title: NF-κB activation impairs somatic cell reprogramming in ageing [NGPS_iPSCs]

status: Public on Jul 01 2015

city: Oviedo

first: Jose

last: Freije

state: Asturias

address: C/ Fernando Bongera s/n

department: Bioquimica y Biologia Molecular

institute: Universidad de Oviedo

summary:
Transcriptional profiling of human control and Néstor-Guillermo Progeria Syndrome (NGPS) fibroblasts and induced pluripotent stem cells (iPSCs).

Somatic cell reprogramming involves rejuvenation of adult cells and relies on the ability to erase age-associated molecular marks. Accordingly, reprogramming efficiency declines with ageing, and age-associated features such as genetic instability, cell senescence or telomere shortening negatively affect this process. However, the regulatory mechanisms that constitute age-associated barriers for cell reprogramming remain largely unknown. Here, by using cells from patients with premature ageing, we demonstrate that NF-κB activation is a critical barrier for the generation of induced pluripotent stem cells (iPSCs) in ageing. We show that NF-κB repression occurs during cell reprogramming towards a pluripotent state. Conversely, ageing-associated NF-κB hyperactivation impairs generation of iPSCs by eliciting reprogramming repressors DOT1L and YY1, reinforcing cell senescence signals and down-regulating pluripotency genes. We also show that genetic and pharmacological NF-κB inhibitory strategies significantly increase the reprogramming efficiency of fibroblasts from Néstor-Guillermo Progeria Syndrome (NGPS) and Hutchinson-Gilford Progeria Syndrome (HGPS) patients, as well as from normal aged donors. Finally, we demonstrate that DOT1L inhibition in vivo ameliorates the accelerated ageing phenotype and extends lifespan in a progeroid animal model. Collectively, our results provide evidence for a novel role of NF-κB in the control of cell fate transitions and reinforce the interest of studying age-associated molecular impairments to implement cell reprogramming methodologies, and to identify new targets of rejuvenation strategies.

overall_design: Control and NGPS fibroblasts were reprogrammed. RNA was extracted and transcriptional profiling was obtained with GeneChip Human Exon 1.0 ST Arrays.

first: Fernando

middle: G

last: Osorio

first: Clara

last: Soria-Valles

middle: M

first: Carlos

last: Lopez-Otin


title: NF-κB activation impairs somatic cell reprogramming in ageing

country: Spain

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

overall_design: Refer to individual Series


title: The MEF2B Regulatory Network - Expression microarray data

city: Vancouver

first: Patrick

last: Plettner

state: BC

address: 100-570 West 7th Avenue

country: Canada

institute: BC Cancer Agency GSC

summary: Myocyte enhancer factor 2B (MEF2B) is a transcription factor with somatic mutation hotspots at K4, Y69 and D83 in diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL). The recurrence of these mutations indicates that they may drive lymphoma development. However, inferring the mechanisms by which they may drive lymphoma development was complicated by our limited understanding of MEF2B’s normal functions. To expand our understanding of the cellular activities of wildtype (WT) and mutant MEF2B, I developed and addressed two hypotheses: (1) identifying genes regulated by WT MEF2B will allow identification of cellular phenotypes affected by MEF2B activity and (2) contrasting the DNA binding sites, effects on gene expression and effects on cellular phenotypes of mutant and WT MEF2B will help refine hypotheses about how MEF2B mutations may contribute to lymphoma development. To address these hypotheses, I first identified genome-wide WT MEF2B binding sites and transcriptome-wide gene expression changes mediated by WT MEF2B. Using these data I identified and validated novel MEF2B target genes.  I found that target genes of MEF2B included the cancer genes MYC, TGFB1, CARD11, NDRG1, RHOB, BCL2 and JUN.  Identification of target genes led to findings that WT MEF2B promotes expression of mesenchymal markers, promotes HEK293A cell migration, and inhibits DLBCL cell chemotaxis. I then investigated how K4E, Y69H and D83V mutations change MEF2B’s activity. I found that K4E, Y69H and D83V mutations decreased MEF2B DNA binding and decreased MEF2B’s capacity to promote gene expression in both HEK293A and DLBCL cells. These mutations also reduced MEF2B’s capacity to alter HEK293A and DLBCL cell movement. From these data, I hypothesize that MEF2B mutations may promote DLBCL and FL development by reducing expression of MEF2B target genes that would otherwise function to help confine germinal centre B-cells to germinal centres. Overall, my research demonstrates how observations from genome-scale data can be used to identify cellular effects of candidate driver mutations. Moreover, my work provides a unique resource for exploring the role of MEF2B in cell biology: I map for the first time the MEF2B ‘regulome’, demonstrating connections between a relatively understudied transcription factor and genes significant to oncogenesis.

overall_design: We analysed Affymetrix Human Exon 1.0 ST array data from HEK293A cells stably transfected with WT or mutant (K4E, Y69H or D83V) MEF2B-V5 and untransfected control cells. Data was collected in triplicate from all cell types under DMSO treatment, as well as from triplicates of WT and untransfected cells that were ionomycin treated (1.5uM for 6hr).

first: Julia

last: Pon

first: Marco

middle: A

last: Marra


title: Mouse bone marrow cells transfected with mmu-miR-142-3p mimic oligo.

status: Public on Jul 23 2015

city: Padova

first: Stefania

last: Bortoluzzi

address: via G. Colombo 3

department: Department of Molecular Medicine

country: Italy

institute: University of Padova

summary:
Tumor progression is accompanied by an altered myelopoiesis that causes the accumulation of cells inhibiting anti-tumor T lymphocytes. We previously reported that immunosuppressive cells can be generated in vitro from bone marrow cells (BM) after four days GM-CSF and IL-6 treatment. Here, we describe that miR-142-3p down-regulation directs macrophage differentiation and determines the acquisition of their immunosuppressive function in cancer. Enforced miR over-expression impaired monocyte to macrophage transition both in vitro and in vivo. Conversely, forced miR down-regulation promoted the generation of immunosuppressive macrophages even during G-CSF-induced granulocytic differentiation. To identify how miR-142-3p regulates MDSC generation and activity, we analyze the gene expression of BM cultures transfected  with either CTRL- or miR 142-3p mimic oligo -transfected before  four days GM-CSF and IL-6 treatment.

Keywords: Expression profiling by array

overall_design: BM cells were transfected either CTRL- or miR 142-3p mimic oligo before GM-CSF and IL-6 treatment to generate in vitro MDSCs during enforced miR over-expression. A triplicate of each sample was considered.Total RNA from obtained in vitro BM-differentiated MDSCs was isolated by Trizol reagent, and cRNA samples were hybridized to the Affymetrix GeneChip MOE430 2.0.

first: Vincenzo

last: Bronte

first: Nada

last: Sonda

first: Francesca

last: Simonato

first: Elisa

last: Peranzoni

first: Bianca

last: Calì

first: Ena

last: Wang

first: Luigi

last: Naldini

first: Bernhard

last: Gentner

first: Christian

last: Trautwein

first: Barbara

last: Molon

first: Andrea

last: Bisognin


title: MicroRNA analysis on epithelial D492 cells and its mesenchymal derivative D492M cells

status: Public on Jul 02 2015

city: Lund

first: Markus

last: Ringner

address: Sölvegatan 35

country: Sweden

institute: Lund University

summary: miRNA analysis of breast epithelial cell line with stem cell properties before and after undergoing endothelial induced epithelial to mesenchymal transition (EMT).

overall_design: miRNA expression anlysis was done on breast epithelial cells before and after endothelial induced EMT. D492 is a breast epithelial cell line with stem cell properties that undergoes EMT in 3D rBM coculture with endothelial cells. Total RNA was isolated from D492 and D492M (a mesenchymal derivative)  at 50% and 90% confluency in monolayer.

first: M


title: Transcriptional profiling of PRDM2 Knock down vs.controlGFPsh Quiescent C2C12 Myoblasts (G0 enriched)

status: Public on Jun 30 2015

city: Bad nauheim

first: Sirisha

last: Cheedipudi

state: Hessen

department: cardiac origin cell lines

country: Germany

institute: Max-planck institue for heart and lung research

summary:
Knockdown of PRDM2 led to precocious differentiation. To understand the molecular basis for this phenotype, we performed microaary analysis of quiescent myoblasts.
Genes differentially regulated by PRDM2 knock down were reveraled by microarray analysis  using affymetrix mouse chips.

overall_design: Control and knock down cells were synchronized at G0 by suspension culture and total RNA was used to perform microarray analysis

first: Deepika

last: Puri

first: Amena

last: Saleh

first: Hardik

last: Gala

first: Mohammed

last: Rumman

first: Malini

middle: S

last: Pillai

first: Prethish

last: Sreenivas

first: Reety

last: Arora

first: Jeeva

last: Sellathurai

first: Henrik

middle: D

last: Schroeder

first: Rakesh

last: Mishra

first: Jyotsna

last: Dhawan


title: miR-7a is regulated in beta-cell dysfunction and couples early and late stages of pancreatic beta-cell differentiation to insulin secretion

city: Rehovot

first: Jean

last: Hausser

address: Herzl St.

country: Israel

institute: Weizmann Institute of Science

summary: Transcriptional and posttranscriptional regulatory networks play a crucial role in the maintenance and adaptation of pancreatic beta-cell function. In this study we show that the levels of the prototypic neuroendocrine miRNA-7 are regulated in islets of obese, diabetic and aged mouse models. Using gain- and loss-of-function models we demonstrate that miR-7 regulates crucial members of the endocrine pancreatic transcriptional network controlling differentiation and insulin synthesis. Importantly, it also directly regulates key proteins in the insulin granule secretory machinery. These results reveal an interconnecting miR-7 genomic circuit that influences beta-cell differentiation, insulin synthesis and release and define a role for miR-7 as an endocrine checkpoint to stabilize beta-cell function during metabolic stress. These findings have implications for miR-7 inhibitors as potential therapies for type 2 diabetes and neurodegenerative diseases.

overall_design: Either miR-7a2 or miR-7b were over-expressed in MIN6 cells using an adenoviral vector. The miR-7a infection was performed in duplicates. In addition, a GFP over-expression in MIN6 using the same viral vector served as control. We also explored the consequence of miR-7a2 deletion in pancreatic beta-cells by generating a beta-cells specific miR-7a2 knock-out using the Lox/Cre system in a C57BL/6 background. We profiled gene expression in mutant and wild-type (control) islets.

first: Mathieu

last: Latreille

first: Ina

last: Stuetzer

first: Quan

last: Zhan

first: Benoit

last: Hastoy

first: Mihaela

last: Zavolan

first: Thomas

last: Ruelicke

first: Patrik

last: Rorsman

last: Stoffel


title: Expression data from E12.5 and E14.5 mouse embryonic gonad of wild type (WT) and Wnt-4 knock-out (KO) mice.

city: Oulu

first: Florence

last: Naillat

address: Aapistie 5A

country: Finland

institute: Oulu University


title: Gene expression profiling of PRDM2 Knockdown in proliferating, quiescent and differentiating myoblasts

first: Sirisha

last: Cheedipudi


title: Gene expression of livers from Lpcat3fl/fl and Lpcat3fl/fl Albumin-Cre mice on chow diet

status: Public on Jun 26 2015

city: los angeles

first: Xin

last: Rong

state: California

address: 675 Charles E Young Dr. South

department: Pathology and Laboratory Medicine

country: USA

institute: UCLA

summary:
The total abundance of phosphatidylcholine (PC) is known to influence lipoprotein production.  However, the role of specific phospholipid species in lipid transport has been difficult to assess due to an inability to selectively manipulate membrane composition in vivo.  Here we show that the LXR-regulated phospholipid remodeling enzyme lysophosphatidylcholine acyltransferase 3 (Lpcat3) is a critical determinant of membrane phospholipid composition and lipoprotein production.  Mice lacking Lpcat3 in the liver show defects in lipoprotein production.
The objective of generating this dataset was to analyze the effects of Lpcat3 loss of function on baseline gene expression in mouse liver.

overall_design: This dataset compares gene expression in Lpcat3fl/fl and Lpcat3fl/fl Albumin-Cre liver samples from 12-week old male mice that were subjected to 6 hr fasting. Each sample contains tissues from 5 mice.

first: Bo

last: Wang

first: Merlow

last: Dunham

first: Per

last: Hedde

first: Enrico

last: Gratton

first: Stephen

last: Young

first: David

last: Ford

first: Peter

last: Tontonoz


title: Dusp9 expression and function in dendritic cells

city: Erlangen

first: Roland

last: Lang

address: Wasserturmstr. 3-5

institute: University Hospital Erlangen

summary: Plasmacytoid dendritic cells (pDC) efficiently produce large amounts of type I interferon in response to TLR7 and TLR9 ligands, whereas conventional DCs (cDC) predominantly secrete high levels of the cytokines IL-10 and IL-12. The molecular basis underlying this distinct phenotype is not well understood. Here, we identified the MAPK phosphatase Dusp9/MKP-4 by transcriptome analysis as selectively expressed in pDC, but not cDC. We confirmed the constitutive expression of Dusp9 at the protein level in pDC generated in vitro by culture with Flt3L and ex vivo in sorted splenic pDC. Dusp9 expression was low in B220- bone marrow precursors and was up-regulated during pDC differentiation, concomitant with established pDC markers. Higher expression of Dusp9 in pDC correlated with impaired phosphorylation of the MAPK ERK1/2 upon TLR9 stimulation. Notably, Dusp9 was not expressed at detectable levels in human pDC, although these displayed similarly impaired activation of ERK1/2 MAPK compared to cDC. Enforced retroviral expression of Dusp9 in mouse GM-CSF-induced cDC increased the expression of TLR7/9-induced IL-12p40 and IFNwhereas IL-10 levels were diminished. Taken together, our results suggest that the species-specific, selective expression of Dusp9 in murine pDC contributes to the differential cytokine/interferon output of pDC and cDC.

overall_design: pDC and cDC subsets were purified from mouse spleens to high purity and analysed by Affymetrix GeneChips.

first: Tim

last: Sparwasser


title: Gene expression of livers from Lpcat3fl/fl and Lpcat3fl/fl Albumin-Cre mice on a western diet

summary:
The total abundance of phosphatidylcholine (PC) is known to influence lipoprotein production.  However, the role of specific phospholipid species in lipid transport has been difficult to assess due to an inability to selectively manipulate membrane composition in vivo.  Here we show that the LXR-regulated phospholipid remodeling enzyme lysophosphatidylcholine acyltransferase 3 (Lpcat3) is a critical determinant of membrane phospholipid composition and lipoprotein production.  Mice lacking Lpcat3 in the liver show defects in lipoprotein production.
The objective of generating this dataset was to analyze the effects of Lpcat3 loss of function on gene expression in mouse liver with a western diet challenge.

overall_design: This dataset compares gene expression in Lpcat3fl/fl and Lpcat3fl/fl Albumin-Cre liver samples from 16-week old male mice that were fed a western diet for 9 weeks since 7 weeks old. Each sample contains tissues from 5 mice.


title: Transcriptional profiling of PRDM2 Knock down vs.controlGFPsh differentiated C2C12 Myoblasts (D28hrs)

summary:
Knockdown of PRDM2 led to precocious differentiation. To understand the molecular basis for this phenotype, we performed microaary analysis of 28hr differentiated myoblasts.
Genes differentially regulated by PRDM2 knock down were reveraled by microarray analysis  using affymetrix mouse chips.

overall_design: Control and knock down cells were grown in differentiating conditions for 28hrs and total RNA was used to perform microarray analysis

first: Deepika

last: Puri

first: Amena

last: Saleh

first: Hardik

last: Gala

first: Mohammed

last: Rumman

first: Malini

last: Pillai

first: Prethish

last: Srinivas

first: Reety

last: Arora

first: Jeeva

last: Sellathurai

first: Henrik

last: Schroeder

first: Rakesh

last: Mishra

first: Jyotsna

last: Dhawan


title: Expression data from E12.5 and E14.5 mouse embryonic gonad of wild type (WT) and Wnt-4 knock-out (KO) mice. [Mouse430_2]

first: Florence

last: Naillat

summary:
Wnt-4 signaling is critical for embryonic female sexual development. When Wnt-4 gene is deleted during embryonic development, the knock-out females present a partial sex reversal.
We used microarrays to detail the global programme of gene expression underlying sexual development and identified distinct classes of up and down-regulated genes during this process.

overall_design: Mouse embryonic gonad from wild type and Wnt-4 knock-out mice (male and female) were selected at two stages of sex determination for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous populations of embryonic gonad at each developmental stage in order to increase the temporal resolution of expression profiles. To that end, we hand-selected embryos according to morphological criteria at two time-points: E 12.5 and E14.5.

first: Seppo

last: Vainio


title: MicroRNA and Gene expression profiling of the prostate biopsy samples from African American and European American prostate cancer patients

status: Public on Jul 27 2015

city: Washington

first: Bi-Dar

last: Wang

state: DC

address: 2300 I street, NW

department: Pharmacology and Physiology

institute: The George Washington University Medical Center

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


title: The impact of P53 loss on transcriptome changes following loss of Apc in the intestine

status: Public on Jun 25 2015

city: Cardiff

first: Karen

middle: Ruth

last: Reed

address: Maindy Road

country: United Kingdom

institute: ECSCRI, Cardiff University

summary:
BACKGROUND: p53 is an important tumor suppressor with a known role in the later stages of colorectal cancer, but its relevance to the early stages of neoplastic initiation remains somewhat unclear. Although p53-dependent regulation of Wnt signalling activity is known to occur, the importance of these regulatory mechanisms during the early stages of intestinal neoplasia has not been demonstrated.
METHODS: We have conditionally deleted the Adenomatous Polyposis coli gene (Apc) from the adult murine intestine in wild type and p53 deficient environments and subsequently compared the phenotype and transcriptome profiles in both genotypes.
RESULTS: Expression of p53 was shown to be elevated following the conditional deletion of Apc in the adult small intestine. Furthermore, p53 status was shown to impact on the transcription profile observed following Apc loss. A number of key Wnt pathway components and targets were altered in the p53 deficient environment. However, the aberrant phenotype observed following loss of Apc (rapid nuclear localisation of beta-catenin, increased levels of DNA damage, nuclear atypia, perturbed cell death, proliferation, differentiation and migration) was not significantly altered by the absence of p53.
CONCLUSION: p53 related feedback mechanisms regulating Wnt signalling activity are present in the intestine, and become activated following loss of Apc. However, the physiological Wnt pathway regulation by p53 appears to be overwhelmed by Apc loss and consequently the activity of these regulatory mechanisms is not sufficient to modulate the immediate phenotypes seen following Apc loss. Thus we are able to provide an explanation to the apparent contradiction that, despite having a Wnt regulatory capacity, p53 loss is not associated with early lesion development.

overall_design: Samples were collected from genetically modified mice. Gene recombination was induced using IP administration of beta-napthoflavone.

first: Owen

last: Sansom

first: Alan

last: Clarke


title: LIF signaling-dependent gene expression

status: Public on Jun 23 2015

city: Taipei

first: Chen-Yun

last: Chen

address: 128 Sec. 2, Academia Rd.

department: Institute of Biomedical Science

country: Taiwan

institute: Acdemia Sinica

summary:
Leukemia Inhibitory Factor (LIF) plays an essential role in the maintenance of pluripotency of mouse embryonic stem cells (mESCs). LIF withdrawal induces mESC differentiation.
To define noval pluripotent factors downstream of LIF signaling, cDNA microarray was used and seveal well-known pluripotent genes were found to respond to LIF withdrawal, including Klf4, Esrrb, Tbx3, and Prdm14.

overall_design: mESCs were cultured in presence or absence of LIF for two days and RNAs extracted from these cells were subjected to microarray analysis

first: Desy

last: Lee


title: The deafness gene DFNA5 induces programmed cell death through mitochondria and MAPK-related pathways [BY4741]

status: Public on Jun 24 2015

city: Edegem

first: Ken

last: Op de Beeck

address: Universiteitsplein 1

country: Belgium

institute: University Of Antwerp

summary: The function of DFNA5 remained unknown for a long time, but previous functional studies by Op de Beeck et al. (2011) revealed that DFNA5 induces a growth defect in mutDFNA5- transfected HEK293T cells, as well as other cells, leading to PCD (Op de Beeck et al., 2011). The cell death-inducing capacity of DFNA5 was not only restricted to human cell lines, but was also observed in the yeast model Saccharomyces cerevisiae (Van Rossom et al., 2012). This inspired us to perform a transcriptomic analysis using two different model organisms (mammalian, HEK293T, and yeast, S.cerevisiae) to further elucidate the mechanisms related to DFNA5.

overall_design: Comparison of 2 transfected yeast cell populations in 2 different growth phases. In total, 4 comparisons were made, each comparison was done in duplo by a colourflip. Every conditions is represented through 2 biol reps.

first: Sofie

last: Van Rossom

first: Vesna

last: Hristovska

first: Joris

last: Winderinckx

first: Guy

last: Van Camp


title: Expression profiling of 40 NSCLC cell lines

status: Public on Jun 22 2015

city: Dallas

first: Luc

last: Girard

state: TX

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

institute: UT Southwestern Medical Center

summary: INTRODUCTION: CDKN2A (p16) inactivation is common in lung cancer and occurs via homozygous deletions, methylation of promoter region, or point mutations. Although p16 promoter methylation has been linked to KRAS mutation and smoking, the associations between p16 inactivation mechanisms and other common genetic mutations and smoking status are still controversial or unknown.  METHODS: We determined all three p16 inactivation mechanisms with the use of multiple methodologies for genomic status, methylation, RNA, and protein expression, and correlated them with EGFR, KRAS, STK11 mutations and smoking status in 40 cell lines and 45 tumor samples of primary non-small-cell lung carcinoma. We also performed meta-analyses to investigate the impact of smoke exposure on p16 inactivation.  RESULTS: p16 inactivation was the major mechanism of RB pathway perturbation in non-small-cell lung carcinoma, with homozygous deletion being the most frequent method, followed by methylation and the rarer point mutations. Inactivating mechanisms were tightly correlated with loss of mRNA and protein expression. p16 inactivation occurred at comparable frequencies regardless of mutational status of EGFR, KRAS, and STK11, however, the major inactivation mechanism of p16 varied. p16 methylation was linked to KRAS mutation but was mutually exclusive with EGFR mutation. Cell lines and tumor samples demonstrated similar results. Our meta-analyses confirmed a modest positive association between p16 promoter methylation and smoking.  CONCLUSION: Our results confirm that all the inactivation mechanisms are truly associated with loss of gene product and identify specific associations between p16 inactivation mechanisms and other genetic changes and smoking status.

overall_design: 40 NSCLC cell lines were profiled on Illumina WG6-V3 expression arrays. They consist of 4 groups of 10 cell lines each: non-smokers with EGFR mutation, non-smokers with EGFR wild-type, smokers with KRAS mutation, smokers with KRAS wild-type. Note that smoking status is not always clear.

first: Adi

last: Gazdar

first: Wei

last: Zhang


title: The deafness gene DFNA5 induces programmed cell death through mitochondria and MAPK-related pathways

sample_organism:
Saccharomyces cerevisiae
Homo sapiens

platform_organism:
Saccharomyces cerevisiae
Homo sapiens


title: The deafness gene DFNA5 induces programmed cell death through mitochondria and MAPK-related pathways [HEK293T]

overall_design: Comparison of two HEK293T transfected cell populations, either with a WT or mutated DFNA5 gene. There are 5 biol reps for the WT transfected cells and 6 biol reps for the mut DFNA5 transfected cells.


title: FOXO1/3 and PTEN Depletion in Granulosa Cells Promotes Ovarian Granulosa Cell Tumor Development

status: Public on Jun 17 2015

city: Houston

first: JoAnne

last: Richards

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: The Forkhead Box, FOXO1 and FOXO3, transcription factors regulate multiple functions in mammalian cells. Selective inactivation of the Foxo1 and Foxo3 genes in murine ovarian granulosa cells severely impairs follicular development and apoptosis causing infertility, and as shown herein, granulosa cell tumor (GCT) formation. Coordinate depletion of the tumor suppressor Pten gene in the Foxo1/3 strain enhanced the penetrance and onset of GCT formation

overall_design: A direct comparison of ovarian granulosa cells from wild type d25 and FOXO/PTEN knockout granulosa cell tumors.

first: Zhilin

last: Liu

first: Yi

last: Ren

first: Stephanie

last: Pangas

first: Diego

middle: H

last: Castrillon

first: Dagmar

last: Wilhelm

last: Zhou


title: Quiescence of Memory CD8+ T Cells Is Mediated by Regulatory T Cells through Inhibitory Receptor CTLA-4

status: Public on Jun 16 2015

city: Seattle

first: Surojit

last: Sarkar

state: WA

address: 1100 Olive Way, Suite 100

department: Department of Pediatrics and Laboratory Medicine

institute: University of Washington School of Medicine

summary:
Immune memory cells are poised to rapidly expand and elaborate effector functions upon reinfection. However, despite heightened readiness to respond, memory cells exist in a functionally quiescent state. The paradigm is that memory cells remain inactive due to lack of TCR stimuli.  Here we report a unique role of Tregs in orchestrating memory quiescence by inhibiting effector and proliferation programs through CTLA-4. Loss of Tregs resulted in activation of genome-wide transcriptional programs characteristic of potent effectors, and both developing and established memory quickly reverted to a terminally differentiated (KLRG-1hi/IL-7R±lo/GzmBhi) phenotype, with compromised metabolic fitness, longevity, polyfunctionality and protective efficacy. CTLA-4, an inhibitory receptor overexpressed on Tregs, functionally replaced Tregs in trans to rescue Treg-less memory defects and restore homeostasis of secondary mediators as well. These studies present CD28-CTLA-4-CD80/CD86 axis as a novel target to potentially accelerate vaccine-induced immunity and improve T-cell memory quality in current cancer immunotherapies proposing transient Treg-depletion.

We used microarray analysis to detail the global programming of gene expression in LCMV GP33-specific CD8 T cells differentiated in the presence or absence of regulatory T cells

overall_design: Differentiation of memory CD8 T cells entails a progressive transition of highly activated effector program to a quiescent memory program. A key question in the field is to understand the factors that aid in the differentiation of memory cells from effector cells. It is a generally accepted paradigm that effector cells transition to a memory state by default after antigen clearance, since TCR stimuli is the key driver of effector programs in CD8 T cells. We hypothesized that the effector to memory transition of CD8 T cells involves active immunological brakes through regulatory T cells (Tregs) that allow the highly activated effector cells to convert into quiescent memory cells. To address this hypothesis, we used FoxP3-DTR mice to deplete Tregs during the window following antigen clearance, during which the effector CD8 T cells convert to long-lived memory cells. To get a deeper understanding of the global transcriptome of CD8 T cells as they transition from an effector to a memory state, we isolated and arrayed the antigen-specific CD8 T cells at day 16 post-infection that have experienced the transitional environment with and without the presence of Tregs.

first: Vandana

last: Kalia


title: caArray_green-00030: 2-methoxyestradiol (2ME2) induces mammary gland differentiation through amphiregulin-EGFR mediated signaling

status: Public on Jun 20 2015

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

summary:
2-methoxyestradiol (2ME2) induces mammary gland differentiation through amphiregulin-EGFR mediated signaling:  molecular distinctions from the mammary gland of pregnant mice.High levels of 2ME2 are observed in the late stages of pregnancy.  We investigated the role of 2ME2 on normal mammary gland development.  Large scale gene expression assays were performed using Affymetrix GeneChips in pursuit of detailed molecular basis.  (1) Mammary glands of wild type FVB mice administered  75 or 150 mg/kg of 2ME2 (2) Mammary glands of normal FVB/Nj mice      (i) at day 16 of pregnancy,      (ii) day 2 of lactation      (iii) day 30 of post-lactation, and (3) mammary epithelial SCp2 cells after 6, 24 and 48 hours of 10 micromol 2ME2 treatment were examined.  In vivo studies revealed that 2ME2 treatment up regulates the expression of amphiregulin.  The clue to the role of 2ME2 in differentiation comes from studies in vitro which detected down regulation of inhibitor of differentiation (Id-1) gene and consequent up regulation of amphiregulin.  The differentiation of E2 negative SCp2 cells by 2ME2 indicate estradiol independent mechanism. For details, please see our paper in Endocrinology 2006.
**NOTE: Migrated from caArray 1.x, identifier='gov.nih.nci.ncicb.caarray:Experiment:1015897590892008:1'

overall_design:
green-00030
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: mg_u74av2, Mouse430_2
Organism: Mus musculus (ncbitax)
Tissue Sites: murine mammary gland
Material Types: cell, synthetic_RNA, organism_part, total_RNA


title: Early neuroinflammatory response precedes Purkinje cell loss in the cerebellum of SCA6 knockin mouse models

status: Public on Jun 14 2015

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

summary: Spinocerebellar ataxia type 6 (SCA6) is a dominantly inherited neurodegenerative disease caused by an expansion of a CAG repeat encoding a polyglutamine (PolyQ) tract in the Cav2.1 voltage-gated calcium channel. Pathologically, it is characterized by selective degeneration of cerebellar Purkinje cells (PCs), which are a common target for PolyQ-induced toxicity among several different SCAs. Mutant Cav2.1 confers toxicity mainly through a toxic gain-of-function mechanism, but subcellular site of expanded Cav2.1 toxicity is controversial and it remains elusive whether SCA6 shares pathogenic cascades with other SCAs. To gain insight into these problems, we studied the cerebellar gene expression patterns of young Sca6 MPI 118Q/118Q knockin (KI) mice, which express mutant Cav2.1 from endogenous locus and faithfully models human SCA6. Comparison of transcriptional changes with those of Sca1 154Q/2Q mice, a faithful KI mouse model of SCA1, revealed that transcriptional signatures in the MPI 118Q/118Q were distinct from those of Sca1 154Q/2Q. Examination of temporal profiles of candidate genes showed that upregulation of those associated with microglial activation was initiated before PC degeneration was apparent and augmented as the disease progressed. Histological analysis of the MPI 118Q/118Q cerebellum confirmed the presence of Iba-1 positive activated microglia. Moreover, predominance of M1-like pro-inflammatory microglia was observed and was concomitant with the increased expression of pro-inflammatory cytokines. These results suggest that the unique transcriptional response, which highlights upregulation of neuroinflammatory genes possibly associated with lysosomal involvement, may play a pivotal role in the pathogenesis. Modulation of innate immune system could pave the way for slowing the progression of SCA6.

overall_design: We used MPI 118Q/118Q and MPI 11Q/11Q mice for Sca6 KI model at six weeks old. Statistical analysis of differently expressed genes was performed using the Linear Models for Microarray Data (limma) package in R/Bioconductor.

first: Tomonori

last: Aikawa

first: Kumiko

last: Iijima

first: Miyano

last: Sakurai

first: Hiroshi

last: Tanaka

first: Hidehiro

last: Mizusawa

first: Kei

last: Watase


title: Expression data from cerebral cortices of bacTRAP transgenic mice

city: New York

first: Awni

last: Mousa

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

summary: We used microarrays of eight different cell types in cortex to conduct specificity index analysis for detailed cell type specific molecular profile.

overall_design: Cerebral cortices of adult bacTRAP transgenic mice were dissected out and subjected to polysomal immunoprecipitation with GFP antibody in accordance with the established protocol (Heiman et al. Cell 2008). Enriched RNAs for each cell type were extracted from corresponding bacTRAP mice and subjected to two cycle RNA amplification and biotin labeling following quality control. Biotin labeled RNAs were hybridized on Mouse Genome 430 2.0 microarray chips and the expression intensity of all 40,000 probesets were analyzed further.

first: Prerana

last: Shrestha

first: Nathaniel

last: Heintz


title: Epression profiling of miR-142 deficient CD19+ B cells

status: Public on Jun 15 2015

city: Duarte

first: Mark

middle: P

last: Boldin

state: CA

address: 1500 E. Duarte Rd

institute: Beckman Research Institute of the City of Hope

summary:
miR-142 gene is specifically and abundantly expressed in hematopoietic cells. Mice that lack this miRNA gene develop immunodeficiency and display altered hematopoeisis.
We used microarrays to detect whole transcriptome changes in miR-142 null B cells.

overall_design: RNA from purified WT(n=3) and miR-142 KO (n=3) CD19+ B cells was extracted and hybridized to Affymetrix GeneChips. Samples in WT and KO groups are biological replicates and were isolated in age and gender matched mice.


title: Gene expression profiles in dorsal skin of hairless mice orally administrated collagen hydrolysate for 1 week

status: Public on Jun 12 2015

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

summary: Dietary collagen hydrolysate has been conjectured to improve skin barrier function. To investigate the effect of long-term collagen hydrolysate administration on the skin, we evaluated stratum corneum water content and skin elasticity in intrinsic aged mice. Female 9-week-old hairless mice were fed a control diet, or a collagen hydrolysate-containing diet, for 12 weeks. The stratum corneum water content and skin elasticity were sequentially decreased by chronological aging in control mice. Intake of collagen hydrolysate significantly suppressed such changes. Moreover, we comprehensively analyzed gene expression in the skin of mouse, which had been administered collagen hydrolysate, using DNA microarray. Twelve weeks after start of collagen intake, no significant differences appeared in gene expression profile compared to that of control group. However, 1 week after administration, 135 genes were up-regulated and 448 genes were down-regulated in collagen group compared to control group. It is indicate that gene changes preceded changes of barrier function and elasticity. We focused on several genes correlated with functional changes in the skin. Gene Ontology terms, especially related to epidermal cell development, were signiﬁcantly enriched in up-regulated genes. These skin function-related genes had properties that facilitate epidermal production and differentiation and suppress dermal degradation. Thus, dietary collagen hydrolysate induced positive gene changes. In conclusion, our results suggest that alteration of gene expression at early stages after collagen administration affect skin barrier function and mechanical properties. Long-term oral intake of collagen hydrolysate improves skin dysfunction by regulating genes related to production and maintenance of the skin tissue.

overall_design: Nine-week-old female Hos:HR-1 hairless mice (Japan SLC Inc., Shizuoka, Japan) were used in this study. All mice were housed in plastic cages (4 mice/cage) in a temperature and humidity controlled room (24 ± 1°C and 50 ± 10% humidity) under a 12 hour light-dark cycle. Mice were given an AIN-93G (Oriental Yeast Co., Ltd., Tokyo, Japan) diet and water. The present study was approved by the Animal Committee of Meiji Seika Kaisha Ltd., Food & Health R&D Laboratories, with the animals receiving care under the Guiding Principles for the Care and Use of Laboratory Animals of this committee. All surgery was performed under isoflurane anesthesia, and all efforts were made to minimize suffering. Sixteen female mice were randomly divided into two groups (n = 8 /group) according to their body weight, stratum corneum water content, and skin elasticity. During the experimental period for 1 week, the control group was fed a control diet (AIN-93G) and the collagen group was fed a collagen diet consisting of a mixture of 2.0 g of collagen hydrolysate and 100 g of the control diet. Fish scale collagen hydrolysate was purchased from Nitta Gelatin Inc. (Osaka, Japan). This amount of collagen hydrolysate is approximately equivalent to oral ingestion of 2.0 g collagen hydrolysate/kg body weight/day.

first: Chisato

last: Oba

first: Kyoko

last: Ito

first: Satomi

last: Ichikawa

first: Masashi

last: Morifuji

first: Tomoko

last: Ishijima

first: Keiko

last: Abe

last: Kawahata


title: Differential gene expression between uninfected and infected U937 derived macrophages with  Leishmania braziliensis

status: Public on Jun 10 2015

city: Bogotá D.C.

first: Clemencia

middle: Elena

last: Ovalle-Bracho

state: Bogotá D.C.

address: Avenida 1 # 13A 61

department: Research office

country: Colombia

institute: Centro Dermatológico Federico Lleras Acosta

summary: The main objective of this study is to identify the list of genes differentially expressed between infected with Leishmania braziliensis  and non-infected macrophage cultures based on gene expression microarray profiling

overall_design: The dataset is comprised by the expression profile of 6 samples from three independent experiments and each experiment had three technical replicates. 3 of the 6 samples were U937 derived macrophages infected by Leishmania braziliensis and the other 3 were U937 derived macrophages without infection with Leishmania braziliensis. A total of 18 microarrays analysis were performed.

first: Carlos

last: Franco-Muñoz

first: Diana

last: Londoño-Barbosa

first: Daniel

last: Restrepo

last: Clavijo


title: Gene expression profiles in dorsal skin of hairless mice orally administrated collagen hydrolysate

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

overall_design: Refer to individual Series


title: Expression data from CD4+ T cells of germ free mice, SPF IQI mice and SPF C57BL/6 mice depletd with Uhrf1

city: Toyama

first: yukihiro

last: furusawa

address: Kurokawa

institute: Toyama Prefectural University

summary:
Commensal bacteria shapes gut immune system. Colonization bacteria increase the frequency of regulatory T cells, however, the molecular mechanisms has not yet been unknown.
To reveal the mechanism, we isolated Treg cells and Non-Treg cells and performed  the global expression analysis.

overall_design: Colonic lamina propria cells were isolated from mice described above. Cells were divided into Treg or Non-Treg cells by FACS AriaIII

first: Koji

last: Hase

first: Yuuki

last: obata

first: Yukihiro

last: Furusawa


title: Gene expression profiles in dorsal skin of hairless mice orally administrated collagen hydrolysate for 12 weeks

last: Nakai

summary: Dietary collagen hydrolysate has been conjectured to improve skin barrier function. To investigate the effect of long-term collagen hydrolysate administration on the skin, we evaluated stratum corneum water content and skin elasticity in intrinsic aged mice. Female 9-week-old hairless mice were fed a control diet, or a collagen hydrolysate-containing diet, for 12 weeks. The stratum corneum water content and skin elasticity were sequentially decreased by chronological aging in control mice. Intake of collagen hydrolysate significantly suppressed such changes. Moreover, we comprehensively analyzed gene expression in the skin of mouse, which had been administered collagen hydrolysate, using DNA microarray. Twelve weeks after start of collagen intake, no significant differences appeared in gene expression profile compared to that of control group. However, 12 weeks after administration, 135 genes were up-regulated and 448 genes were down-regulated in collagen group compared to control group. It is indicate that gene changes preceded changes of barrier function and elasticity. We focused on several genes correlated with functional changes in the skin. Gene Ontology terms, especially related to epidermal cell development, were signiﬁcantly enriched in up-regulated genes. These skin function-related genes had properties that facilitate epidermal production and differentiation and suppress dermal degradation. Thus, dietary collagen hydrolysate induced positive gene changes. In conclusion, our results suggest that alteration of gene expression at early stages after collagen administration affect skin barrier function and mechanical properties. Long-term oral intake of collagen hydrolysate improves skin dysfunction by regulating genes related to production and maintenance of the skin tissue.

overall_design: Nine-week-old female Hos:HR-1 hairless mice (Japan SLC Inc., Shizuoka, Japan) were used in this study. All mice were housed in plastic cages (4 mice/cage) in a temperature and humidity controlled room (24 ± 1°C and 50 ± 10% humidity) under a 12 hour light-dark cycle. Mice were given an AIN-93G (Oriental Yeast Co., Ltd., Tokyo, Japan) diet and water. The present study was approved by the Animal Committee of Meiji Seika Kaisha Ltd., Food & Health R&D Laboratories, with the animals receiving care under the Guiding Principles for the Care and Use of Laboratory Animals of this committee. All surgery was performed under isoflurane anesthesia, and all efforts were made to minimize suffering. Sixteen female mice were randomly divided into two groups (n = 8 /group) according to their body weight, stratum corneum water content, and skin elasticity. During the experimental period for 12 weeks, the control group was fed a control diet (AIN-93G) and the collagen group was fed a collagen diet consisting of a mixture of 2.0 g of collagen hydrolysate and 100 g of the control diet. Fish scale collagen hydrolysate was purchased from Nitta Gelatin Inc. (Osaka, Japan). This amount of collagen hydrolysate is approximately equivalent to oral ingestion of 2.0 g collagen hydrolysate/kg body weight/day.


title: Ileal gene expression in Duoxa-/- mice and cohoused littermate controls

city: Ann Arbor

first: Helmut

last: Grasberger

state: MI

address: 1150 West Medical Center Drive

institute: University of Michigan

summary: Dual oxidases play a role in innate host defense at barrier epithelia. We examined the effect of loss of dual oxidase function (duoxa-/-) on gene expression in the mouse terminal ileum at homeostasis. To control for cage/litter effects, duoxa-/- were cohoused with wild type littermate controls.

overall_design: Ileal mucosal samples were obtained from duoxa-/- mice and cohoused wild type littermates from three separate cages (litters). For each cage, RNA was pooled from n=2-3 animals per genotype.


title: Tetraspanin 3 is Required for the Development and Propagation of Acute Myelogenous Leukemia

status: Public on Jun 04 2015

city: La Jolla

first: Roman

last: Sasik

address: 9500 Gilman Dr.

department: Center for Computational Biology and Bioinformatics

institute: UCSD

summary: Msi2 is a critical regulatior of myeoid leukemia, and these data identify genes that are changed following Msi2 deletion in bcCML and de novo AML stem cells.

overall_design:
Leukemic stem cells were extracted from wild-type and Msi2 mutant MLL-AF9 driven AML and BCR-ABL/NUP98-HOXA9 driven bcCML, in triplicate. RNA was extracted and hybridized on Affymetrix microarrays.
The mouse strain was a genetic trap Msi2 mutant made by Center for Animal Resources and Development (CARD) of Kumamoto University.
They call their strain B6;CB-Msi2Gt(pU-21T)2Imeg, see also

http://cardb.cc.kumamoto-u.ac.jp/transgenic/strainsDetailAction.do?strainId=834


title: Identification of activity-induced Npas4-regulated genes in cortical inhibitory and excitatory neurons (array)

city: Boston

first: Ivo

last: Spiegel

state: MA

address: 220 Longwood Ave

department: Department of Neurobiology

institute: Harvard Medical School

summary: To identify the activity-induced gene expression programs in inhibitory and excitatory neurons, we analyzed RNA extracted from cultured E14 mouse MGE- and CTX-derived neurons (DIV 10) after these cultures were membrane-depolarized for 0, 1 and 6 hrs with 55mM extracellular KCl. To identify the gene programs regulated in these cells by the activity-induced early-response transcription factor Npas4, we repeated the same experiment in the MGE- and CTX-cultures lacking Npas4 (Npas4-KO).

overall_design: Littermate mouse E14 MGE- or CTX-derived neurons (WT or KO for Npas4) were cultured for 9 days, quieted overnight with TTX and AP-5 and then membrane-depolarized for 0, 1 or 6 hours by raising the extracellular KCl-concentration to 55mM. RNA was then extracted and analyzed using Affymetrix GeneChip Mouse Expression Set 430 2.0 microarray platform.

first: I

first: A

middle: R

last: Mardinly

first: M

middle: E

last: Greenberg


title: Gene Expression of primary rat hippocampal neurons after Ncoa3 knockdown

status: Public on Jun 01 2015

city: Marburg

first: Peter

middle: Harry

last: Störchel

address: Karl-von-Frisch-Str. 1

department: Institut für Physiologische Chemie

institute: Philipps-Universität Marburg

summary: We identified Ncoa3 as a regulator of neuronal morphology and microRNA activity. In order to uncover target genes of this transcriptional coactivator we performed this microarray analysis.

overall_design: The Expression of Ncoa3 was diminshed by AAV-mediated Ncoa3 shRNA expression. Gene expression was compared to control shRNA expressing cells. Three biological replicates are included in this analysis.

first: Jelena

last: Pistolic

first: Vladimir

last: Benes

first: Gerhard

last: Schratt


title: Expression of cytokine-sensitive genes in islets from diabetes-prone mice

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

summary: Genome-wide association studies in human type 2 diabetes (T2D) have renewed interest in the pancreatic islet as a major site of T2D risk. In this study, microarray data collected from mouse islets were used to identify genes that are regulated by cytokines at levels consistent with the chronic low-grade inflammation observed in T2D.  The most cytokine-sensitive genes were then examined for association of single nucleotide polymorphisms (SNPs) with acute insulin response to glucose (AIRg) measured in the Genetics UndeRlying DIAbetes in HispaNics (GUARDIAN) study. In GUARDIAN, there was evidence of association of AIRg with SNPs in ARAP3 (5q31.3), F13A1 (6p25.3), KLHL6 (3q27.1), NID1 (1q42.3), PAMR1 (11p13), RIPK2 (8q21.3), and STEAP4 (7q21.12). These data support the mouse islet microarray data in detection of seven novel genes with potential importance to islet dysfunction in T2D. To further assess each gene, murine islets were exposed for 48-hrs to the following stressors representing models of beta-cell failure: 20nM rotenone (oxidative stress), 100nM thapsigargin (ER stress), 10pg/ml IL-1B + 20pg/ml IL-6 (cytokines/low-grade inflammation), 28mM glucose (hyperglycemia), or 50uM palmitate + 100uM oleate + 50uM linoleate (lipotoxicity). RT-PCR revealed that F13a1 was downregulated 3.3-fold by cytokines (P<0.05) and 2.6-fold by rotenone (P<0.05), Klhl6 was upregulated 4.3-fold by thapsigargin (P<0.01), Ripk2 was mildly (1.5-3-fold) but significantly upregulated by all stressors (P<0.05), and STEAP4 was profoundly cytokine-sensitive (167-fold upregulation, P<0.01). These findings reveal promising leads in elucidating islet dysfunction during the development of T2D.

overall_design: Islets were isolated from prediabetic male BKS.Cg-m+/+Leprdb/J (db/db) mice and non-diabetic heterozygous controls. Islets were treated with proinflammatory cytokines overnight or left untreated and then collected for mRNA. Microarray analysis of Affymetrix chips was performed by the UVA Biomolecular Research Facility.

first: Craig

last: Nunemaker


title: TLR4 senses oxidative stress mediated by partially oxidized microvesicles.

city: Domzale

first: Simon

last: Horvat

address: Groblje 3

department: Animal Science

country: Slovenia

institute: University of Ljubljana; Biotechnical faculty

summary: Oxidative stress is a hallmark of inflammation in infection or sterile tissue injury. We show that partially oxidized phospholipids of microvesicles (MVs) from plasma of patients with rheumatoid arthritis or cells exposed to oxidative stress induce activation of TLR4. MVs from healthy donors or reconstituted synthetic MVs can be converted to TLR4 agonists by limited oxidation, while prolonged oxidation abrogates the activity. Activation by MVs mimics the mechanism of TLR4 activation by LPS. However, LPS and MVs induce significantly different transcriptional response profile in mouse BMDMs with a strong inflammation-resolving component induced by the endogenous signals. MVs thus represent a ubiquitous endogenous danger signal released under the oxidative stress, which underlies the pervasive role of TLR4 signaling in inflammation.

overall_design: BMDMs (bone marrow derived macrophages) from C57BL/6J strain were stimulated with LPS (100ng/ml), oxidative stress-derived MVs (5000 MV/ml) or MVs-FR (5000 MV/ml). RNA was extracted 4 hours after stimulation. 3 biological replicates (BMDM cells isolated from three different mice) per group.

first: Mateja

last: Manček-Keber

first: Mojca

last: Frank

first: Iva

last: Hafner-Bratkovič

first: Anže

last: Smole

last: Zorko

first: Nina

last: Pirher

first: Silvia

last: Hayer

first: Veronika

last: Kralj-Iglič

first: Blaž

last: Rozman

first: Nejc

last: Ilc

last: Jerala


title: FGFR1/KLB regulated genes in mouse brown adipose tissues

status: Public on Jun 02 2015

city: South San Francisco

first: Matthew

last: Brauer

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

summary: We aimed to identify genes that are regulated at downstream of FGFR1/KLB receptor complex in brown adipose tissues of adult male mice on high fat diet by injecting anti-FGFR1/KLB agonistic antibody or human FGF21.

overall_design: A three condition experiment with five biological replicates per condition.  Interscapular brown adipose tissues were isolated from adult male mice on high fat diet at day 5 after a single intraperitoneal injection of 10 mg/kg anti-FGFR1/KLB agonistic antibody (bFKB1) or after injection of human FGF21 at 1 mg/kg b.i.d. (2 mg/kg/day) for 5 days.

middle: J

first: Junichiro

last: Sonoda

first: Mark

middle: Z

last: Chen

first: Robert

last: Soriano


title: Chronic binge alcohol administration accentuates expression of pro-fibrotic and inflammatory genes in the skeletal muscle of simian immunodeficiency virus-infected macaques

city: New Orleans

first: Patricia

last: Molina

state: Louisiana

address: 1901 Perdido St.

department: Physiology

institute: LSU health Sciences Center

summary:
We studied the effect of alcohol admistration on the gene profiles of skeletal muscle of SIV-infected macaques. We found that alcohol-treated SIV-infected monkeys had altered gene patterns associated with ECM remodeling including TIMP-1, MMP2 and MMP9
In addition, hydroxyproline content and picrosirius staining reflected greatest collagen deposition in the alcohol-SIV muscle tissue.

overall_design: Animals were infused intragastrically with alcohol or sucrose daily for three months prior to intravenous SIV inoculation with 10,000X the ID50SIV mac251 for about 13 months

first: Tracy

last: Dodd

first: Liz

last: Simon

first: Nicole

last: LeCapitaine

first: Jovanny

last: Zabaleta

first: Jason

last: Mussell

first: Paul

last: Berner

last: Ford

last: Dufour

first: Gregory

last: Bagby

first: Steve

last: Nelson


title: Expression data from pre-B ALL tumors isolated from ingeneered mice from the indicated genotypes

status: Public on May 30 2015

first: yue

last: kang

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana Farber Cancer Institute

summary:
The Ink4a/Arf tumor supressors play crucial roles in inhibiting cell cycle progression at the G1/S checkpoint.  Activating mutations in the KrasG12D oncogene is one of the most frequent changes in human cancer, with resultant constitutive mitogenic signaling within the cell. We generated cohorts of  CD19Cre; KrasG12D/+; Ink4a/ArfL/+ mice to evaluate the  combined contributions of Ink/Arf loss and KrasG12D activation in pre-B ALL lymphomas.
In this data set we include the expression data obtained from pre-B ALL lymphomas isolated from  mice with simultaneous deletion of the Ink/Arf locus and activation of KrasG12D oncogene (and CD19Cre; KrasG12D/+; Ink4a/ArfL/+ mice).

overall_design: A total 10 mRNA samples were isolated from pre-B ALL arising in CD19Cre; KrasG12D/+; Ink4a/ArfL/+ mice.

first: Kumar

last: Sukhdeo

first: Ruben

last: Carrasco


title: Immediate Effects of Extracellular Phosphate on Gene Expression in Primary Murine Osteoblasts

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

institute: University Medical Center Hamburg-Eppendorf

summary: That phosphate homeostasis is tightly linked to skeletal mineralization is probably best underscored by the fact that the phosphaturic hormone FGF23 is primarily expressed by terminally differentiated osteoblasts/osteocytes, and that increased circulating FGF23 levels are causative for different types of hypophosphatemic rickets.  In contrast, FGF23-inactivation results in hyperphosphatemia, and unexpectedly this phenotype is associated with severe osteomalacia in Fgf23-deficient mice.  In this context it is interesting that different types of bone cells have been shown to respond to extracellular phosphate, thereby raising the concept that phosphate can act as a signaling molecule.  To identify phosphate-responsive genes in primary murine osteoblasts we performed genome-wide expression analysis with cells maintained in medium containing either 1 mM or 4 mM sodium phosphate for 6 hours.  As confirmed by qRT-PCR, this analysis revealed that several known osteoblast differentiation markers (Bglap, Ibsp or Phex) were unaffected by raising extracellular phosphate levels.  In contrast, we found that the expression of Enpp1 and Ank, two genes encoding inhibitors of matrix mineralization, was induced by extracellular phosphate, while the expression of Sost and Dkk1, two genes encoding inhibitors of bone formation, was negatively regulated.  The ability of osteoblasts to respond to extracellular phosphate was dependent on their differentiation state, and shRNA-dependent repression of the phosphate transporter Slc20a1 in MC3T3-E1 cells partially abolished their molecular response to phosphate.  Taken together, our results provide further evidence for a role of extracellular phosphate as a signaling molecule and raise the possibility that severe hyperphosphatemia can negatively affect skeletal mineralization.

overall_design: Primary osteoblasts were obtained from the calvariae of 5 days old mice.  Cells were isolated by sequential digestion with collagenase/dispase and subsequently cultured in a-MEM (including 10 % FBS) for 3 days, until they were 80 to 90 % confluent.  Thereafter, they were cultured in non-modified-a-MEM or phosphate enriched a-MEM. The expression patterns of the modified culture was then compared to the non-modified culture.

first: Thorsten

last: Schinke


title: Expression data from CD19-positive B-cells and pre-B ALL tumors isolated from ingeneered mice from the indicated genotypes


title: Modeling Clostridium difficile infections

status: Public on May 29 2015

city: Houston

first: Frank

last: McKeon

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

summary: Clostridium difficile (Cd) is a gram-positive, spore-forming bacterium and the primary cause of nosocomial diarrhea and pseudomembranous colitis. The pathogenicity of Cd has been linked to its production of TcdA and TcdB. While they cause fluid secretion, inflammation, and colonic damage, their respective and synergistic roles have been difficult to ascertain. In infection animal model, TcdB has been demonstrated to be a key virulence factor, and TcdB causes obvious damage in human and porcine colonic explants. Using the colonic epithelia derived from cloned colonic stem cells, we have developed a model to test the response to TcdB. Epithelia generated in air-liquid interface cultures from cloned transverse colon stem cells were challenged with TcdB at different concentrations and durations.

overall_design: Colonic stem cells were differentiated in air-liquid interface cultures and treated with C. difficile toxin B at different doses (100 pM, 250 pM, and 500 pM) and times (8 hrs, 16 hrs and 24 hrs). At appropriate time points, membranes with ALI structure were collected for histology and microarray analysis.

first: Xia

last: Wang

first: Yusuke

last: Yamamoto

first: Lane

last: Wilson

first: Ting

last: Zhang

first: Benoit

last: Chevalier

first: Wa

last: Xian


title: Expression data from CD19-positive B-cells isolated from splenocytes from 8 week-old ingeneered mice from the indicated genotypes

summary:
The Ink4a/Arf tumor supressors play crucial roles in inhibiting cell cycle progression at the G1/S checkpoint.  Activating mutations in the KrasG12D oncogene is one of the most frequent changes in human cancer, with resultant constitutive mitogenic signaling within the cell. We generated cohorts of CD19Cre,  CD19Cre; KrasG12D, CD19Cre; Ink4a/ArfL/+, and CD19Cre; KrasG12D/+; Ink4a/ArfL/+ mice to evaluate the isolated or combined contributions of Ink/Arf loss and KrasG12D activation in B-cell development.
In this data set we include the expression data obtained CD19-positive B-cells isolated from premalignant (8 weeks old ) mice.

overall_design: A total 8 mRNA samples were preppared with two biological of CD19-positive B-cells isolated from the spleen of mice of the indicated genotypes.


title: Cloning and Variation of Ground State Intestinal Stem Cells

summary: Despite major advances with embryonic and induced pluripotent stem cells or lineage-committed, p63-expressing stem cells of stratified epithelia, we know less about the indigenous stem cells of the gastrointestinal tract, pancreas, liver, and other columnar epithelia which collectively resist cloning in their elemental states.  Here we demonstrate the cloning of highly immature epithelial stem cells from defined regions of the human intestine and colon.  We show that single cell-derived pedigrees can be propagated indefinitely while often sustaining minimal copy number and sequence variation.  Despite prolonged cultivation, these pedigrees from disparate regions of the intestinal tract respond to identical differentiation signals by formation of epithelia with eponymous structural and gene expression features.  These data suggest developmental patterning of cell-autonomous commitment programs in stem cells that enforce specialization along the gastrointestinal tract and predict the utility of these cells in disease modeling and regenerative medicine.

overall_design: Stem cell clones and air-liquid interface of the stem cells from 6 parts of human fetal intestine

first: Lingyan

last: Wu

first: Gang

last: Ning

first: Yue

last: Hong

first: Chiea

middle: C

last: Khor

first: Brooke

last: Howitt

first: Ho

middle: K

last: Yu

first: Christopher

last: Crum


title: Human ileum stem cell differentiation by air-liquid interface

summary: Despite major advances with embryonic and induced pluripotent stem cells or lineage-committed, p63-expressing stem cells of stratified epithelia, we know less about the indigenous stem cells of the gastrointestinal tract, pancreas, liver, and other columnar epithelia which collectively resist cloning in their elemental states.  Here we demonstrate the cloning of highly immature epithelial stem cells from defined regions of the human intestine and colon.  In this study, we have isolated ileal stem cells and performed air-liquid interface method to induce differentiation of human ileal stem cells. The differentiated structure showed villi-like epithelia which contains enterocytes, goblet cells, endocrine cells and paneth cells.

overall_design: Human ileal stem cells are differentiated by air-liquid interface method and total RNA was collected for microarray preparation.


title: Expression data from aging study on mouse spermatogonial stem/progenitor cell population

status: Public on May 24 2015

city: Shatin

first: Alfred

middle: Chun Shui

last: LUK

address: LKS Integrated Biomedical Sciences Building, Area 39, The Chinese University of Hong Kong, Shatin

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: In mouse, spermatogonial stem/progenitor cells are the progenitor cell which develop to mature sperms through a series of mitotic and meiotic divisions and differentiation. Gfra1 is an established surface marker for mouse spermatogonial stem/progenitor cells. In this study, we used a transcriptomic approach to investigate the effect of aging on Gfra1-positive and -negative populations of mouse male germ cells.

overall_design: Spermatogonial stem/progenitor cells were isolated from testes of mice at ages 6-day, 21-day, 60-day, and 8-months by magnetic assisted cell sorting (MACS) technique using Gfra1 marker. Transcriptomes among different ages and Gfra1 status were compared.

first: Maria

last: Kokkinaki

first: Tin-Lap

last: Lee

first: Zuping

last: He

first: Jiji

last: Jiang

first: Nady

last: Golestaneh

first: Marie-Claude

last: Hofmann

first: Wai-Yee

last: Chan

first: Martin

last: Dym


title: Gonadal Identity in the Absence of pro-Testis Factor SOX9 and pro-Ovary Factor beta-catenin

status: Public on May 26 2015

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary:
The main goal of our study is to identify the molecular events that determine the gonadal identity in mammals. Although testis and ovary arise from a common embryonic primordium, they represent outcomes of opposing fate determination. This decision to differentiate into a testis or an ovary hinges upon the balance between two antagonizing factors, pro-testis SOX9 and pro-ovary β-catenin.
This microarray analysis led to the identification of the genes involved in the fate of XX and XY gonads in absence of SOX9 and beta-catenin

overall_design: We developed mouse genetic models that lack either Sox9, β-catenin, or both specifically in the somatic cells. All embryos used in this study resulted from the crossing between Ctnnb1f/f; Sox9f/f females with Sf1-cre+/Tg ; Ctnnb1+/f; Sox9+/f males. XX and XY fetal gonads were collected at embryonic day E14.5

first: Barbara

last: Nicol

first: Humphrey

last: Yao


title: Changes in gene expression caused by loss of Med1 in the mouse prostate

status: Public on May 22 2015

city: Piscataway

first: Wei

state: NJ

address: 675 Hoes Lane West

department: Pharmacology

institute: Rutgers

summary:
MED1 is a transcriptional coactivator for gene-specific activators involved in growth and development, we were interested in identifying MED1 target genes potentially involved in prostate development by cDNA microarray. Med1 was conditional knocked out in mice prostate. We performed cDNA microarray with two sets: (1) RNA isolated from three WT ventral prostates and three MT ventral prostates; (2) RNA isolated from three WT lateral prostates and three MT lateral prostates.
We used microarrays to detail the global programme of gene expression underlying how Med1 was involved in mice prostate development by regulating targeted genes expression

overall_design: 12 mice prostate samples were divided into two groups: (1) three WT ventral prostates and three MT ventral prostates; (2) three WT lateral prostates and three MT lateral prostates.

first: Joseph

last: Fondell


title: Polycomb group proteins adjust the threshold for retinoic acid mediated signaling during early proximal-distal patterning in forelimb development

status: Public on May 27 2015

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

type: Genome binding/occupancy profiling by array

summary:
Polycomb group (PcG) proteins play a pivotal role in epigenetically silencing development-related genes, restricting their expression to appropriate tissues. However, in some instances PcG target genes must also be dynamically regulated in response to developmental signals encountered during morphogenesis. Here we examine the role of PcG factors in early forelimb bud patterning, a process that relies on various morphogenetic signals.
Depletion of Ring1 proteins, which are essential components of Polycomb repressive complex-1 (PRC1), led to dramatic deficiencies in forelimb formation and proximal-distal regionalization. Gene expression analysis identified Meis2 and Meis1 as critical PRC1 targets genes in early distal specification, with PcG proteins counteracting retinoic acid (RA) signaling to control their expression. Importantly, in this system, PcG factors appear to function by adjusting the threshold for RA signaling, revealing an unexpected role of polycomb proteins in dynamic gene regulation during development.

overall_design:
[Affymetrix] Mouse E10.5 forelimb buds of Ring1A-KO, Ring1A/B-dKO and RA-treated wild type were used for RNA extraction and hybridization on Affymetrix microarrays.
[Agilent] ChIP analysis of mouse E10.5 whole forelimb buds against anti-H3K27me3 antibody.

first: N

last: Yakushiji-Kaminatsui

first: T

first: H

last: Koseki


title: RTN1 IS A NOVEL MEDIATOR FOR PROGRESSION OF KIDNEY DISEASE

status: Public on May 20 2015

city: New York

first: Chengguo

last: Wei

state: NY

address: 1428 Madison Ave1468 Madison Ave

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

summary: Gene expression profiling of kidneys from the murine model of HIV-associated nephropathy (HIVAN) identified an association between the expression of an endoplasmic reticulum (ER)-associated protein reticulon-1, RTN1, and the severity of kidney disease. Of the three known RTN1 isoforms, only RTN1A protein expression was increased in kidneys of murine models of HIVAN, diabetic nephropathy (DN), and renal fibrosis and humans with HIVAN and DN. Both mRNA and protein expression of RTN1-A in the kidneys correlated inversely with estimated glomerular filtration rate (eGFR) in patients with DN. In kidney cells, RTN1 overexpression induced ER stress/apoptosis, whereas RTN1 knockdown attenuated tunicamycin-, and hyperglycemia-induced ER stress/apoptosis. Incubation of kidney cells with high glucose media induced RTN1A expression likely through oxidative pathway, while knockdown of RTN1A inhibited high glucose-induced apoptosis. RTN1A interacts with PERK and mutation of its N- or C-terminal domain abolished its effects on ER stress/apoptosis. In vivo, knockdown of Rtn1a expression either before or after kidney injury attenuated renal fibrosis in mice with unilateral ureteral obstruction (UUO) and tubular epithelial cell-specific knockdown of Rtn1a also ameliorated ER stress and renal fibrosis in the UUO mice. Finally, knockdown of Rtn1a also attenuated proteinuria, glomerular hypertrophy, and mesangial expansion in STZ-induced diabetic mice, which were associated with suppression of ER stress markers. Taken together, these data suggest that RTN1 is a mediator of kidney disease progression that exacerbates kidney injury through ER stress and apoptosis.

overall_design:
Animal studies: All animal studies were approved by the IACUC committee of Mount Sinai School of Medicine. HIV-1 transgenic mice, Tg26, and their littermates were generated and genotyped as described. Only male heterozygous Tg26 in the FVB/N background were used in the study, because homozygous HIV-transgenic mice are not viable for more than few weeks postnatally. UUO and folic acid-induced nephropathy models were created as described . Mice were grouped as wild type, Tg26 with mild kidney injury, Tg26, with serious kidney injury. The kidneys were collected from these mice for histology, western blot, real-time PCR analysis, and microarray studies. Kidney disease was confirmed by measurement of proteinuria, renal function, and histologic analysis.
Microarray studies: Affymetrix gene expression microarrays were performed at the Mount Sinai Institution Microarray Core Facility. The Affymetrix GeneChip® Mouse Genome 430 2.0 Array was used to profile gene expression in the kidney cortex of Tg26 and WT mice 37. One-way analysis of variance test (ANOVA) was applied to the dataset to identify the genes that were differentially expressed between the two groups.  P-values were corrected using Benjamini–Hochberg false discovery rate (FDR) with a threshold of 0.05.

first: Ying

last: Fan

first: Wenzhen

last: Xiao

first: Zhengzhe

last: Li

first: Xuezhu

first: Peter

last: Chuang

first: Belinda

last: Jim

first: Weijia

last: Zhang

first: Niansong

last: Wang

first: Weiping

last: Jia

first: Huabao

last: Xiong

first: Kyung

first: John


title: mRNA Expression Changes Induced by Myocardial MCU Inhibition

status: Public on Jun 07 2015

city: Iowa City

first: Tyler

middle: Paul

last: Rasmussen

state: IA

address: 285 Newton Rd.

department: Internal Medicine

institute: University of Iowa

summary:
Mitochondrial calcium is an important second-messenger controlling fight-or-flight responses in the heart.  The molecular identity of MCU (Mitochondrial Calcium Uniporter) was recently discovered allowing us to test this hypothesis in vivo by expressiing a myocardial delimited dominant negative form of MCU.
We queried mRNA expression changes induced by dominant negative MCU expression in the heart.

overall_design: Neonatal (< 24 h) and 6 week old hearts were harvested from mice expressing the dominant negative MCU contruct or wild-type littermates.

first: Mark

last: Anderson

first: Fenhuang

last: Zhan


title: The transferrin receptor is required for intestinal epithelial homeostasis

status: Public on May 19 2015

city: Durham

first: Nancy

last: Andrews

state: North Carolina

address: Duke University Medical Center Box 3813, 450 Research Drive, LSRC C-125

department: Pharmacology and Cancer Biology

institute: Duke University

summary: The role of Tfr1 in non-erythroid tissues remains elusive due to the embryonic lethality of the Tfr1 global knockout mouse model.  To bypass this problem, we generated a mouse model in which Tfr1 was conditionally deleted in intestinal epithelial cells (IECs).  These mice developed severe IEC disruption, characterized by blunted villi, edema, loss of proliferative intervillus IECs, accumulation of lipids, and early neonatal lethality.  Strikingly, a wide range of genes associated with epithelial-to-mesenchymal transition were highly upregulated in IEC lacking Tfr1.  Additionally, candidate vesicular transport and sorting genes implicated in lipid absorption and trafficking were downregulated.  Surprisingly, the presence of a mutant allele of Tfr1, which is unable to bind to iron-loaded transferrin, was capable of rescuing the lethality, intestinal epithelial homeostasis, and proliferation in a majority of the Tfr1 conditional knockout mice.

overall_design: 9 samples (3 wildtype, 3 knockout, 3 rescue) were prepared from the intestinal epithelial cells isolated from the small intestine and proximal colon.

first: Alan

last: Chen


title: Expression data from differentiating murine embryonic stem cells

status: Public on May 21 2015

city: Cologne

first: Dina

last: Ivaniuk

address: Robert Koch Str.39

institute: Istitute for Neurophysiology University of Cologne

summary:
Various substances have been reported to enhance the cardiac differentiation of embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). Ascorbic Acid had a cardiogenic effect in mESC CGR8 cell line. Transcriptome of AA-treated CGR8 ESCs did not reveal any significant changes in gene expression as compared to untreated cells.
We performed a global gene expression analysis to better understand the mechanism of Ascorbic acid-induced cardiac differentiation.

overall_design:
Differentiating murine embryonic stem cells from CGR cell line were selected at stages of Day 0 (undifferentiated cells), Day 2, Day 3 and Day 5 of differentiation for RNA extraction and hybridization on Affymetrix microarray chip. Samples were collected in 3 biological replicate and were either treated with Ascorbic acid or nontreated (control group). Only those samples were processed for further analysis in which we were able to confirm that AA significantly enhanced cardiac differentiation efficiency at later stages (day 8 and 12) of differentiation by assessing the number of beating EBs in control and AA-treated groups.
Cardiac efficiency was evaluated later on this study. But samples that were analyzed by microarray analysis was limited till Day 5. We did not perform whole genome study for these later days of differentiation ( day 8 or 12).

middle: A

last: Gaspar

first: Umesh

last: Chaudhari

first: Tomo

last: Saric


title: Lovastatin effect on breast tumors in HER2/neu transgenic mice

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

institute: CNB, CSIC

summary:
The statins are a family of inhibitors of the 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase enzyme, which converts acetyl-CoA into mevalonic acid.  Since HMG-CoA reductase catalyzes the rate-limiting step in the mevalonate pathway of cholesterol biosynthesis, it was thought that the major clinical benefit of statins was to reduce cholesterol levels in the bloodstream; statins are thus in wide clinical use for the prevention and treatment of cardiovascular disease. Nonetheless, mevalonate is also the precursor of isoprenoid compounds, which are substrates for the post-translational modification of many proteins involved in cell signaling.  The blockade of isoprenoid synthesis might explain the pleiotropic effects described for statins in extrahepatic tissues, including inhibition of pathogen infection and anti-inflammatory and immunomodulatory activities.
We used microarrays to find differentially expressed genes in spontaneous breast tumors from mice treated with lovastatin (Lov) or vehicle (ethanol) as control.

overall_design: Standard single channel experimental design with biological replicates: gene expression signals from 5 treated tumor samples were compared to 5 non-treated tumor samples using Affymetrix GeneChips (MG430 v2.0).

first: Emilia

last: Mira

first: Lorena

last: Carmona

first: Alicia

last: González-Martín

first: Manuel

last: Tardáguila

first: Luis

last: Almonacid

first: Santos

last: Mañes


title: Gene expression profiles of control and EWS-FLI1-transduced neural crest stem cells

status: Public on May 15 2015

city: Ann Arbor

first: Elizabeth

last: Lawlor

address: 1600 Huron Parkway, NCRC Bldg 520

institute: University of Michigan

summary:
Expression profiles were generated from hESC-derived neural crest stem cells following transduction with GFP control vector or EWS-FLI1 vector. Expression was analyzed in stem cell conditions 5 days after transduction (undifferentiated conditions) and after 6 weeks in differentiation media (differentiation conditions).
Changes in gene expression over time were compared between control and EWS-FLI1 expresssing cells.

overall_design: Total RNA was extracted from 3 replicates for each of 4 conditions (undifferentiated control, undifferentiated EWS-FLI1, differentiated control and differentiated EWS-FLI1. Samples were analyzed by Affymetrix exon arrays using standard procedures.


title: Gene expression profiling of proximal versus distal mouse colon during AOM/DSS-induced colitis-associated carcinogenesis.

city: HERAKLION

first: ARISTIDES

last: ELIOPOULOS

state: CRETE

address: UNIVERSITY CAMPUS

department: MEDICAL SCHOOL

country: Greece

institute: UNIVERSITY OF CRETE

summary: In humans with UC, low-grade dysplasia also develops predominantly in the distal colon, progresses more rapidly to neoplasia than proximal colon low-grade dysplasia and associates with worse patient prognosis. In a mouse model of colitis-associated carcinogenesis induced by administration of the mutagen AOM and the luminal toxin DSS, tumors also develop exclusively in the distal part of the large intestine. We monitored global changes in the transcriptome of mouse proximal and distal colon during exposure to AOM/DSS with the aim to define biological pathways and processes that characterize regional responses of the large intestine to colitis-associated carcinogenesis.

overall_design: Female C57BL/6J mice were injected intaperitoneally with 10mg/kg body weight azoxymethane (AOM) when their weight was approximately 18-20 g (day 1) and 96 hours later 2.5% DSS was administered in their drinking water for five days, followed by 14 days of regular water. This cycle was repeated once (EARLY TREATMENT GROUP) or three times more (LATE TREATMENT GROUP) before mice were sacrificed on days 42 and 120 respectively. Macroscopic and histological analyses showed dysplasias and intramucosal adenocarcinomas in the distal colon of the late treatment group and areas of dysplasia in the early treatment group.  The proximal part of the colon remained unaffected. At least three (3) animals (biological replicates) were used to isolate tissue from proximal and distal areas of the large intestine under different treatment conditions (early vs late AOM/DSS treatment and untreated controls) which was processed for RNA isolation and gene expression profiling.

first: Aristides

middle: G

last: Eliopoulos

first: George

last: Pavlopoulos


title: Murine bone marrow gene expression profiling

status: Public on May 18 2015

city: Boston

first: Aldo

last: Roccaro

address: 450 Brookline Av

institute: Dana-Farber Cancer Institute

summary: Mice have been treated with NOX-A12. Whole BM cells have been harvested, RNA isolated,  and gene expression profiling was performed on cDNA using Mouse Genome 430 2.0 array. Untreated mice have been used as control.

first: Irene

last: Ghobrial


title: Expression data of CD4+T cells from Idiopathic CD4+ T cells lymphopenia (ICL) patients, Sarcoidosis (SARC) and Healthy individuals

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

summary: This work focuses on understanding the molecular basis of the immune dysfunctions in Idiopathic CD4+ T cells lymphocytopenia (ICL). ICL is a rare haematological disorder of unknown origin, characterized by a profound and persistent CD4+ T-cell defect, which predisposes to life threatening opportunistic infections very similar to those seen in AIDS. To analyse more in depth the functional pathways involved in ICL pathogenesis, we conducted gene expression profiling of CD4+ T-cells isolated from blood samples from ICL, sarcoidosis and healthy individuals. Our analyses have revealed specific CD4+ T-cells gene expression signatures in ICL associated with defective TCR activation threshold, expansion of the Treg-cell compartment and interestingly with accelerated immune aging.

overall_design: 25 Total samples were analyzed. We generated the following pairwise comparisons using GenoSplice technology. We permormed multiple anlayses including : ICL vs Healthy (All or paired samples), ICL vs SARC (All or paired samples) and SARC vs Healthy (All or paired sample). Paired samples means that a same healthy individual was using in comparaison of a ICL or SARC subjects. Genes with a Fold-change ≥ 1,5 and  P-Value ≤ 0,05 were selected.

first: Karl

last: Balabanian


title: Analysis of the role of miR-21 in liver regeneration after partial hepatectomy (PHx) in chronic ethanol-treated rats through in vivo inhibition using LNAs

status: Public on Sep 01 2015

city: Philadelphia

first: Egle

last: Juskeviciute

state: PA

address: 1020 Locust st. JAH 527

department: Pathology

institute: Thomas Jefferson University

summary: In this study, we analyzed the role of miR-21 in liver regeneration after partial hepatectomy (PHx) in chronic ethanol-treated rats. Male Sprague-Dawley rats were fed a liquid diet containing 36% of total calories derived from ethanol for 5 weeks; corresponding pair-fed calorie-matched controls were fed diets in which ethanol calories were replaced by carbohydrate. After 5 weeks, locked nucleic acid (LNA)-modified oligo antisense to miR-21 (AM21, Exiqon, Vedbaek, Denmark) was used to inhibit miRNA in vivo, and rats were subjected to 70% PHx. Liver samples were collected at 24h after the surgery. The excised liver samples at t=0 served as within-animal controls. Rat Gene 2.0 ST (Affymetrix, Santa Clara, CA) arrays were used to obtain global gene expression data from pooled liver samples (pools of 3 or 4 biological replicates/array, total 8 arrays).

overall_design: Gene expression was profiled in AM21 treated or untreated chronic ethanol-fed (EtOH) and carbohydrate control pair-fed (CHO) rat liver prior to (control, t=0) and 24 h after 70% partial hepatectomy (PHx).

first: Rachael

last: Dippold

first: Rajanikanth

last: Vadigepalli

first: Jan

middle: B

last: Hoek


title: Expression data from WT and IL-2 secondary CD4 T cell effectors responding towards infuenza A virus infection

status: Public on May 14 2015

city: Worcester

first: Susan

middle: L

last: Swain

address: 55 Lake Avenue North

institute: University of Massachusetts Medical School

summary:
How IL-2 produced by secondary CD4 T cell effectors, derived from resting memory cells, impacts memory CD4 T cell function and survival to memory following antigen re-encounter is unknown.
We used microarrays to detail the global programme of gene expression underlying differences between WT and IL-2 deficient secondary CD4 T cell effectors purified from the lung on day 7 following A/PR8/34-OVAII influenza infection.

overall_design: Congenic primed memory DO11.10 TCR trangenic CD4 T cells were sort purifed from the lungs of infected mice on day 7 post infection for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain only CD4 T cell populations that had entered into the immune response by also sorting and collecting only those cells that had divided at least 5 times by CFSE analysis.

last: McKinstry

first: Tara

middle: M

last: Strutt


title: Gene expression during ligands activation of RXR in activated RAW264.7 cells

city: Suzhou

first: feng

last: ma

state: Jiangsu

address: 218 Xinghu Street, B5-527

department: Suzhou Institute of Systems Medicine

country: China

institute: CAMS

summary: Ligands activation of RXR modulate host antivarl response. We used microarray to determine if 9cRA could regulate the antiviral gene expression in LPS- and polyI:C triggered RAW264.7 cells.

overall_design: RAW 264.7 cells were pre-treated with DMSO or 100nM of 9cis-retinoic acid for 16hours.  The cells were then stimulated with polyI:C (6ug transfected) or LPS (500ng/mL) for 2 hours.

first: Feng

last: Ma

first: Su-Yang

last: Liu

first: Bahram

last: Razani

first: Neda

last: Arora

first: Bing

last: Li

first: Hiroyuki

last: Kagechika

first: Peter

last: Tontonoz

first: Vanessa

last: Núñez

first: Mercedes

last: Ricote

first: Genhong

last: Cheng


title: Expression data from  Shp2f/f and SCSKO mice testis

city: Xaimen

first: Zhongxian

last: Lu

state: Fujian

address: Xiangan Nanlu Road

department: School of Pharmaceutical Sciences

institute: Xiamen University

summary: The ability of male reproduction is seriously dependent on Sertoli cells. However, the mechanisms governing the functional integrity of Sertoli cells remained largely unexplored. Tyrosine phosphatase protein Shp2 is expressed in germ, Leydig and Sertoli cells of mice testes. But the physiological role of Shp2 in the spermatogenesis was not fully understood. Thus, we conditionally deleted Shp2 gene in Sertoli cells using two transgenic models, and demonstrated that Shp2 deficiency caused infertility, excessive differentiation of SSCs and abnormal BTB in mice. To further discover the underlying mechanism of Shp2 regulation, we collected the mRNA of testes from wild type or knockout mice at 16.5 fetal day, Postnatal 3 days, 1 weeks, 2 weeks, and then screened the gene expression.

overall_design: Testis tissues from Shp2f/f and SCSKO mice were for RNA extraction and hybridization on Affymetrix microarrays.

last: LV

first: Xiaope

last: Hu

first: Zhenzhou

last: Tang


title: Sox9 controls self-renewal of oncogene targeted cells and links tumor initiation and invasion [Affymetrix]

status: Public on May 13 2015

city: Brussels

first: Jean-Christophe

last: Larsimont

state: Brussels

address: 808, route de Lennik

department: Faculté de médecine

institute: Université Libre de Bruxelles (ULB)

summary: Sox9 is a transcription factor expressed in most solid tumors. However, the molecular mechanisms underlying Sox9 function during tumorigenesis remain unclear. Here, using a genetic mouse model of basal cell carcinoma (BCC), the most frequent cancer in human, we show that Sox9 is expressed from the earliest step of tumor formation in a Wnt/β-catenin dependent manner. Deletion of Sox9 together with the constitutive activation of Hedgehog (HH) signaling completely prevents BCC formation and leads to a progressive loss of oncogene expressing cells. Transcriptional profiling of oncogene expressing cells with Sox9 deletion, combined with in vivo ChIP-sequencing uncovers a cancer-specific gene network regulated by Sox9 that promotes stemness, extracellular matrix (ECM) deposition and cytoskeleton remodeling while repressing epidermal differentiation. Our study identifies the molecular mechanisms regulated by Sox9 that links tumor initiation and invasion.

overall_design: Basal interfolicular cells expressing SmoM2 in presence or absence of Sox9 were FACS isolated and RNA was extracted before being hybridized Affymetrix microarrays. We then obtained a genes of list deregulated in absence of Sox9 by comparing Sox9 wild type and conditional knock-out SmoM2 expressing cells.

first: Cédric

last: Blanpain


title: Inhibition of Lymphotoxin-LIGHT Signaling Reduces the Interferon Signature in Rheumatoid Arthritis Patients

city: Cambridge

first: Jadwiga

last: Bienkowska

address: 45 Fayette Str Apt 3

institute: BiogenIdec

summary: Whole blood expression was profiled in Rheumatoid Arthiritis and SLE (Systemic LUPUS Erythomatosus) patients.

overall_design:
Expression in the whole blood of RA and SLE patients, comparing  gene expression signatures in SLE, and RA DMARD-IR and RA TNF-IR patients.
This is baseline whole blood expression data for 3 patient populations (SLE, RA DMARD-IR and RA TNF-IR) and 20 Controls.

first: Norm

last: Allaire

first: Jeff

last: Browning


title: Concurrent progress of reprogramming and gene-correction to overcome limitation of gene therapy of ALK2 mutant iPSCs

status: Public on May 12 2015

city: Daejeon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

country: South Korea

institute: Korea Institute of Oriental Medicine

summary: To ameliorate the cumbersome processes of reprogramming and subsequent gene-editing in vulnerable iPSCs, we have developed a greatly simplified one-step procedure, simultaneously introducing reprogramming and gene-editing components into human fibroblast cells. This not only serves to save time, labor, and costs, but opens up a new arena of research that is beyond the current application of gene-editing methodologies due to restrictive reprogramming concerns, inhibitory pluripotency maintenance requirements, and vulnerability of single-cell dissociated iPSCs.

overall_design: We generated iPSCs (mALK2-iPSCs) derived from Fibrodysplasia ossificans progressiva (FOP)-fibroblast cells carrying the ACVR1 p.R206H mutation and gene-corrected ALK2-iPSCs (cALK2-iPSCs). To identify gene-correction effects on global gene expression, gene expression profiling was measured in cALK2-iPSCs and mALK2-iPSCs, calibrated to WT-iPSCs with duplication.

first: Sun

last: Chung

first: Bu

middle: Y


title: Gene expression profiling of basal cells in rat epididymis

city: laval

first: Daniel

last: Cyr

state: Québec

address: 531 boulevard des Prairies

country: Canada

institute: INRS-IAF

summary: Basal cells represent a specific cell type in the epididymis, with specific functions. We performed gene expression analysis to detect differentially regulated genes in basal cells versus other, non-basal, cells in rat epididymis, in order to understand basal cell functions.

overall_design: Epididymides from 3 48-days old rats were isolated using magnetic separation to obtain basal cell and non-basal cell fractions. RNA was extracted and hybridized on Affymetrix RaGene 2.0 ST array. Experiments were done in triplicate.

first: Marion

last: Mandon


title: Cloning and Variation of Ground State Intestinal Stem Cells Super [expression & SNP studies]

city: Houston

first: Frank

last: McKeon

state: TX

address: 3455 Cullen Blvd

institute: University of Houston

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

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

overall_design: Refer to individual Series


title: IL-10 from intestinal macrophages prevents excessive innate immune responses to bacteria by limiting IL-23 synthesis

city: LA JOLLA

first: Jason

last: Greenbaum

state: CA

address: 9420 Athena Circle

department: Bioinformatics Core Facility

institute: LIAI

summary: Innate immune responses must be regulated in the intestine to prevent excessive inflammation. Here, using gene reporter mice, we show that a subset of mouse colonic macrophages constitutively produced the anti-inflammatory cytokine IL-10.  In mice infected with Citrobacter rodentium, which is considered similar to enteropathogenic Escherichia coli infection in humans, macrophage IL-10 was required to prevent intestinal pathology and to promote survival.  The synthesis of the proinflammatory cytokine IL-23 was significantly increased in infected mice with a myeloid cell specific deletion of IL-10 and the addition of IL-10 reduced in vitro IL-23 production by intestinal macrophages.  Furthermore, blockade of IL-23 led to reduced morbidity and mortality in the context of macrophage IL-10 deficiency.  Transcriptome analysis indicated that the reporter positive and negative colonic macrophage subsets were highly similar, but the reporter positive cells differed for the expression of CD163, an IL-10 target gene, suggesting an autocrine IL-10 signal, and when obtained from infected mice, they had reduced IL-23p19 mRNA.  Interestingly, only transfer of the reporter positive cells could rescue IL-10 deficient infected mice.  Therefore, these data indicate a pivotal role for a subset of intestinal macrophages that constitutively produces IL-10, perhaps acting in part in autocrine fashion, in controlling excessive innate immune activation, regulation of IL-23 production, and prevention of tissue damage after an acute bacterial infection in the intestine.

overall_design: Two replicates each of IL10+ and IL10- large intestinal macrophages. Data were normalized with the 'rma' function of the Bioconductor package, along with several GEO (GSM616132, GSM616136, GSM616140, GSM868296, GSM868297, GSM868298) and ArrayExpress (E-MEXP-3216: 04-M2WT, 05-M2WT, 06-M2WT) datasets.

first: Petra

last: Krause

first: Venetia

last: Morris

first: Yoon

last: Park

first: Unni

last: Bjoerheden

first: Tracy

last: Muffley

first: Jr-Wen

last: Shui

first: Gisen

first: Hilde

last: Cheroutre

first: Yun-Cai

last: Liu

first: Bjoern

last: Peters

first: Mitchell

last: Kronenberg

first: Masako

last: Murai


title: Exon array profiles of primary human Ewing sarcoma tumors

first: Elizabeth

middle: R

last: Lawlor

state: MI

summary: Affymetrix exon array data were generated from total RNA that was isolated from localized Ewing sarcoma biopsy specimens. Expression of transcript summarized data was compared to data generated from normal stem cells and normal adult tissues.

overall_design: Total RNA was extracted from 32 archived tumor biopsy specimens obtained from patients with localized Ewing sarcoma. Samples were analyzed by Affymetrix exon arrays using standard procedures. Data were compared to human neural crest and mesenchymal stem cells (in triplicate: GSE21511) as well as to 33 normal adult tissues (Affymetrix tissue controls; 11 tissues in triplicate: cel files obtained from: http://www.affymetrix.com/support/technical/sample_data/exon_array_data.affx). Normalization was achieved by RMA using Parkek Genomics Suite


title: Expression data from wildtype and Tfr1 heart KO mice

city: Durahm

first: Nancy

last: Andrews

address: 450 Research Drive

institute: Duke University

summary: We deleted Tfr1 in the heart to determine the role of Tfr1 in iron uptake in normal cardiac funciton  We used microarrays to identify global gene changes associated with deletion of Tfr1 in skeletal muscle

overall_design: We isolated RNA from WT and Tfr1 KO hearts at both postnatal day 5 and postnatal day 10.RNA was labaled and hibridized to Affymetrics microarrays.

first: Wenjing

last: Xu


title: Whole Blood Transcriptional Response to Pediatric Influenza Infection

city: Dallas

first: Damien

last: Chaussabel

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

summary: The objective of this study was to identify the transcriptional siganture of influenza infection in a pediatric populationfor comparison with other disease datasets.

overall_design: Pediatric influenza patients (n=19) had whole blood samples collected into Tempus tubes upon presentation at local hospital with follow up confirmation of influenza infection.  Age matched healthy controls were also collected (n=12) for microarray anlysis


title: Atlantic salmon (Salmo salar) liver transcriptome response to diets containing camelina products

city: St. John's

first: Xi

last: Xue

state: NL

address: 1 Marine Lab Road

department: Department of Ocean Sciences

institute: Memorial University of Newfoundland

summary: This study was performed to investigate assess the impacts of CO and/or CM containing diets on Atlantic salmon hepatic gene expression in order to identify candidate molecular biomarkers of responses to camelina-containing diets. Atlantic salmon were fed diets with complete or partial replacement of FO and/or FM with camelina oil (CO) and/or camelina meal (CM) in a 16-week trial (Control diet: FO; Test diet: 100% FO replacement with CO, with solvent-extracted FM and inclusion of 10% CM (100COSEFM10CM). A 44K microarray experiment identified liver transcripts that responded to 100COSEFM10CM (associated with reduced growth) compared to FO controls at week 16.

overall_design: Atlantic salmon were fed for 16 weeks with the FO or 100COSEFM10CM diet (three tanks per diet). Liver samples were taken from 7 fish from each tank at week 16. A universal reference design was used for the microarray experiment. For the test samples, RNA was used from individual livers of fish from the 2 treatment groups: FO and 100COSEFM10CM. For each treatment group we used 9 biological replicates (3 fish from each of 3 tanks). All test samples were labeled with Cy5. The common reference was a pool of 18 RNA samples from livers of fish from all individuals invovled in microarray experiment. The common reference was labeled with Cy3. Each individual test sample was hybridized together with the common reference sample on an array, so the experiment consisted of 18 arrays

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