title: Analysis of the vascular gene expression profile following a chronic nitrate supplementation in old mice

status: Public on Mar 16 2015

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

institute: University of Duesseldorf

summary: Analyses of the vascular changes that occur following a chronic nitrate supplementation in old mice at a gene expression level and transcriptional profile have not been elucidated in depth. To determine the changes of the vascular transcriptome, we conducted gene expression microarray experiments on aortas of old and old nitrate treated mice, in which age-related vascular dysfunction was confirmed by endothelial dysfunction.

overall_design: C57BL/6 mice (n=6) obtained from Janvier (Saint Berthevin, France) were 20 months old. Standard rodent chow were fed ad libitum. Mice were treated with 1g/L NaNO3 dissolved in the drinking water for 8 weeks. For aortic RNA Analysis, the vessel was flushed thoroughly with ice-cold phosphate-buffered saline (PBS), through the left ventricle of the heart, cleaned of periadventitial fat and connective tissues, and snap-frozen in liquid nitrogen and stored at -80 °C.

first: Christos

last: Rammos

first: Ulrike

last: Hendgen-Cotta

first: Rene

last: Deenen


title: Expression data from a variant monocyte population following dendritc cell depletion

status: Public on Apr 01 2015

city: London

first: Stephen

last: Henderson

address: Paul O'Gorman Building

department: Cancer Institute

country: United Kingdom

institute: UCL

summary: Ly6C+ ‘classical’ monocytes respond rapidly to inflammation, either directly as effector cells or by differentiating into inflammatory macrophages and dendritic cells (DC).  In the absence of DC, elevated levels of serum Flt3L and G-CSF induce a monocytosis although the properties of this expanded population have not been addressed.  Here, we show that depletion of DC using the CD11c-DTR model results in rapid and CCR2-independent expansion of a variant population of splenic MHC Class II+ CD64+ Ly6C+ monocytes that are distinct from both circulating blood Ly6C+ monocytes and their tissue counterparts, but resemble Ly6C+ cells mobilized by exogenous G-CSF and Flt3L. The CD64+ Ly6C+ monocyte population is characterized by up-regulation of TLR signalling apparatus and an increased capacity to produce TNF-a following stimulation. Therefore, perturbation within the mononuclear phagocytic system in the absence of inflammation induces an alternative differentiation pathway that drives expansion of monocytes poised for innate immune activation.

overall_design:
Monocytes populations were purified from CD11c-DTR mice which were injected with PBS or diphtheria toxin 48 hours previously. Common monocyte progenitors (cMoP) were isolated from untreated C57BL/6 mice.
48 hours after injection of PBS or DT, monocytes were purified from the spleen after collagenase digestion and flow sorted directly into Qiagen RLT buffer. cMoP were purified directly from the bone marrow without digestion enzymes.

first: Clare

last: Bennett

first: Ronjon

last: Chakraverty

first: Shivajanani

last: Sivakumaran


title: Eomes+ natural Th1 (nTh1) T cells share functional features with classical Th1 (cTh1) cells.

status: Public on Mar 24 2015

city: Seoul

first: Seonghoe

last: Park

address: 71, Ihwajang-gil

department: Department of Pathology

country: South Korea

institute: Seoul National University, College of Medicine

summary: Identification of intrathymic Eomes+ natural Th1 cells creates a novel idea that there is more than one way for the generation of innate CD4 T cells. To more deeply characterize this type of innate T cells, we compared the gene expression profile between nTh1 cells generated in CIITAtg mice and classic Th1 cells differentiated from naive CD4 T cells in Th1-polarizing condition.

overall_design: We compared data from four different cells: Naïve (CD4+CD62Lhi) CD4 T cells from wild-type spleen, TT Naive (CD4+CD62L+CXCR3-) thymocytes from CIITAtg mice, classic Th1 cells (naive T cells of wild-type spleen differentiated in Th1-polarizing condition), nTh1 cells (CD4+CD62L+CXCR3+ thymocytes from CIITAtg mice). Total RNA was extracted using Rneasy Micro Kit (qiagen) and then subjected to Affymetrix gene array. 1 sample for each cell type was used for analysis.

first: B

middle: H

last: Kang


title: Identification of genes activated under CoCl2 treatment in an Sp1 dependent manner in an ovarian cancer cell line

city: Yokohama

first: Shiro

last: Koizume

state: Please Select

address: 2-3-2 Nakao Asahi-ku

country: Japan

institute: Kanagawa Cancer Center Research Institute

summary: To identify genes activated under CoCl2 treatment of a cancer cell line in an Sp1 dependent manner, we performed cDNA microarray analysis with an ovarian cancer cell line, in which Sp1 is silenced via RNA interference.

overall_design: Cells were transfected with scramble or Sp1 siRNA and cultured for 40 h. Cells were further cultured for 4 h under 0.5 mM CoCl2 exposure. Total RNA was isolated for cDNA microarray analysis.


title: The transcription factor IRF1 and guanylate-binding proteins target activation of the AIM2 inflammasome by Francisella infection

status: Public on Mar 04 2015

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

country: USA

institute: St Jude Childrens Research Hospital

summary: Inflammasomes are critical for mounting host defense against pathogens. The molecular mechanisms that control activation of the AIM2 inflammasome in response to different cytosolic pathogens remain unclear. Here we found that the transcription factor IRF1 was required for the activation of the AIM2 inflammasome during infection with the Francisella tularensis subspecies novicida (F. novicida), whereas engagement of the AIM2 inflammasome by mouse cytomegalovirus (MCMV) or transfected double-stranded DNA did not require IRF1. Infection of F. novicida detected by the DNA sensor cGAS and its adaptor STING induced type I interferon-dependent expression of IRF1, which drove the expression of guanylate-binding proteins (GBPs); this led to intracellular killing of bacteria and DNA release. Our results reveal a specific requirement for IRF1 and GBPs in the liberation of DNA for AIM2 sensing depending on the pathogen encountered by the cell.

overall_design: We used microarrays to explore the gene expression profiles differentially expressed in Francisella-infected bone marrow-derived macrophages (BMDMs) isolated from Irf1-/-, Ifnar1-/-, Aim2-/- and wild-type mice.

first: Si

middle: M

last: Man

first: Thirumala

middle: D

last: Kanneganti


title: Expression data from diseased Ezh2 KO Lineage-c-Kit+Sca-1+ (LSK) bone marrow cells

status: Public on Mar 14 2015

city: Chiba

first: Makiko

last: Mochizuki-Kashio

address: 1-8-1 Inohana

institute: Chiba University

summary:
Recent studies have shown that epigenetic regulator are mutated in myelodysplastic syndrome (MDS) patients.  Ezh2 is frequently mutated in hematopoietic malignant patients, however, the pathophysiological role of Ezh2 mutations has not been elucidated yet.  In this study, we examined the function of Ezh2 in murine hematopoietic disease.
Ezh2 deleted mice with myeloid malignancies including MDS, Myelodysplasia/myeloneoplasm(MDS/MPN), Myelodysplasia/myeloneoplasm_thrombocytosis(MDS/MPN_TC)

overall_design: In this study, we utilized Ezh2 conditional knockout mice.  We harvested bone marrow stem/progenitor (LSK) cells from Cre-ERt (Wild) and Ezh2 deletion mice (n=3) at 3 months after transplanted and induced Tamoxifene to delete Ezh2.  We also collected bone marrow stem/progenitor (LSK) cells  at 9-12 months-post transplantation and induced Tamoxifen.

first: Atsushi

last: Iwama


title: Profiling of TGF-beta regulated genes in immortal and tumor cell-lines

city: Bangalore

first: Neeraj

last: KUMAR

address: Indian Institute of Science Bangalore

department: MRDG

country: India

institute: Indian Institute of Science Bangalore

summary: The study was carried out to delineate distinct TGF-beta target genes in immortal fibroblasts (HFhTERT), transformed fibroblasts (hFhTERT-LTgRAS) and tumor cells (HT1080). The data would help us in understanding the dual nature of TGF-beta.

overall_design: Control_HF_1hr vs TGFb_HF_1hr, Control_HF_4hr vs TGF-b_HF_4hr, Control_HF_12hr vs TGF-b_HF_12hr, Control_HT_1hr vsTGF-b_HT_1hr, Control_HT_4hr vs TGF-b_HT_4hr, Control_HT_12hr vs TGF-b_HT_12hr, Control_LTgRAS_1hr vsTGF-b_LTgRAS_1hr,  Control_LTgRAS_4hr vsTGF-b_LTgRAS_4hr, Control_LTgRAS_12hr vsTGF-b_LTgRAS_12hr

first: Sunita

last: Chopra

last: Kumar

first: Paturu

last: Kondaiah


title: Gene expression profiles of DKO172 cells expressing DICER1 wildtype or hotspot mutants

city: Vancouver

first: Jiamin

last: Chen

state: BC

department: OvCaRe

country: Canada

institute: bc cancer agency

summary: DICER1 plays a critical role in microRNA (miRNA) biogenesis. Recurrent somatic “hotspot” mutations at four mental binding sites within the RNase IIIb domain of DICER1, were identified in ovarian sex cord-stromal tumors and have since been described in other pediatric tumors. In this study, we identified and characterized DICER1 hotspot mutations in endometrial cancers derived from The Cancer Genome Atlas (TCGA) and our local tumor bank. DICER1 hotspot mutations are found in ~2% of endometrial tumors. Using Illumina and Sanger targeted resequencing we observed biallelic DICER1 mutations in more than 50% of cases with hotspot mutations and identified an additional recurrent mutation G1809R in 2 cases. Through small RNA deep sequencing and real-time PCR, we demonstrated mutations that add a positively charged side chain to residue 1809 have similar detrimental effects on 5p miRNA production as mutations at metal binding sites. In one case G1809R was compound heterozygous with a germline S839F mutation, which contributes to loss of DICER1 expression by promoting protein degradation. As expected, 5p miRNAs are globally reduced in tumors and cell lines with hotspot mutations. Pathway analysis of gene expression profiles indicated that genes derepressed due to loss of 5p miRNAs are strongly associated with cell cycle related pathways. Using a Dicer null cell line model, we demonstrated that DICER1 hotspot mutants abolished the inhibitory effects of wildtype DICER1 on cell proliferation upon re-expression. Furthermore, targets of let-7 family miRNAs are enriched among the upregulated genes, suggesting loss of let-7 may be impacting downstream pathways.

overall_design: DKO172 cells were seeded in 6-well plates at 200,000 cells per well the day before transfection. DKO172 cells were transfected with 2ug of pLD-hygro-EnVM vectors expressing DICER1 WT, D1709N, G1809R, or GFP control. The cells were harvested after 24 hours and re-plated into P60 plates. Cells were then selected with 300ug/ml hygromycin for 84 hours before harvested for RNA extraction.


title: Retinoic acid signaling constrains the plasticity of Th1 cells and prevents development of pathogenic Th17 cells [Agilent experiments]

status: Public on Mar 10 2015

first: Venu

middle: Madhav

last: Pullabhatla

address: Great Maze Pond

department: Guy's Hospital

institute: Biomedical Research Centre

summary: CD4+ T cells differentiate into phenotypically distinct T-helper cells upon antigenic stimulation. Regulation of plasticity between these CD4+ T-cell lineages is critical for immune homeostasis and prevention of autoimmune diseases. However, the factors that regulate lineage stability are largely unknown. Here we investigate a role for retinoic acid (RA) in the regulation of lineage stability using T helper 1 (Th1) cells, traditionally considered the most phenotypically stable Th subset. We found that RA, through its receptor RARa, sustains stable expression of Th1 lineage specifying genes as well as repressing genes that instruct Th17 cell fate. RA signaling is essential for limiting Th1 cell conversion into Th17 effectors and for preventing pathogenic Th17 responses in vivo. Our studies identify RA-RARa as a key component of the regulatory network governing Th1 cell fate and define a new paradigm for the development of pathogenic Th17 cells. These findings have important implications for autoimmune diseases in which dysregulated Th1-Th17 responses are observed.

overall_design: Th1 cells; comparing dnRARa to WT

first: Chrysothemis

middle: C

last: Brown

first: Randolph

middle: J

last: Noelle


title: Human hepatic stem cells transplanted into a fulminant hepatic failure Alb-TRECK/SCID mouse model exhibit liver reconstitution and drug metabolism capabilities

city: Yokohama City

first: Yasuharu

last: Ueno

state: Kanagawa

address: 3-9  Fuku-ura, Kanazawa-ku

department: Graduate School of Medicine

institute: Yokohama City University

summary: Comparison of liver developmental gene expression of human hepatic stem cells (HpSCs), human primary fetal liver cells (FLCs), human adult hepatocyte (AH) and HpSCs or FLC-derived humanized liver.

overall_design: 8 Samples were analyzed

first: Yun-Wen

last: Zheng


title: Expression data from the Lateral Habenula (LHb) and the Medial Habenula (MHb) of the mouse (C57BL/6) brain after nicotine self-administration (mRNA)

city: Seongbuk-gu, Seoul

first: Heh-In

last: Im

address: 5, Hwarang-ro 14-gil

institute: Korea Institute of Science and Technology

summary:
After intarvenouse catheter surgery, nicotine self-administration using an operant self-administration chamber, was conducted for 44 days with various doses of nicotine solution.
Age-matched mice were used for control. After the self-administration, the Lateral Habenual (LHb) and the Medial Habenula (MHb) of the mouse brain were collected.

overall_design: We used microarrays to detail the mRNA expression profile of the Lateral Habenual (LHb) and the Medial Habenula (MHb) after the nicotine self-administration.

first: Sangjoon

last: Lee


title: Gene expression response to high radiation treatment in MCF7 breast cancer cell line

status: Public on Jun 11 2015

city: Cefalù

first: Valentina

last: Bravatà

address: Contrada Pietrapollastra Pisciotto

country: Italy

institute: IBSBC CNR

summary: Intraoperative radiotherapy (IOERT) is a high radiation therapeutic technique which administers a single high dose of ionizing radiation (IR) immediately after surgical tumor removal in order to destroy the residual cancer cells in the site at high risk for recurrence. IR is able to regulate several genes and factors involved in cell-cycle progression, survival and/or cell death, DNA repair and inflammation modulating an intracellular response radiation dependent producing an imbalance in cell fate decision. In this study, we examined changes in gene expression in MCF7 breast cancer cell line exposed to 9Gy and 23Gy high single dose of IR delivered by IOERT.

overall_design: Changes in gene expression in MCF7 breast cancer cell line exposed to 9Gy and 23Gy high single dose of IR (named MCF7_9Gy and MCF7_23Gy respectively), were analyzed as two-color hybridizations using Agilent Technologies whole human genome 4x44K microarrays


title: Identification of genes activated under CoCl2 treatment in an Sp1 dependent manner and under hypoxia without serum condition in an ovarian cancer cell line

first: Shiro

last: Koizume

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

overall_design: Refer to individual Series


title: Expression data from the Lateral Habenula (LHb) and the Medial Habenula (MHb) of the mouse (C57BL/6) brain after nicotine self-administration

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

platform_organism:
Mus musculus
synthetic construct


title: Gene expression analysis of FACS-isolated mammary stromal cells (Fsp1-expressing) between stromal Gli2 wild type control and stromal Gli2 ablated mice

status: Public on Mar 13 2015

city: Stanford

first: CHEN

last: ZHAO

state: CA

address: 265 Campus Dr.

department: Biochemistry

institute: Stanford University

summary:
The capacity of stem cells to maintain and regenerate organs is critically dependent on the niche, a complex signaling microenvironment that sustains and regulates stem cell activity. Niche function in the mammary gland must integrate local homeostatic activities with hormonally regulated events, such as pregnancy or the onset of puberty. In the human disorder CPHD (combined pituitary hormone deficiency) breast growth defects at puberty are associated with mutations disrupting the transcription factor, GLI2. Here we find that Gli2 functions in mouse mammary stromal cells to shape a niche signaling program that sustains mammary epithelial stem cells.  Ablation of Gli2 in stromal cells thus leads to a disorganized mammary gland, associated with collapse of the niche signaling environment, with a five-fold decrease in functional mammary stem cell activity, and with attenuated response to the mammatrophic hormones estrogen and growth hormone. Consistent with a niche defect, aspects of Gli2-deficient mammary gland architecture can be rescued by local supplementation with IGF and WNT protein signals. Our findings thus identify GLI2 as a critical coordinator of local and hormonal influences on the niche signaling program, and suggest that mammary pathogenesis in CPHD patients results from dysfunction of the mammary epithelial stem cell niche.
We used microarrays to identify gene expression signatures associated with stromal Gli2 expression

overall_design: To identify stromal factors induced by Gli2 activity, we compared gene expression of FACS-isolated Fsp1Cre-marked stromal cells from Gli2∆S or Gli2WT littermates by microarray analysis, and identified genes encoding paracrine factors such as Igf1, Wnt2, Hgf, Fgf7, and Bmp7; we also identified down-regulated genes encoding estrogen receptor (Esr1), growth hormone receptor (Ghr), and other genes typically expressed in stromal cells. Of particular interest among the paracrine factors, WNT signals sustain the activity of MaSCs and in ex vivo culture, and functional inactivation of Igf1 or its epithelially expressed receptor, Igf-1r, both lead to development of hypoplastic mammary glands with terminal end bud abnormalities similar to the defects we observe in Gli2∆S mice. The down-regulation of these genes was confirmed by qRT-PCR of bulk stromal cells from Gli2WT and Gli2∆S mice, and was further quantified by qRT-PCR from single cells

first: Chen

last: Zhao

first: P

middle: A

last: Beachy


title: Expression data from CpG treated Common Lymphoid Progenitors

status: Public on Mar 01 2015

city: Philadelphia

first: Edward

last: Behrens

state: Pennsylvania

institute: The Children's Hospital of Philadelphia

summary: Common Lymphoid Progenitors (CLPs) have two subsets, Ly-6d- which are mutli-potent, and Ly-6d, which derive from Ly-6d- and are committeed to the B-cell fate.  Treatment of a mouse with CpG DNA causes an inflammatory response that alters both subsets.  We used expression data to understand the changes in transcription in the transition of Ly-6d- CLPs to Ly-6d+ CLPs ion the presence and absence of CpG induced inflammation.

overall_design: C57BL/6 mice were treated over 10 days with either PBS or 50 ug of CpG1826.  On day 10, bone marrow was harvested and CLPs populations were sorted by flow cytometry directly into RNAeasy buffer (Qiagen).

first: Sheena

last: Baratono


title: Effects of thyroxine on the Craniosynostotic Phenotype

status: Public on Feb 21 2015

city: Charleston

first: James

last: Cray

state: South Carolina

address: 173 Ashley Avenue, BSB230B

department: Oral Health Sciences

institute: Medical University of South Carolina

summary:
Thyroid hormone is know to effect growth and development. However little is know about the hormone thyroxine's effect on craniofacial growth and suture development.
We used microarray as one tool to determine gene expression profile of wild type and craniosynostotic (Twist 1 +/-) suture cells after thyroxine exposure.

overall_design: We isolated whole RNA from Wild type C57BL6 and Twist 1 +/- suture derived calvarial cells and treated with proliferation media and with thyroxine 10^-6 mol/liter for 3 or 7 days in culture. We then used an Affymetrix array and compared expression profiles between control and experimental treatments.

last: Cray Jr.

first: Jeremy

middle: L

last: Barth


title: Retinoic acid signaling constrains the plasticity of Th1 cells and prevents development of pathogenic Th17 cells [Affymetrix experiments]

last: Pullabhatla

overall_design: IFN-gamma+ Th1 cells from IFNgeYFP reporter mouse; comparing dnRARa to WT

first: Matthew

last: Arno


title: Polyploidy can drive rapid adaptation in yeast

status: Public on Feb 28 2015

city: Boston

first: Anna

last: Selmecki

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

type: Genome variation profiling by genome tiling array

summary: Analysis of copy number variation in evolved haploid, diploid, tetraploid strains.

overall_design: All experimental samples were compared to the same reference strain S288C. The samples include the progenitor strains for the haploid, diploid, and tetraploid evolution experiments, and single colony isolates (clones) from the evolving populations at given time points. Evolved clones were analyzed at generation 250 unless the name is followed by gen35, gen55 or gen500, in which case those generations were analyzed.

first: David

middle: S

last: Pellman


title: Functions of BET proteins in GATA1-mediated transcription [expression array]

status: Public on Feb 23 2015

first: Aaron

middle: James

last: Stonestrom

state: PA

address: 315 ARC 3615 Civic Center Blvd

department: Hematology

institute: Children's Hospital of Philadelphia

summary:
Role of bromodomain and extra-terminal motif (BET) proteins in GATA1-null erythrolbasts (G1E) and in differentiation induced by activation of conditional GATA1 tested by addition of BET inhibitor JQ1 (250nM)
Array protocols were conducted as described in the Ambion WT Expression Manual and the Affymetrix GeneChip Expression Analysis Technical Manual by the University of Pennsylvania Molecular Profiling Core.

overall_design: Two-factor design (+/- JQ1, +/- GATA1). External RNA spike-in controls (ERCC controls, Ambion) added to each sample in proportion to cell number at the time of RNA harvest.


title: Expression data from mouse mast cell progenitors, mature mast cells and innate lymphoid cells of type 2

status: Public on Mar 07 2015

city: Solna

first: Joakim

last: Dahlin

address: CMM, Visionsgatan 18

department: Department of Medicine, Solna

country: Sweden

institute: Karolinska Institutet

summary:
Mast cells originate from the bone marrow and develop into c-kit+ FcεRI+ cells. As both mast cell progenitors and mature mast cells express these cell surface markers, ways validated to distinguish between the two maturation forms with flow cytometry have been lacking.
We identified and sorted two distinct populations of mast cells from mouse peritoneum. Gene expression microarray analyses were used to confirm the maturation statuses of the mast cell populations.

overall_design: Gene expression microarray analyses were performed on mast cell progenitors, mature mast cell, and innate lymphoid cells of type 2. The cells were extracted from the peritoneal cavity of five naïve BALB/c mice. Individual variations were minimized by pooling the cells from all mice. Fluorescence-activated cell sorting was used to isolate the mast cell progenitors, the mature mast cells, and the innate lymphoid cells of type 2. Innate lymphoid cells of type 2 were included in the study as they are distantly related to mast cells.

first: Zhoujie

last: Ding

first: Jenny

last: Hallgren


title: Comparison of gene expression in aorta and CD115+ isolated circulating cells from apoE-/- versus apoE-/-LTbR-/- mice

first: Karl

last: Koehrer

country: Germany

institute: University of Duesseldorf

summary: Affymetrix Microarrays were used to analyse gene expression in aortas and circulating CD115+ cells of ApoE- and ApoE/Lymphotoxin beta receptor (LTbR)-double-deficent mice fed a Western diet from 8 to 12 weeks of age in order to identify regulated genes and pathways leading to reduced atherosclerosis in ApoE-/-/LTbR-/- mice compared to ApoE-/- littermate controls.

overall_design: Gene expression was analysed in aorta and CD115+ circulating blood cells in ApoE-and ApoE/LTbR-double deficient mice after 4 weeks feeding a high-fat, high-cholesterol Western type diet.

first: M

last: Grandoch

first: K

last: Feldmann

first: J

middle: R

last: Göthert

first: S

last: Homann

first: L

last: Dick

middle: K

last: Bayer

first: C

last: Klatt

middle: N

last: Waldheim

first: B

last: Rabausch

first: N

last: Nagy

first: A

last: Oberhuber

first: R

last: Deenen

last: Köhrer

last: Lehr

last: Homey

last: Pfeffer

middle: W

last: Fischer


title: In vivo response of microglia to Aβ and prostaglandin-E2 EP2 receptor signaling

status: Public on Feb 20 2015

first: Katrin

last: Andreasson

address: 1201 Welch Road, MSLS P210

department: Neurology and Neurological Sciences

summary:
Microglia, the innate immune cells of the central nervous system, perform critical inflammatory and non-inflammatory functions to maintain homeostasis and normal neural function.  However in Alzheimer’s disease (AD), these beneficial functions become progressively impaired, contributing to synapse and neuron loss and cognitive impairment. The inflammatory cyclooxygenase-PGE2 pathway, including the PGE2 receptor EP2, is implicated in AD development, both in human epidemiology and in transgenic models of AD.
To test the transcriptional responses of EP2-deficient microglia to Aβ in vivo, we used mice in which the EP2 receptor is conditionally deleted in microglia using the CD11b-Cre transgene and floxed alleles of the EP2 gene. By injecting these mice with Aβ ICV and isolating microglia from the brains, we have been able to establish the transcriptional response of microglia to Aβ in vivo and test how EP2 deletion in microglia affects this response.

overall_design: 8 month-old C57BL/6 mice, of the genotype CD11b-Cre; EP2+/+ or CD11b-Cre; EP2lox/lox, were injected I.C.V. with either Aβ or vehicle. 48 hours after injection, the mice were sacrificed and transcardially perfused with cold heparinized 0.9% NaCl. Brains were then removed from the mice and pooled, two brains of the same genotype per sample, to ensure adequate cell and RNA yield. The brains were then enzymatically dissociated for microglia isolation using the Neural Tissue Dissociation Kit (P), MACS Separation Columns (LS), and magnetic CD11b Microbeads from Miltenyi Biotec according to the manufacturer's protocol. Immediately after isolating the microglia, RNA was extracted from the cells for microarray analysis.

middle: U

last: Johansson

first: Nathaniel

last: Woodling

middle: I


title: Bacterial c-di-GMP reorganizes hematopoietic stem/progenitors and niches through STING

status: Public on Feb 13 2015

city: Tokyo

first: Keiyo

last: Takubo

address: 1-21-1 Toyama Shinjuku-ku

department: Department of Stem Cell Biology

institute: National Center for Global Health and Medicine

summary: Upon systemic bacterial infection, hematopoietic stem and progenitor cells (HSPCs) migrate to the periphery in order to supply a sufficient number of immune cells. Although pathogen-associated molecular patterns (PAMPs) reportedly mediate HSPC activation, how HSPCs detect pathogen invasion in vivo remains elusive. Bacteria use the second messenger bis-(3’-5’)-cyclic dimeric guanosine monophosphate (c-di-GMP) for a variety of activities. Here we report that c-di-GMP comprehensively regulates both HSPCs and their niche cells through an innate immune sensor, STING, thereby inducing entry into the cell cycle and mobilization of HSPCs, while decreasing the number and repopulation capacity of long-term hematopoietic stem cells (LT-HSCs). Furthermore, we show that type I IFN acts as a downstream target of c-di-GMP to inhibit HSPC expansion in the spleen, while  TGF-β1 is required for c-di-GMP-dependent splenic HSPC expansion. Our results define novel machinery underlying dynamic regulation of HSPCs and their niches during bacterial infection through c-di-GMP/STING signaling.

overall_design: Ten-week-old mice were intraperitoneally administered PBS or 200 nmol c-di-GMP, and CD150+ CD41- CD48- CD34- Flt3- LSK cells of pooled bone marrow from 10 mice per group were sorted 3 days later. mRNA was then extracted using RNeasy micro (Qiagen). Likewise, CD45- Ter-119- CD31- CD140a+ CD51+ MSCs and CD45- Ter119- CD31+ endothelial cells from c-di-GMP-treated or untreated mice were sorted and mRNA was extracted. cDNA was synthesized from mRNA and hybridized to gene chip Mouse60k (Agilent Technologies) and expression levels analyzed.

first: Hiroshi

last: Kobayashi

first: Chiharu

first: Ayako

last: Nakamura-Ishizu

first: Daiki

last: Karigane

last: Haeno

first: Taku

last: Sato

first: Toshiaki

last: Ohteki

first: Yoshihiro

last: Hayakawa

first: Glen

last: Barber

first: Mineo

last: Kurokawa

first: Toshio

last: Suda


title: Transcriptomic analysis of mouse lung tissue exposed to two multiwalled carbon nanotubes (NRCWE-26 and NM-401)

status: Public on Feb 18 2015

city: Roskilde

first: Sarah

middle: Søs

last: Poulsen

state: Denmark

address: Knud den Stores Vej 39B, 2.MF

country: Denmark

institute: The National Research Centre for the Working Environment

summary: Multi-walled carbon nanotubes (MWCNTs) are extensively produced and used in composite materials and electronic applications, thus increasing risk of worker and consumer exposure. MWCNTs are an inhomogeneous group of nanomaterials that exist in various lengths, shapes and with different metal compositions, which makes hazard evaluation difficult. However, several studies suggest that length plays an important role in the toxicity induced by MWCNTs. How the length influences toxicity at the molecular level is yet to be characterized.  We used high-content genomics tools to compare pulmonary responses after exposure to a short, entangled MWCNT to the pulmonary responses after exposure to a long, stiffer MWCNT at the global transcriptomic level. Female C57BL/6 mice were exposed by single intratracheal instillation to 18, 54 or 162 µg/mouse of a short MWCNT (NRCWE-26 (NC-7000), 847±102 nm in length) or long MWCNT (NM-401 (CP-0006-SG), 4048±366 nm in length). Lung tissues were harvested 24 h, 3 d and 28 d after exposure.

overall_design: This experiment examined the pulmonary transcriptional response of female C57BL/6 mice exposed to NRCWE-26, a short multi-walled carbon nanotube, and NM-401, a long multi-walled carbon nanotube, at three doses: D1 (18 μg), D2 (54 μg), D3 (162 μg), and vehicle control. Each dose group was examined 1, 3 or 28 days post-exposure. Each dose group had 5-6 biological replicates. There were a total of 139 samples included in the final analysis using a two-color reference design.

first: Anne

middle: T

last: Saber

first: Andrew

last: Williams

first: Ole

last: Andersen

first: Carsten

last: Købler

first: Rambabu

last: Atluri

first: Mariaelena

last: Pozzebon

first: Stefano

middle: P

last: Mucelli

first: Monica

last: Simion

first: Roberto

last: Hanoi

first: David

last: Rickerby

first: Kristian

last: Mølhave

first: Nicklas

last: Jacobsen

first: Carole

last: Yauk

first: Håkan

last: Wallin

first: Sabina

last: Halappanavar

first: Ulla

last: Vogel


title: CDK6 as key regulator of hematopoietic and leukemic stem cell activation.

city: Madrid

first: Marcos

last: Malumbres

address: Melchor Fernandez Almagro 3

department: Molecular Oncology

country: Spain

institute: Centro Nacional de Investigaciones Oncológicas (CNIO)

summary: The cyclin-dependent kinases (CDK) CDK6 and CDK4 have redundant functions in regulating cell-cycle progression. We describe a novel role for CDK6 in hematopoietic and leukemic stem cells (HSCs and LSCs) that exceeds its function as cell-cycle regulator. Although hematopoiesis appears regular under steady state conditions Cdk6-/- HSCs do not efficiently repopulate upon competitive transplantation and Cdk6-deficient mice are significantly more susceptible to 5-fluorouracil (5-FU) treatment. We find that activation of HSCs requires CDK6, which interferes with transcription of key regulators including Egr1. The central role of Egr1 is supported by transcriptional profiling of HSCs. The impaired repopulation capacity extends to BCR-ABLp210+ leukemic stem cells. Transplantation with BCR-ABLp210+-infected bone marrow (BM) from Cdk6-/- mice fails to induce disease although recipient mice do harbor LSCs. Egr1 knock-down in cdk6-/- BCR-ABLp210+ LSKs significantly enhances colony formation underlining the importance of the Cdk6-Egr1 axis. Our findings define CDK6 as an important regulator of stem cell activation and as essential component of a transcriptional complex that suppresses Egr1 in HSCs and LSCs.

overall_design: Four-condition experiment, Untreated or polyI:C-treated CDK6-/- cells versus untreated or polyI:C-treated wild-type cells. Biological replicates: 3 untreated replicates, 3 polyI:C-treated replicates.

first: Veronika

last: Sexl


title: Whole transcriptome analysis of laser capture microdissected tissues reveals site-specific programming of the host epithelial transcriptome by the gut microbiota [short period of bacteria colonization]

status: Public on Feb 12 2015

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

summary:
The mammalian gut harbors a diverse microbial community (gut microbiota) that mainly consists of bacteria. Their combined genomes (the microbiome) provide biochemical and metabolic functions that complement host physiology. Maintaining symbiosis seems to be a key requirement for health as dysbiosis is associated with the development of common diseases. Previous studies indicated that the microbiota and the host’s epithelium signal bidirectional inducing transcriptional responses to fine-tune and maintain symbiosis. However, little is known about the host’s responses to the microbiota along the length of the gut as earlier studies of gut microbial ecology mostly used either colonic or fecal samples. This is of importance as not only function and architecture of the gut varies along its length but also microbial distribution and diversity. Few recent studies have begun to investigate microbiota-induced host responses along the length of the gut. However, these reports used whole tissue samples and therefore do not allow drawing conclusions about specificity of the observed responses. Which cells in the intestinal tissue are responsible for the microbially induced response: epithelial, mesenchymal or immune cells? Where are the responding cells located? Furthermore, the gut microbiota has been implicated in epigenetic regulation of the host’s transcriptional profile.
We used using extensive microarray analysis of laser capture microdissection (LCM) harvested ileal and colonic tip and crypt fractions from germ-free mice before and during the time course of colonization with a normal microbiota (on days 1, 3, 5 and 7) to investigate the microbiota-induced transcriptional responses and their kinetics in specific and well-defined cell populations of the host’s epithelium.
Ileum and colon segments were dissected from germ-free 10-12 weeks old female C57Bl/6 mice and on day 1, 3, 5 and 7 after colonization, washed and frozen as OCT blocks. Cryosections were prepared from these OCT blocks and tip/crypt fractions isolated using laser capture microdissection.

overall_design: To investigate the microbiota-induced transcriptional responses specific for specific subpopulations of intestinal epithelial cells and their kinetics, tip and crypt fractions of ileal and colonic epithelium of germ-free 10-12 weeks old female C57Bl/6 mice before and during the time course of colonization with a normal microbiota (on days 1, 3, 5 and 7) were harvested using laser capture microdissection and probed in an extensive microarray analysis.

first: Felix

last: Sommer

first: Nina

last: Adam

first: Per

last: Fogelstrand

first: Fredrik

last: Bäckhed


title: Expression data from 10 months old sciatic nerves of Sterol regulatory element binding factor 1c (SREBF-1c) KO mice and relative littermates

status: Public on Feb 10 2015

city: Milan

first: Nico

last: Mitro

state: MI

address: Via Balzaretti 9

department: Pharmacological and biomolecular sciences

institute: Università degli studi di Milano

summary:
SREBF-1c is a transcription factor regulating fatty acid biosynthesis. We have charaterized the impact of the abcence of SREBF-1c on the development of peripheral neuropathy
In this dataset we included expression data from dissected sciatic nerve from 10 months old SREBF-1c KO mice and relative littermates.

overall_design: 6 total samples were analyzed (3 wild type and 3 SREBF-1c KO). Data handling was mainly done using TAC and Partek Genomic Suite software. The Robust Multichip Average (RMA) method was employed to calculate probe set intensity. RMA is a robust multi-chip average expression method that estimates the probe-level data from a set of chips: the perfect-match (PM) values are background-corrected, normalized and finally summarized resulting in a set of expression measures. The identification of differentially expressed genes was addressed using Fold Change (FC) and ANOVA. For each experimental condition the probesets whose fold change are higher or equal than 1.5 with an ANOVA unadjusted p-value lower than 0,05 are selected as significantly modulated.

first: Gaia

last: Cermenati

first: Matteo

last: Audano

first: Silvia

last: Giatti

first: Valentina

last: Carozzi

first: Carla

last: Porretta-Serapiglia

first: Emanuela

last: Pettinato

first: Cinzia

last: Ferri

first: Maurizio

last: D’Antonio

first: Emma

last: De Fabiani

last: Crestani

first: Samuele

last: Scurati

first: Enrique

last: Saez

first: Iñigo

last: Azcoitia

first: Guido

last: Cavaletti

first: Luis-Miguel

last: Garcia-Segura

last: Melcangi

first: Donatella

last: Caruso


title: Hepatic Gene Expression in LIRKO Mice

status: Public on Feb 05 2015

first: Sudha

last: Biddinger

state: Massachusetts

address: CLSB 16027 300 Longwood Ave

department: Endocrinology

institute: Boston Children's Hospital

summary:
Control and Liver Insulin Receptor KO mice (LIRKO) were sacrificed in the non-fasted state. RNA was prepared from liver samples and subjected to expression microarray analysis
Each array was hybridized with sample derived from 2-3 mice of the same genotype.

overall_design: Three arrays per group were used.


title: Epigenetic effects of antidepressants to neuroprotective genes in neuronal cultured cells

status: Public on Jan 30 2015

city: Chuoshi

first: Kunio

last: Miyake

state: Yamanashi

address: 1110 Shimokato

institute: Yamanashi University

summary: Antidepressants are widely used for treatment of depression. Imipramine, a typical antidepressant, is recently known to have an effect to restore the expression of brain-derived neurotrophic factor gene, which is decreased in depressed patients, by increasing histone acetylation. However, it is largely unknown whether other antidepressants have similar epigenetic effects to change gene expression. To address this question, we examined the effect of five antidepressants (imipramine, citalopram, duloxetine, amitriptyline, mirtazapine) on expression of genes associated with mental and neurodegenetative disorders. We found that 48-hour treatment with imipramine, citalopram, amitriptyline, mirtazapine, but not duloxetine, caused a large number of differentially expressed genes in primary neocortical neurons in mice. Focused on genes relating to neural protection and neuroplasticity, we discovered that amitriptyline not only enhanced the expression of atf3 and cox2 by increasing histone H3 Lys4 trimethylation (H3K4me3), but also protected neurons against oxygen-glucose deprivation and staurosporine-induced apoptosis. Our study will shed a new insight in understanding of the molecular and epigenetic mechanism of antidepressants.

overall_design: Mouse primary neuronal cultures were used to evaluate 48 hour effects of antidepressants. Briefly, cultured neurons at day in vitro 3 (DIV3) were treated with 5µM imipramine, 10 µM citalopram, 0.1 µM duloxetine, 5 µM amitriptylline, 50 µM mirtazepine. These cultures were harvested after 48 hours (DIV5).

first: An

last: Nguyen

first: Miyake

last: Kunio

first: Kubota

last: Takeo


title: Expression data from Ezh2 epithelial knock-out mouse lungs at E14.5

status: Public on Feb 04 2015

first: Michael

middle: Patrick

last: Morley

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary:
Ezh2 epigenetically suppresses developmentally-regulated genes. Ezh2 is highly expressed during development, including in the lung. We knocked out Ezh2 in the developing lung epithelium using a Shh-cre driver which is active in foregut endoderm prior to lung morphogenesis. Many developmentally regulated genes became derepressed in the mutant lungs, leading to defects in lung development.
Microarray analysis of genes upregulated in Ezh2 epithelial knock-out mouse lungs compared to Shh-cre controls.

overall_design: We generated Ezh2 epithelial mutant lungs by crossing the Ezh2-floxed line (Su et al., 2003) with the Shh-cre line (Harfe et al., 2004). We isolated RNA from whole mouse lungs at embryonic day 14.5 from 4 Shh-cre:Ezh2-flox/flox embryos (M1-M4) and 4 Shh-cre embryos (C1-C4). Littermates are as follows: C1+C2; C3+C4; M1+M2; M3+M4.

first: Melinda

middle: E

last: Snitow

first: Komal

last: Rathi

first: Edward

last: Morrisey


title: Characterization of protoporphytin IX effects on X-ray irradiation in Hela cells in vitro

status: Public on Jan 21 2015

city: Tsukuba

first: Junko

last: Takahashi

state: Ibaraki

address: 1-1-1 Umezono

institute: National Institute of Advanced Industrial Science and Technology　(AIST)

summary: Hela cells were used to evaluate the protoporphytin IX (PpIX) effects on X-ray irradiation. Treatment conditions were (1) control group (untreated cells); (2) cells treated with 1 μg /ml PpIX for 6 hours; (3) cells irradiated with 3Gy X-rays; (4) cells treated with 1 μg /ml PpIX for 6 hours prior to irradiation with 3Gy X-rays.

overall_design: Hela cells gene expressions in 4 groups were measured at 24 hours after exposure to 0 and 3 Gy X-rays plus treatment with PpIX prior to irradiation.

first: Masaki

last: Misawa

first: Hitoshi

last: Iwahashi


title: Changes in cholesterol homeostasis and acute phase response following pulmonary exposure to multi-walled carbon nanotubes links carbon nanotube exposure to risk of cardiovascular disease

status: Public on Feb 02 2015

first: Sarah

last: Poulsen

summary:
Adverse lung effects in rodents following pulmonary exposure to multi-walled carbon nanotubes (MWCNT) are well documented. However, systemic effects are less understood. Prospective epidemiological studies have shown increased cardiovascular disease risk after pulmonary exposure to airborne particles, which has led to concerns that inhalation exposure to MWCNT might pose similar risks.
We used high-content genomics tools to compare hepatic responses after exposure to a short, entangled MWCNT to the hepatic responses after exposure to a long, stiffer MWCNT at the global transcriptomic level. Female C57BL/6 mice were exposed by single intratracheal instillation to 162 µg/mouse of a short MWCNT (NRCWE-26 (NC-7000), 847±102 nm in length) or long MWCNT (NM-401 (CP-0006-SG), 4048±366 nm in length). Liver tissues were harvested 24 h, 3 d and 28 d after exposure.

overall_design: This experiment examined the pulmonary transcriptional response of female C57BL/6 mice exposed to NRCWE-26, a short multi-walled carbon nanotube, and NM-401, a long multi-walled carbon nanotube, at three doses: D1 (18 μg), D2 (54 μg), D3 (162 μg), and vehicle control. Each dose group was examined 1, 3 or 28 days post-exposure. Each dose group had 6 biological replicates. There were a total of 72 samples included in the final analysis using a two-color reference design.

last: Søs Poulsen

first: Anne

last: Saber

first: Alicja

last: Mortensen

first: Józef

last: Szarek

first: Dongmei

last: Wu

first: Andrew

last: Williams

first: Ole

last: Andersen

first: Nicklas

last: Jacobsen

first: Carole

last: Yauk

first: Håkan

last: Wallin

first: Sabina

last: Halappanavar

first: Ulla

last: Vogel


title: Relation between T CD4+: Regulatory cells and IL-2 producing cells

status: Public on Feb 01 2015

city: Paris

first: Antonio

middle: Angelo

last: Freitas

address: 25 Rue du Dr. Roux

department: Lymphocyte Population Biology Unit

country: France

institute: Institut Pasteur

summary:
We previously proposed that lymphocyte homeostasis is achieved by a quorum-sensing like mechanism, based on the paracrine sensing of IL-2 by Foxp3(+) regulatory T CD4(+) cells. In turn, these cells will suppress IL-2 producing cells, thereby controlling the total number of T CD4(+) cells. As CD4(+) T regulatory cells are unable to produce IL-2, such control mechanism assumes the complete segregation of both lymphocyte subsets, that is to say they constitute distinct compartments. In the present study, we re-evaluate the above-described quorum-sensing mechanism by considering the non-exclusive possibility that a fraction of IL-2-producing cells might acquire regulatory function, implying the existence of a role for an autocrine sensing of IL-2 in the homeostasis  of the regulatory compartment.

According to the mouse models used in these experiments, RFP is used as a reporter for the Foxp3 expression. The transcription factor Foxp3 is the main hallmark of T CD4(+) regulatory cells. Therefore RFP(+) cells are associated to T CD4(+) regulatory cells. According to the mouse model, and our last publication (PMID: 24249704), the GFP is a reporter for cells that having activated the IL-2 locus within the last 2-3 weeks. This subset of cells is called IL-2p cells.

overall_design: 4 populations of conventional CD4+ T cell are analysed. 5 replicats for each.

first: Julien

last: Berges


title: Higher maternal folic acid during gestation dysregulates expression of several genes in mice offspring cerebellum

status: Public on Jan 26 2015

city: Staten Island

first: Mohammed

middle: A.

last: Junaid

state: NY

address: 1050 Forest Hill Road

department: Developmental Biochemistry

institute: New York State Institute for Basic Research in Developmental Disabilities

summary: Maternal vitamins and micronutrients during gestational periods have profound impact on the developmemt of newborns as well as influence susceptibility to chronic conditions. Folic acid is indicated to women during pregnancies to prevent occurrence of neural tube defects in infants. Recently, evidence is emerging of the epigenetic effects of folic acid. Since epigenetic changes are crucial in developing fetus, we investigated the effect of maternal higher folic acid supplementation on the gene expression in offspring brains to identify if brain development may be affected. Our results revealed that maternal exposure of higher dose FA diet during gestation dysregulates expression of several genes in the cerebellum of both male and female pups.  Dysregulated genes included several transcriptional factors, imprinted genes, neurodevelopmental genes and genes associated with autism spectrum disorder.

overall_design: Adult, 8- to 10-week-old C57BL/6J mice were used in all the experiments and handled according to the protocol reviewed and approved by the Institute for Basic Research Institutional Animal Care and Use Committee.  One week prior to mating and throughout the pregnancy two groups of female mice were fed with custom AIN-93G amino acid–based diet (Research Diet, Inc. New-Brunswick, NJ), which contained folic acid (FA) at 2mg/kg and 20 mg/kg diet.  At postnatal day one (P1), from FA at 2 mg/kg group: male pups’ n=3 and female pups’ n=3 were sacrificed by cervical dislocation and cerebellum tissues were collected.  From FA at 20 mg/kg group: male pups’ n=6 and female pups n=6 were similarly processed.  All tissues were snapped frozen and stored at -80°C until downstream analysis was performed.

first: Subit

last: Barua

first: Salomon

last: Kuizon


title: Whole transcriptome analysis of laser capture microdissected tissues reveals site-specific programming of the host epithelial transcriptome by the gut microbiota [germ free vs conventional mice]

first: Intawat

last: Nookaew

summary:
The mammalian gut harbors a diverse microbial community (gut microbiota) that mainly consists of bacteria. Their combined genomes (the microbiome) provide biochemical and metabolic functions that complement host physiology. Maintaining symbiosis seems to be a key requirement for health as dysbiosis is associated with the development of common diseases. Previous studies indicated that the microbiota and the host’s epithelium signal bidirectional inducing transcriptional responses to fine-tune and maintain symbiosis. However, little is known about the host’s responses to the microbiota along the length of the gut as earlier studies of gut microbial ecology mostly used either colonic or fecal samples. This is of importance as not only function and architecture of the gut varies along its length but also microbial distribution and diversity. Few recent studies have begun to investigate microbiota-induced host responses along the length of the gut. However, these reports used whole tissue samples and therefore do not allow drawing conclusions about specificity of the observed responses. Which cells in the intestinal tissue are responsible for the microbially induced response: epithelial, mesenchymal or immune cells? Where are the responding cells located?
We used using extensive microarray analysis of laser capture microdissection (LCM) harvested ileal and colonic tip and crypt fractions from germ-free and conventionally-raised mice to investigate the microbiota-induced transcriptional responses in specific and well-defined cell populations of the host’s epithelium.
Ileum and colon segments were dissected from germ-free and conventionally-raised 10-12 weeks old female C57Bl/6 mice, washed and frozen as OCT blocks. Cryosections were prepared from these OCT blocks and tip/crypt fractions isolated using laser capture microdissection.

overall_design: To investigate the microbiota-induced transcriptional responses specific for specific subpopulations of intestinal epithelial cells, tip and crypt fractions of ileal and colonic epithelium of germ-free and conventionally-raised 10-12 weeks old female C57Bl/6 mice were harvested using laser capture microdissection and probed in an extensive microarray analysis.

first: Felix

last: Sommer

first: Nina

last: Adam

first: Per

last: Fogelstrand

first: Fredrik

last: Bäckhed


title: Early reprogramming stages and regulators identified by prospective isolation and single cell mass cytometry

status: Public on Jan 31 2015

first: Marius

last: Wernig

address: 265 Campus Drive, 3rd Floor

department: Pathology

institute: Stanford University

summary: In the context of most induced pluripotent stem (iPS) cell reprogramming methods,  heterogeneous populations of nonproductive and staggered productive intermediates arise at different reprogramming time points1-11. Despite recent reports claiming substantially increased reprogramming efficiencies using genetically modified donor cells12,13 prospectively isolating distinct reprogramming intermediates remains an important goal to decipher reprogramming mechanisms. Previous attempts to identify surface markers of intermediate cell populations were based on the assumption that during reprogramming the cells progressively lose donor cell identity and gradually acquire iPS cell properties1,2,7,8,10. Here, we report that iPS cell and epithelial markers, such as SSEA1 and EpCAM, respectively, are not predictive of reprogramming during early phases. Instead, in a systematic functional surface marker screen we find that early reprogramming-prone cells express a unique set of surface markers, including CD73, CD49d and CD200 that are absent in fibroblasts and iPS cells.  Single cell mass cytometry and prospective isolation show that these distinct intermediates are transient and bridge the gap between donor cell silencing and pluripotency marker acquisition during the early, presumably stochastic reprogramming phase2. Expression profiling revealed that the transcriptional regulators Nr0b1 and Etv5 are specifically expressed in this early reprogramming state, preceding activation of key pluripotency regulators such as Rex1, Dppa2, Nanog and Sox2. Both factors are required for the generation of the early intermediate state and fully reprogrammed iPS cells, and thus mark some of the earliest known regulators of iPS cell induction.  Our study shows an ordered sequence of transitions during the earliest steps of iPS cell reprogramming that deconvolutes the first steps in a hierarchical series of events that lead to pluripotency acquisition.

overall_design: Samples for poised (CD73+ or CD49d+) and non-poised (CD73-) reprogramming samples were FACS sorted 6 and 9 days after induction of Klf4, Oct4, Sox2 and cMyc in Rosa-rtTA +/- mouse embryonic fibroblasts (MEFs).  'Total' populations are expression analyses for unsorted populations analyzed at the same time points.  Control populations were also sampled: mouse embryonic fibroblasts (MEFs), partially reprogrammed cells (SC4) and mouse embryonic stem cell (ESC).

first: Ernesto

last: Lujan


title: Characterization of cyclobutane pyrimidine dimer-dependent modulation of gene expression in human keratinocytes following UVB exposure

status: Public on Jan 16 2015

city: Debrecen

first: Gabor

last: Boros

address: Nagyerdei krt. 98.

department: Department of Dermatology

country: Hungary

institute: University of Debrecen

summary: To address CPD-dependent UVB activities, a model system was established in which transfection of keratinocytes with pseudouridine-modified mRNA (Ψ-mRNA) encoding CPD-photolyase resulted in 90% reduction of CPDs within 6 and 24 hours after UVB exposure. Microarray analysis of this model system demonstrated that more than 50 % of the gene expression altered by UVB were changed in a CPD-dependent manner. The expression of most of the CPD-dependent genes was changed at 6 h after UVB as compared to 24 h likely due to the higher CPD levels. Nine genes (ATF3, CCNE1, CDKN2B, EGR1, ID2, PTGS2, RUNX1, SNAI1, SNAI2) regulated by CPDs were selected for further investigation (qPCR, Western blot) based on the microarray data.

overall_design: Gene expression modulated by UVB irradiation in HaCaT keratinocytes was measured at 6 and 24 hours after the exposure to dose of 20 mJ/cm2 UVB. Three independent experiments were performed at each time (6 or 24 hours) using different passages for each experiment.

first: Gábor

first: Edit

last: Miko

first: Hiromi

last: Muramatsu

first: Drew

last: Weissman

first: Eszter

last: Emri

first: Gijsbertus

middle: J

last: van der Horst

first: Irén

last: Horkay

first: Gabriella

first: Katalin

last: Karikó

first: Éva

last: Remenyik


title: Gene expression signature of carcinoma cell response to extracellular matrix

city: Bethesda

first: Kenneth

middle: M.

last: Yamada

state: MD

address: 30 Convent Dr.

department: LCDB

institute: NIDCR, NIH

summary: To evaluate changes in gene expression in MDA-MB-231 cancer cells upon interaction with different extracellular matrices

overall_design: Gene expression in MDA-MB-231 cells was assayed after overnight incubation of the cells on gelatin or dense fibrillar collagen (HDFC) matrices at the presence or absence of serum in tissue culture medium. Five repeats were performed

first: Vira

middle: V

last: Artym

middle: M


title: The p53 Signaling Pathway is Activated in Response to Hydroxyurea Embryotoxicity During Organogenesis

status: Public on Jan 15 2015

city: Montreal

first: Nazem

last: El Husseini

state: QC

address: 3655 Promenade Sir William Osler

department: Pharmacology & Therapeutics

institute: McGill University

summary:
Hydroxyurea (HU), an anticancer agent and potent teratogen, is used as a model drug to study the embryonic stress response during organogenesis. Previously, we demonstrated that HU activates a DNA damage response (DDR) pathway in the gestation day (GD) 9 mouse embryo (Toxicol Sci. 2013 133(2):298-308). The p53 tumor suppressor gene is a possible downstream effector of this pathway. P53 plays an important role in embryonic development, however its response to teratogens is debatable. We hypothesize that HU exposure at the organogenesis stage activates p53 which then mediates cell cycle arrest and cell death that result in the observed malformations.
To test this hypothesis, CD-1 embryos at GD9 were exposed in vivo to saline (Control-CO) or two doses of HU (HU400= 400 mg/kg; HU600= 600 mg/kg); embryos were extracted after 3 hours and samples prepared to examine gene and protein expression. Microarray analysis of embryos in the HU400 group showed that the expression of 1346 genes significantly changed compared to control and that they were significantly associated with the p53 signaling pathway. The active form of p53 (phospho-p53) was significantly upregulated in HU-exposed embryos; Western blot and confocal microscopy showed increasing protein concentrations and nuclear translocation in major embryonic tissues. qRT-PCR showed that p53-regulated genes (Cdkn1A, Fas, p53inp1) were significantly upregulated and p53inp1 protein increased in a dose-dependent fashion with HU. Together, these data show that p53 signaling is the main pathway activated in response to HU during organogenesis, and leads to the upregulation of cell cycle arrest and cell death promoting factors.

overall_design: Gestational day 9 mouse embryos were treated with saline or 400 mg/kg hydroxyurea by intraperitoneal injection. Dams were euthanized after 3 hours and embryos explanted. 4 independent experiments were performed and analyzed for each sample.

first: Ava

last: Schlisser

first: Barbara

last: Hales


title: Long term culture of genome-stable bipotent progenitor cells from adult human liver

city: Dresden

first: Meritxell

last: Huch

address: Pfotenhauerstrasse 108

institute: Max Planck Institute of Molecular Cell Biology and Genetics

summary: Despite the enormous replication potential of the human liver, there are currently no culture systems available that sustain hepatocyte replication and/or function in vitro. We have shown previously that single mouse Lgr5+ liver stem cells can be expanded as epithelial organoids in vitro and can be differentiated into functional hepatocytes in vitro and in vivo. We now describe conditions allowing long-term expansion of adult bile duct-derived bi-potent progenitor cells from human liver. The expanded cells are highly stable at the chromosome and structural level, while single base changes occur at very low rates. The cells can readily be converted into functional hepatocytes in vitro and upon transplantation in vivo. Organoids from α1-antitrypsin deficiency and Alagille Syndrome patients mirror the in vivo pathology. Clonal long-term expansion of primary adult liver stem cells opens up experimental avenues for disease modeling, toxicology studies, regenerative medicine and gene therapy.

overall_design: We generated arrays from whole human liver tissue, and human liver derived cultures maintained in our defined medium. Genes 4 fold differentially expressed  were used for the clustering analsyis (see matrix 1). For the genes enriched in organoid cultures grown in ERFHNic+A compared to ERFHnic we normalized the arrays by substracting the liver tissue 1 array to the culture arrays. Then we calculated the fold difference between the ERFHNic+A and the ERFHNic samples (see matrix 2).

first: Hans

last: Clevers


title: Transcriptome analysis of bone marrow mesenchymal stromal cells from patients with Primary Myelofibrosis

status: Public on Jan 10 2015

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

institute: university Paris Sud11

summary:
Primary myelofibrosis (PMF) is a clonal myeloproliferative neoplasm whose severity and treatment complexity is attributed to the presence of bone marrow (BM) fibrosis and alterations of stroma impairing the production of normal blood cells.  Despite the recently discovered mutations including the JAK2V617F mutation in about half of patients, the primitive event responsible for the clonal proliferation is still unknown. In the highly inflammatory context of PMF, the presence of fibrosis associated with a neoangiogenesis and an osteosclerosis concomitant to the myeloproliferation and to the increase number of circulating hematopoietic progenitors suggests that the crosstalk between hematopoietic and stromal cells is deregulated in the PMF BM microenvironment. Within these niches, Mesenchymal Stromal Cells (BM-MSC) play a supportive role in the production of growth factors and extracellular matrix which regulate the proliferation, differentiation, adhesion and migration of hematopoietic progenitors. A transcriptome analysis of BM-MSC in PMF patients will help to characterize their molecular alterations and to understand their involvement in the hematopoietic progenitor deregulation that features PMF.
Primary Myelofibrosis, mesenchymal stroma cells, bone marrow, myeloproliferative disorders

overall_design: Transcriptome analysis was performed on BM-MSC amplified in vitro after 3 to 5 passages. Agilent Whole Human Genome Oligo Microarrays were used to compare expression profiling of BM-MSC from PMF patients and healthy donors.

first: Christophe

last: Martinaud

last: Desterke

first: Joahnna

last: Konopacki

first: Alessandro

last: Vannucchi

first: Paola

last: Guglielmelli

first: Laetitia

last: Boutin

first: Jean-Jacques

last: Lataillade

first: Marie-Caroline

last: Le Bousse-Kerdilès


title: Human MCF-7 breast cancer cells: control vs. treated with conditioned medium of cancer associated adipose tissue

status: Public on Jan 07 2015

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

summary: Transcriptional profiling of human MCF-7 breast cancer cells comparing MCF-7 cells treated with control medium (DMEM/F12 + 0,5% BSA) with MCF-7 cells treated with conditioned medium of cancer-associated adipose tissue (CMCAAT) obtained from 2 breast cancer patients. Goal was to determine the effects of CMCAAT treatment on global MCF-7 gene expression.

overall_design: Two-condition experiment: MCF-7 control vs. CMCAAT treated cells. Biological replicates: 3 control replicates pooled as 1 (LL 1-2-4), 4 CMCAAT replicates (LL 6, LL 8, LL 9, LL 10)

first: Lore

last: Lapeire

first: Olivier

last: De Wever


title: Gene expression signatures of human plasma cells isolated from different territories

status: Public on Jan 05 2015

city: Cádiz

first: Antonio

last: Campos-Caro

state: Cádiz

address: Avda. Ana de Viya, 21

department: Unidad Investigación

institute: Hospital Universitario Puerta del Mar

summary: In vivo antigen (Ag)-induced differentiation of B lymphocytes into plasma cells (PCs) takes place in extra-follicular foci and germinal centers of the secondary lymphoid organs (SLOs). Most of these SLO PCs are short-living and only relatively few PCs, characterized by secreting high-affinity antibodies (Ab), travel through the circulation and finally home in specialized survival niches of the bone marrow (BM) and, at a lesser extent, in the SLOs, where they become long-living Ab-secreting PCs. We have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish between human circulating Ag-induced PCs in comparison with tonsil and BM PCs distinctively regulate genes involved in cell proliferation.

overall_design: Gene expressions in human plasma cells isolated from tonsil (7 samples), blood (6 samples) and bone marrow (7samples) were measured. Each sample was isolated from a different donor.

first: Ana

last: Ramos-Amaya

first: Beatriz

last: Rodríguez-Bayona

first: Rubén

last: Pérez-Blanco

first: Eloisa

last: Andújar

first: Mónica

last: Pérez-Alegre

first: José

middle: A

last: Brieva


title: Development of mRNA and lincRNA expression signatures of MEFs deficient in ER stress mediators for tunicamycin treatment

status: Public on Jan 18 2015

city: Tokushima

first: Seiichi

last: Oyadomari

state: Tokushima

address: 3-18-15 Kuramoto

department: Division of Molecular Biology

institute: Institute for Genome Research

summary: To further development of our mRNA or lincRNA expression approach to ER stress, we have employed whole genome microarray expression profiling as a discovery platform to identify ER stress-responsible genes.   Mouse embryonic fibroblasts (MEFs) deficient in each ER stress mediator (XBP1, ATF4, ATF6a or ATF6b) were treated with tunicamycin for 12 or 24 hrs. Genes responsible for tunicamycin in each mediator-dependent manner were extracted and categorized by Gene Ontology. Among them, expression of five ER-related genes (Derl1, Ssr3, Magt1, Bet1 and Mcfd2) was quantified in the RNA samples from COS7 cells by real-time PCR, confirming existence of similar mechanisms of trancriptional activation in ER stress by tunicamycin treatment.

overall_design: Mouse embryonic fibroblasts (MEFs) deficient in each ER stress mediator (XBP1, ATF4, ATF6a or ATF6b) were treated with 2ug/mL tunicamycin for 12 or 24 hrs. Two independent experiments were performed for each mediator-deficient MEF at each time (untreated, 12 or 24 hrs). Genes responsible for tunicamycin in each mediator-dependent manner were extracted and categorized by Gene Ontology in GeneRanker program of Genomatix platform.

first: Taiji

last: Ito

first: Tomoko

last: Mori

first: Robert

last: Zheng

first: Chinobu

last: Miyamoto

first: Kazue

last: Tsugawa

first: Kiyoe

last: Kurahashi

first: Mari

last: Funahashi

first: Ryosuke

last: Sato

first: Naoko

last: Miura

first: Kazuna

last: Takahara

first: Miho

first: Masato

last: Miyake


title: Transcriptome analysis of in vitro MSC-derived osteoblastic cells from patients with Primary Myelofibrosis

first: christophe

last: desterke

summary: Primary myelofibrosis (PMF) is a clonal myeloproliferative neoplasm whose severity and treatment complexity is attributed to the presence of bone marrow (BM) fibrosis and alterations of stroma impairing the production of normal blood cells.  Despite the recently discovered mutations including the JAK2V617F mutation in about half of patients, the primitive event responsible for the clonal proliferation is still unknown. In the highly inflammatory context of PMF, the presence of fibrosis associated with a neo-osteogenesis and an osteosclerosis concomitant to the myeloproliferation and to the increase number of circulating hematopoietic progenitors suggests that the crosstalk between hematopoietic cells and the osteoblastic niche is deregulated in the PMF BM microenvironment. Osteoblastic niche is well known to be an important support to regulate hematopoietic stem cell functions in bone marrow. A transcriptome analysis of bone marrow mesenchymal stem cells (BM-MSC) induced in vitro to differentiate in osteoblasts will help to understand the role of these cells in pathophysiology of PMF.

overall_design:
Transcriptome analysis was performed on BM-MSC at J0 and J21 of in vitro osteoblastic differentiation. Agilent Whole Human Genome Oligo Microarrays were used to compare expression profiling of BM-MSCs from PMF patients and healthy donors before and after osteoblastic differentiation.
Primary Myelofibrosis, mesenchymal stroma cells, bone marrow, myeloproliferative disorders

first: Christophe

last: Martinaud

last: Desterke

first: Joahnna

last: Konopacki

first: Alessandro

last: Vannucchi

first: Paola

last: Guglielmelli

first: Laetitia

last: Boutin

first: Jean-Jacques

last: Lataillade

first: Marie-Caroline

last: Le Bousse-Kerdilès


title: CD98 marks a subpopulation of head and neck squamous cell carcinoma cells with stem cell properties

status: Public on Jan 24 2015

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

country: Netherlands

institute: Vrije Universiteit Medical Center

summary: The application of compounds specifically targeting the cancer stem cells (CSCs), in addition to routinely used therapeutics, would likely improve the clinical outcome of head and neck squamous cell carcinoma (HNSCC). The previously described monoclonal antibody K984 (now found to recognize CD98) was used to identify, select and isolate a specific tumor subpopulation. These cells were molecularly characterized and subjected to serial transplantation experiments to determine the CSC properties. We show that CD98high cells, in contrast to CD98low cells, are able to generate tumors in immunodeficient mice and that the CD98high subpopulation expresses high levels of cell cycle control and DNA repair genes, while the CD98low fraction shows expression patterns that represent the more differentiated cells forming the bulk of the tumor.

overall_design: Transcriptional profiling of CD98high cells (n=4 fractions) of VU-SCC-OE xenograft tumors compared to CD98low cells (n=3 fractions) from the corresponding tumors.

first: Sanne

middle: R

last: Martens-de Kemp

first: Arjen

last: Brink

first: Marijke

last: Stigter-van Walsum

first: J

last: Damen

first: François

last: Rustenburg

first: Thijs

last: Wu

first: Wessel

last: van Wieringen

first: Gerrit

last: Schuurhuis

first: Boudewijn

last: Braakhuis

first: Monique

last: Slijper

first: Ruud

middle: H

last: Brakenhoff


title: Mapping of Hepatic Expression Quantitative Trait Loci (eQTLs) in a Han Chinese Population [Expression analysis]

status: Public on Jan 02 2015

city: Shanghai

first: Zhiqiang

last: Li

address: Huashan Road No.1954

department: Bio-X Institutes

country: China

institute: Shanghai Jiao Tong University

summary: Elucidating the genetic basis underlying the variation in hepatic gene expression is of importance to understand disease etiology and drug metabolism variances. To date, no genome-wide eQTL analysis has been conducted in the Han Chinese, the largest ethnic group in the world. We performed a genome-wide eQTL mapping in a set of Han Chinese liver tissue (n=64).

overall_design: Normal (non-diseased) liver tissues were previously collected from 64 Chinese donors who provided informed consent. All samples were stored frozen at -80℃ from collection until processing for RNA and DNA extraction. DNA /Total RNA of the human liver tissue samples were extracted by using the RNA/DNA Mini Kit (Qiagen, Hilden, Germany).each RNA sample were labeled and hybridized to the One-Color Agilent 60-mer Whole Human Genome Microarray (G4112F, GPL4133) at the Agilent Microarray Facility of Shanghai genomePilot Technology, Inc. The genome-wide scan was performed using the Affymetrix Genome-Wide Human SNP Array 6.0. We tested all expression traits for their associations with each of the QC passed SNPs using PLINK's assoc function for quantitative traits, which correlates allele dosage with changes in the trait.

first: Xiaoliang

last: Wang

first: Huamei

last: Tang

first: Mujian

last: Teng

first: Jianguo

first: Junwei

last: Fan

first: Lin

last: Zhong

first: Xing

last: Sun

first: Junming

last: Xu

first: Guoqing

last: Chen

first: Dawei

first: Zhaowen

first: Tonghai

last: Xing

first: Jinyan

last: Zhang

first: Li

last: Huang

first: Shuyun

first: Xiao

last: Peng

first: Shengying

last: Qin

first: Yongyong

last: Shi

first: Zhihai


title: IL-2Rβ- and CD103-dependent genes in regulatory T cells in the gut mucosa

status: Public on Jan 06 2015

city: Miami

first: Thomas

last: Malek

state: FL

address: 1600 NW 10th Avenue

department: Microbiology/Immunology

institute: University of Miami

summary: This study determined the genes that are differentially expressed when regulatory T cells (Tregs) were isolated from the lamina propria of the small and large intestine from mice with impaired IL-2Rβ signaling (designated Y3) or impaired IL-2Rβ signaling and lack of CD103 expression (designated Y3/CD103-/-) when compared to Tregs from WT mice. 204 unique annotated mRNAs were differentially expressed by ≥1.5 fold between these 3 groups (Fig. 6B). Very few mRNAs were uniquely up or down regulated in relationship to impaired IL-2Rβ signaling or the combination of impaired IL-2Rβ signaling and lack of CD103 expression. Thus, lack of CD103 does not obviously regulated signaling in Tregs in the gut mucosa and most differentially expressed genes were due to impaired IL_2Rβ signaling. Gene enrichment analysis of these differentially expressed genes identified 4 major enrichment groups (EG) are: EG1, Cytokine-cytokine receptor interaction and the JAK-STAT signaling pathway; EG2, regulation of lymphocyte activation and proliferation; EG3, regulation of cell death and the caspase pathway in apoptosis; and EG4, transcription.

overall_design: Mouse regulatory T cells (Tregs) cells were FACS purified based on expression of red fluorescent protein linked to the Foxp3 gene. These cells were obtained from the lamina propria of the small and large intestine from WT, Y3, and Y3/CD103-/- mice. Total RNA was prepared and processed to probe Affymetrix mouse Gene ST2.0 arrays.


title: Expression data from AMPK deficient MLL-AF9 leukemia initiating cells and whole leukemia cells

status: Public on Jan 01 2015

city: Houston

first: Yusuke

last: Saito

state: TX

address: One Baylor Olaza

institute: Baylor college of medicine

summary: Deletion of AMPK significantly extended the onset of leukemogenesis and depleted leukemia initiating cells (LICs). To identify how AMPK regulates LICs, we performed gene expression profiling of LICs isolated from AMPK wild type leukemic mice or AMPK-deficient leukemic mice.

overall_design: 4 groups were analyzed; 1) Whole leukemia (GFP+) from AMPK WT ( AMPKfl/fl) mice, 2) Whole leukemia  (GFP+) from AMPK-deficient ( AMPKΔ/Δl) mice, 3) LICs=L-GMP  (GFP+,lin-,c-kit+, CD16/32+,CD34+) cells from  AMPK WT ( AMPKfl/fl) mice, 4) LICs=L-GMP  (GFP+,lin-,c-kit+, CD16/32+,CD34+) cells from AMPK-deficient ( AMPKΔ/Δl)  mice.

first: Y

first: D

last: Nakada


title: NOTCH and WNT pathways regulate stemness and differentiation in human fallopian tube long term organoid culture

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: We report the establishment of a stable 3D in vitro organoid culture procedure from human fallopian tube samples and confirming experimentally the existence of adult stem cells in this epithelial tissue. Long term growth and the differentiation of the organoids depend on the interplay between the paracrine signaling pathways Wnt, NOTCH and BMP, since R spondin 1 and Wnt3a are required for preservation of stemness in concert with continuous suppression of TGF-beta activity. Microarray analysis revealed that inhibition of NOTCH signaling by the gamma-secretase inhibitor DBZ leads to down-regulation of a gene cluster associated with pluripotency, as the adult stem cell signature is significantly enriched in the list of downregulated targets.

overall_design: Microarray experiments were performed as dual-color hybridizations on Agilent human whole genome catalog 44K arrays. To compensate for dye-specific effects, a dye-reversal color-swap was applied.

first: Mirjana

last: Kessler

last: Meyer


title: IFNγ signaling endows DCs with the capacity to control type I inflammation during parasitic infection through promoting T-bet+ regulatory T cells

city: La Jolla

first: Li-Fan

last: Lu

state: CA

address: 9500 Gilman Dr., NSB 5314

department: Biological Sciences

institute: University of California, San Diego

summary:
Transcriptome analysis of IFNγ-insensitive DCs
IFNγ signaling drives dendritic cells (DCs) to promote type I T cell (Th1) immunity. Here, we show that activation of DCs by IFNγ is equally crucial for the differentiation of a population of T-bet+ regulatory T (Treg) cells specialized to inhibit Th1 immune responses. Conditional deletion of IFNγ receptor in DCs but not in Treg cells resulted in a severe defect in this specific Treg cell subset, leading to exacerbated immune pathology during parasitic infections. Mechanistically, IFNγ-unresponsive DCs failed to produce sufficient amount of IL-27, a cytokine required for optimal T-bet induction in Treg cells. Thus, IFNγ signalling endows DCs with the ability to efficiently control a specific type of T cell immunity through promoting a corresponding Treg cell population.

overall_design: We analyzed 3 WT DC samples and 3 IFNγR2 KO DC samples isolated from unmanipulated mice. In addition, we analyzed 3 WT DC samples and 3 IFNγR2 KO DC samples isolated from mixed BM chimeras (WT + IFNgR2KO) day 8 T. gondii infected.

first: Hyang-Mi

last: Lee

first: Aly

last: Khan

first: Sunglim

last: Cho

first: Ling-Li

last: Lin

first: Duc

last: Nguyen


title: Transcriptomic analyses of duodenum from wild type and VDR-null mice

status: Public on Apr 16 2015

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

institute: IGBMC

summary: As duodenum is an important Vitamin D target organ, transcriptomic analyses were performed in this tissue.

overall_design: We analysed RNA extracted from duodenum of three 10 week-old wild-type and VDR-null mice using the Affymetrix Mouse Gene 2.0 ST.

first: Tiphaine

last: Huet

first: Gilles

last: Laverny

first: Fabrice

last: Ciesielski

first: Thanuja

middle: G

last: Ramamoorthy

first: Ferdinand

last: Molnár

first: Anna

middle: Y

last: Belorusova

first: Pierre

last: Antony

first: Noelle

last: Potier

first: Daniel

last: Metzger

first: Dino

last: Moras

first: Natacha

last: Rochel


title: Development of mRNA and miRNA expression signatures of MEFs deficient in ER stress mediators for tunicamycin treatment

first: Seiichi

last: Oyadomari

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

overall_design: Refer to individual Series


title: Astrocyte transcriptome from Mecp2-deficient mice

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

institute: Université Paris-Saclay

summary: Mutations in the gene encoding the transcriptional modulator methyl-CpG binding protein 2 (MeCP2) are responsible for the neurodevelopmental disorder Rett syndrome that is one of the most frequent sources of intellectual disability in women. It has been shown that mutant astrocytes contribute to neuronal defects, probably as a result of aberrant secretion of soluble factor(s). Based on the hypothesis that this irregular secretion of soluble factor is the result of abnormal transcription of those factors, we have compared the gene expression profiles of wild type and mutant astrocytes from Mecp2 308/y mice by using Affymetrix mouse 2.0 microarrays.

overall_design: P0 newborns from pregnant Mecp2 308/+ heterozygous mice were used for the preparation of dissociated cortical astrocyte cultures. Four wild-type and four mutant confluent astrocytes cultures were used for total RNA extraction with the Qiagen RNeasy kit (Qiagen, Courtaboeuf, France) as described by the manufacturer. The gene expression profiles of wild type and mutant astrocytes from Mecp2 308/y mice have been assayed by using Affymetrix mouse 2.0 microarrays.

first: Chloe

last: Delepine

first: Thierry

last: Bienvenu


title: Tobacco-induced mRNAs profile alterations in human spermatozoa: a preliminary study for further knowledge of toxical spermatogenesis impairment

city: MARSEILLE CEDEX 09

first: Aurelie

last: Bergon

address: parc scientifique de Luminy, case 928

institute: TAGC INSERM U1090

summary:
Tobacco smoking generates deleterious effects on human semen quality but mechanisms by which cigarettes smoking can impact spermatogenesis are poorly understood. Recent works have shown that spermatozoa RNAs can be used to understand mechanisms involved in tobacco induced spermatogenesis impairment. We performed a prospective study of 8 smoker and 8 non-smoker patients in an university hospital. All patients were selected according to an occupational exposure standardized questionnaire and the sperm parameters. We performed gene expression and miRNA microarrays using RNA extracts from spermatozoa of 8 smokers and 8 non-smokers. Quantification of selected miRNA was performed using quantitative RT-PCR.
We show that 16 genes were differentially expressed between smokers and non-smokers, of which 5 were upregulated and 11 were down regulated in smokers. 23 microRNAs were differentially expressed, of which 16 were upregulated and 7 were down regulated in smokers. Quantitative RT-PCR confirmed the down regulation in smokers for 3 microRNAs. Moreover in smokers, one of the upregulated genes is a putative target for one down regulated microRNA.

This is a preliminary and innovating study on spermatozoa RNA extracts in the field of infertility. This preliminary study shows that large scale approaches are non invasive diagnostic tools that may help elucidate the mechanisms that mediate the response to tobacco smoke exposure on human spermatogenesis. This could be used to design biomarkers of human spermatogenetic damage, and help elucidate the fine regulatory mechanisms that mediate responses to environmental agent exposure during human spermatogenesis.

overall_design: Total RNAs were extracted from spermatozoa of 11 patients including: 5 non-smokers and 6 smokers

first: Catherine

last: Metzler-Guillemain

first: Cyrille

last: Lepoivre

first: Geneviève

last: Victorero

first: Aurélie

first: Jeanne

last: Perrin

first: Irène

last: Sari-Minodier

first: Nicolas

last: Boulanger

first: Pascal

last: Rihet

last: Nguyen


title: miR-302-367 regulates cardiomycyte proliferation and differentiation during development

city: Philadelphia

first: Michael

last: Morley

address: 3400 Civic Center Blvd, Bldg 421

institute: Perelman School of Medicine at the University of Pennsylvania

summary: To define the role of miR-302-367 cluster in cardiac development, we overexpressed miR-302-367 cluster in mouse heart by using R26R-miR-302-367; Nkx2.5-Cre mice. This data set contains the microarrays examining gene expression in the hearts of R26R-miR-302-367; Nkx2.5-Cre mice at postnatal day 14.

overall_design: We overexpressed miR-302-367 cluster in developing mouse heart using Nkx2.5-Cre mouse line

first: Ying

last: Tian

first: Edward

last: Morrisey


title: Transciptome of ex vivo-isolated Foxp3+/-RORγt+/- CD4+ T cell populations

status: Public on Dec 31 2014

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary: Foxp3-expressing regulatory (Treg) T cells are essential for immunological tolerance, where loss of this transcription factor leads to uncontrolled T cell responses and their associated clinical presentation of systemic autoimmunity in mice and humans. Importantly, Foxp3+ Tregs result from different origins and are either generated in the thymus (tTreg) or from conventional CD4+ T cells in the periphery (pTreg). In addition, Treg cells may adopt specific effector Treg phenotypes, reflecting the diversity of functional demands in the different tissues of the body. Here, we report that Foxp3+ T cells expressing the Th17 master transcription factor, RORγt, represent a stable effector Treg lineage that is specifically enriched in intestinal organs and gut-associated lymphoid tissues in mice possessing a complex microbial microflora. Simultaneous expression of Foxp3 and RORγt promotes the transcription of both Treg- and Th17-associated genes in Foxp3+RORγt+ T cells; however, epigenetic profiling of the Treg-specific demethylated region (TSDR) and other Treg-associated genes revealed a high degree of similarity between conventional Tregs and Foxp3+RORγt+ T cells, indicating that these cells have a stable regulatory, rather than inflammatory, function. Indeed, adoptive transfer of Foxp3+RORγt+ T cells in the context of T cell transfer colitis not only confirmed their Treg function and lineage stability in vivo, it also revealed a significantly enhanced regulatory capacity as compared to RORγt+ Treg cells. Thus, our data suggest that RORγt expression in Tregs is essential for optimal regulation of gut-specific immune responses, which renders them an important effector Treg lineage in the intestinal system.

overall_design: To study the global relationship in their gene expression profiles, we sorted Foxp3-RORγt- CD4+ T cells, Foxp3+(RORγt-) Treg cells, RORγt+(Foxp3-)  and Foxp3+RORγt+ T cells from splenocytes, peripheral LN and mesenteric LN cells pooled together in order to avoid bias due to a specific tissue location.

first: Stefanie

last: Hagemann

first: Bi-Huei

last: Yang


title: Gene expresson profiles of hPER1S714G and hPER1S714 in liver and white adipose at ZT1 and ZT13

city: Guangzhou

first: Lehang

last: Lin

address: 107, West Yanjiang Road

institute: Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University

summary: To discover the influence of S714G mutation in PER1, we used whole genomic array to analyze the changes in liver and white adipose.

overall_design: Both hPER1S714G and hPER1S714 control mice were entrained to LD cycles for 10 days, liver and white adipose samples were taken at ZT1 and ZT13. Three independent repeats were performed for each sample at each time point.

first: Zhiwei

last: Liu

first: Moli

last: Huang


title: High-throughput identification of adaptive mutations in experimentally evolved yeast populations

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

summary:
High-throughput sequencing has enabled genetic screens that can rapidly identify mutations that occur during experimental evolution. The presence of a mutation in an evolved lineage does not, however, constitute proof that the mutation is adaptive, given the well-known and widespread phenomenon of genetic hitchhiking, in which a non-adaptive or even detrimental mutation can co-occur in a genome with a beneficial mutation and the combined genotype is carried to high frequency by selection. We approximated the spectrum of possible beneficial mutations in Saccharomyces cerevisiae using sets of single-gene deletions and amplifications of almost all the genes in the S. cerevisiae genome. We determined the fitness effects of each mutation in three different nutrient-limited conditions using pooled competitions followed by barcode sequencing. Although most of the mutations were neutral or deleterious, ~500 of them increased fitness. We then compared those results to the mutations that actually occurred during experimental evolution in the same three nutrient-limited conditions. On average, ~35% of the mutations that occurred during experimental evolution were predicted by the systematic screen to be beneficial. We found that the distribution of fitness effects depended on the selective conditions. In the phosphate-limited and glucose-limited conditions, a large number of beneficial mutations of nearly equivalent, small effects drove the fitness increases. In the sulfate-limited condition, one type of mutation, the amplification of the high-affinity sulfate transporter, dominated. In the absence of that mutation, evolution in the sulfate-limited condition involved mutations in other genes that were not observed previously—but were predicted by the systematic screen. Thus, gross functional screens have the potential to predict and identify adaptive mutations that occur during experimental evolution.

Previously version available on bioRXiv.

overall_design: Each array is a comparative genomic hybridization of a test sample DNA versus wt genomic DNA. Two of the experiments compare the DNA content of an experimentally evolved population against the ancestral DNA. The remaining 6 arrays are CGH of population samples from pooled library competition studies versus a wt strain. Data were normalized according to the default Agilent settings.

first: Celia

last: Payen


title: Sex-specific transcriptional differences between non-treated male and female human umbilical vein endothelial cells (HUVEC)

first: Mario

last: Lorenz

address: Hessische Strasse 3-4

institute: Charité-Universtitätsmedizin Berlin

summary: Significant sex differences exist in cardiovascular diseases. It is largely unknown whether sexually dimorphic gene expression plays a role, and whether cells themselves show intrinsic sex differences. We therefore performed whole genome expression analyses in human umbilical vein endothelial cells (HUVEC) from five sample pools with equal amounts of four individual RNAs from either male or female donors (altogether 20 male and 20 female donors) and compared levels of gene transcription between the sexes. Genes indicative for greater immune responsiveness were stronger expressed in female compared to male HUVEC. There was a significant enrichment of 77 immune-related genes in female HUVEC.

overall_design: RNA derived from HUVEC of 20 male and 20 female donors were used. Five sample pools with equal amounts of four individual RNAs from either male or female HUVEC were generated.


title: Gene expression and functional annotation of choroid plexus epithelium failure in Alzheimer disease

first: Sarah

last: Janssen

address: Meibergdreef 47

department: Ophthalmogenetics

institute: Netherlands Institute for Neuroscience

summary: We investigated the gene expression of the human CPE in Braak stadia 0, 3 and 6.We isolated CPE cells with laser dissection microscopy from healthy human donor choroid plexus tissues and from human choroid plexus tissue from brains that were post-mortem staged in Braak 3 and Braak 6 Alzheimer disease stages . Next, we performed RNA isolation, amplification, labeling and hybridization against 44k Agilent microarrays.

overall_design: We performed the microarrays against a common reference sample, namely human RPE/choroid RNA. We performed 7 replicates of human CPE-Braak-0 (healthy) samples from 7 different donors, 7 replicates of human CPE-Braak-3 from 7 different donors and 7 replicates of human CPE-Braak-6 from 7 different donors.

middle: F

first: Arthur

last: Bergen


title: Tobacco-induced microRNAs and mRNAs profile alterations in human spermatozoa: a preliminary study for further knowledge of toxical spermatogenesis impairment

first: Aurelie

last: Bergon

first: Catherine

last: Metzler-Guillemain

first: Cyrille

last: Lepoivre

first: Geneviève

last: Victorero

first: Aurélie

first: Jeanne

last: Perrin

first: Irène

last: Sari-Minodier

last: Boulanger


title: Gene knockdown suggests a new paradigm for transcription factor TFIIB functionality

city: Quebec

first: Dimcho

last: Bachvarov

state: Quebec

address: 9, rue McMahon

institute: CHU-Q, Centre de recherche-HDQ

summary: Experimental and bioinformatic studies of transcription initiation by RNA polymerase II (RNAP2) have revealed a mechanism of RNAP2 transcription initiation less uniform across gene promoters than initially thought. However, the general transcription factor TFIIB is presumed to be universally required for RNAP2 transcription initiation. Based on bioinformatic analysis of data, TFIIB knockdown in primary and transformed cell lines, and in vitro transcription experiments, we report that TFIIB is dispensable for transcription of most human promoters, but is essential for HSV-1 gene transcription and replication. We report a novel cell cycle TFIIB regulation and involvement of the acetylated TFIIB variant in chromosomal condensation.  Taken together, these results establish a new paradigm for TFIIB functionality as a determinant of the human transcriptome, which when downregulated has potent anti-viral effects.

overall_design: HeLa cells are electroporated with TFIIB specific siRNA and control siRNA to identify if all human genes require TFIIB for transcription. Sixty hours post electroporation with siRNA, when the cellular TFIIB protein content was nearly undetectable by anti- human TFIIB in western blotting and immunofluorescence cells were harvested and total RNA was isolated. The gene expression profile of cells that received TFIIBsiRNA was compared to the gene expression profile of cells that received control siRNA by applying  Agilent Whole Human Genome Oligo Microarray. Some data were confirmed by RT-PCR. RNAs for which the array data and the RT-PCR data differ have been excluded.   The microarray experiments were performed in duplicates, as two hybridizations were carried out for the TFIIB -suppressing cell clone against the corresponding control, using a fluorescent dye reversal (dye-swap) technique.


title: Global gene expression in Head and neck squamous carcinoma (KB) cells treated with the combination of 2-DG + 6-AN followed by irradiation (2-Gy)

city: New Delhi

first: Pradeep

last: Sharma

email: praddybiotech@gmail.com, ravipathak@aol.in, raghuram98@hotmail.com, rvarshney@rediffmail.com, dwarakanathdrbs@gmail.com

state: Delhi

address: Lucknow Road, Timarpur

department: Division of radiation biosciences

institute: Institute of Nuclear medicine and allied sciences (INMAS, DRDO)

summary: Whole genome expression profiling of head and neck squamous carcinoma (KB) cells comparing control untreated cells as well as irradited (2 Gy) alone cells with carcinoma cells treated with the combination of 2-DG and 6-AN followed by irradiation (2 Gy). Goal of this study was to study the global gene expression involved in radiosensitization of Head and neck squamous carcinoma (KB cells) treated with the combination of two metabolic modifers namely 2-deoxy-D-Glucose (2-DG) and 6-Aminonicotinamide (6-AN) followed by irradiation (2 Gy). This will enable us to understand the role of metabolic oxidative stress (MOS) involved in the radiosensitization of cancer cells and regulation between complex molecular circuits to develop better therapeutic approaches/ protection against oxidative damage.

overall_design: Agilent two-color experiment, Organism: Human, Agilent-14850 Agilent Whole Genome Human 4x44k (AMADID No: 14850), Labeling kit: Agilent Low RNA Input Linear amplification Kit (Part number:5184-3523)

middle: K

first: Richa

last: bhardwaj

first: Ravi

last: Pathak

first: Bilikere

middle: S

last: Dwarakanath

first: Nandula

last: Raghuram

first: Rajeev

last: Varshney


title: Sex-specific transcriptional differences between male and female human umbilical vein endothelial cells (HUVEC) after shear stress.

first: Mario

last: Lorenz

summary: To assess whether there is a sex-specific response to stress, we subjected male and female HUVEC to laminar shear of 6 dyn/cm2 for 24 hours and analysed changes in gene expression. 6.7 % of all mRNAs were regulated by shear stress. Female HUVEC showed a more pronounced transcriptional response to shear than did their male counterparts. In addition to quantitative differences, a number of genes were regulated in the opposite direction between the two sexes by shear stress.

overall_design: HUVEC from 12 male and female donors were isolated and cultured. HUVEC from four individual male or female donors at passage 2 were grown to confluence, trypsinized and cell numbers were counted. Equal numbers of cells were mixed, seeded, and cultured to confluence. Three male and female cell pools were generated in this way. Laminar shear stress of 6 dyn/cm2 was applied for 24 hours to fully confluent cell monolayers (passage 3) using a cone-and-plate system. Cells cultured under static conditions served as controls.


title: Color-flu: multi-spectral fluorescent reporter influenza viruses as powerful tools for in vivo studies

status: Public on Dec 24 2014

city: Minato

first: Yoshihiro

last: Kawaoka

state: Tokyo

address: Shirokanedai 4-6-1

department: ERATO Influenza-induced Host Responses Project

institute: Japanese Science and Technology Agency

summary: We sorted macrophages (known to be infected by influenza viruses from the lungs of mice infected with MA-Venus-PR8 on the basis of their fluorescent protein expression and performed microarray analysis. Macrophages isolated from the lungs of mice inoculated with PBS (naive macrophages) served as controls.

overall_design: 15 samples

first: Jason

last: Shoemaker

first: Satoshi

last: Fukuyama

first: Dongming

last: Zhao


title: Alterations in hepatic gene expression induced by chronic exposure to low levels of the SV40 LT/st oncoproteins (4C)

status: Public on Dec 22 2014

city: New York

first: Nikolaus

last: Schultz

address: 1275 York Ave, Box 460

department: Computational Biology Center

institute: Memorial Sloan-Kettering Cancer Center

summary: Hepatic gene expression induced by chromic exposure to low levels of the SV40 LT/st oncoproteins (4P)

overall_design: Affymetrix mouse genome U74Av2 platform was used, duplicate measurements for wild-type and transgenic animals

first: Sarah

last: Comerford

first: Sharon

middle: L

last: Milgram

first: Robert

last: Hammer