title: AMPKα stimulates skeletal muscle fatty acid utilization during in vivo exercise in mice

city: Aarhus

first: Kasper

last: Thorsen

address: Brendstrupgaardsvej

country: Denmark

institute: Aarhus University Hospital

summary: Existing controversy regarding the importance of AMP-activated protein kinase (AMPK) in fatty acid (FA) oxidation in skeletal muscle with contraction/exercise may to some extent pertain to redundant AMPKα1 signaling. Using a mouse model lacking both AMPKα1 and -α2 in skeletal muscle specifically (mdKO) we hypothesized that FA utilization would be impaired in skeletal muscle. Calorimetric analysis showed a similar respiratory exchange ratio (RER) of AMPKα WT and mdKO mice when fed normal chow, a high fat diet or with prolonged fasting. Though, in vivo treadmill exercise at the same relative intensity induced a higher RER in mdKO mice compared to WT (WT=0.81; mdKO=0.87; p<0.01) indicating a decreased utilization of FA. Ex vivo incubation of soleus muscle revealed that basal and contraction-induced FA oxidation was impaired in mdKO mice, suggesting that the increased RER during in vivo running exercise originated from decreased skeletal muscle FA oxidation. A decreased muscle protein expression of CD36 and FABPpm (by 17-40%) together with abolishment of TBC1D1 Ser237 phosphorylation in mdKO mice, may result in lower FA transport capacity and FA transport protein translocation to sarcolemma, respectively. In summary this study shows that the catalytically active AMPKα subunits are required for normal stimulation of FA utilization during exercise and contractions.

overall_design: Four wild type and 3 AMPKα1α2 double knockout mice were used.

first: Joachim

last: Fentz

first: Jørgen

middle: F

last: Wojtaszewski


title: mmu-miR-709 gene targets

status: Public on Sep 30 2015

city: Indianapolis

first: Núria

last: Morral

state: IN

address: 975 West Walnut, IB130

department: Medical and Molecular Genetics

country: USA

institute: Indiana University School of Medicine

summary: We analyzed miRNA profiles in normal liver and identified miR-709, a highly abundant miRNA in this tissue. Through microarray analysis, gene targets were identified. Thirty-six genes were significantly down-regulated >2-fold in the miR-709-treated relative to the control group, and at least three of them, including Ras-related protein 11b (Rab11b), phosphatidylcholine transfer protein (Pctp), and carboxylesterase 1g (Ces1g), are direct targets. miR-709 regulates genes implicated in cytoskeleton organization, extracellular matrix attachment, cell proliferation and fatty acid metabolism, suggesting a coordinated response during cell division, when cytoskeleton remodeling requires substantial changes in gene expression.

overall_design: Mouse primary hepatocytes were transfected with miR-709 or the control miRNA Cel-239b (1 µg) (Dharmacon, Lafayette, CO), and harvested 24 hours later. Gene expression profiles were then generated using Affymetrix mRNA microarrays.

first: Nuria

first: Sneha

last: Surendran


title: Identification of transcriptional signatures overlapping in pancreatic ductal development, acute pancreatitis and KrasG12D-driven carcinogenesis

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

summary: To determine the molecular basis of gene regulation in pancreatic ductal epithelial cells, we developed methods for the isolation of this cell population during mouse development and normal adult homeostasis, as well as in conditions with ductal features (acinar-to-ductal metaplasia (ADM), pancreatic intraepithelial neoplasia (PanIN) and pancreatic ductal adenocarcinoma (PDAC)). Our technique utilizes the specificity of Dolichos biflorus Agglutinin (DBA) lectin marking the entire normal ductal tree, including terminal intercalated ducts (putative sites of stem or progenitor cells) and ductal structures in ADM and PanIN. We used ferromagnetic-labeled DBA lectin to isolate ductal structures. Ductal cells were isolated under the following conditions: (1) Embryonic Development in wild type mice: E14.5, E15.5, E16.5, and postnatal day 1 (P1); (2) Injury and regeneration (pancreatitis) 0, 1, 3, 5 days following cerulein-induced acute pancreatitis. Cerulein is a cholecystokinin analog which produces a self-limited pancreatitis with injury and subsequent regeneration and repair, completed five days after insult; and (3) Pdx1-Cre;LSL-KrasG12D/+ mice aged 10 and 20 weeks that harbor PanIN lesions and a subset develop PDAC. Ductal/PanIN cells were isolated from these mice and appropriate control mice (Pdx1-Cre;Kras+/+).

overall_design: Expression profiling of ductal cells at embryonic days 14.5, 15.5, 16.5 and post-natal day 1 as well as days 0, 1, 3 and 5 after acute ceruelin-induced pancreatitis and 10/20 weeks aged Pdx1-Cre;LSL-KrasG12D/+ mice.

first: M

last: Reichert

first: J

middle: S

last: Lee

first: A

middle: K

last: Rustgi


title: Enriching glioma stem cells by intracranial implantation and developing clinically relevant model for therapeutic intervention

city: Columbus

first: Kamalakannan

last: Palanichamy

state: OHIO

address: 400 W. 12th Ave., Rm#385E, Wiseman Hall

department: Radiation Oncology

institute: The Ohio State University Medical Center

summary: It is becoming better understood that radiation resistance in glioblastomas (GBMs) may be secondary to a self-renewing subpopulation of cells in the bulk tumor that form neurospheres in culture. This population has been referred to as Glioma stem cells (GSCs). One of the limitations regarding the use of GSCs is that these studies require fresh tumor biopsy samples obtained from patients, and can be extremely difficult to culture, propagate, and perform treatment-response assays. This report describes the generation of a self-renewing population of GSCs derived from commercially available U87 cells using NOD-SCID mice as carrier. The tumors were dissociated to obtain GSCs that demonstrate stem-like properties and high degree of chemo and radiation resistance. Pathological analysis of tumors obtained using GSCs exhibit all the histological hallmarks of human GBMs which is quite uncommon in GBM rodent models and hence could serve as a better model for pre-clinical study. We have shown that MGH87GSCs have an enhanced tumorogenicity than parental U87 and about 500 cells are sufficient to form tumors. To understand the transcriptome and accompanied proteome better, we explored the gene expression profiles of MGH87GSC and U87. We have shown that these GSCs are plastic like stem cells and can be directed towards a particular progeny within neural lineage by providing suitable growth factor. Our objective was to understand the genetic and biochemical mechanisms that control the self-renewal phenotype, asymmetric subdivision, chemo and radiation resistance and the role of the GSC niche in regulating the biological properties of GSC. Through this model we anticipate to devise therapeutic strategies to target this sub population of GSCs within GBMs to eradicate treatment resistance and tumor recurrence.

overall_design: The experiments were conducted in two batches. The first batch consisting of U87 and MGH87GSC obtained from the tumors (1st implant). The second batch consists of U87 cells (duplicates) and MGH87GSC (2nd implant – triplicates). Eventually we are submitting three and four ‘CEL’ files for U87 and MGH87GSC respectively.

first: Arnab

last: Chakravarti


title: An immediate transcriptional signature predicts response to the histone deacetylase inhibitor Givinostat in T acute lymphoblastic leukemia xenografts

city: Padova

first: Chiara

last: Borga

address: Corso Stati Uniti,4

country: Italy

institute: University of Padua

summary: Gene expression analysis of three sets of patient-derived T-ALL xenografted murine lines treated or not treated with Givinostat, to investigate the immediate anti-leukemic effects after 6 hours of in vivo treatment with this histone deacetylase inhibitor.

overall_design: Three different sets of class comparisons between Givinostat-treated and un-treated murine models xenografted with three different human primary pediatric T-ALL cells.

first: Marica

last: Pinazza

first: Geertruy

last: te Kronnie

first: Stefano

last: Indraccolo


title: Targeting the WNT pathway for repigmenting vitiligo

status: Public on Oct 01 2015

city: Sophia Antipolis

first: Florence

last: joly

address: 2400 route des Colles

department: Research.

country: France

institute: Galderma R&D

summary: Vitiligo is an acquired depigmentation of the skin inducing a marked alteration of the quality of life of affected individuals. Halting the disease progression and repigmenting the lesional skin represent the two faces of the therapeutic challenge in vitiligo. So far, none of them has been successfully addressed. Oxidative stress and immune system in genetically predisposed individuaLesionalparticipate to the complex pathophysiology of vitiligo. We performed a transcriptome and proteomic analysis on lesional, perilesional and non-depigmented skin of vitiligo patients compared to matched skin controLesionalof healthy subjects. Our results show that the WNT pathway, implicated in melanocytes differentiation, was found to be altered in vitiligo skin. We demonstrated that the oxidative stress decreases WNT expression/activation in keratinocytes and in melanocytes. We developed an ex vivo skin model that remains functional up to 15 days. We then confirmed the decreased activation of the WNT pathway in human skin subjected to oxidative stress. Finally, using pharmacological agents that activate the WNT pathway, we treated the ex vivo depigmented skins from vitiligo patients and successfully induced the differentiation of resident stem celLesionalinto pre-melanocytes supporting further exploration of WNT activators to repigment vitiligo lesions.

overall_design: Total of 40 chips. 10 patients (3 biospies per patient: 1 lesional , 1 perilesional and 1 non lesional) ; 10 healthy volunteers (1biopsy in matched anatomical areas)

first: F

last: Joly


title: Gene Expression of Double Positive LCK:Hdac3 KO 3w old mice

status: Public on Sep 29 2015

city: Nashville

first: Scott

last: Hiebert

state: TN

address: 2220 Pierce Ave

department: Biochemistry

institute: Vanderbilt University

summary:
Analysis of gene expression in double positive (DP) thymoctes from 3w old LCK Hdac3 conditional KO mice.
In this data set we sorted GFP double positive (DP) thymocytes from 3w old mice to identify possible signaling and transcripitonal programs that might explain the DP to single positive block in cell maturation

overall_design: Total RNA was pooled from 2 WT and 2 LCK:Hdac3 KO mice for a total of 3 biological replicates.

first: Kristy

last: Stengel

first: Yue

last: Zhao

first: Nicholas

middle: J

last: Klus

first: Jonathan

last: Kaiser

first: Laura

middle: E

last: Gordy

first: Sebastian

last: Joyce

middle: W

first: Alyssa

middle: R

last: Summers


title: Effect in MOLM-14 cells of 3hr cortistatin A treatment on gene expression

status: Public on Sep 25 2015

city: Cambridge

first: Matthew

middle: D.

last: Shair

state: MA

address: 12 Oxford Street

department: Chemistry and Chemical Biology

institute: Harvard University

summary:
We characterized the marine natural product cortistatin A (CA) as an inhibitor of CDK8 to determine whether pharmacologic inhibition of CDK8 regulates super-enhancer function and inhibits AML proliferation.
In this series, we examine the transcriptional effect on MOLM-14 cells of 3hrs exposure to CA to identify immediate effects.

overall_design: MOLM-14 cells were treated in triplicate with either DMSO or CA for 3hrs. RNA was harvested and hybridized to microarrays to assess transcriptional changes.

first: Henry

last: Pelish

first: Brian

middle: B

last: Liau

first: Diogo

middle: H

last: Da Silva

first: Madeleine

last: Lemieux

middle: D


title: Effect in K562 cells of 3hr cortistatin A treatment on gene expression

summary:
We characterized the marine natural product cortistatin A (CA) as an inhibitor of CDK8 to determine whether pharmacologic inhibition of CDK8 regulates super-enhancer function and inhibits AML proliferation.
In this series, we examine the transcriptional effect on K562 cells of 3hrs exposure to CA to identify immediate effects.

overall_design: K562 cells were treated in triplicate with either DMSO or CA for 3hrs. RNA was harvested and hybridized to microarrays to assess transcriptional changes.


title: Epigenetics and Preeclampsia: Defining Functional Epimutations in the Preeclamptic Placenta Related to the TGF-β Pathway [gene expression]

status: Public on Sep 24 2015

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

summary:
Placental Tissue Samples from 36 women (17 normotensive women, denoted with a P, and 19 preeclamptic women, denoted with a Q) were analyzed for differenital methylation
Preeclamptic womene were compared direclty to normotensive women controlling for gestational age, race, maternal age, and baby sex

overall_design: 36 samples were analyzed: 17 normotensive, 19 preeclamptic

first: Elizabeth

last: Martin

first: Paul

last: Ray

first: Lisa

last: Smeester

last: Grace

first: Kim

last: Boggess

middle: C


title: Functional Retinal Pigment Epithelium-like Cells from Human Fibroblasts

status: Public on Sep 23 2015

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: The retinal pigment epithelium (RPE) provides vital support to photoreceptor cells and its dysfunction is associated with the onset and progression of age-related macular degeneration (AMD). Surgical provision of RPE cells may ameliorate AMD and thus it would be valuable to develop sources of patient-matched RPE cells for this application of regenerative medicine. We describe here the generation of functional RPE-like cells from fibroblasts that represent an important step toward that goal.  We identified candidate master transcriptional regulators of RPEs using a novel computational method and then used these regulators to guide exploration of the transcriptional regulatory circuitry of RPE cells and to reprogram human fibroblasts into RPE-like cells.  The RPE-like cells share key features with RPEs derived from healthy individuals, including morphology, gene expression and function, and thus represent a step toward the goal of generating patient-matched RPE cells for treatment of macular degeneration.

overall_design: Expression analysis was performed on induced retinal pigment epithelium-like cells.

first: Ana

last: D'Alessio

first: Zi

middle: P

last: Fan

first: Tony

middle: I

last: Lee


title: Transformation of Human Fallopian Tube Stem Cells and high grade serous ovarian cancer

first: Frank

last: McKeon

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

summary: High-grade serous ovarian cancer (HGSOC) progresses to advanced stages without symptoms and the 5-year survival rate is a dismal 30%.  Recent studies of ovaries and oviducts in patients with BRCA mutations revealed that premalignant HGSC is found almost exclusively in the fallopian tube.  To validate this notion, we cloned and transformed the fallopian tube stem cells (FTSC).  We demonstrated that the tumors derived from the transformed fallopian tube stem cells (FTSCt)  share the similar histological and molecular feature of high-grade serous cancer.  In addition, a whole-genome transcriptome analysis comparing between FTSC, immortalized fallopian tube stem cells (FTSCi), and FTSCt showing a clear molecular progression, which is mimicked by the gene expression comparison between laser captured normal oviducts and HGSOC ( cancer and paired normal samples from 10 patients).

overall_design: FTSCs were immortalized or transformed with retroviral infection of hTERT, SV40 and c-myc and then subcutaneously transplanted into highly immunocompromised NSG (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) mice.  Total RNA was isolated from FTSC, immortalized FTSC, transformed FTSC, xenografting tumors. For contarol samples, we also use HGSOC and paired normal oviduct samples from 10 independent patients (samples were isolated laser captured microdissection (LCM)). We used Affymetrix chips (HG-U133_Plus_2).

first: Yusuke

last: Yamamoto

first: Gang

last: Ning

first: Karishma

last: Mehra

first: Alicia

last: Tay

first: Christopher

last: Crum

first: Wa

last: Xian


title: Expression data for analysis of genes affected by CHD4 in alveolar rhabdomyosarcoma cell line Rh4

city: Zurich

first: Beat

last: Schäfer

state: ZH

address: Balgrist Campus Lengghalde 5

department: Oncology

country: Switzerland

institute: University Childrens Hospital

summary:
CHD4 is an ATPase able to use the energy from ATP to shift or remove nucleosomes from specific sites in the chromatin, thereby affecting accessability of gene regulatory elements. It is part of the NuRD complex.
The effect of CHD4 on global gene expression was evaluated in Rh4 alveolar rhabdomyosarcoma cells.

overall_design: A Dox-inducible shRNA construct directed against CHD4 was stably transduced into Rh4 cells and used for silencing of CHD4.  A scrambled shRNA construct was used as control. RNA used for expression profiling was isolated from these Rh4 cells after 24, 48 and 72h of shRNA induction. Scrambled controls were performed in duplicate at each time point, whereas single expression profiles were measured for the CHD4 directed construct at each time point.

first: Maria

last: Böhm

first: Marco

last: Wachtel


title: Expression data from UMUC3 cells transduced with non-targeted shRNA and shRNA specific to AGL

status: Public on Sep 26 2015

city: Novato

first: Yuanbin

last: Ru

state: CA

address: 105 Digital Dr

institute: BioMarin Pharmaceutical Inc.

summary:
Loss of Amylo-alpha-1-6-glucosidase-4-alpha-glucanotransferase (AGL) drives bladder cancer growth. Low AGL expression predicts poor patient outcome. Currently no specific therapeutically tractable targets/pathways exist that could be used to treat patients with low AGL expressing bladder tumors.
To address this issue we carried out a transcriptome analysis in human bladder cancer cells with and without AGL expression to identify pro-tumorigenic pathways upregulated with AGL loss. We identified and validated that hyaluronic acid (HA) synthase 2 (HAS2) expression and subsequent HA synthesis is upregulated with AGL loss. We validated that HAS2 and consequent HA synthesis drive tumor growth and that genetic and pharmacologic inhibition of these respectively is a viable therapeutic option in xenograft models. We further established that bladder cancer patients with low AGL expression and high HAS2 expression have poor outcome. Together, this data provide preclinical evidence for personalized targeting of HAS2/HA signaling in patients with low AGL expressing tumors.

overall_design: AGL knockdown in UMUC3 was achieved using shRNA TRCN0000035082 (Sigma-Aldrich). MISSION® pLKO.1-puro non-mammalian shRNA control plasmid DNA (SHC002, Sigma-Aldrich) was used as control. Each condition had two biological replicates.

first: Dan

last: Theodorescu


title: Effect in MOLM-14 cells of 24hr cortistatin A treatment on gene expression

first: Matthew

last: Shair

summary:
We characterized the marine natural product cortistatin A (CA) as an inhibitor of CDK8 to determine whether pharmacologic inhibition of CDK8 regulates super-enhancer function and inhibits AML proliferation.
In this series, we examine the transcriptional effect on MOLM-14 cells of 24hrs exposure to CA.

overall_design: MOLM-14 cells were treated in triplicate with either DMSO or CA for 24hrs. RNA was harvested and hybridized to microarrays to assess transcriptional changes.

first: Henry

last: Pelish

first: Brian

last: Liau

first: Deepti

last: Banka

first: Scott

last: Armstrong

first: Madeleine

last: Lemieux


title: Epigenetics and Preeclampsia: Defining Functional Epimutations in the Preeclamptic Placenta Related to the TGF-β Pathway

first: Rebecca

last: Fry

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Expression data from toll-like receptor 9 (TLR9) knockout macrophages stimulated with β-1,3 glucan beads

status: Public on Sep 28 2015

city: Boston

first: Fei

last: Ji

address: 185 Cambridge St

institute: Massachusetts General Hospital

type: Expression profiling by high throughput sequencing

summary: Dectin1 controls the recruitment of TLR9 to β-1,3 glucan beads containing phagosomes. We sought to determine whether Dectin-1 also plays a role in controlling TLR9 dependent gene expression.

overall_design: We stimulated wild-type and TLR9KO immortalized macrophages with β-1,3 glucan beads for 4 h, harvested RNA, and conducted a microarray analysis to identify differentially expressed genes

first: Nida

last: Khan

first: Jatin

last: Vyas

first: Ruslan

last: Sadrayev


title: Epigenetics and Preeclampsia: Defining Functional Epimutations in the Preeclamptic Placenta Related to the TGF-β Pathway [methylation]

overall_design: 36 samples were analyzed, 18 in each group

first: Elizabeth

last: Martin

first: Paul

last: Ray

first: Lisa

last: Smeester

last: Grace

first: Kim

last: Boggess


title: Escherichia coli MG1655 gene expression in glucose minimum media

city: New York

first: Gregory

last: Boel

state: NY

address: 1212 Amsterdam Ave.

department: Biological Sciences

institute: Columbia University

summary:
M9 glucose minimum media were analyzed for RNA expression.
We use this expression information to show that mRNA level correlate with codon efficiency (Boel et al., Nature 2015)

overall_design: Cells were grown in M9 glucose media until an OD600 of 1 for RNA extraction and hybridization on Affymetrix microarrays.

first: Jhon

last: Hunt


title: Fibrinogen promotes autoimmunity and demyelination via chemokine release and antigen presentation [Mm]

status: Public on Sep 16 2015

city: San Francisco

first: Katerina

last: Akassoglou

address: 1650 Owens St

institute: Gladstone Institutes

summary:
Determination of the mechanism by which fibrinogen, a central blood coagulation protein drives immunological responses targeted to the CNS. Results identify the factors involved in the regulation and provide mechanistic basis.
We subjected fibrinogen-injected corpus callosum to microarray to determine the genes involved in innate and adaptive immune responses by fibrinogen deposited in the CNS after blood-brain barrier disruption.

overall_design: Corpus callosum tissues were isolated from mice received stereotactic injection of fibrinogen or ACSF at 12 hr. Tissues were subjected for RNA extraction and hybridization on Affymatrix microarrays. Two ACSF and two fibrinogen samples were generated.

first: Jae

last: Ryu


title: Novel IDH1 Mutant Inhibitors for Treatment of Acute Myeloid Leukemia (expression)

status: Public on Sep 21 2015

city: Bronx

first: Britta

last: Will

state: NEW YORK

address: 1300 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

summary: Neomorphic mutations in isocitrate dehydrogenase 1 (IDH1) are driver mutations in acute myeloid leukemia (AML) and other cancers. We report the development of new allosteric inhibitors of mutant IDH1. Crystallographic and biochemical results demonstrated that compounds of this chemical series bind to an allosteric site and lock the enzyme in a catalytically inactive conformation, thereby enabling inhibition of different clinically relevant IDH1 mutants. Treatment of IDH1 mutant primary AML cells uniformly led to a decrease in intracellular 2-HG, abrogation of the myeloid differentiation block and induction of granulocytic differentiation at the level of leukemic blasts and more immature stem-like cells, in vitro and in vivo. Molecularly, treatment with the inhibitors led to a reversal of the DNA cytosine hypermethylation patterns caused by mutant IDH1 in AML patients’ cells. Our study provides proof-of-concept for the molecular and biological activity of novel allosteric inhibitors for targeting different mutant forms of IDH1 in leukemia. To obtain insight into the molecular mechanism for the induction of granulocytic differentiation and cell death following inhibition of IDH1 mutant protein in primary AML cells, we performed gene expression microarrays following treatment with either GSK321 IDH1 inhibitor or Controls (DMSO or GSK990 inactive inhibitor).

overall_design: Primary IDH1 mutant acute myeloid leukemia (AML) mononuclear (MNC) cells were treated in suspension cultures in differentiating media for 6 days with 3 microM GSK990 or GSK321 and an equal volume of DMSO. Followed by microarray analysis after RNA extraction.

first: U

last: Okoye-Okafor

last: Steidl


title: Gene expression data from Zeb2WT, Zeb2KO, T-betWT and T-betKO effector CD8+ T cells during infection

status: Public on Sep 19 2015

city: Stanford

first: Howard

middle: Y

last: Chang

state: California

address: 269 Campus Drive

institute: Stanford University

summary: ZEB2 is a multi-zinc-finger transcription factor known to play a significant role in early neurogenesis and in EMT-dependent tumor metastasis. While the function of ZEB2 in T lymphocytes is unknown, activity of the closely related family member ZEB1 has been implicated in lymphocyte development. Here, we find that ZEB2 expression is upregulated by activated T cells, specifically in the KLRG1hi effector CD8+ T cell subset. Loss of ZEB2 expression results in a significant loss of antigen-specific CD8+ T cells following primary and secondary infection with a severe impairment in the generation of the KLRG1hi effector-memory cell population. We show that ZEB2, which can bind DNA at tandem, consensus E-box sites, regulates gene expression of several E-protein targets and may directly repress CD127 and IL-2 in CD8+ T cells responding to infection.  Furthermore, we find that T-bet binds to highly conserved T-box-sites in the ZEB2 gene and that T-bet and ZEB2 regulate similar gene-expression programs in effector T cells, suggesting that T-bet acts upstream and through regulation of ZEB2. Taken together, we place ZEB2 in a larger transcriptional network that is responsible for the balance between terminal differentiation and formation of memory CD8+ T cells.

overall_design: Zeb2WT, Zeb2KO, T-betWT and T-betKO effector CD8+ T cells were sorted into Trizol at day 6 of infection. Two or more replicates per sample were analyzed

first: Kyla

last: Omilusik

first: J

last: Best

first: Bingfei

last: Yu

first: Ananda

last: Goldrath


title: Microarray analysis of mice with thyroid hormone receptor and RAS mutations.

status: Public on Sep 22 2015

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

summary: Affymetrix GeneChip Mouse Gene 1.0 ST Array was used to study gene expression profiles in three groups of mice: with thyroid hormone receptor ThrbPV (ThrbPV/PV) mutation only, with RAS mutation (KrasG12D) only, and with both ThrbPV/PV and KrasG12D mutations.

overall_design: Three groups mice: with thyroid hormone receptor ThrbPV (ThrbPV/PV) mutation only, with RAS mutation (KrasG12D) only, and with both ThrbPV/PV and KrasG12D mutations.   Each group has three biological replicates.

first: Sheue-yann

last: Cheng

first: Dong

last: Kim

first: Xuguang


title: Expression data from mice brain implanted GSC272 glioma stem cells or POSTN knockout

first: Soon Young

last: Park

address: 6767 Bertner Ave BSRB S5.8224

department: Neuro-oncology

institute: UT MD Anderson Cancer Center

summary:
Differential mRNA expression patterns were seen in GSC272-vector compared to GSC272-POSTN shRNA tumors.
We used microarrays to POSTN regulated gene expression in glioma stem cells.

overall_design: Gene expression comparisons were shown between: 1. mRNA control from GSC272 glioma stem cells implanted mouse brain tumor at 7 weeks after implantation, and 2. mRNA deplection of POSTN from  knock down of POSTN of GSC272 glioma stem cells implanted mouse brain tumor  at 7 weeks after implantation.

first: Soon-Young

first: Yuji

last: Piao

first: Kang-Jin

last: Jeong

first: John

middle: F

last: de Groot


title: Regulation of HSF1-mediated transcriptional programs by PGC-1alpha

first: Neri

last: Minsky

address: 1230 York Avenue

institute: Rockefeller University

summary:
We examined global gene expression patterns in response to PGC-1 expression in cells derived from liver or muscle.
As our study revealed regulation of HSF1 by PGC-1alpha, in some experiments we knocked-down HSF1 using siRNAs in addition to inducing PGC-1alpha expression.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Cells were grown in 24-well plates and adenoviruses encoding either GFP ("Ad-GFP"), PGC-1alpha ("Ad-PGC-1alpha") or PGC-1beta ("Ad-PGC-1beta") were directly added to the culture medium. For experiments involving siRNA transfections, cells were transfected with the indicated siRNAs 48hr prior to infection with adenoviruses encoding either GFP ("Ad-GFP") or PGC-1alpha ("Ad-PGC-1alpha").

first: Robert

middle: G

last: Roeder


title: Effect in MV4;11 cells of 3hr cortistatin A treatment on gene expression

first: Matthew

last: Shair

summary:
We characterized the marine natural product cortistatin A (CA) as an inhibitor of CDK8 to determine whether pharmacologic inhibition of CDK8 regulates super-enhancer function and inhibits AML proliferation.
In this series, we examine the transcriptional effect on MV4;11 cells of 3hrs exposure to CA to identify immediate effects.

overall_design: MV4;11 cells were treated in triplicate with either DMSO or CA for 3hrs. RNA was harvested and hybridized to microarrays to assess transcriptional changes.

first: Henry

last: Pelish

first: Brian

last: Liau

first: Diogo

last: Da Silva

first: Madeleine

last: Lemieux


title: DNA methylation landscapes of human fetal development

city: Leiden

first: Roderick

last: Slieker

address: PO Box 9600

department: Medical Oncology

country: Netherlands

institute: Leiden University Medical Center

summary: Here we assessed the genome-scale DNA methylation of 472,703 autosomal CpG sites in 4 tissues (muscle, amnion, pancreas and adrenal glands) on 3 time-points (9, 18 and 22 weeks) using the Illumina 450k array.   We identified 52,134 CpG sites with dynamic DNA methylation during fetal development (gain or loss >20% from 9 to 22 weeks), where the period between 9 and 18 weeks was most dynamic. Loss in DNA methylation (25,579 CpGs), displayed clear tissue-specific patterns near genes enriched for a role in tissue-specific processes. Gain in DNA methylation (26,555  CpGs) occurred often near genes involved in (tissue-specific) developmental processes.

overall_design: Comparison of DNA methylation of four fetal human tissues on three time points of gestation: 9, 18 and 22 weeks of gestation.

first: R

first: M

middle: S

last: Roost

first: L

last: van Iperen

first: H

last: Suchiman

first: E

last: Tobi

first: F

last: Carlotti

first: EJ

last: de Koning

first: P

last: Slagboom

first: B

middle: T

last: Heijmans

first: S

middle: M

last: Chuva de Sousa Lopes


title: ERG promotes the maintenance of hematopoietic stem cells by restricting their differentiation

city: Copenhagen

first: Nicolas

last: Rapin

address: Ole Maaloes vej 5

department: Finsen Laboratory

institute: Copenhagen University

summary: To investigate the role of the transcription factor ERG in hematopoiesis we generated Erg heterozygous knockout and conditional Erg knockout mice. We found that several hematopoietic cell types were decreased in these mice. To define Erg downstream target genes in hematopoietic stem cells, we sorted Lineage-, Sca-1+, c-kit+, CD150+, CD48- cells from Erg +/- mice for gene expression analysis. To define Erg downstream target genes in hematopoietic progenitors, we sorted multipotent progenitors (Lineage-, Sca-1+, c-kit+, CD150-) from Erg -/- mice for gene expression analysis.

overall_design: We generated Erg heterozygous knockout mice and provide 3 replicates for wild type (Erg +/+) populations of stem cells (HSC) and 3 replicates for Erg +/- mices. We also generated a conditional Erg knockout mice. We provide 3 replicates for Erg fl/fl and 3 replicates for Erg (-/-) mice.

last: Porse

last: Rehn


title: The epigenetic signature of subcutaneous fat cells is linked to altered expression of genes implicated in lipid metabolism in obese women

status: Public on Sep 15 2015

city: Huddinge

first: Ingrid

last: Dahlman

address: Hälsovägen 7

department: Department of Medicine

country: Sweden

institute: Karolinska Institute

summary:
Background
Obesity is associated with changes in fat cell gene expression and metabolism. What drives these changes is not well understood. We aimed to explore fat cell epigenetics, i.e., DNA methylation, as one mediator of gene regulation, in obese women. The global DNA methylome for abdominal subcutaneous fat cells was compared between 15 obese case (BMI 41.4 ± 4.4 kg/m 2 , mean ± SD) and 14 never-obese control women (BMI 25.2 ± 2.5 kg/m 2 ). Global array-based transcriptome analysis was analyzed for subcutaneous white adipose tissue (WAT) from 11 obese and 9 never-obese women. Limma was used for statistical analysis.

Results
We identified 5529 differentially methylated DNA sites (DMS) for 2223 differentially expressed genes between obese cases and never-obese controls (false discovery rate <5 %). The 5529 DMS displayed a median difference in beta value of 0.09 (range 0.01 to 0.40) between groups. DMS were under-represented in CpG islands and in promoter regions, and over-represented in open sea-regions and gene bodies. The 2223 differentially expressed genes with DMS were over-represented in key fat cell pathways: 31 of 130 (25 %) genes linked to “adipogenesis” (adjusted P = 1.66 × 10 −11 ), 31 of 163 (19 %) genes linked to “insulin signaling” (adjusted P = 1.91 × 10 −9 ), and 18 of 67 (27 %) of genes linked to “lipolysis” (P = 6.1 × 10 −5 ). In most cases, gene expression and DMS displayed reciprocal changes in obese women. Furthermore, among 99 candidate genes in genetic loci associated with body fat distribution in genome-wide association studies (GWAS); 22 genes displayed differential expression accompanied by DMS in obese versus never-obese women (P = 0.0002), supporting the notion that a significant proportion of gene loci linked to fat distribution are epigenetically regulated.

Conclusions
Subcutaneous WAT from obese women is characterized by congruent changes in DNA methylation and expression of genes linked to generation, distribution, and metabolic function of fat cells. These alterations may contribute to obesity-associated metabolic disturbances such as insulin resistance in women.

overall_design: The global DNA methylome in abdominal subcutaneous fat cells was compared between 15 obese cases (BMI 41.4±4.4 kg/m2, mean ± SD) and 14 never-obese control women (BMI 25.2±2.5 kg/m2).

first: Peter

last: Arner

first: Indranil

last: Sinha

first: Anders

last: Thorell

first: Mikael

last: Rydén

first: Karin

last: Dahlman-Wright


title: ELABELA Is an Endogenous Growth Factor that Sustains hESC Self-Renewal Via the PI3K/AKT Pathway

status: Public on Sep 20 2015

city: singapore

first: Lena

last: Ho

state: -- Please Select --

address: 8A BIomedical Grove 05-40 Immnuos

country: Singapore

institute: Institute of Medical Biology

summary: ELABELA (ELA) is a peptide hormone required for heart development that signals via the Apelin Receptor (APLNR, APJ). ELA is also abundantly secreted by human embryonic stem cells (hESCs), which do not express APLNR.  Here we show that ELA signals in a paracrine fashion in hESCs to maintain self-renewal. ELA inhibition by CRISPR/Cas9-mediated deletion, shRNA or neutralizing antibodies causes reduced hESC growth, cell death and loss of pluripotency. Global phosphoproteomic and transcriptomic analyses of ELA-pulsed hESCs show that it activates PI3K/AKT/mTORC1 signaling required for cell survival. ELA promotes hESC cell cycle progression and protein translation, and blocks stress-induced apoptosis.  INSULIN and ELA have partially overlapping functions in hESC medium, but only ELA can potentiate the TGFβ pathway to prime hESCs towards the endoderm lineage. We propose that ELA, acting through an alternate cell-surface receptor, is an endogenous secreted growth factor in human embryos and hESCs that promotes growth and pluripotency.

overall_design: Global Transcriptomic Analysis of INSULIN versus ELA-pulsed human embryonic stem cells was performed to elucidate the functional overlap between these two ligands

first: Bruno

last: Reversade


title: Epigenome analysis of IDH1 mutant and IDH1/2 wild-type patient derived glioblastoma tumorsphere lines.

first: Kensuke

last: Tateishi

state: Massachusetts

address: 185 cambridge street

department: Neurosurgery

summary: The aim of ths study is to compare global methylation status between 1) IDH1 mutant and IDH1/2 wild-type glioblastoma tumorsphere cells and 2) MGG152 (IDH1 mutant) with DMSO and IDH1 inhibitor treatment. Genome wide DNA methylation profiling of patient derived glioblastoma tumorsphere and HT1080 cells. The Illumina Infinium  Human DNA methylation Beadchip450  was used to obtain DNA methylation profiles.

overall_design:
Bisulphite converted DNA from the 10 samples and one control were hybridised to the Illumina Infinium  Human Methylation Beadchip450.
Please note that the MGG (in the sample title) represents patient-derived MGH glioblastoma cell lines.
Regarding MGG152 samples, sample no.1 is low passage number and used for comparison between IDH1 mt and wild-type.
Sample no. 2-4 were used for assessing DNA methylation change after short term or long term IDH1 inhibiting treatment.

first: Daniel

last: Cahill

first: Andrew

last: Chi


title: Fibrinogen promotes autoimmunity and demyelination via chemokine release and antigen presentation

first: Katerina

last: Akassoglou

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus


title: Everolimus protects podocytes via stabilizing TUBB2B and DCDC2 expression

status: Public on Sep 09 2015

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

summary: Glomerular podocytes are highly differentiated cells that are key components of the kidney filtration units. The podocyte cytoskeleton builds the basis for the dynamic podocyte cytoarchitecture and plays a central role for proper podocyte function. Recent studies implicate that immunosuppressive agents including the mTOR-inhibitor everolimus have a protective role directly on the stability of the podocyte cytoskeleton.  To elucidate mechanisms underlying mTOR-inhibitor mediated cytoskeletal rearrangements, we carried out microarray gene expression studies to identify target genes and corresponding pathways in response to everolimus. We analyzed the effect of everolimus in a puromycin aminonucleoside experimental in vitro model of podocyte injury.  Upon treatment with puromycin aminonucleoside, microarray analysis revealed gene clusters involving cytoskeletal-associated pathways, adhesion, migration and extracellular matrix composition to be affected. Everolimus is capable of protecting podocytes from injury, both on the transcriptome and protein level. Rescued genes included TUBB2B and DCDC2, both involved in microtubule structure formation in neuronal cells but not identified in podocytes so far. Confirming gene expression data, Western-blot analysis in cultured podocytes showed an increase of TUBB2B and DCDC2 protein after everolimus treatment, and immunohistochemistry in healthy control kidneys confirmed a podocyte-specific expression. Microtubule-inhibitor experiments led to a maldistribution of TUBB2B and DCDC2 as well as an aberrant reorganization of the actin cytoskeleton. Tubb2bbrdp/brdp mice showed a delay in glomerular podocyte and capillary development.  Taken together, our study suggests that off-target, non-immune mediated effects of the mTOR-inhibitor everolimus on the podocyte cytoskeleton might involve regulation of microtubules, revealing a potential novel role of TUBB2B and DCDC2 in glomerular podocyte development

overall_design: We analyzed the effect of everolimus on gene expression in a puromycin aminonucleoside experimental in vitro model of podocyte injury using microarrays

first: Stefanie

last: Jeruschke

last: Weber


title: SKBR3 cells treated with epirubicin or hypoxia

first: Christine

last: Loreth

address: 610 Main St

institute: Pfizer

summary:
Intratumoral heterogeneity may generate a diversity of resistance mechanisms that could cause different therapeutic responses in different cell populations.
Gene expression profiles were generated for breast cancer cells that had survived two different treatment and were also sorted by the cancer stem cell marker CD44.

overall_design: SKBR3 cells were treated with epirubicin or hypoxia, and then flow sorted by CD44 expression and processed for expression profiles.  3 or 4 biological replicates were generated for each condition.

first: Siobhan

middle: K

last: O'Brien

first: Liang

last: Chen

first: Wenyan

last: Zhong

first: Douglas

last: Armellino

first: Jiyang

last: Yu

first: Maximillian

last: Follettie

first: Marc

last: Damelin


title: Gene expression analysis of leukemia-initiating cells of compound URE-/+::Msh2-/- mice

status: Public on Sep 07 2015

first: Britta

last: Will

address: 1300 Morris Park Avenue

summary: Expression profiling of FACS purified Lin-cKit+ cells from compound URE-/+::Msh2-/- mice with AML and control animals

overall_design: Analysis of gene expression in Lin-cKit+ cells from three URE-/+::Msh2-/- mice and four wild type controls

first: Ulrich

last: Steidl


title: Inflammation promotes a conversion of astrocytes into neural progenitor cells via NF-kB activation

city: Belvaux

first: Enrico

last: Glaab

state: Capellen

address: 6, avenue du Swing

country: Luxembourg

institute: University of Luxembourg

summary:
Brain inflammation, a common feature in neurodegenerative diseases, is a complex series of events, which can be detrimental and even lead to neuronal death. Nonetheless, several studies suggest that inflammatory signals are also positively influencing neural cell proliferation, survival, migration and differentiation. Recently, correlative studies suggested that astrocytes are able to dedifferentiate upon injury, and may thereby re-acquire neural stem cells (NSC) potential. However, the mechanism underlying this dedifferentiation process upon injury remains unclear. In this study, we find that during the early response of reactive gliosis, inflammation induces a conversion of mature astrocytes into neural progenitors. A TNF treatment induces the decrease of specific astrocyte markers, such as GFAP or genes related to glycogen metabolism, while a subset of these cells re-express immaturity markers, such as CD44, Musashi-1 and Oct4. Thus, TNF treatment results in the appearance of cells that exhibit a neural progenitor phenotype and are able to proliferate and differentiate into neurons and/or astrocytes.
This dedifferentiation process is maintained as long as TNF is present in the culture medium. In addition, we identify a role for Oct4 in this process, since the TNF-induced dedifferentiation can be prevented by inhibiting Oct4 expression. Our results show that activation of the NF-kB pathway through TNF plays an important role in the dedifferentiation of astrocytes via the re-expression of Oct4. These findings indicate that the first step of reactive gliosis is in fact a dedifferentiation process of resident astrocytes mediated by the NF-kB pathway.    This dedifferentiation process is maintained as long as TNF is present in the culture medium. In addition, we identify a role for Oct4 in this process, since the TNF-induced dedifferentiation can be prevented by inhibiting Oct4 expression. Our results show that activation of the NF-kB pathway through TNF plays an important role in the dedifferentiation of astrocytes via the re-expression of Oct4. These findings indicate that the first step of reactive gliosis is in fact a dedifferentiation process of resident astrocytes mediated by the NF-kB pathway.

overall_design: Cultures of primary mouse astrocytes were treated with TNF (50 ng/mL) for 24 hours. Cells were collected and immediately homogenized in cooled down RNA NOW reagent (OZYME). Total RNA was extracted according to RNA NOW manufacturer's recommendations with -20C overnight incubation for small RNA precipitation. Total RNA integrity and purity were assessed using the Agilent 2100 Bioanalyzer and RNA 6000 Nano LabChip kits (Agilent Technologies). Only good-quality RNA (no contamination or degradation, RIN > 9) was used and further processed. Total RNA samples were reverse-transcribed to double-stranded cDNA using specific primers, which reduce the priming of rRNA. cRNA was generated by in vitro transcription and reverse transcribed into a sense single-stranded cDNA. The cDNA was fragmented, labeled, and hybridized onto Affymetrix GeneChip Mouse Gene 1.0 ST Arrays according to the Ambion Whole Transcript Expression kit for Affymetrix GeneChip Whole Transcript Expression Array Protocol (P/N 4425209 Rev.B 05/2009) and GeneChip WT Terminal Labeling and Hybridization User Manual for use with the Ambion Whole Transcript Expression kit (P/N 702808 Rev.6). Microarrays were then washed, stained, and scanned according to the manufacturer's instructions. The samples cover two conditions (TNF and Control), with three replicates per condition.

first: Luc

last: Grandbarbe

first: Sébastien

last: Gabel

first: Eric

last: Koncina

first: Gauthier

last: Dorban

first: Tony

last: Heurtaux

first: Cindy

last: Birck

first: Alessandro

last: Michelucci

first: Paul

last: Heuschling


title: Toxicogenomics on mice liver of coumarins from Calophyllum brasiliense

status: Public on Sep 06 2015

city: Mexico City

first: Juan

middle: Carlos

last: Gomez-Verjan

state: Distrito Federal

address: Circuito Exterior, Ciudad Universitaria, Delegación Coyoacán C.P. 04510, México, D.F.

department: Productos Naturales

country: Mexico

institute: Instituto de Quimica

summary:
A toxicogenomic analysis from liver of different pharmacological active coumarins (mammea A/BA+A/BB 3:1 and soulatrolide ) was performed on mice treated (20mg/kg/daily) for a whole week  to evaluate if such compounds possess or could develop  a hazardous profile on liver.
In this dataset, we include the expression data obtained from dissected liver mouse treated with active coumarins (obtained from Calophyllum brasiliense) and control (SSI) for a whole week. Livers from 4 animals per treatment and control were subjected to RNA extraction. These data showed 46 genes up and 72 downregulated genes for mammea coumarins and 665 up and 1077 downregulated genes .

overall_design:
Expression data from liver of mice treated with different coumarins (mammea and soulatrolide) from Calophyllum brasiliense
12 Total samples were analyzed. Liver from 4 animals per treatment groups were subjected to mRNA expression analysis. We generated the statistical computing and metrics in the arrayQualityMetrics data were normalized with RMA method and differential expressed genes obtained with Ingenuity Software. Genes with an FDR≤10% and a fold-change ≥2 were selected.

first: Ricardo

last: Reyes-Chilpa


title: Comparison of M. tuberculosis and M. bovis BCG in diluted whole blood cultures

status: Public on Sep 10 2015

city: London

first: Jackie

last: Cliff

address: Keppel Street

department: Immunology and Infection

country: United Kingdom

institute: London School of Hygiene & Tropical Medicine

summary: Despite wide scale vaccination with Mycobacterium bovis BCG, the prevalence of tuberculosis remains high, reflecting the global variable efficacy of this vaccine against adult pulmonary TB.  Characterisation of different immune responses to M. tuberculosis and M. bovis BCG would increase understanding of pathology following M. tuberculosis infection or reactivation, and would facilitate the rational design of a new vaccine. Gene expression profiling was conducted on samples from diluted whole blood cultures from three healthy donors following incubation with live mycobacteria for six days.  Approximately 8,000 gene entities were at least two-fold up- or down- regulated by the mycobacteria, and both mycobacteria induced similar expression changes in approximately 2,300 genes. Strikingly, many genes exhibited qualitatively different expression patterns, with over 1,000 genes up-regulated in response to M. bovis BCG but not changed by M. tuberculosis. Gene Ontology analysis revealed that the genes which failed to upregulate in M. tuberculosis-infected cultures included a large proportion of genes with lysosomal function. The inhibited up-regulation of expression of IFN-γ-inducible protein 30, acid phosphatase 2, cathepsin B and GM2 ganglioside activator was verified in samples from six biologically independent donors by qRT-PCR. The failure to up-regulate these genes in response to M. tuberculosis may constitute an immune evasion mechanism, preventing intracellular killing and antigen presentation.

overall_design: Blood from three healthy BCG-vaccinated donors was diluted with growth medium and incubated alone or with live M. tuberculosis (H37Rv), M. bovis BCG for 6 days. RNA samples were pooled before hybridisation.

first: Jacqueline

first: Nicholas

last: Constantinou

first: Jang-Eun

last: Cho

first: Iryna

middle: N

last: Andrade

first: Hazel

last: Dockrell


title: Gene expression profiling of effector and regulatory T-cells from peripheral blood of rheumatoid arthritis (RA) patients and healthy volunteers.

status: Public on Sep 05 2015

city: Måløv

first: Klaus Stensgaard

last: Frederiksen

address: Novo Nordisk Park F9.1.07

department: Molecular Genetics

institute: Novo Nordisk A/S

summary: Objective: Conflicting evidence exists regarding the suppressive capacity of Tregs from the peripheral blood (PB) of patients with rheumatoid arthritis (RA). Our aim was to determine whether Tregs are intrinsically defective in RA using a wide range of read-out assays.  Methods: CD3+CD4+CD25+CD127low Tregs from CD45RO+ and CD45RA+ compartments of PB from patients with RA and healthy controls (HC) were analysed for phenotype, cytokine expression profile (ex vivo and after in vitro stimulation), suppression of effector T-cell proliferation and cytokine production, suppression of monocyte-derived cytokine/chemokine production, and gene expression profiling.   Results: No differences were observed between patients with RA and HC regarding Treg frequency, ex vivo phenotype (CD4, CD25, CD127, CD39, CD161) or pro-inflammatory cytokine profile (IL-17, IFN-gamma, TNF-alpha). FOXP3 expression was increased in Tregs from RA blood. The ability of Tregs to suppress T-cell proliferation or cytokine (IFN-gamma, TNF-alpha) production upon co-culture with autologous CD45RO+ effector T-cells and monocytes was not significantly different between patients with RA and HC. CD45RO+ Tregs from RA blood showed a slightly impaired ability to suppress production of some cytokines/chemokines by autologous LPS-activated monocytes (IL-1-beta, IL-1Ra, IL-7, CCL3, CCL4), but this was not true for all patients and other cytokines/chemokines (TNF-alpha, IL-6, IL-8, IL-12, IL-15, CCL5) were suppressed in the majority of patients similarly to HC. Finally, gene expression profiling of CD45RA+ or CD45RO+ Tregs from PB revealed no statistically significant differences between patients with RA and HC.   Conclusions: Our findings suggest that Tregs isolated from PB of patients with RA are not intrinsically defective.

overall_design: Sorted regulatory and effector T-cells were isolated from peripheral blood (6 healthy controls and 6 patients with rheumatoid arthritis). Total RNA was isolated and profiled using Affy HG-U133_Plus_2 chips.

first: Klaus

first: Leonie

last: Taams


title: Expression data from human GBMs

status: Public on Sep 08 2015

city: Philadelphia

first: Matthew

middle: J

last: Lazzara

address: 220 South 33rd Street

institute: University of Pennsylvania

summary: Analysis of human glioblastoma multiforme tumors revealed genes that are upregulated in tumors expressing EGFRvIII compared to those expressing wild-type EGFR

overall_design: We examined gene expression in 52 primary GBM tumors, which were stratified based on the presence or absence of EGFRvIII expression using EGFRvIII-specific RT-PCR (Tykocinski et al., 2012).  The extracted RNA samples from these tumors were subjected to microarray analysis using HG-U133 2.0 Plus Affymetrix gene chips.  Average expression of all transcripts were compared between EGFRvIII-positive and -negative GBMs.

first: Alice

last: Walsh

first: Gurpreet

last: Kapoor

first: Yingtao

last: Bi

first: Ramana

middle: V

last: Davuluri

first: Donald

last: O'Rourke


title: Excessive Cytolytic Responses Predict Tuberculosis Relapse After Apparently Successful Treatment

summary:
Background
Identification of patients at risk of tuberculosis relapse following treatment would revolutionize clinical trials of new drugs and regimens and facilitate clinical management. The study aim was to determine whether tuberculosis patients who subsequently suffer relapse have different immune responses to mycobacteria in vitro compared to patients who remain cured for two years post-treatment.
Methods
First episode pulmonary tuberculosis patients were recruited into a surrogate marker study in Cape Town, South Africa. Peripheral blood samples were collected at diagnosis and after two and four weeks of tuberculosis treatment. Diluted blood was cultured with live Mycobacterium tuberculosis for six days and cellular RNA was frozen. Gene expression in samples from ten patients who subsequently relapsed, confirmed by stain genotyping, was compared to those who remained cured using Affymetrix microarrays.
Results
At diagnosis, the expression of 668 genes was significantly different in samples from patients who subsequently relapsed compared to successfully cured patients, and these differences persisted for at least four weeks. Gene Ontology and biological pathways analyses revealed the most significant difference was up-regulation of genes involved in cytotoxic cell-mediated killing, such as perforin, granulysin and fas ligand. Results were confirmed by qRT-PCR in a wider patient cohort.
Conclusions
These data show that patients who will subsequently relapse exhibit altered immune responses at diagnosis, including excessively robust cytolytic responses to M. tuberculosis in vitro, compared to patients who will achieve durable cure. Together with microbiological and clinical indices, these differences could be exploited for patient stratification in drugs trials, or for host-directed therapy development.

overall_design: Venous blood samples were diluted in culture medium and stimulated with live M. tuberculosis for 6 days. Samples from 10 TB patients who subsequently relapsed and 10 patients whore remained disease-free for 2 years. Samples collected at TB diagnosis and after 2 weeks or 4 weeks of treatment of first TB episode.

first: Ji-Sook

last: Lee

first: Katharina

last: Ronacher

first: Elizabeth

last: King

first: Paul

middle: D

last: Van Helden

first: Gerhard

last: Walzl


title: Expression data of Langerhans cells purified from Il34+/LacZ and Il34LacZ/LacZ mice after UV treatment

status: Public on Nov 04 2015

city: Saint Louis

first: Marco

last: Colonna

state: MO

address: 660 S Euclid Ave.

department: Pathology and Immunology

institute: Washinton University School of Medicine

summary: We examined the impact of IL-34 on repopulation of Langerhans cells after inflammation

overall_design: Langerhans cells were FACS-purified from Il34+/LacZ and Il34LacZ/LacZ mice after UV treatment

first: Yaming

last: Wang


title: Gene expression analysis of leukemia-initiating cells of preleukemic compound URE-/+::Msh2-/- mice

first: Britta

last: Will

institute: Albert Einstein College of Medicine

summary: Expression profiling of FACS purified Lin-cKit+ cells from preleukemic compound URE-/+::Msh2-/- mice and control animals (two separate pools of 3 mice each)

overall_design: Analysis of gene expression in Lin-cKit+ cells from two URE-/+::Msh2-/- mice and wild type control animals  (two pools of three animals each)

first: Ulrich

last: Steidl


title: Expression data from control, aged and activated neutrophils in mouse blood

status: Public on Sep 24 2015

first: Dachuan

last: Zhang

address: 1301 Morris Park Avenue, Price Center 113

summary:
Neutrophils provide immune protection against pathogens but also may promote tissue injury in inflammatory diseases. Although neutrophils are generally considered as a relatively homogeneous population, evidence for heterogeneity is emerging. Under steady-state conditions, neutrophil heterogeneity may arise from ageing and the replenishment by newly released neutrophils from the bone marrow.
We used microarray to globally analyze gene expression in aged neutrophils and characterize the inflammatory programs that are activated during the aging process in the circulation.

overall_design: Control, aged and activated neutrophils were sorted directly from mouse blood for RNA extraction and hybridization on Affymetrix microarrays. We transfused whole blood and harvested donor neutrophils marked by the CD45.1 allele 6h later to derive neutrophils that had truly aged in vivo. Sorted neutrophils were compared to control donor neutrophils that had been transferred for only 10 min. Additionally, we harvested circulating neutrophils from TNF-α treated mice for comparison with neutrophils activated by systemic inflammation.

last: Frenette


title: Gene expression analysis of leukemia-initiating cells of URE-/+::Msh2-/- mice

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

overall_design: Refer to individual Series


title: Genomic profiles for human peripheral blood T cells, B cells, natural killer cells, monocytes, and polymorphonuclear cells: comparisons to ischemic stroke, migraine, and Tourette syndrome

status: Public on Sep 03 2015

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

institute: CIML

summary:
Blood genomic profiling has been applied to disorders of the blood and various organ systems including brain to elucidate disease mechanisms and identify surrogate disease markers. Since most studies have not examined specific cell types, we performed a preliminary genomic survey of major blood cell types from normal individuals using microarrays. CD4+ T cells, CD8+ T cells, CD19+ B cells, CD56+ natural killer cells, and CD14+ monocytes were negatively selected using the RosetteSep antibody cocktail, while polymorphonuclear leukocytes were separated with density gradient media.
Genes differentially expressed by each cell type were identified. To demonstrate the potential use of such cell subtype-specific genomic expression data, a number of the major genes previously reported to be regulated in ischemic stroke, migraine, and Tourette syndrome are shown to be associated with distinct cell populations in blood. These specific gene expression, cell-type-related profiles will need to be confirmed in larger data sets and could be used to study these and many other neurological diseases.

overall_design: This study includes data from major blood cell types from normal individuals. These cell types include CD4+ T cells, CD8+ T cells, CD19+ B cells, CD56+ natural killer cells, CD14+ monocytes and PMN (polymorphonuclear cells). The data were hybridized on 3 separate batches of gene chips.

first: X

last: Du

first: Y

last: Tang

first: H

last: Xu

first: L

last: Lit

first: W

last: Walker

first: P

last: Ashwood

first: J

last: Gregg

first: F

middle: R

last: Sharp


title: Simultaneous Host-Pathogen transcriptome analysis during Granulibacter bethesdensis infection of normal and chronic granulomatous disease neutrophils

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: Polymorphonuclear leukocytes (PMN) from patients with chronic granulomatous disease (CGD) fail to produce microbicidal concentrations of reactive oxygen species due to mutations in NOX2.  Patients with CGD suffer from severe, life-threatening infections and inflammatory complications.  Granulibacter bethesdensis is an emerging Gram-negative pathogen in CGD that resists killing by CGD PMN and inhibits PMN apoptosis through unknown mechanisms.  Microarray analysis was used to study mRNA expression in normal and CGD PMN during incubation with G. bethesdensis and, simultaneously, in G. bethesdensis with normal and CGD PMN.  We detected upregulation of anti-apoptotic genes (e.g., XIAP, GADD45B) and downregulation of pro-apoptotic genes (e.g., CASP8, APAF1) in infected PMN.  Transcript and protein levels of inflammation and immunity-related genes were also altered.  Upon interaction with PMN, G. bethesdensis altered expression of ROS-resistance genes in the presence of normal but not CGD PMN.  Bacterial stress response genes, including ClpB, increased during phagocytosis by both normal and CGD PMN demonstrating responses to oxygen-independent PMN antimicrobial systems.  Antisense knock down demonstrated that ClpB is dispensable for extracellular growth but is essential for bacterial resistance to both normal and CGD PMN.  Metabolic adaptation of Granulibacter growth in PMN included upregulation of pyruvate dehydrogenase.  Pharmacologic inhibition of pyruvate dehydrogenase by triphenylbismuthdichloride was lethal to Granulibacter.  This study expands knowledge of microbial pathogenesis by Granulibacter in cells from permissive (CGD) and non-permissive (normal) hosts and identifies potentially druggable microbial factors, such as pyruvate dehydrogenase and ClpB, to help combat this antibiotic-resistant pathogen.

sample_organism:
Homo sapiens
Granulibacter bethesdensis

platform_organism:
Coxiella burnetii
Rickettsia rickettsii
Homo sapiens
Chlamydia muridarum
Chlamydia pneumoniae AR39
Staphylococcus epidermidis RP62A
Staphylococcus epidermidis ATCC 12228
Staphylococcus aureus subsp. aureus MW2
Borreliella burgdorferi B31
Coxiella burnetii RSA 493
Chlamydia caviae GPIC
Chlamydia trachomatis D/UW-3/CX
Staphylococcus haemolyticus JCSC1435
Granulibacter bethesdensis

overall_design: pathogen time series 0-1-4-24 in CGD subjects and normals : host time series 0-1-4-24 in CGD subjects and normals non-infected and infected with Gb

first: David

middle: E

last: Greenberg

first: Daniel

first: Kimberly

last: Marshall-Batty

first: Jessica

last: Chu

first: Anthony

last: Pettinato

first: Kimmo

last: Virtaneva

first: John

last: Lane

first: Bruce

middle: L

last: Geller

first: Stephen

last: Porcella

last: Gallin

first: Steven

last: Holland

first: Kol

middle: A

last: Zarember


title: Gene expression profiling in mature OT-II TCR transgenic CD4 SP thymocytes, either Jmjd3- and Utx-deficient or -sufficient.

status: Public on Sep 17 2015

first: Sugata

last: Manna

state: Maryland

address: 37 Convent Dr. Room 3032A

department: Laboratory of Immune Cell Biology

institute: National Cancer Institute, National Institute of Health

summary:
The biological functions of histone demethylases Jmjd3 and Utx remain poorly understood. We assessed such functions in developing T cells, using conditional (CD4-Cre-mediated) gene disruption, by inactivating Kdm6a and Kdm6b, respectively encoding Utx and Jmjd3, in immature CD4+CD8+ thymocytes. We compared microarray gene expression in mature (Va2hi CD24lo) mutant and wild-type CD4+CD8- thymocytes carrying the OT-II TCR transgene.
We show that Jmjd3 and Utx redundantly promote H3K27Me3 removal at, and expression of, a specific subset of genes involved in terminal thymocyte differentiation, especially S1pr1, encoding a sphingosine-phosphate receptor required for thymocyte egress.

overall_design: Mature (Va2hi CD24lo) CD4 thymocytes were sorted from freshly prepared single-cell suspensions OT-II TCR transgenic thymocytes deficient for Utx and Jmjd3 (dKO, CD4-Cre conditional deletion of floxed Kdm6a and Kdm6b alleles), and from Cre-negative controls (wild-type). Total RNA was extracted from sorted thymocytes using the RNeasy Plus Mini Kit (Qiagen) and processed for microarray analyses (Affymetrix Mouse Exon 1.0 ST array) at the NCI microarray facility, following the manufacturer’s recommendation. Data is generated from 3 replicates from each experiment.

first: Rémy

last: Bosselut


title: Rapid, high efficiency isolation of pancreatic ß-cells

status: Public on Sep 04 2015

city: Boston

first: James

last: Mohan

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

summary: The ability to isolate pure pancreatic ß-cells would greatly aid multiple areas of diabetes research. We developed an exendin-4-like neopeptide conjugate for the rapid purification and isolation of functional pancreatic ß-cells. By targeting the glucagon-like peptide-1 receptor, ß-cells were isolated within an hour and were >99% pure. These studies were confirmed by immunostaining, confocal microscopy and microarray analysis on isolated cells. Gene expression profiling studies of the cytofluorometrically sorted ß-cells provided new insights into the genetic programs at play of different ages and stages during type-1 diabetes development. The described isolation method should have broad applicability to the ß-cell field.

overall_design:
Microarray profile of beta cells from isolated islets from 4 and 12 week old NOD mice.
Cells were stained with 50 nM Ex4+ probe and sorted on FACS ARIA. DAPI and CD45+ cells were excluded.

first: Jim

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Expression of genes at the 45 min time point relative to that at 0 min time after release from initiation-arrest in either presence or absence of TorR

status: Public on Sep 01 2015

city: Hohhot

first: yao

last: yuan

state: Inner Mongolia

address: No. 235, Da xue West Road,

department: School of Life Sciences

country: China

institute: Inner Mongolia University

summary: We find that the response regulator TorR protein of the TorR/TorS two-component signal transduction system localizes to the old poles of the Escherichia coli cells, forming a functional focus. Interestingly, TorR co-localizes with the nucleoid in a cell-cycle-dependent mode, implying a cell-cycle-dependent interaction of TorR with its target genes.

sample_organism: Escherichia coli str. K-12 substr. W3110

overall_design: We choosed the samples collected at 0min and 45min after being synchronized regarded as Z0 cells and Z45 cells expressed TorR respectively, beacuse there was significant difference between these different time intervals. In order to rule out the interference factor coming from the regulation only in a cell-cycle dependent way, we used the samples collected at 0min and 45min after being synchronized without TorR, regarded as W0 cells and W45 cells. And then we made comparisons of gene expression between different groups. Firstly, we made a comparison between Z45 cells and Z0 cells in treated group. Secondly, we presented a comparison between W45 cells and W0 cells in untreated control group.

first: Yuan

last: Yao


title: MicroRNA-15/16 Antagonizes c-Myb to Control Natural Killer Cell Maturation

first: Todd

last: Fehniger

address: 660 S. Euclid Ave Campus Box 8007

department: Internal Medicine / Oncology

institute: Washington University in St. Louis School of Medicine

summary: NK cells develop in the bone marrow and complete their maturation in peripheral organs, but the molecular events controlling maturation are incompletely understood. Utilizing an NK cell-specific miR-15/16 deficient genetic model (15aKO), we identified a critical role for miR-15/16 family microRNAs in the normal maturation of NK cells in vivo, with a specific reduction in mature CD11b+CD27- NK cells in multiple tissues. The mechanism responsible was a block in differentiation, since accelerated NK cell death was not evident, and earlier intermediates of NK cell maturation were expanded. Further, we identified Myb as a direct target of miR-15/16 in NK cells, with Myb expression increased in immature 15aKO NK cells. Following adoptive transfer, immature 15aKO NK cells exhibited defective maturation, which was rescued by ectopic miR-15/16 expression or Myb knockdown. Moreover, Myb overexpression resulted in defective NK cell maturation. Thus, miR-15/16 regulation of Myb controls the normal NK cell maturation program.

overall_design: 3 technical replicates each of CD27+ 15a/16-1FKO NK cells, and CD27+ Ctrl NK cells

first: Ryan

middle: P

last: Sullivan


title: Low-dose, long-wave UV light does not affect gene expression of human mesenchymal stem cells

status: Public on Sep 02 2015

city: Los Angeles

first: Andrea

last: Kasko

address: 410 Westwood Plaza, 4121 Engineering V

department: Bioengineering

institute: University of California, Los Angeles

summary:
This experiment was conducted to test multiple hypotheses: 1) long-wave 365 nm UV light exposure at low fluences does not alter gene expression of hMSC, 2) presence of radical species during polymerization causes DNA damage in hMSC, 3) 3D encapsulation of hMSC causes changes in gene expression of hMSC compared with traditional 2D culture, 4) Differencesin 3D hydrogel networks induce gene expression changes in hMSC
The first publication derived from this data set concerns UV exposure and reactive radical species. Light is a non-invasive tool that is widely used in a range of biomedical applications.  Techniques such as photopolymerization, photodegradation and photouncaging can be used to alter the chemical and physical properties of biomaterials in the presence of live cells. Long-wave UV light is an easily accessible and commonly used wavelength.  Although exposure to low doses of long-wave UV light is generally accepted as biocompatible, most studies only investigate cell viability, ignoring other possible non-toxic effects. Since light exposure could potentially induce phenotypic changes (i.e. if damage repair mechanisms are activated), we examined changes in gene expression of human mesenchymal stem cells exposed to light under various 2D and 3D culture conditions. While exposure to long-wave UV light did not induce any significant changes in gene expression regardless of culture conditions, significant changes were observed due to scaffold fabrication chemistry and between cells plated in 2D versus 3D scaffolds.

overall_design: In total, 24 samples were analyzed. Three different culture conditions were created: 2D(plated), 3DR (encapsulated, radical polymerization), and 3DC (encapsulated, conjugate addition). Each culture condition was further subjected to UV radiation or no UV radiation, for 6 total experimental groups. Each experimental group was performed in triplicate. The 2D experimental groups, with and without UV, were additionally performed twice, once simultaneously with the 3DR samples, and once simultaneously with the 3DC samples. 3DR: encapsulated cells using radical polymerization (APS/TEMED) in a poly(ethylene glycol) (MW=4,000 g/mol) hydrogel in PBS. 3DC: encapsulated cells using conjugate addition with a four-arm PEG-Thiol (pentaerythritol tetrakis(3-mercaptopropionate) (PETMP) ) as the cross-linker in PBS.

first: Darice

middle: Y

last: Wong

first: Thanmayi

last: Ranganath


title: DNA methylation screening of small bowel adenocarcinoma

city: Cambridge

first: Muhammad

middle: Abdullah

last: Alvi

address: Addenbrooke's site

institute: University of Cambridge

summary:
Illumina Infinium 450k screening of normal and tumour tissue in a retrospective 28 sample cohort of small bowel adenocarcinoma patients.
Average signal and beta values normalised to internal Illumina controls.

overall_design: Comparing DNA methylation differences in a matched normal tumour cohort of 28 small bowel adenocarcinoma patients.

first: Manuel

last: Salto-Tellez


title: Deficiency of multidrug resistance 2 contributes to cell transformation through oxidative stress

city: Paris

first: Guillaume

last: soubigou

address: 25 rue du Docteur Roux

institute: Institut Pasteur

summary:
Mdr2 is the transporter of phosphatidylcholine, which is an essential component of bile. Deficiency of mdr2 causes hepatic inflammation, liver fibrosis and hepatocellular carcinoma. Mdr2-/- MEFs show increased proliferation, spontaneous transformation and tumorigenesis.
We used microarray to obtain genome-wide profiling of gene expression underlying the changes in mdr2-/- MEFs.

overall_design: MEFs derived from wt and mdr2-/- littermate embyos were subjected to passage according to 3T3 protocols. RNA was extracted from cells on passage 40 and hybridized on Affymetrix microarrays.

first: Ali

last: Tebbi

first: Florence

last: Levillayer

last: Soubigou

first: Hugo

last: Varet

first: Yu

last: Wei


title: Transcription changes due to TET1 knockdown in HCT116 colorectal cancer cells.

city: Tokyo

first: Yotaro

last: Kudo

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

department: Gastroenterology

country: Japan

institute: University of Tokyo

summary: Transcriptional profiling of HCT116 cells transfected with either control siRNA or TET1 siRNA was analyzed using whole human genome microarrays.

overall_design: To identify genes regulated by TET1 in colorectal cancer, HCT116 cells were transfected with either control siRNA or TET1 siRNA, and total RNA was extracted from biologically duplicated samples.

first: Keisuke

last: Tateishi

first: Genta

last: Nagae

last: Yamamoto

first: Takuma

last: Nakatsuka

first: Naoto

last: Fujiwara

first: Kiyokazu

last: Shirai

first: Masato

last: Yonezawa

first: Motoaki

last: Seki

first: Asuka

last: Kamio

first: Yasuo

last: Tanaka

first: Hideaki

last: Ijichi

first: Hiroyuki

last: Aburatani

first: Kazuhiko

last: Koike


title: The DNA methylation signature of human TCRαβ+CD4-CD8- double negative T cells reveals CG demethylation and a unique epigenetic architecture permissive to a broad stimulatory immune response

city: OKC

first: Jonathan

middle: Daniel

last: Wren

state: OK

address: 825 NE 13th St

department: Arthritis & Clinical Immunology

institute: Oklahoma Medical Research Foundation

summary: T cell receptor (TCR) αβ+ CD4- CD8- double negative T cells represent a rare T cell subset implicated in the pathogenesis of several autoimmune diseases. In this study, we investigated the DNA methylation signature of double negative T cells to gain insight into the epigenetic architecture and transcriptional capacity of peripheral blood primary human double negative T cells compared to autologous CD4+ and CD8+ T cells.  We identified 2,984 CG sites across the genome with unique loss of DNA methylation in double negative T cells, and showed significant reduction in mRNA expression of DNA methyltransferases DNMT1, DNMT3A, and DNMT3B. DNA methylation was increased in CD8A/CD8B and CD4 consistent with epigenetic repression of both the CD8 and CD4 genetic loci in double negative T cells. Curiously, we show consistent increase in non-CG methylation in double negative T cells, a finding suggestive of pluripotency and previously only known to occur in embryonic stem cells and developing brain tissue. Network analyses of genes hypomethylated in double negative compared to CD4+ and CD8+ T cells indicate a strong relationship between double negative T cells and functions related to cell-cell interaction, cell adhesion, and cell activation pathways. Our data also suggest a robust pro-inflammatory epigenetic signature in double negative T cells, consistent with a transcriptional permissiveness to produce key inflammatory cytokines including IFNγ, IL-17F, IL-12B, IL-5, IL-18, TNFSF11 (RANKL), and TNFSF13B (BLYS or BAFF). These findings highlight an epigenetic basis for a role of double negative T cells in autoimmunity and extend the potential pathogenic transcriptional capacity of this unique T cell subset.

overall_design: Peripheral blood mononuclear cells (PBMCs) were isolated from fresh blood samples of 7 unrelated healthy women (age range 25-60) (Supplementary Table 1) by Ficoll-gradient centrifugation (GE Healthcare Bio-Sciences AB, Uppsala, Sweden). Subsequently, T cells were negatively-selected using the Human Pan T Cell Isolation II kit (Miltenyi Biotec, Cambridge, MA). T cells were then analyzed and sorted into TCRαβ+ CD4+ T cells, TCRαβ+ CD8+ T cells, and TCRαβ+ DN T cell subsets by flow cytometry. DNA was isolated from CD4+, CD8+, and DN T cell subsets using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA), then bisulfite-converted using the EZ DNA Methylation kit (Zymo Research, Irvine, CA) for DNA methylation studies.

first: Paul

last: Renauer

first: Patrick

last: Coit

first: Amr

middle: H

last: Sawalha


title: Characterization of the cartilage DNA methylome in knee and hip osteoarthritis.

city: Newcastle upon Tyne

first: Andrew

middle: James

last: Skelton

state: Tyne and Wear

address: Framlington Place

department: Bioinformatics

institute: Newcastle University

summary:
The aim of this study was to characterise the genome-wide DNA methylation profile of osteoathritis (OA) chondrocytes from both knee and hip cartilage, providing the first comparison of DNA methylation between OA and non-OA hip cartilage, and between OA hip and OA knee cartilage. The study was performed using the Illumina Infinium HumanMethylation450 BeadChip array. Genome-wide methylation was assesed in chondrocyte DNA extracted from 23 OA hip, 73 OA knee and 21 healthy hip controls (NOF - neck of femure samples).

Keywords: Methylation profiling by array

overall_design: Bisulphite converted DNA from the 97 samples were hybridised to the Illumina Infinium HumanMethylation450 BeadChip array.

first: A

first: L

last: Reynard

first: J

last: Loughlin

first: Michael

last: Rushton


title: MicroRNA-15/16 Antagonizes c-Myb to Control Natural Killer Cell Maturation (c-Myb overexpression)

first: Todd

last: Fehniger

overall_design: KY-1 and KY-2 cell lines overexpressing c-Myb

first: Ryan

last: Sullivan


title: mRNA Expression Changes with Cofilin-2 Deficiency

first: Sarah

last: Morton

state: MA

address: 300 Longwood Ave

institute: Boston Children's Hospital

summary: mRNA Expression in Quadriceps Muscle from Cofilin-2 Null Mice Compared to WT Littermates on Day 7

overall_design: Quadriceps muscle resected on day 7 from cofilin-2 deficient mice and wildtype littermates were collected and mRNA was isolated.  Expression changes were analyzed by microarray.

first: Pankaj

last: Agrawal


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

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. The different populations are left unstimulated or are stimulated with LPS

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


title: Expression data from of HD-iPSC and CON-iPSC neuron derivatives

city: Taipei

first: Hung-Chih

last: Kuo

address: No.128, Sec. 2 Academia Rd

department: Institute of Cellular and Organismic Biology

country: Taiwan

institute: Academia Sinica

summary:
Compared the global gene expression profiles of HD- and CON-iPSC-derived neurons
We used microarrays to detail the global programme of gene expression for comparing the global gene expression profiles of HD- and CON-iPSC-derived neurons and facilitating studies of medium spiny neurons (MSN)-degenerative processes of Huntington's Disease (HD).

overall_design: By using a step-wise in vitro differentiation protocol combining EB formation, neural induction by small molecules, treatment with inhibitors of the TGFß pathway (SB431542) and the BMP pathway (LDN193189), and mechanical isolation/purification of neural progenitors and neurons, we induced 60-70% of control iPSCs or HD-iPSCs to differentiate into GABA- and DARPP-32- double positive neurons.

first: Feng-Lan

last: Chiu

first: Chun-Ying

last: Yu


title: Gene Expression Changes in Nemaline Myopathy

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

overall_design: Refer to individual Series


title: Beclin-1 is dispensable for chromosome congression and proper outer kinetochore assembly

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

institute: Eurac Researc

summary: Chromosomal instability (CIN) is defined by the propensity to acquire structural and/or numerical aberration in the normal cellular karyotype and is often associated with cancer. Autophagy is a catabolic process that leads to the recycling of cellular components that may positively or negatively impact on cancer development and progression, depending on the context. Recent work postulated that the depletion of the pro-autophagic and tumor suppressive protein Beclin 1 triggers CIN by interfering with mitotic chromosome segregation, providing a possible mechanism for how Beclin 1 can act as a tumor suppressor (Fremont et al., PMID: 23478334). Here, we present data supporting the notion that the phenotypes described in Fremont et al., depend on a siRNA off-target effect. The transcriptomic analysis shown here was designed to identify the factor(s) that are responsible for such phenotype.

overall_design: HeLa cells synchronized in mitosis have been transfected in 3 independent experiments with either Beclin 1-ER or Beclin 1-II siRNA. RNA was extracted and subjected to gene expression profiling. Differentially expressed probe sets/genes have been identified between the ER and II siRNA using the moderated t-test from Bioconductor's limma package with the resulting p-values being adjusted for multiple hypothesis testing using the method from Benjamini and Hochberg.

first: Luca

last: Fava

first: Manuel

last: Haschka

first: Stephan

last: Geley

first: Andreas

last: Villunger


title: Revisiting the transcriptional analysis of primary tumors and associated nodal metastases with enhanced biological and statistical controls: application to thyroid cancer

city: Anderlecht

first: Maxime

last: Tarabichi

state: Bruxelles

address: Route de Lennik 808

country: Belgium

institute: IRIBHM

summary: The biology underlying nodal metastasis is poorly understood. Transcriptome profiling has helped to characterize both primary tumors seeding nodal metastasis and the metastasis themselves. The interpretation of these data, however, is not without ambiguities. Here we profiled the transcriptomes of 17 papillary thyroid cancer (PTC) nodal metastases, associated primary tumors and primary tumors from N0 patients. We also included patient-matched normal thyroid and lymph node samples as controls to address some limits of previous studies. We found that the transcriptomes of patient-matched primary tumors and metastases were more similar than of unrelated metastases/primary pairs, a result also reported in other organ systems, and that part of this similarity reflected patient background. We found that the comparison of patient-matched primary tumors and metastases was heavily confounded by the presence of lymphoid tissues in the metastasis samples. An original data adjustment procedure was developed to circumvent this problem. It revealed a differential expression of stroma-related gene expression signatures also regulated in other organ systems. The comparison of N0 vs. N+ primary tumors uncovered a signal irreproducible across independent PTC datasets. This signal was also detectable when comparing the normal thyroid tissues adjacent to N0 and N+ tumors, suggesting a cohort specific bias also likely to be present in previous studies with similar statistical power. Classification of N0 vs. N+ yielded an accuracy of 63%, but additional statistical controls not presented in previous studies, revealed that this is likely to occur by chance alone. To address this issue, we used large datasets from The Cancer Genome Atlas and showed that N0 vs. N+ classification rates could not be reached randomly for most cancers. Yet, it was significant, but of limited accuracy (<70%) for thyroid, breast and head and neck cancers.

overall_design: We profiled the transcriptomes of 11 primary PTCs with no detectable nodal invasion, 17 primary PTCs with nodal invasion and 17 patient-matched nodal metastases. We also profiled a number of control samples. These included 24 patient-matched normal thyroid tissues (11 from N0, 13 from N+ patients), and 4 normal lymph nodes; technical and biological replicates including additional nodal metastasis for 3 patients, adjacent blocks for 5 primary tumors, 4 normal thyroid tissues and 1 nodal metastasis.

last: Saiselet

first: Christophe

last: Trésallet

first: Catherine

last: Hoang

first: Denis

last: Larsimont

first: Guy

last: Andry

first: Carine

last: Maenhaut

first: Vincent

last: Detours


title: MDSC exacerbate acute hepatitis, mature and loose suppressor function CD40 dependent

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: Myeloid-derived suppressor cells (MDSC) represent a heterogeneous population of immature myeloid cells that accumulate in blood, liver, spleen and tumors upon chronic inflammation and tumor development in patients and mice. Acute hepatitis is characterized by a fast infiltration of inflammatory cells in the liver and increased enzymatic activity at this organ that could lead into liver fibrosis and cirrhosis. We have studied the biology of hepatic MDSC in acute hepatitis. Unexpectedly, hepatic MDSC, which accumulate in the liver of mice bearing subcutaneous tumors, failed to suppress inflammatory responses upon Con A injection, but instead were responsible for exacerbating acute liver damage. Phenotypic, genetic and functional studies demonstrated rapid changes of hepatic MDSC from a suppressor phenotype into a pro-inflammatory subset as early as 3 hours after Con A injection. An increase in the expression of pro-inflammatory cytokines, costimulatory molecules such as CD80, CD86 and CD40 along with a loss of suppressor function was noticed in mice upon Con A treatment. These changes were CD40-dependent and not found in CD40-/- MDSC. Interestingly, CD40 ligation of human MDSC in vitro resulted in down-regulation of arginase I expression and suppressor function. Finally, blockade of ROS production in hepatic MDSC ameliorated hepatocyte damage suggesting that MDSC mediated toxicity was ROS dependent. We believe that these findings reflect how MDSC plasticity can be modulated to promote inflammation, opening a new path for therapies targeting innate suppressive cells in cancer patients.

overall_design: EL4 tumors were established in C57BL/6 mice, then mice were injected either with PBS (n=3) or 12.5mg/kg Con A (n=3). Three hours later mice were sacrificed, liver CD11b+Gr-1+ cells were sorted and samples were processed for gene expression analysis.


title: Expression data from HaCaT cells stimulated by IL-22

status: Public on Aug 27 2015

city: Jinan

first: Meng

last: Jiang

state: Shandong

address: lixia street

institute: Qilu hospital

summary:
Psoriasis is an inflammatory skin disease and the exact pathogenesis has not been fully illuminated yet. It has been demonstrated that interleukin-22 (IL-22) plays a significant role in the pathogenesis of psoriasis.
Our study aimed to explore the role of IL-22 and its target miRNAs in pathogenesis of psoriasis.

platform_organism:
Homo sapiens
synthetic construct

overall_design: Differentially expressed miRNAs and mRNAs in HaCaT cells with IL-22 stimulation were analysed through miRNA and mRNA microarrays. qRT-PCR assay was conducted to validate microarrays results.

first: Qing

last: Sun


title: Exploration of hydroxymethylation in Kagami-Ogata syndrome caused by hypermethylation of imprinting control regions

city: Setagaya-ku

first: Keiko

last: Matsubara

state: Tokyo

department: Department of Molecular Endocrinology

institute: National Research Institute for Child Health and Development

summary:
5-hydroxymethylcytosine (5hmC), converted from 5-methylcytosine (5mC) by Tet enzymes, has recently drawn attention as the ‘sixth base’ of DNA since it is considered to be an intermediate of the demethylation pathway. Nonetheless, it remains to be addressed how 5hmC is linked to the development of human imprinting disorders. In this regard, conventional bisulfite (BS) treatment is unable to differentiate 5hmC from 5mC. It is thus hypothesized that BS conversion-derived ‘hypermethylation’ at imprinting control regions (ICRs), which may cause human imprinting disorders, would in fact be attributable to excessively increased levels of 5hmC as well as 5mC. To test this hypothesis, we applied the newly developed oxidative BS (oxBS) treatment to detect 5hmC in blood samples from Kagami-Ogata syndrome (KOS14) patients caused by perturbed expression of clustered imprinted genes on 14q32.2 resulting from the hypermethylation of ICRs at this locus, IG-DMR and MEG3-DMR.
oxBS with pyrosequencing and cloning-based sequencing revealed that there were few amounts of 5hmC at the hypermethylated IG-DMR in blood samples from KOS14 patients. oxBS with genome-wide methylation array analysis demonstrated that global levels of 5hmC were very low with similar distribution patterns in blood samples from KOS14 patients and normal controls. We also confirmed the presence of a large amount of 5hmC in the brain sample from a normal control.
5hmC is not a major component in abnormally hypermethylated ICRs or at a global level, at least in blood from KOS14 patients. As the brain sample contained a large amount of 5hmC, the neural tissues of KOS14 patients are promising candidates for analysis in elucidating the role of 5hmC in the neurodevelopmental context.

overall_design: We generated illumina 450k DNA methylation data for BS or oxBS converted samples of three KOS14 blood samples, one control pooled blood sample and one control brain sample with two technical replicates for each sample.

first: K

first: M

last: Kagami

last: Nakabayashi

last: Hata

last: Fukami

first: T

last: Ogata

last: Yamazawa


title: Analysis of the gene expression profile in cutaneous squamous cell carcinoma cells after EphB2 knockdown

city: Turku

first: Liisa

last: Nissinen

address: Medisiina D, 5th floor; Kiinamyllynkatu 10

department: Dermatology

country: Finland

institute: University of Turku

summary:
The role of Eph/ephrin signaling in numerous biological processes has been established. However, Eph/ephrin signaling has been shown to have complex role in tumor progression. The role of EphB2 receptor in the progression of cutaneous squamous cell carcinoma (cSCC) has not been studied before.
EphB2 is significantly overexpressed in cSCC cells compared with normal human epidermal keratinocytes (NHEKs). We used microarray based global gene expression profiling to study the effect of EphB2 knockdown on the expression of different genes in cSCC cells.

overall_design: cSCC cell lines (n=3) were transfected with either control or EphB2 siRNA (75 nM) and incubated for 72 hours. Total RNA was extracted and processed expression profiling with GeneChip 3’ IVT Express Kit according to manufacturer’s protocol.

first: Mehdi

last: Frashchian

first: Veli-Matti

last: Kähäri


title: Analysis of the gene expression profile in normal human epidermal keratinocytes and cutaneous squamous cell carcinoma cell lines

summary:
The incidence of keratinocyte-derived skin cancer, cutaneous squamous cell carcinoma (cSCC) is increasing worldwide making it the second most common metastatic skin cancer.
We used microarrays to characterize gene expression profile in normal human epidermal keratinocytes (NHEK) and cSCC cell lines.

overall_design: Total RNAs from normal human epidermal keratinocytes (n=5) and cSCC cell lines (n=8) were extracted. The samples were processed for Affymetrix 3´ IVT Express Kit according to manufacture’s protocol.

last: Farshchian

first: Risto

last: Ala-aho


title: ATF7 mediates lipopolysaccharide-induced epigenetic changes in macrophages involved in innate immunological memory

status: Public on Aug 31 2015

city: Tsukuba

first: Keisuke

last: Yoshida

state: Ibaraki

address: 3-1-1 Koyadai,

institute: RIKEN

type: Genome binding/occupancy profiling by genome tiling array

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


title: Immune cell subsets and their gene expression profiles from human PBMC isolated by Vacutainer Cell Preparation Tube and standard density gradient

status: Public on Aug 28 2015

city: St. John's

first: Tomasz

middle: I

last: Michalak

state: NL

address: 300 Prince Philip Dr.

department: Division of BioMedical Sciences

country: Canada

institute: Memorial University of Newfoundland and Labrador

summary: High quality genetic material is an essential pre-requisite when analyzing gene expression using microarray technology. Peripheral blood mononuclear cells (PBMC) are frequently used for genomic analyses, but several factors can affect the integrity of nucleic acids prior to their extraction, including the methods of PBMC collection and isolation. In this study, we compared the Ficoll-Paque density gradient centrifugation and BD Vacutainer cell preparation tube (CPT) protocols to determine if either method offered a distinct advantage in preparation of PBMC-derived immune cell subsets for their use in gene expression analysis. We compared gene expression in PBMC and individual immune cell types from Ficoll and CPT isolation protocols using Affymetrix microarrays.

overall_design: PBMC from 3 healthy donors were isolated using Ficoll-Paque gradient or BD Vacutainer CPT methods. Subsequently, immune cell subsets were separated by positive selection from PBMC obtained by both methods. RNA was extracted from total PBMC isolated by both protocols and from their subsets, followed by analysis of gene expression using Affymetrix microarrays. Gene expression was compared between Ficoll and CPT samples for a given cell type.

first: Christopher

last: Corkum

first: Danielle

last: Ings

last: Burgess

first: Sylwia

last: Karwowska

first: Werner

last: Kroll


title: Expression data from thalamus or parietal lobe of FFI patients and normal human.

status: Public on Aug 30 2015

city: Beijing

first: chan

last: tian

address: Changbai Road, Changping district

institute: Chinese Center for Disease Control and Prevention, China CDC

summary:
Fatal familial insomnia (FFI) is a special subtype of genetic human prion diseases that is caused by the D178N mutation of the prion protein gene (PRNP). In this study, global expression patterns of the thalamus and parietal cortex from three patients with FFI were analyzed by Affymetrix Human Genome U133+ 2.0 chip.
We used microarrays to detail the global gene expression in tissues from normal human and FFI patients thalamus, or parietal lobe.

overall_design: Tissues from normal human and FFI patients' thalamus, or parietal lobe were for RNA extraction and hybridization on Affymetrix microarrays.

first: Chan

last: Tian

first: Xiaoping

last: Dong

first: Di

last: Liu


title: Low dose of DNA-demethylating agents target colorectal cancer-initiating cells by activation of RIG1/MAVS signaling pathway

city: Toronto

first: Daniel

last: De Carvalho

state: ON

address: 101 College St

institute: Princess Margaret Cancer Centre

summary: Genome wide DNA methylation profiling of 3 patient-derived colorectal cancer samples with different CIMP profiles. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs

overall_design: Bisulphite converted DNA from the 3 samples were hybridised to the Illumina HumanMethylation450 BeadChip

first: Rajat

last: Singhania


title: EphB2 promotes progression of cutaneous squamous cell carcinoma

last: Nissinen


title: ATF7 mediates lipopolysaccharide-induced epigenetic changes in macrophages involved in innate immunological memory (expression)

summary: Immunological memory is generally thought to be mediated exclusively by lymphocytes such as memory T and B cells. However, enhanced innate immune responses caused by a previous infection increase protection against reinfection suggesting the presence of innate immunological memory. Here, we describe expression profile of peritoneal macrophages from wild-type mice pre-administrated with TLR ligands or from ATF7 knockout mice. ATF7 suppresses a group of innate-immunity genes in macrophage by recruiting H3K9 dimethyltransferase G9a. TLR ligands induce ATF7 phosphorylation, leading to release of ATF7 from chromatin and reduction in H3K9me2 level. Partially disrupted chromatin structure and increased basal expression on target genes are maintained for a long period, increasing resistance pathogens. Therefore we speculate ATF7 is important factor in controlling innate immunological memory.

overall_design: This series contains seven sets of exression array data. For all sample, we use four CEL files generated by four biological-independent experiments.

first: Toshio

last: Maekawa

first: Claire

last: Renard-Guillet

first: Bruno

last: Chatton

first: Ken-ichi

last: Ishibashi

first: Naohito

last: Ohno

first: Katsuhiko

last: Shirahige

first: Shunsuke

last: Ishii