouse Gene 1.0 ST Array which contains 28853 transcripts was used to study the gene differential expression between wild type and A2a-R TG mice.


title: Granulocyte colony-stimulating factor reprograms bone marrow stromal cells to actively suppress B lymphopoiesis in mice

status: Public on Mar 21 2015

city: St. Louis

first: Daniel

last: Link

state: MO

address: 660 S. Euclid, Campus Box 8007

institute: Washington University

summary: G-CSF treatment targets CXCL12-abundant reticular (CAR) cells to suppress their production of a number of B trophic factors, including CXCL12, IL-6, IL-7, IGF-1, and Flt3 ligand.

overall_design: CAR cells were sorted from the bone marrow of Cxcl12-gfp mice treated with G-CSF or saline alone for 5 days

first: Ryan

last: Day


title: Genome-wide Scan for Methylation Profiles in head and Neck Cancer

city: Detroit

first: Maria

last: Worsham

state: MI

address: 1 Ford Place

department: Otolaryngology

institute: Henry Ford Health System

summary: Genome wide DNA methylation profiling of HPV positive and HPV negative head and neck squamous cell cancer (HNSCC) samples. The Illumina Infinium 450k Human DNA methylation Beadchip v1.1 was used to obtain DNA methylation profiles across approximately 485577 CpGs in 4 HPV positive and 4 HPV negative HNSCC tumors

overall_design: Bisulphite converted DNA from the 8 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip v1.1

first: Dhananajay

last: Chitale

first: George

last: Divine

first: Indrani

last: Datta

first: Kang

last: Chen

first: Josena

last: Stephen


title: Expression data of human neuroblastoma IMR32 cells treated with the DHODH inhibitor Teriflunomide [118 µM]

status: Public on Mar 27 2015

city: Essen

first: Sven

last: Lindner

address: Hufelandstraße 55

institute: University Hospital Essen

summary: Neuroblastoma is an embryonal tumor which originates from neural crest progenitor cells that fail to differentiate along their predefined route to sympathetic neurons or sympatho-adrenergic adrenal cells. It is the most common extracranial tumor of childhood and accounts for 15% of all childhood cancer deaths. Especially patients suffering from high grade or relapsed neuroblastoma have poor outcome in spite of aggressive treatment regimens including autologous stem cell transplantation. Those patients are in urgent need of additional effective therapies which demands the development of targeted approaches. Dihydroorotatedehydrogenase (DHODH) is the fourth enzyme of the pyrimidine synthesis pathway which oxidizes dihydroorotate to orotate. In recent past it became a potential drug target for cancer treatment because of its keyrole in processing essential pyrimidine nucleotides. On the basis of the existing data, functional inhibition of DHODH is considered to be promising therapeutic option for several tumor entities like advanced colorectal, breast or lung-cancers. Leflunomide is an established drug in treatment of the autoimmune diseases rheumatoid arthritis and multiple sclerosis. In the liver Leflunomide becomes converted to its active metabolite called Teriflunomide, which inhibits the activity of DHODH directly. In recent times Leflunomide is also used for therapy against the Cytomegalovirus and the BK virus. Also for Melanoma was shown recently a decreased growth rate due to Leflunomide treatment in a zebrafish and a mouse model. As Melanoma is a malignant tumor of the skin, which derives also from neural crest progenitor cells, a coherent investigation of effictivity of Leflunomide in neuroblastoma celllines showed first promising results. The aim of our study was to reanalyse the effectivity of Leflunomide in Neuroblastoma and to shed further light in its biological mode of action.

overall_design: Three+B52 biological samples of the human neuroblastoma cell line IMR32 were treated with DMSO or Teriflunomide [118 µM]

first: Johannes

last: Schulte


title: Radiation and Dual Checkpoint Blockade Activates Non-Redundant Mechanisms in Cancer

status: Public on Mar 16 2015

city: Philadelphia

first: Andy

last: Minn

state: PA

address: 421 Curie Blvd

institute: University of Pennsylvania

summary: Response to immune checkpoint inhibitors may be improved through combinations with each other and other therapies, raising questions about non-redundancy and resistance. We report results from parallel studies of melanoma patients and mice treated with anti-CTLA4 and radiation (RT). Although combined treatment improved responses, resistance was common. Computational analyses of immune and transcriptomic profiles (provided here) revealed that resistance in mice was due to upregulation of tumor PD-L1 that drives T cell exhaustion. Accordingly, optimal response requires RT, anti-CTLA4, and anti-PD-L1. Anti-CTLA4 inhibits Tregs, RT diversifies and shapes the TCR repertoire, and anti-PD-L1 reinvigorates exhausted T cells. Together, all three therapies promote the expansion of clonotypes with distinct TCR traits. Similar to mice, patients with melanoma showing high PD-L1 did not respond to RT + anti-CTLA4, demonstrated persistent T cell exhaustion, and rapidly progressed. Thus, the combination of RT, anti-CTLA4, and anti-PD-L1 promotes response through distinct mechanisms.

overall_design: Mice with bilateral flank B16-F10 tumors were treated with radiation to one tumor combinated with CTLA4 blockade. From unirradiated tumors that were resistant or relapsed after therapy, cell lines were isolated. After confirming the resistance phenotype by reimplantation, tumors from these resistant cells and control sensitive cells were profiled by microarray.


title: Expression data from intermediate monocytes from healthy donors and autoimmune uveitis patients

status: Public on Mar 17 2015

city: Bethesda

first: Baoying

last: Liu

address: 9000 Rockville Pike

institute: NEI

summary: Human peripheral monocytes have been categorized into three subsets based on differential expression levels of CD14 and CD16. However, the factors that influence the distribution of monocyte subsets and the roles which each subset plays in autoimmunity are not well studied. To compare the gene expression profiling 1) on intermediate monocytes CD14++CD16+ monocytes between healthy donors and autoimmune uveitis patients and 2) among 3 monocyte subsets in health donors, here we purified circulating intermediate CD14++CD16+ monocytes from 5 patients with autoimmune uveitis (labeled as P1-5) and 4 healthy donors (labeled as HD1-4) by flow cytometry and isolated total RNA to proceed microarray assay. In addition, we also purified CD14+CD16++ (non-classical monocytes) and CD14++CD16- (classical monocytes) from 4 healthy donors to do microarray. We demonstrate that CD14++CD16+ monocytes from patients and healthy control donors share a similar gene expression profile. The CD14+CD16++ cells (non-classical monocytes) display the most distinctive gene expression profiling when compared to intermediate CD14++CD16+ monocytes and classical CD14++CD16- monocytes.

overall_design:
Pheripharal blood from 5 autoimmune uveitis patients and 4 healthy donors were collected. Immediately after collection, we purified circulating intermediate CD14++CD16+ monocytes from 5 patients with autoimmune uveitis ( Sample 13-17; titled as P intermediate 1-5) and 4 healthy donors (Sample 1, 4, 7, 10; titled as HD intermediate 1-4) by flow cytometry and isolated total RNA to proceed microarray assay. In addition, we also purified CD14+CD16++ (Sample 3, 6, 9, 12; titled HD non-classical 1-4) and CD14++CD16- (Sample 2, 5, 8, 11; titled HD classical 1-4) from 4 healthy donors to do microarray.

Please note that data processing was performed in two groups;
[1] HD intermediate, classical and non-classical samples (total 12 samples)
[2] HD intermediate samples reanalyzed with P intermediate samples (total 9 samples).


title: STIM1 controls T cell mediated immune regulation and inflammation in chronic infection

city: New York City

first: Stefan

last: Feske

state: NY

address: 550 First Avenue

department: Pathology

institute: New York University

summary:
Influence of STIM1 on the transcriptome of CD4+ T cell subsets
STIM1 is critical for the regulation of the intracellular Ca2+ homeostasis in CD4+ T cell. Loss of function mutations in STIM1 in patients result in severe immuno deficiency and recurrent infections. Using conditional knock out mice for STIM1, we  investigated the role of STIM1 in T cells during chronic infections by in-vivo and in-vitro experiments. We found that STIM1 is required for T cell-mediated immunity to chronic infection with Mycobacterium tuberculosis (Mtb) as STIM1-deficient mice succumb to infection faster than littermate controls, have increased mycobacterial burdens and severe pulmonary infiltration with myeloid and lymphoid cells .Using the Affymetrix Mouse Exon 1.0 platform,  we analyzed  the influence of STIM1 expression on the transcriptom of  CD4+T cells in-vitro.  We found that STIM1 is required for the regulation of apoptosis related genes after TCR stimulation as well as for the induction of a transcriptonal program that polarizes naive CD4+ T cells into inducible CD4+ T regulatory cells (iTreg).  Together with our in-vivo findings, these experiments  reveal that STIM1  is essential for immune regulation to prevent an injurious inflammatory response during chronic infection.

overall_design: For microarry analysis, CD4+ T cells from WT or Stim1CD4 mice were isolated and stimulated with anti- CD3 and anti-CD28 antibodies for 48h in the presence or absence of TGFβ. Total RNA was isolated using the RNeasy micro RNA isolation kit (Quiagen). Biotin-labeled amplified aRNA was prepared and hybridized to 1.0 Exon expression chips (Affymetrix) according to the manufacturer’s protocols. The values in the sample data tables  were derived from the Expression Console Software (Affymetrix) by performing a gene-level normalization and signal summarization on the raw CEL files (gene-level analysis). Obtained  CHP files were subsequently analyzed and visualized using TAC software (Affymetrix) and IPA pathway analysis software (Qiagen). 3 age matched  mice per group and condition were used, no technical replicates were used.

first: Ludovic

last: Desvigne

first: Carl

last: Weidinger

first: Patrick

last: Shaw

first: Martin

last: Vaeth

first: Theo

last: Ribierre

first: Menghan

first: Lina

last: Kozhaya

first: Lauren

last: McVoy

first: Derya

last: Unutzmaz

first: Joel

last: Ernst


title: Analysis of Klf4 factor stoichiometry effects during iPS cell derivation from mouse embryonic fibroblasts

status: Public on Mar 13 2015

city: Kyoto

first: Knut

last: Woltjen

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

department: Reprogramming Science

institute: CiRA, Kyoto University

summary:
Oct3/4, Sox2, Klf4, and c-Myc re-wire somatic cells to achieve induced pluripotency (iPS cells). However, subtle differences in reprogramming methodology may confound comparative studies of reprogramming-induced gene expression changes. We specifically focused on the design of polycistronic reprogramming constructs, which encode all four factors linked with 2A peptides. Notably, publically available cassettes were found to employ one of two Klf4 variants (Klf4S and Klf4L; GenBank Accession No’s: AAC52939.1 and AAC04892.1), differing only by nine N-terminal amino acids. In a polycistronic context, these two variants generated dissimilar protein stoichiometry, where Klf4L vectors produced more Klf4 protein than those encoding Klf4S.
Employing piggyBac transposons, we systematically assessed gene expression changes during mouse embryonic fibroblast (MEF) reprogramming using a panel of novel and publically available polycistronic cassettes (Klf4S: OKMS, STEMCCA, EB-C5, WTSI; Klf4L: OSKM, MKOS, OK+9MS, OKN-HAMS). Strikingly, global gene expression patterns elicited by the panel of polycistronic cassettes at an intermediate stage of reprogramming (day6) diverged according to the Klf4 variant they encoded. Klf4L expressing vectors induced gene expression changes in MEFs similar to over-expression of Klf4 alone. Moreover, we found that these gene expression clusters were associated with differences in reprogramming hallmarks, including colony formation frequencies and the stabilization of transgene-independent pluripotency. Our data exposes a Klf4 reference cDNA variation that alters polycistronic factor stoichiometry, implicating a threshold in determining reprogramming outcomes. We hope this study will help to guide the comparison of compatible public gene expression data sets.

overall_design: 11 samples were analyzed. MEFs were transfected with one of eight different polycistronic reprogramming vectors or one of two Klf4 variants, followed by FACS sorting for transgene-positive cells. A MEF cell sample, mock transfected with a lacZ expression vector, was used as a reference for all intermediate reprogramming populations. All samples were compared to reveal construct-specific and common gene expression changes.

first: Shin

middle: I

last: Kim

first: Takuya

last: Yamamoto


title: Expression data from WT and TREM2 deficient microglia in a mouse model of Alzheimer's disease

city: Saint Louis

first: Marco

last: Colonna

address: 660 S Euclid Ave.

department: Pathology and Immunology

institute: Washinton University School of Medicine

summary: We examined the role of TREM2 on microglia responses to amyloid-beta deposition in a mouse model of Alzheimer's disease

overall_design: Microglia were FACS-purified from 8.5 month old WT, Trem2-/-, 5XFAD, and Trem2-/- 5XFAD mice

first: Yaming

last: Wang


title: Histone deacetylase inhibitors cause the selective depletion of bromodomain containing proteins

status: Public on Mar 10 2015

city: Heidelberg

last: Beck

state: Baden-Wurttemberg

address: Meyerhofstraße 1

department: Structural and Computational Biology

institute: European Molecular Biology Laboratory

summary: Histone deacetylases (HDACs) and acetyltransferases control the epigenetic regulation of gene expression through modification of histone marks. Histone deacetylase inhibitors (HDACi) are small molecules that interfere with histone tail modification thus altering chromatin structure and epigenetically controlled pathways. They promote apoptosis in proliferating cells and are promising anti-cancer drugs. While some HDACis have already been approved for therapy and others are in different phases of clinical trials, the exact mechanism of action of this drug class remains elusive. Previous studies have shown that HDACis cause massive changes in chromatin structure but only moderate changes in gene expression. To which extent these changes manifest at the protein level has never been investigated on a proteome-wide scale. Here, we have studied HDACi-treated cells by large-scale mass spectrometry based proteomics. We show that HDACi treatment affects primarily the nuclear proteome and induces a selective decrease of bromodomain containing proteins (BCPs), the main readers of acetylated histone marks. By combining time-resolved proteome and transcriptome profiling, we show that BCPs are affected at the protein level as early as 12 hours after HDACi treatment and that their abundance is regulated by a combination of transcriptional and post-transcriptional mechanisms. Using gene silencing, we demonstrate that the decreased abundance of BCPs is sufficient to mediate important transcriptional changes induced by HDACi. Our data reveals a new aspect of the mechanism of action of HDACi that is mediated by an interplay between histone acetylation and the abundance of BCPs.

overall_design: HeLa cells treated with trichostatin A and sodium butyrate for 12 and 48 hours

first: Marie-Therese

last: Mackmull

first: Murat

last: Iskar

first: Luca

last: Parca

first: Stephan

last: Singer

first: Peer

last: Bork

first: Alessandro

last: Ori


title: Comparison of Transcriptome Signatures between Meniscus and Articular Cartilage from Knees Undergoing Arthroscopic Partial Meniscectomy

status: Public on Mar 06 2015

first: Muhammad Farooq

last: Rai

address: 660 S. Euclid Ave.

department: Orthopaedic Surgery

institute: Washington University School of Medicine

summary:
Background:  Meniscus tears are the most common injury in the knee and are associated with an increased risk of osteoarthritis (OA). The molecular profile of knees with meniscus tears is not well-studied. Therefore, to advance our understanding of the early response of the knee to injury, we compared the gene expression profile of meniscus and articular cartilage within the same knees following meniscus injury.  Hypothesis/Purpose:  To identify differences between the molecular signatures of meniscus and articular cartilage from knees with intact articular cartilage undergoing arthroscopic partial meniscectomy.  Study Design: Descriptive laboratory study Methods:  Patients (n=12) with a known isolated medial meniscus tear without any knee chondrosis or radiographic OA were consented prior to surgery. During arthroscopic partial meniscectomy, a sample of their injured meniscus and a sample of their articular cartilage off the medial femoral condyle were procured. The transcriptome signatures, as measured through Affymetrix microarray, were compared between the two tissues and underlying biological processes were explored computationally.
Results:  3566 gene transcripts were differentially expressed between meniscus and articular cartilage. Gene transcripts down-regulated in articular cartilage were associated with extracellular matrix organization, wound healing, cell adhesion, and chemotaxis. Gene transcripts up-regulated in articular cartilage were associated with blood vessels morphogenesis and angiogenesis. Examples of individual genes with significant differences in expression between the two tissues include IBSP (23.76 fold; P < 0.001), upregulated in meniscus, and TREM1 (3.23 fold; P = 0.006), upregulated in meniscus. Conclusion:  The meniscus and articular cartilage have distinct gene expression profiles in knees with meniscus tears and intact articular cartilage.

overall_design: Total RNA obtained from injured meniscus and normal articular cartilage from patients undergoing partial meniscectomy.

first: Muhammad

middle: F

first: Linda

last: Sandell

first: Rick

middle: W

last: Wright

first: Robert

last: Brophy


title: Microarray data of FACS purified population isolated from AML patients.

city: Copenhagen

first: Nicolas

last: Rapin

address: Ole Maaloes vej 5

department: Finsen Laboratory

country: Denmark

institute: Copenhagen University

summary: We isolated hematopoietic stem and progenitor cells from AML patients by FACS.

overall_design:
Mononuclear bone marrow cells from AML patient were enriched for 34+ and leukemic Granulocyte Macrophage Progenitors (L-GMP) cells were sorted by FACS and hybridized to Affymetrix HG-U133 Plus 2.0 GeneChips. see 1-2 for details.
1. Rapin N, Bagger FO, Jendholm J, et al. Comparing cancer vs normal gene expression profiles identifies new disease entities and common transcriptional programs 1n AML patients. Blood. 2014;123(6):894?904.
2. Mora-Jensen H, Jendholm J, Fossum A, et al. Technical advance: immunophenotypical characterization of human neutrophil differentiation. J. Leukoc. Biol. 2011;90(3):629?634.

first: Johan

last: Jendholm

first: Kim

last: Theilgaard-Mönch


title: Evolutionary changes in promoter and enhancer activity during human corticogenesis (human)

city: New Haven

first: Steven

last: Reilly

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Evolutionary changes in gene regulation during cortical development likely contributed to the expansion and specialization of the cortex in humans. However, the lack of a regulatory map of the human embryonic cortex has hindered identification of these changes and the biological processes they influenced. We performed genome-wide epigenetic profiling to compare promoter and enhancer activity during corticogenesis in human, rhesus, and mouse. We identified 2,855 promoters and 8,996 enhancers that have gained activity in human based on increased epigenetic marking. To detect biological pathways enriched for these changes, we mapped promoters and enhancers exhibiting epigenetic gains onto modules of co-expressed genes constructed using spatio-temporally rich expression data from developing human cortex. We identified multiple modules enriched in human lineage epigenetic gains. Gains in enriched modules were associated with genes functioning in neuronal proliferation and migration, cortical patterning, and the extracellular matrix. Gain-enriched modules also showed correlated gene expression patterns and similar transcription factor binding site enrichments in promoters and enhancers, suggesting they are connected by common regulatory mechanisms. Our results reveal coordinated patterns of potential regulatory changes associated with conserved developmental processes in corticogenesis, providing insight into human cortical evolution.

overall_design: For Human and Mouse samples, two biological replicates from four   cortical tissue stages, each stage  with separate  H3K27ac and H3K4me2 ChIPs as well as an input control. Identical ChIPs for two replicates at two stages in Rhesus cortex, and one rhesus stage without replication.

first: James

last: Noonan


title: Expression data from ethanol and saline exposed mice

status: Public on Mar 07 2015

city: Toronto

first: Eric

last: Chater-Diehl

state: ON

address: 686 Bay St.

country: Canada

institute: SickKids Research Institute

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

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

platform_organism:
Mus musculus
synthetic construct

overall_design: Refer to individual Series


title: Gene expression profiling from pooled samples of subcutaneous adipose tissue of NAPE-WT or NAPE-KO mice fed either with a control diet or a high-fat diet.

city: Brussels

first: Jean-Baptiste

last: Demoulin

address: av Hippocrate 75, B1.74.05

department: de Duve Institute

institute: Université catholique de Louvain

summary: Mice knocked-out or wild type for the NAPE PLD gene specifically in adipose tissue, were recruited for this expression profiling experiment. Each group of mice (WT versus cKO) were fed with a control diet or a high fat diet. Then mice were sacrificed and adipose tissue samples form the subcutaneous adipose tissue were processed for RNA extraction. Total RNA of each sample was then pooled with those of the same group and treatment for microarray hybridization.

overall_design: two groups of mice: (I) NAPE PLD WT and NAPE PLD KO. Each group was submitted to a diet treatment: (I) control diet and (II) high fat diet.

first: Lucie

last: Geurts

first: Ahmed

last: Essaghir

first: Patrice

middle: D

last: Cani


title: Transcriptional regulation by EVI1 in the absence or presence of TPA

status: Public on Mar 14 2015

city: Vienna

first: Rotraud

last: Wieser

address: Waehringer Guertel 18-20

department: Clinic of Medicine I

country: Austria

institute: Medical University of Vienna

summary: To investigate whether and how expression of the oncogenic transcription factor EVI1 influences gene regulation by phorbol esters and vice versa, the human myeloid cell line U937 was transduced with an EVI1 expression vector or empty vector as a control. Cells were treated with 12-Otetradecanoylphorbol 13-acetate (TPA) or its solvent ethanol as a control. RNA was extracted and subjected to gene expression microarray analysis.

overall_design: U937 cells transduced with an EVI1 expression vector or empty vector as a control were treated with 50 ng/ml TPA or an equivalent amount of ethanol (solvent) for 24 h prior to gene expression microarray analysis. 3 biological replicates were performed.

first: Birgit

last: Steinmetz

first: Hubert

last: Hackl


title: CMV infection drives adaptive epigenetic diversification of NK cells

city: Stockholm

first: Yenan

last: Bryceson

address: Karolinska University Hospital Huddinge

department: Department of Medicine

institute: Karolinska Institutet

summary: The mechanisms underlying human NK cell phenotypic and functional heterogeneity are unknown. Here, we describe the emergence of diverse subsets of human NK cells selectively lacking expression of signaling proteins following cytomegalovirus (CMV) infection. The absence of B and myeloid cell-related signaling protein expression in these NK cell subsets correlated with promoter DNA hypermethylation. Intriguingly, geneome-wide analyses revealed patterns of DNA methylation that were strikingly similar between CMV-associated adaptive NK cells and cytotoxic effector CD8+ T cells, but differed from those of canonical NK cells.

overall_design: A total of 23 samples were analyzed (4 sorted NK cell subsets and 2 sorted T cell subsets each from 4 individual donors). In one donor only 5 subsets were analyzed. Bisulfite-converted genomic DNA was hybridized to the Illumina Human Methylation450 BeadChip

middle: T

first: Frank

last: Cichocki

first: Bianca

last: Tesi


title: Expression data from murine Treg subsets defined by CD103 and ICOS expression before and after activation by an in vitro CD4 T cell suppression assay

status: Public on Mar 08 2015

city: Campus de Cantoblanco

first: Alberto

last: Pascual-Montano

state: Madrid

address: Darwin 3

country: Spain

institute: National Center for Biotecnology

summary: Regulatory T cells (Treg) are pivotal for the maintenance of peripheral tolerance by controlling self-reactive, chronic and homeostatic T cell responses. We now report that the increase in Treg suppressive function observed in lymphopenic mice correlates with the degree of lymphopenia and is caused by a higher frequency of a novel subpopulation of CD103posICOSpos cells among peripheral Treg that differentially express multiple Treg signature genes.

overall_design: Treg subsets were sorted from wild type mice based on their expression of CD103 and ICOS. Gene expression profile was analysed directly after sorting and after activation of the subsets in a standard CD4 T cell suppression assay.  Two independent experiments were performed.

first: Thomas

last: Barthlott

first: Angela

last: Bosch

first: Caroline

last: Berkemeier

first: Ruben

last: Nogales-Cadenas

first: Lukas

last: Jeker

first: Marcel

last: Keller

first: Georg

middle: A

last: Holländer


title: Anticancer effects of pycnogenol, catechin, epicatechin, taxifol and resveratrol on human fibrosarcoma cells

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

summary: We assessed the apoptotic and antiproliferative effects of resveratrol, pycnogenol and its metabolites on HT1080 human fibrosarcoma cells in vitro. Viability, apoptosis and necrosis were quantified by FACS analysis (Propidiumiodide/AnnexinV staining). Gene expression was analysed by RNA-Microarray. Cell proliferation was analysed by BrdU ELISA assay.

overall_design: We used microarrays to investigate differential gene expression in HT1080 fibrosaroma cells after incubation with pycnogenol, catechin, epicatechin, taxifolin and resveratrol. Microarray analysis revealed differential gene expression patterns of HT1080 after incubation with compounds.

first: L

first: K

last: Harati

first: A

last: Daigeler


title: Multiple Overlapping Mammalian Chromatin Remodeling Systems Collaborate Genome-wide at Dynamic Chromatin Transitions [Affymetrix]

status: Public on Mar 05 2015

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

summary:
Expression data from 3134  mouse mammary epithelial cell line -/+ Tet-inducible chromatin remodeler mutant variants
ATP-dependent chromatin remodeling is an essential process required for the dynamic organization of chromatin structure. Here we describe the genome-wide location and activity of three remodeler proteins with diverse physiological functions in the mouse genome: Brg1, Chd4 and Snf2h. The localization patterns of all three proteins substantially overlap with one another and with regions of accessible chromatin. Furthermore, using inducible mutant variants, we demonstrate that the catalytic activity of these proteins contributes to the remodeling of chromatin genome wide and that each of these remodelers can independently regulate chromatin reorganization at distinct sites. Many regions require the activity of more than one remodeler to regulate accessibility. We also examined effects of mutant remodeler variants on selective gene expression by global analysis of RNA expression patterns and found more than 800 genes are deregulated by these variants. These findings provide a dynamic view of chromatin organization and highlight the differential contributions of remodelers to chromatin maintenance in higher eukaryotes.

overall_design: Flag tagged dominant negative variants of the chromatin remodelers Brg1, Chd4, and Snf2h were each stably integrated into a cell line containg the tetracycline transactivator regulatory system (3134Tet (7110)). The 3134Tet control cells and each of the dominant-negative remodeler cell lines were grown in media with or without tetracycline for 48 hrs to induce expression of the tetracycline transactivator alone (3134Tet cells) or tetracycline transactivator and dominant negative remodeler variant. Following  treatment, cells were harvested for RNA extraction and hybridization to Affymetrix Mouse Gene 1.0 ST arrays.

first: Stephanie

last: Morris


title: Genome-wide Scan for Methylation Profiles in Breast Cancer

status: Public on Mar 11 2015

first: Maria

last: Worsham

address: 1 Ford Place

institute: Henry Ford Health System

summary: Genome wide DNA methylation profiling of normal and breast cancer samples. The Illumina Infinium 450k Human DNA methylation Beadchip v1.1 was used to obtain DNA methylation profiles across approximately 485577 CpGs in breast cancer and normal samples. Samples included 40 normal, 80 breast cancer samples.

overall_design: Bisulphite converted DNA from the 120 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.1

first: Dhananajay

last: Chitale

first: George

last: Divine

first: Indrani

last: Datta

first: Kang

last: Chen


title: Epigenetic and transcriptional characterisation of CMV driven diversification of NK cells

first: Yenan

last: Bryceson


title: Expression data from CSC and Non-CSC of three HCC cell lines

city: Beijing

first: Yanying

last: Wang

address: 15 Datun Road, Chaoyang District,Beijing 100101, China

country: China

institute: Institute of Biophysics, Chinese Academy of Sciences

summary:
Hepatocellular carcinoma (HCC) represents the major subtype of liver cancer, characterized with a high rate of recurrence and heterogeneity. Liver cancer stem cells (CSCs) may account for a hierarchical organization of heterogeneous cancer cells. However, how liver CSCs sustain their self-renewal remains largely unknown.
We used microarrays to discover the long non-coding RNAs (lncRNAs) expression underlying cell stem cell (CSC) and non cell stem cell (non-CSC) and identified distinct lncRNAs during this process.

overall_design: We sorted CD13+CD133+ and CD13-CD133- cells from Hep3B, Huh7, and PLC/PRF/5 HCC cell lines as liver CSCs and non-CSCs, then hybridized on Affymetrix microarrays. We sought to identify distinct lncRNAs in liver CSCs.


title: Epigenome analysis of human epidermal and dermal samples with aging and sun exposure

city: Baltimore

first: Andrew

last: Feinberg

address: 855 N. Wolfe St

institute: Johns Hopkins University School of Medicine

summary: Genome wide DNA methylation profiling of epidermal and dermal samples obtained from sun-exposed and sun-protected body sites from younger (<35 years old) and older (>60 years old) individuals. The Illumina Infinium 450k Human DNA methylation Beadchip  was used to obtain DNA methylation profiles across approximately 450,000 CpGs in dermal and epidermal samples. Samples included 10 younger sun protected dermal samples, 10 younger sun exposed dermal samples, 10 older sun protected dermal samples, 10 older sun exposed dermal samples, 9 younger sun protected epidermal samples, 9 younger sun exposed epidermal samples, 10 older sun protected epidermal sample, 10 older sun exposed epidermal samples.

overall_design: Bisulphite converted DNA from the 78 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip.

first: Amy

middle: R

last: Vandiver


title: KSHV G-protein-coupled receptor (GPCR) induced gene transcription in HUVEC cells

city: Wuhan

first: Junjie

last: Zhang

state: Hubei

address: Donghu Road, No. 115

department: Medical Research Institute

institute: Wuhan University

summary:
We used microarrays to compare the gene transcription level between HUVEC-kGPCR and HUVEC-vector stable cells. The goal is to identify the genes that are affected by KSHV kGPCR expression.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

overall_design: HUVEC cells were infected with kGPCR or control lentivirus and selected with puromycin to get stable cells. Then RNA was extracted from these cells and microarray analysis was performed.

first: Pinghui

last: Feng


title: Expression data from shlncTCF7 and shCtrl of hepatocellular carcinoma (HCC) clinical sample

summary:
To explore the target genes of long noncoding RNA lncTCF7, we established lncTCF7-silenced HCC primary CSC cells and conducted transcriptome microarray analysis.
We used microarrays to identify distinct gene expression underlying shCtrl and shlncTCF7 of hepatocellular carcinoma sample stem cells.

overall_design: We cultured shlncTCF7 and shCtrl cells from hepatocellular carcinoma (HCC) clinical sample, then hybridized on Affymetrix microarrays. We sought to identify distinct target genes of lncTCF7 in liver cancer stem cells (CSCs).


title: Gene expression profiling of perinatal or adult medullary thymic epithelial cells (MECs)

status: Public on Mar 02 2015

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: A comparative analysis of gene expression of perinate or adult Aire-GFP+ and GFP- MECs in WT or Aire-KO thymus

overall_design: Aire+ and Aire- MECs were sorted from adults (5 weeks old) or perinates (0-3 days old) of Aire-driven Igrp-GFP (Adig) mice in Aire-WT and -KO background. RNA from whole samples was amplified, labeled, and hybridized to Affymetrix Mouse Gene 1.0 ST Arrays.

first: Noriyuki

last: Fujikado

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Effects of Low-Dose Irradiation Using Unsealed Caesium-137 on Cultured Normal Human Cells

status: Public on Mar 15 2015

city: Tokyo

first: Mari

last: Katsura

address: 2-11-16 Yayoi, Bunkyo-ku

department: Isotope Science Center

institute: The University of Tokyo

summary: Caesium-137 (Cs-137) is one of the major radionuclides appearing in the natural environment after nuclear power plant accidents. However, the biological effects of low-dose internal irradiation with this radionuclide remain unclear. We developed an experimental model for studying low-dose internal irradiation using cultured human cells. The cells were incubated in the culture medium supplemented with unsealed Cs-137 chloride. We used the Monte Carlo simulation method for measuring internal irradiation because making direct measurements was not possible. The simulation revealed that 96.40%?99.70% of the internal irradiation involved ?-particles and other electrons. During the experiment, a gradual incorporation of Cs-137 in the cells, and the absorbed dose rate increased in a time-dependent manner. In addition, the number of ?-H2AX and 53BP1 nuclear foci in the cells increased by internal irradiation in a dose-dependent manner. Microarray analysis revealed time-dependent alterations in gene expression caused by the radiation. These results demonstrate that our experimental system can be useful in the investigation of the effects of low-dose internal irradiation.

overall_design: HUVECs synchronized in G1 cell cycle phase were irradiated by unsealed cesium-137 in culture medium at 0.0146 mGy per minute (0.675 mGy) externally and 0.0152 mGy per minute (2.09 mGy/ hr), 0.0159 mGy per minute (4.66 mGy/ hr)for 1, 3 and 6 h, respectively. Experiments were biologically duplicated.

first: Azusa

last: Ishizaki

first: Hiromasa

last: Nakamine

first: Takahide

last: Kohro

first: Kazuyuki

last: Tao

first: Kazunori

last: Watanabe

first: Tsuyoshi

last: Inoue

first: Kaneki

last: Kaneki

first: Akashi

last: Taguchi

first: Mika

last: Kobayashi

first: Shota

last: Amagasa

first: Masataka

last: Komori

first: Yasushi

last: Iwamoto

first: Mikoto

last: Tamura

first: Rie

last: Mizuno

first: Norio

last: Nogawa

first: Toshiyuki

last: Kaji

first: Hideko

last: Sone

first: Kenichi

last: Ijiri

first: Tatsuhiko

last: Kodama

first: Youichiro

last: Wada

first: Kiyoshi

last: Miyagawa

first: Nobuyoshi

last: Akimitsu


title: Expression data from Keap1 overexpression and Nrf2 knockdown lung cancer cell

status: Public on Mar 04 2015

city: Taipei

first: Kuo-Tai

last: Hua

address: No. 1, Sec. 1, Jen-Ai Rd.

country: Taiwan

institute: National Taiwan University

summary:
Keap1 overexpressed and Nrf2 depleted CL1-5 cells were used to identify genes regulated by Keap1/Nrf2 axis-dependent gene regulations
We used microarrays to detail the global programme of gene expression underlying metastasis and identified distinct classes of Keap1/Nrf2-regulated genes during this process.

overall_design: CL1-5 cells stably expressed Keap1 expressing construct and Nrf2-specific shRNA were analyzed compared to control cells

first: Min-Liang

last: Kuo

first: Ming-Hsien

last: Chien


title: Pathogenic pathways are activated in each major cell type of the glomerulus in the Cd2ap mutant   mouse model of focal segmental glomerulosclerosis

status: Public on Mar 03 2015

city: Cincinnati

first: Steven

last: Potter

state: OH

address: 3333 Burnet Ave.

department: Developmental Biology

institute: Children's hospital Medical Center

summary: Mutations in several genes expressed in podocytes, including Cd2ap, have been associated with focal segmental glomerulosclerosis in humans. Mutant mouse models provide an opportunity to better understand the molecular pathology that drives these diseases. In this report we use a battery of transgenic-GFP mice to facilitate the purification of all three major cell types of the glomerulus from Cd2ap mutant mice. Both microarrays and RNA-seq were used to characterize the gene expression profiles of the podocytes, mesangial cells and endothelial cells, providing a global dual platform cross-validating dataset. The mesangial cells showed increased expression of profibrotic factors, including thrombospondin, Tgfb2 and Tgfb3, as well as the angiogenesis factor Vegf. They also showed upregulation of protective genes, including Aldh1a2, involved in retinoic acid synthesis, and Decorin, a Tgfb antagonist. Of interest, the mesangial cells also showed significant expression of Wt1, which has generally been considered podocyte specific. The Cd2ap mutant podocytes showed upregulation of proteases as well as genes involved in muscle and vasculature development, and showed a very strong gene expression signature indicating programmed cell death. Endothelial cells showed increased expression of the leukocyte adhesion associated factors Vcam1 and Sele, as well as Midkine (promoting angiogenesis), endothelin, and many genes responsive to cytokines and interferons. This study provides a comprehensive analysis of the changing properties of the three cell types of the glomerulus in Cd2ap mutants, identifying activated and repressed pathways and responsible genes, thereby delivering a deeper molecular understanding of this genetic disease.

overall_design: All three major cell types of the glomerulus were FACS purified from CD2AP-/- mutant mice and normal controls and gene expression profiled with Affymetrix Mouse Exon 1.0 ST arrays. Data was analyzed with GeneBASE software.  Biological triplicates were performed.

first: S

middle: S

first: Eric

last: Brunskill


title: Tumorgrafts as in vivo surrogates for women with ovarian cancer.

status: Public on Mar 09 2015

city: Rochester

first: Marc

last: Becker

state: MN

address: 200 First St SW

department: Medical Oncology

institute: Mayo Clinic

summary:
Purpose:Ovarian cancer has a high recurrence and mortality rate. A barrier to improved outcomes includes a lack of accurate models for preclinical testing of novel therapeutics.
Experimental Design:Clinically-relevant, patient-derived tumorgraft models were generated from sequential patients and the first 168 engrafted models are described. Fresh ovarian, primary peritoneal, and fallopian tube carcinomas were collected at the time of debulking surgery and injected intraperitoneally into severe combined immunodeficient mice.
Results:Tumorgrafts demonstrated a 74% engraftment rate with microscopic fidelity of primary tumor characteristics. Low-passage tumorgrafts also showed comparable genomic aberrations with the corresponding primary tumor and exhibit gene set enrichment of multiple ovarian cancer molecular subtypes, similar to patient tumors. Importantly, each of these tumorgraft models are annotated with clinical data and for those that have been tested, response to platinum chemotherapy correlates with the source patient.
Conclusions:Presented herein is the largest known living tumor bank of patient-derived, ovarian tumorgraft models that can be applied to the development of personalized cancer treatment.

overall_design: Microarrays were employed to elucidate global transcription in 36 ovarian tumorgrafts and identify differentially expressed genes in platinum resistant vs. sensitive models.

first: Saravut

last: Weroha

first: Paul

last: Haluska


title: Calcitriol deregulates AR signaling to inhibit prostate cancer progression in the TRAMP model

city: buffalo

first: Dan

last: Wang

address: Elm & Carlton Streets

institute: RPCI

summary: The mechanism of action of vitamin D in prostate cancer (PCa) remains poorly defined, with most mechanisms identified being highly cell type and model specific. One of the underlying factors for these diverse mechanisms may be the use of overly simplistic in vitro model systems to study the complex biology of vitamin D response. Here we use the more complex and in vivo transgenic adenocarcinoma of mouse prostate (TRAMP) model to better determine the mechanism by which vitamin D inhibits PCa growth. In these studies early stage TRAMP mice were treated ± 20μg/kg calcitriol (vitamin D) on a Monday/Wednesday/Friday schedule and tissue was procured 12 and 24 hours post treatment to assess changes in PCa transcriptomes using Affymetrix gene expression arrays.

overall_design: 15 total samples were analyzed. 10 week old TRAMP mice were treated IP ± 20 ug/kg calcitriol on a Monday/Wednesday/Friday (MWF) schedule, and prostate tissue was procured 12 (N=3, control; N=4, calcitriol) and 24 hours (N=4, control; N=4, calcitriol) post treatment for use in affymetrix studies.

first: Jason

last: Kirk

first: Bryan

last: Gillard

first: Ellen

last: Karasik

first: Mike

last: Moser

first: Song

last: Liu

first: Barbara

last: Foster


title: DNA methylation profiles of brain samples from Down Syndrome subjects and controls.

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

summary:
Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 486,000 CpGs. Dataset included 71 samples from multiple brain regions (cerebellum, temporal/occipital/frontal cortex). The goal was to evalute the effect of trisomy 21 on DNA methylation levels and epigenetic age.
Explanation of characteristics variables in supplementary file Explanation_of_characteristic_variables2.docx

overall_design: Bisulphite converted DNA from the 71 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip. Trisomy 21 (Down syndrome status) was related to CpGs.


title: Integrative profiling of follicular lymphoma at diagnosis and relapse

city: Houston

first: Michael

last: Green

state: TX

address: 1515 Holcombe Blvd, Unit 903

department: Lymphoma/Myeloma

institute: MD Anderson Cancer Center

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

summary: Follicular lymphoma (FL) is incurable with conventional therapies and has a clinical course typified by multiple relapses after therapy. These tumors are genetically characterized by B-cell leukemia/lymphoma 2 (BCL2) translocation and mutation of genes involved in chromatin modification. By analyzing purified tumor cells, we identified additional novel recurrently mutated genes and confirmed mutations of one or more chromatin modifier genes within 96% of FL tumors and two or more in 76% of tumors. We defined the hierarchy of somatic mutations arising during tumor evolution by analyzing the phylogenetic relationship of somatic mutations across the coding genomes of 59 sequentially acquired biopsies from 22 patients. Among all somatically mutated genes, CREBBP mutations were most significantly enriched within the earliest inferable progenitor. These mutations were associated with a signature of decreased antigen presentation characterized by reduced transcript and protein abundance of MHC class II on tumor B cells, in line with the role of CREBBP in promoting class II transactivator (CIITA)-dependent transcriptional activation of these genes. CREBBP mutant B cells stimulated less proliferation of T cells in vitro compared with wild-type B cells from the same tumor. Transcriptional signatures of tumor-infiltrating T cells were indicative of reduced proliferation, and this corresponded to decreased frequencies of tumor-infiltrating CD4 helper T cells and CD8 memory cytotoxic T cells. These observations therefore implicate CREBBP mutation as an early event in FL evolution that contributes to immune evasion via decreased antigen presentation.

overall_design:
[copy number]  B-cells were purified from cyropreserved tumor cell suspensions by FACS, DNA isolated, and interogated using Affymetrix 250K Nsp SNP microarrays.
Aim: To track the evolution of genetic alterations during progression of follicular lymphoma.
One array per tumor.

[gene expression]  Gene expression profiling of purified B and T cells from follicular lymphoma tumors at diagnosis and relapse
Tumor B-cells (CD19+CD20+CD10+) and tumor-infiltrating T-cells (CD5+CD19-) were sorted from cryopreserved follicular lymphoma biopsies by fluorescence activated cell sorting. DNA and RNA were isolated using Qiagen AllPrep kits, and RNA was interrogated using Affymetrix U133plus2 gene expression microarray.

first: Ash

last: Alizadeh


title: Expression data from ethanol and saline exposed mice [mRNA]

last: Chater-Diehl

address: 686 Bay St.

institute: SickKids Research Institute

summary: Mouse models of Fetal Alcohol Spectrum Disorder can be used to assess molecular changes underlying the disorder. Neonatal ethanol exposure in mice can be used to model third trimester ethanol exposure in humans.

overall_design: Mice were injected with 2.5 g/kg twice on each of postnatal days 4 and 7. Mice were allowed to reach postnatal day 70, at which time whole-hippocampus was isolated and snap frozen. Tissue was thawed and RNA was isolated. RNA run on affymetrix gene expression array according to standard protocol.  Each array was a pool of three mice, for a total n=9 ethanol-exposed and 9 control mice. All mice were male.

last: Diehl

first: Shiva

last: Singh


title: Expression data from Smarcd1 knockdown R1 embryonic stem cells

status: Public on Mar 01 2015

city: Jerusalem

first: Eran

last: Meshorer

address: Edmond J. Safra Campus

country: Israel

institute: The Hebrew University of Jerusalem

summary: We used microarrays to identify the gene expression changes after Smarcd1 knockdown in ESCs and 4 day RA differentiated ESCs

overall_design: Actively growing ESCs and 4d RA differentiated ESCs were harvested and RNA was extracted immediately.

first: Adi

last: Alajem


title: S-adenosylmethionine (SAM) changes DNA methylation patterns in prostate cancer cells

city: Vancouver

last: Stefanska

state: BC

address: 2205 East Mall

department: Land and Food Systems

institute: The University of British Columbia

summary: Genome-wide DNA methylation profiling of human PC3 invasive prostate cancer cell line treated with vehicle control (SAH, S-adenosylhomocysteine) and with SAM (S-adenosylmethionine) as well as of untreated human LNCaP non-invasive prostate cancer cell line. The Illumina Infinium 450k Human DNA Methylation BeadChip v1.2 was used to obtain DNA methylation profiles across approximately 450,000 CpGs in human cell lines exposed to described treatments. Samples included biological triplicate of PC3 control (SAH treated), biological triplicate of PC3 treated with SAM, and biological duplicate of LNCaP untreated.

overall_design: Bisulfite-converted DNA from the 8 samples were hybridised to the Illumina Infinium 450k Human Methylation BeadChip v1.2.

first: Nicholas

last: Shukeir

first: Surabhi

last: Parashar

first: Flora

last: Chik

first: Ani

last: Arakelian

first: Moshe

last: Szyf

first: Shafaat

last: Rabbani


title: The combinatorial code governing cellular responses to complex stimuli

city: London

first: Raphael

last: Zollinger

state: London

address: Charterhouse Square

country: United Kingdom

institute: Barts Cancer Institute (QMUL)

summary: Integration of multiple signals shapes cell adaptation to their microenvironment through synergistic and antagonistic interactions. The combinatorial complexity governing signal integration for multiple cellular output responses has not been resolved. For outputs measured in the conditions 0 (control), signals X, Y, X+Y, combinatorial analysis revealed 82 possible interaction profiles, which we biologically assimilated to 5 positive, and 5 negative interaction modes. To experimentally validate their use in living cells, we designed an original computational workflow, and applied it to transcriptomics data of innate immune cells integrating physiopathological signal combinations. Up to 9 of the 10 defined modes coexisted in context-dependent proportions. Each integration mode was enriched in specific molecular pathways, suggesting a coupling between genes involved in particular functions, and the corresponding mode of integration. We propose that multimodality and functional coupling are general principles underlying the systems level integration of physiopathological and pharmacological stimuli by mammalian cells.

overall_design: The general experiment design : No stimulus (Medium), stimulus X, stimulus Y and combination treatment X+Y was applied for 6 or 24 hours, with different stimuli combinations. Every experimental condition was carried out in 3 independent biological replicates.

first: Antonio

last: Cappuccio

first: Vassili

last: Soumelis


title: Expression data from mouse arthritis tarsal joints

city: Copenhagen N

first: Thomas

last: Litman

state: Outside the US or Canada

address: Blegdamsvej 3C

department: ISIM

institute: University of Copenhagen

summary: Pathological bone changes differ considerably between inflammatory arthritic diseases, and most studies have focused on bone erosion. Collagen Induced Arthritis (CIA) is a model for Rheumatoid Arthritis, which, in addition to bone erosion, demonstrates bone formation at the time for clinical manifestations. The objective of this study was to use the CIA model to study bone remodelling by performing a gene expression profiling time-course study on the CIA model.

overall_design: Three tarsal joints were sampled per clinical phase from the following clinical phases: Duration of clinical arthritis 0-3 days, duration of clinical arthritis 1-2 weeks, duration of clinical arthritis 3-4 weeks and duration of clinical arthritis minimum 3 weeks and declining (Twelve joints in total). For the clinical phase  “Decline” the joints had had a clinical score of 3 for minimum 3 weeks, after which the clinical score had declined minimum 1 score when the joint was sampled. For all other joints, the clinical score was 3 at the sampling time. The twelve joints were compared to three joints from non-induced control animals. The joints were processed and analysed separately (unpooled ). The joints were snap-frozen in liquid N2 and stored at -80˚C. RNA was extracted using the mirVanaTM miRNA isolation kit (Ambion, Denmark), amplified and labelled using the Pico amplification kit (Nugen, San Carlos, USA), according to the manufacturers´ instructions, followed by hybridisation to Mouse Gene 1.0ST microarrays (Affymetrix, Santa Clara, USA). The quality of the RNA was evaluated using RNA integrity numbers (RIN) and only samples with values of minimum 8.4 were chosen for further analysis.

first: Katja

last: Denninger

first: Troels

last: Marstrand


title: Loss of p21 expression enhances DNA damage, cholestasis and hepatocarcinogenesis in the liver

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: Overexpression of p21 in NEMOΔhepa animals protects against DNA damage, acceleration of hepatocarcinogenesis and cholestasis. As strengthened by our LPS stimulation experiments, we identified a novel protective role of p21 against DNA damage.

overall_design: Expression profiling of livers from wild type, NEMO, and NEMO-P21 null mice.

first: Haksier

last: Ehedego

first: Mark

last: Boekschoten

first: Wei

last: Hu

first: Carina

last: Doler

first: Johannes

last: Haybaeck

first: Nikolaus

last: Gaßler

first: Michael

last: Müller

first: Christian

last: Liedtke

last: Trautwein


title: Expression data for childhood BCP-ALL xenografts

city: Albuquerque

first: Richard

last: Harvey

state: NM

department: Pathology

institute: University of New Mexico

summary: Primary xenografts were made from a variety of different high-risk childhood BCP-ALL leukemia samples.

overall_design: 13 primary BCP-ALL samples were used to generate the 38 xenografts in NOD/SCID mice.


city: Copenhagen

first: Anders

last: Lund

address: Ole Maaloes Vej 5

department: Biotech Research and Innovation Centre

summary:
The PR-domain family (PRDMs) encodes transcriptional regulators, several of which are deregulated in cancer. We found that loss of Prdm11 accelerates MYC-driven lymphomagenesis in the Eµ-Myc mouse model.
Expression data from EμMyc;Prdm11 WT and EμMyc;Prdm11 KO end-stage splenic tumors to identify genes deregulated by loss of Prdm11

overall_design: 9  EμMyc;Prdm11 WT and 9 EμMyc;Prdm11 KO end-stage splenic tumors

first: Cathrine

last: Fog


title: Gene expression profiling of perinatal or adult regulatory T cells (Tregs)

status: Public on Feb 27 2015

first: CBDM

last: Lab

state: MA

summary: A comparative analysis of gene expression of 3 different experiments; 1. Perinate or adult-tagged GFP+YFP+ and bulk GFP+YFP- Tregs, 2. FL or BM-derived Tregs 3. Perinate or adult thymic Tregs.

overall_design:
1. Foxp3-eGFP-Cre-ERT2 x Rosa26-YFP lineage-reporter mice were injected ip with tamoxifen (4 injections, every third day) between 0-10 (perinate) or 35-45 (adult) days of age, and keep until 8 weeks of age. Perinate or adult-tagged GFP+YFP+ cells and bulk GFP+YFP- were double-sorted.

2. Hematopoietic progenitor cells were isolated from E18.5 fetal liver of CD45.1 congenic mice or from bone marrow of 5 weeks old CD45.2 B6 mice via negative selection of Thy1.2+ cells. The two populations were mixed at a 1:1 ratio, and were iv-transferred into irradiated (1000 rad) Rag-1-KO mice. FL or BM-derived Tregs were double sorted after reconstitution. 3. Foxp3-GFP+ Tregs were double-sorted from perinate (4 days old) or adult (5 weeks old) thymi. RNA from whole samples was amplified, labeled, and hybridized to Affymetrix Mouse Gene 1.0 ST Arrays.

first: Fujikado

last: Noriyuki

first: Yang

last: Siyoung

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Gene expression data from the ATAD3A stable knockdown MDA-MB-231 cells and the control cells

city: AUGUSTA

first: yong

last: teng

institute: GRU

summary:
From our previous data, we found that loss of ATAD3A gene expression in breast cancer cells results in loss of cell motility in vitro and metastasis in vivo. To obtain a better understanding of oncogenic pathway of ATAD3A, we have established the stable ATAD3A knockdown MDA-MB-231 cells using lentiviral strategy.
We used the whole genome microarrays to detail the global programme of gene expression after depleting of ATAD3A and identified distinct classes of up or down-regulated metastmir associated with breast cancer cells migration

overall_design: Total RNA was extracted from ATAD3A stable knockdown cells (shATAD3A) and the control cells (shGFP). The labeled RNA was hybridized on U133 plus 2.0 Array. To identify altered gene expression patterns with or without ATAD3A expression, we compared average mRNA expression levels between the ATAD3A knockdown and control MDA-MB-231 cells.

first: Yong

last: Teng

first: J

last: Cowell


title: Memory CD8+ T cells induce precocious effector differentiation of naive T cells through quorum sensing-like behavior

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

summary: Some unicellular organisms exhibit collective decision-making through intercellular communication once a quorum of members sense an environmental stress. Whether T cells at different states of differentiation may also synchronize their behavior on a population basis through direct interactions remains unclear. We report that memory CD8+ T cells (TMem) directly interact with naive T cells (TN) during priming, affecting the phenotypic, functional, transcriptional and metabolic differentiation of TN-derived progeny. This previously unrecognized, contact and concentration-dependent interaction between naive (TN) and memory CD8+ T cells (TMem) directly enhanced TN effector differentiation through non-apoptotic Fas signaling resulting in downstream Akt pathway activation. TN primed with TMem exhibited significantly impaired persistence and antitumor activity compared with TN primed alone. Disruption of FasL-Fas signaling in TN cells limited differentiation and enhanced anti-tumor immunity while provision of exogenous FasL in the absence of TMem impaired anti-tumor immunity by augmenting TN differentiation. These findings reveal that the full therapeutic potential of TN-derived cells for adoptive immunotherapy requires physical separation from TMem prior to priming or antagonism of Fas-signaling.

overall_design: FACS-sorted in vitro differentiated TMem samples were without stimulation (0 hours) (n=3), and FACS-sorted in vitro differentiated TMem samples were stimulated using CD3-specific and CD28-specific antibodies and IL-2 for 18 (n=3) and 96 (n=3) hours. FACS-sorted naive Pmel-1 CD8+ T cell samples were without stimulation (0 hours) (n=3), and FACS-sorted TN-derived Pmel-1 CD8+ T cell samples were stimulated using CD3-specific and CD28-specific antibodies and IL-2 for 18 (n=3) and 96 (n=3) hours. FACS-sorted TN-derived Pmel-1 CD8+ T cell samples were stimulated in the presence of TMem using CD3-specific and CD28-specific antibodies and IL-2 for 18 (n=3) and 96 (n=3) hours. FACS-sorted in vitro differentiated TMem samples were stimulated in the presence of TN using CD3-specific and CD28-specific antibodies and IL-2 for 18 (n=3) and 96 (n=3) hours. All samples were done in triplicate as biological repeats.


title: Expression data of T follicular helper cells (Tfh) from follicular lymphoma lymph nodes (FL) or non malignant tonsils (TONS)

status: Public on Feb 28 2015

city: Rennes

first: Patricia

last: Amé-Thomas

address: 2 Avenue du Pr Léon Bernard

department: Faculté de Médecine

country: France

institute: INSERM UMR1236

summary: GEP on Affymetrix U133+2.0 microarrays was performed on ex vivo cell-sorted Tfh from FL or TONS

overall_design: GEP was performed on 7 Tfh from FL and 7 Tfh from TONS

first: Jérôme

last: Le Priol

first: Karin

last: Tarte


title: Gene expression profile of GM-CSF derived bone marrow dendritic cell subsets

first: Julie

last: Helft

address: 44 Lincoln's Inn Fields

department: London Research Institute

institute: Cancer Research UK

summary:
GM-CSF derived bone marrow cultures contain several subsets of CD11c+MHCII+ mononuclear phagocytes
Using Affymetrix microarrays we compared gene expression of the different mononuclear phagocytes within the bone marrow culture

overall_design: The Affymetrix GeneChip Mouse Gene 1.0 arrays were used to define gene expression profiles in the different population.


title: Gene expression profiling of FFPE breast cancer samples [Affymetrix vs. Illumina]

status: Public on Feb 25 2015

city: Milan

first: Maurizio

last: Callari

address: Via Amadeo, 42

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

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

overall_design: Refer to individual Series

first: Valeria

last: Musella

first: Vera

last: Cappelletti

first: Maria

middle: G

last: Daidone


title: Investigation of the mechansim underlying the inflammatory phenotype in Group A ependymoma

city: Aurora

first: Andrew

last: Donson

state: CO

department: Pediatrics

country: USA

institute: CU Anschutz Medical Campus

summary:
Inflammatory response has been identified as a molecular signature of high-risk Group A ependymoma (EPN). To better understand the biology of this phenotype and aid therapeutic development, transcriptomic data from Group A and B EPN patient tumor samples, and additional malignant and normal brain data, were analyzed to identify the mechanism underlying EPN group A inflammation.
Gene expression profiles of Group A and B EPN were contrasted to identify inflammatory transcriptional profiles (GSEA analysis). Candidate inflammatory mechanism genes were examined across a broader cohort of pediatric and adult brain tumor types and normal brain.

overall_design: Gene expression profiles were generated from surgical tumor and normal brain samples (n=149) using Affymetrix HG-U133plus2 chips (Platform GPL570).


title: The basal transcription complex component TAF3 transduces changes in nuclear phosphoinositides into transcriptional output

city: Southampton

first: nullin

last: divecha

address: Highfield Campus

department: Biological Sciences

institute: University of southampton

summary: The aim of the experiment was to determine if changes in nuclear phosphoinositides induced by depletion of PIP4K2B impacts on gene expression through a specific phosphoinositide interaction site on TAF3.  TAF3 is a core promoter complex protein that contains a PHD finger that interacts with H3K4me3.  We determined that The TAF3 PHD finger also interacted with phosphoinositides and generated mutants of TAF3 that were unable to interact with phosphoinositides but still were capable of interacting with H3K4me3.  PIP4K2B depletion enhances C2C12 myoblast differentiation. We depleted the endogenous TAF3 from C2C12 myoblast cells and rescued the cells with either a wild type TAF3 or a mutant unable to interact with PI (KK-TAF3). These cells were then maintained as controls or depeleted of  PIP4K2B.  The cells were then differentiated for two days or were treated wtih a etoposide.  We aimed to identify genes that were reguated by PIP4K2B that required an intact phosphoinositide binding site.

overall_design: Triplicate biological samples were analysed for each point after differentiation for three days or etoposide treatment for seven hours.

first: Nullin

last: Divecha


title: Gene expression profiling of FFPE breast cancer samples [Affymetrix platform]

summary: The use of Affymetrix U133 2.0 Plus chips on FFPE samples when coupled with a qPCR-based sample pre-assessment step, yielded satisfactory results from the point of view of biological reliability. When compared with the Illumina DASL WG platform, specifically designed for degraded RNA, the data generated with the Affymetrix platform showed a wider interquartile range (IQR 1.32 vs 0.57, p<2.2x10-16) suggesting a superior discriminatory power within samples as indicated by the good agreement with the immunohistiochemically derived ER status.

overall_design:
FFPE primary breast cancer samples profiled using Affymetrix HG-U133 Plus 2.0 microarray platform after RNA amplification with the Nugen WT-Ovation FFPE System
The following criteria were considered for a direct comparison of 12 GEPs obtained from Affymetrix and DASL platforms: gene variability as defined by IQR, ESR1 expression in ER status subgroups defined by IHC, distribution of fold changes for predefined ER related genes when comparing ER positive and negative samples.


title: Whole transcriptome analysis of erlotinib treatment in EGFR-mutant cells

city: Charlestown

first: Stephen

middle: Michael

last: Rothenberg

address: 13th Street, Bldg. 149, 7th Floor

department: Cancer Center

institute: Massachusetts General Hospital

summary: We were interested in characterizing the transcriptional changes that occur on a genome-wide scale following treatment of EGFR-mutant lung cancer cells with targeted therapies.

overall_design: HCC827 human lung cancer cells harboring an amplified EGFR allele with an activating in frame deletion of 15 nucleotides in exon 19 were treated in triplicate with 1uM erlotinib (EGFR inhibitor), AZD-6244 (MEK inhibitor) or BEZ-235 (PI3-Kinase/mTOR inhibitor) for 6 hours, followed by total mRNA isolation and whole transcriptome analysis using Affymetrix U133 Plus 2.0 expression arrays.


title: Blood methylomic signatures of pre-symptomatic dementia in elderly subjects with Type 2 Diabetes Mellitus

city: Exeter

first: Rebecca

middle: Georgina

last: Smith

state: Devon

address: RILD, RD and E

department: Medical School

institute: University of Exeter

summary: Due to an increasingly aging population, the incidence of dementias such as Alzheimer’s disease are steadily rising, with recent estimates predicting >115million dementia sufferers by 2050.   The ability to identify early markers in blood, which appear before the onset of clinical symptoms is of considerable interest to allow early intervention, particularly in “high risk” groups such as those with Type 2 Diabetes (T2D). Here we present longitudinal genome-wide DNA methylation data comparing 18 elderly individuals with T2D who developed pre-symptomatic dementia within an 18 month period following baseline assessment to 18 age, sex and education matched controls who maintained normal cognitive function. We identified a highly significant overlap in the effect size of the top-ranked methylation sites at baseline and follow-up, and identified 8 robust loci, some of which have been previously related to neurodegenerative processes, which were consistently differentially methylated prior to symptoms at baseline, and at 18 month follow up, when a diagnosis of pre-symptomatic dementia had been provided. Finally we show a significant overlap in the effect size of the top-ranked methylation sites in converters, only after they develop symptoms of pre-symptomatic dementia, with changes at the same loci in blood samples from patients with clinically-diagnosed Alzheimer’s disease.

overall_design: 18 elderly individuals with T2D who developed pre-symptomatic dementia within 18 months following baseline assessment and 18 age, sex and education matched controls who maintained normal cognitive function

first: Katie

last: Lunnon

first: Itzik

last: Cooper

first: Lior

last: Greenbaum

first: Michal

last: Beeri

first: Jonathan

last: Mill


title: Type-1-cytokines synergize with oncogene inhibition to induce tumor growth arrest

status: Public on Feb 20 2015

first: Francesco

last: Marincola

summary: Both targeted inhibition of oncogenic driver mutations and immune-based therapies show efficacy in treatment of patients with metastatic cancer but responses are either short-lived or incompletely effective. Oncogene inhibition can augment the efficacy of immune-based therapy but mechanisms by which these two interventions might cooperate are incompletely resolved. Using a novel transplantable BRAFV600E-mutant murine melanoma model (SB-3123), we explore potential mechanisms of synergy between the selective BRAFV600E inhibitor vemurafenib and adoptive cell transfer (ACT)-based immunotherapy. We found that vemurafenib cooperated with ACT to delay melanoma progression but surprisingly did not enhance tumor infiltration or effector function of endogenous or adoptively transferred CD8+ T cells as previously observed. Instead, we found that the T cell cytokines IFN-gamma and TNF-alpha synergized with vemurafenib to induce cell cycle arrest of tumor cells in vitro. This was recapitulated in vivo as continuous vemurafenib administration was required to delay melanoma progression following ACT. The unexpected finding that immune cytokines synergize with oncogene inhibitors to induce growth arrest have major implications for understanding cancer biology at the intersection of oncogenic and immune signaling and provides a basis for design of combinatorial therapeutic approaches for patients with metastatic cancer.

overall_design: SB-3123p cells were treated in triplicate (biological replicates) under the following conditions for 96 hours: DMSO vehicle (control) (n=3); mouse IFNgamma (2.4 ng/ml) and mouse TNFalpha (0.24 ng/mL) (n=3); Vemurafenib (1uM) (n=3); and mouse IFNgamma (2.4 ng/ml), mouse TNFalpah (0.24 ng/mL) and Vemurafenib (1uM) (n=3).


title: Methylation data of pediatric B-cell acute leukemias

status: Public on Feb 23 2015

city: San Francisco

first: Seung-Tae

last: Lee

address: 1450 3rd Street

institute: UCSF

summary:
We investigated DNA methylomes of 227 pediatric B-cell acute lymphoblastic leukemias (B-ALLs) using whole-genome bisulfite sequencing and high-definition microarrays, along with RNA expression profiles.
The current study identified a link between DNA methylome of B-cell acute lymphoblastic leukemias (B-ALLs) and embryonic stem cell (ESC) bivalency, through which tumor cells can mimic the pluripotency of ESCs.

overall_design: A total of 231 pediatric patients with B-ALL were utilized from the California Childhood Cancer Study. After informed consent, bone marrow specimens packed with leukemic blasts were obtained in each patient. Expression and methylation data of purified Pre-B cells in four developmental stages were retrieved from our previous study (Lee et al., Nucleic Acids Res 2012).

first: Joseph

middle: L

last: Wiemels


title: Gene expression data from patients with colorectal cancer

city: Shanghai

first: Lisha

last: Wang

address: 270 DongAn Road

institute: Fudan University Shanghai Cancer Center

summary:
Microarray analyses for the identification of differences in gene expression patterns have increased our understanding of the molecular genetic events in colorectal cancer.
We used gene expression analysis data from recurrent and non-recurrent patients with colorectal cancer to identify differentially expressed probes.

overall_design: Tumor tissues were taken from 81 patients with colorectal cancer, rapidly frozen in RNAlater, and isolated using Trizol. Gene expression proﬁles were determined using Affymetrix HG-U133 Plus 2.0 GeneChips.We aimed to identify a molecular signature that can reliably identify colorectal cancer patients at high risk for recurrence.

first: Zhimin

first: Xiang

last: Du