title: Distinct effects of  topoisomerase II inhibitors on tumor cell lines (part 2)

status: Public on Jun 04 2013

city: Palo Alto

first: Baoxu

last: Pang

state: CALIFORNIA

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

summary: One major class of anti-cancer drugs targets topoisomerase II to induce DNA double-strand breaks and cell death of fast growing cells.  Here, we compare three members of this class - the antracyclines doxorubicin and aclarubicin, and a chemically unrelated compound, etoposide. Aclarubicin does not induce DNA breaks. We define a new activity for the antracyclines: unsupported histone eviction from ´open´ or loosely packed chromosomal areas reflecting exon and promoter regions. As a result, the epigenome and the transcriptome are strongly affected.

overall_design: Tissue culture cells were treated with doxorubicin, aclarubicin or etoposide for 2 hours. Then drugs were removed by extensive washing. cells were further cultured for indicated days before total RNA were extracted and compared to un-treated control.

first: Arno

last: Velds

first: Ron

last: Kerkhoven

first: Jacques

last: Neefjes


title: Generation of hematopoietic progenitor cell lines with myeloid and lymphoid potential using a conditional form of Hoxb8

status: Public on Jun 05 2013

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

country: USA

institute: St Jude Children's Research Hospital

summary: Investigation of immune-cell differentiation and function is limited by shortcomings of suitable and scalable experimental systems. Here we show that retroviral delivery of an estrogen-regulated form of Hoxb8 into mouse bone marrow cells can be used along with Flt3 ligand to conditionally immortalize early hematopoietic progenitor cells (Hoxb8-FL cells). Hoxb8-FL cells have lost self-renewal capacity and potential to differentiate into megakaryocytes and erythrocytes but retain the potential to differentiate into myeloid and lymphoid cells. They differentiate in vitro and in vivo into macrophages, granulocytes, dendritic cells, B lymphocytes and T lymphocytes that are phenotypically and functionally indistinguishable from their primary counterparts. Quantitative in vitro assays indicate that myeloid and B-cell potential of Hoxb8-FL cells is comparable to that of primary lymphoid-primed multipotent progenitors, whereas T-cell potential is diminished. The simplicity of this system and the unlimited proliferative capacity of Hoxb8-FL cells will enable studies of immune-cell differentiation and function.

overall_design: Hoxb8 expressing immortalized cells

first: Vanessa

last: Redecke

first: Ruiqiong

last: Wu

first: Jingran

last: Zhou

first: Vandana

last: Chaturvedi

first: Anthony

middle: A

last: High

first: Hans

last: Häcker


title: Expression data from wild-type and Dazap1 mutant mouse testes

status: Public on Jun 01 2013

city: Taipei

first: Hsiang-Ying

last: Chen

address: 128 Sec. 2, Academia Rd.

country: Taiwan

institute: IBMS

summary: Deleted in Azoospermia Associated Protein 1 (DAZAP1) is a ubiquitous RNA-binding protein that is highly expressed in the testis. It is a component of the hnRNP particles and shuttles between the nucleus and the cytoplasm. Mice expressing the DAZAP1-Fn mutant protein manifest both growth retardation and spermatogenic arrest before meiosis I. To elucidate the biological function(s) of DAZAP1 and to search for its natural RNA substrates, we compared the expression profiles of wild-type and Dazap1 mutant testes by cDNA microarrays.

overall_design: We used wild-type and Dazap1 mutant mouse testes. Each genotype has three replicates. 6 total samples were analyzed.

first: Hsiang

middle: Y

first: Paulin

last: Yen


title: Differentially regulated genes and exons from wild-type and Dazap1 mutant mouse testes

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

overall_design: Refer to individual Series


title: Expression data from clone sorted tumor endothelial subsets

city: Stanford

first: Daniel

last: Corey

state: Ca

address: 265 Campus Drive

institute: Stanford Univeristy

summary: Competitive interactions between emerging blood vessels determine the clonogenic contribution to developing vascualture. Using a multi-color cre reporter, CD31+CD45-VeCad+ clones were isolated and analyzed for expression differences.

overall_design: Tamoxifen labeled CD31+, CD45-VeCad+ tumor endothelial cells were isolated by FACS for analysis from separate tumors. The most frequent clone was compared to the least frequent clone between and across tumors.  The strain of mice is C57BL/6.


title: Non-telomeric role for Rap1 in regulating metabolism and protecting against obesity

city: New York

first: Frank

last: Yeung

state: New York

address: 540 First Ave

institute: Skirball Institute of Biomolecular Medicine

summary:
The mammalian telomere-binding protein Rap1 was found to have additional non-telomeric functions, acting as a transcriptional cofactor and a regulator of the NF-kB pathway. Here, we assess the effect of disrupting mouse Rap1 in vivo, and report on its unanticipated role in metabolic regulation and body weight homeostasis. Rap1 inhibition causes dysregulation in hepatic as well as adipose function. In addition, using a separation-of-function allele, we show that the metabolic function of Rap1 is independent of its recruitment to TTAGGG binding elements found at telomeres, and at other interstitial loci.
We have utilized microarrays to outline gene expression changes resulting from Rap1-deficiency when compared to the wild-type controls.

overall_design: Total RNA was isolated from the liver and intra-abdominal white adipose tissue of 3 female Rap1 deficient mice and 3 control littermates at 6-8 weeks of age. Rap1 deficient mouse embryonic fibroblasts (MEF) were isolated from 13.5 day embryos, immortalized with SV40LgT, and stably infected with vector, Rap1-wildtype, or Rap1 carrying an isoleucine to arginine mutation at amino acid 312. Total RNA was extracted from MEFs following a similar protocol. The samples were labeled, hybridized, and scanned using standard protocols by the Core Facility at NYU Langone Medical Center on Affymetrix GeneChip Mouse Genome 430 2.0 Arrays.

first: Cristina

middle: M

last: Ramirez

first: Pedro

last: Mateos-Gomez

first: Alexandra

last: Pinzaru

first: Giovanni

last: Ceccarini

first: Shaheen

last: Kabir

first: Carlos

last: Fernández-Hernando

first: Agnel

last: Sfeir


title: Expression analysis of control and low protein fed mouse offspring subsequently treated with multiple low doses of STZ

city: Houston

first: Aaron

middle: R

last: Cox

state: TX

address: 1102 Bates Ave.

department: Pediatrics - Endocrinology and Diabetes

institute: Baylor College of Medicine

summary:
Low protein (LP) during gestation leads to low birth weight and poor fetal growth, with altered islet development and glucose intolerance in adulthood. Additionally, LP offspring fail to regenerate their β-cells following depletion with streptozotocin (STZ), in contrast to control-fed offspring that are capable of β-cell regeneration.
Our objective was to identify genes and signalling pathways that may be critically altered in LP offspring rendering them susceptible to develop long term glucose intolerance and decreased β-cell plasticity.

overall_design: Pregnant Balb/C mice were place on a control (20% protein) or isocaloric low protein (8%) diet for the period of gestation, and then all dams were switch to the control diet at birth. Female offspring were injected with streptozotocin (35 mg/kg body weight; sodium citrate buffer 0.1 mol/L, pH 4.5) or vehicle (sham). Total RNA was extracted from pancreas of 30 day old female offspring (n=3) and hybridized to Affymetrix GeneChips.

first: David

last: Carter

first: Edith

middle: J

last: Arany

last: Hill


title: SAM domain polymerization links subnuclear clustering of PRC1 to silencing (Affymetrix)

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

summary: Polycomb group (PcG) proteins mediate heritable but reversible silencing of developmental regulator genes by modifying their chromatin configuration. Accumulating evidence documents a role for PcG proteins in regulating higher order chromatin structures likely by their clustering, however, underlying mechanisms and its impact on transcriptional regulation remain obscure. In this study, we found that subnuclear clustering of PRC1 at canonical PcG target genes depended on head-to-tail polymerization property of SAM domain of Phc2 and likely Phc1. We show that Phc2-SAM polymerization limits the dynamic nature of PRC1, thereby promotes stable association of PRC1 with PcG target genes and contributes to their robust silencing. Our findings suggest a novel model by which SAM polymerization of Phc2 modulates the structural organization of PcG complexes to enable robust yet reversible PcG-mediated repression during development.

overall_design: Wild type and Phc2L307R/L307R MEFs were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Rie

last: Suzuki


title: Impact of KLF2 expression on T cell genetic program

status: Public on May 31 2013

city: Dundee

first: Gavin

middle: Charles

last: Preston

address: 4 Old Hawkhill

department: Cell Signaling & Immunology

country: United Kingdom

institute: University of Dundee

summary:
On triggering of the T cell receptor CD8 T lymphocytes downregulate expression of the transcription factor KLF2.  KLF2 expression remains low as these cells differentiate to Cytotoxic T lymphocytes (CTL) but may be re-expressed depending on the local environmental signals.
We used retroviral transduction to enforce KLF2 expression in CTL to determine the impact of it re-expression on the CTL genetic program.

overall_design: T lymphocytes with a transgenic T cell receptor (P14 LCMV) isolated from murine spleens were activated with gp33-41 peptide for 2 days and transduced with empty vector (evGFP) or GFP-KLF2.  After differentiation to CTL in culture with Interleukin-2 for 2 further days, cells positive for GFP were isolated by Fluorescence Activated Cell Sorting and the RNA extracted for microarray analysis.

middle: C

first: Doreen

last: Cantrell


title: Pancreatic cancer biomarkers in mouse saliva

status: Public on Jun 12 2013

city: Los Angeles

first: Tristan

last: Grogan

state: CA

address: 911 Broxton Ave, 3rd floor

institute: UCLA

summary:
This is a pilot study.  We are trying to detect potential salivary biomarkers in mice with a pancreatic tumor.
Global gene expression profiling has shown great promise in high-throughput biomarker discovery for early disease detection in body fluids such as saliva, which is accessible, cost-effective, and non-invasive. However, this goal has not been fully realized because saliva, like many clinical samples, contains partially fragmented and degraded RNAs that are difficult to amplify and detect with prevailing technologies. Here, using nanogram scale salivary RNA as a proof-of-principle example, we describe our progress with a novel poly-A tail independent mRNA amplification strategy combined with the Affymetrix GeneChip Exon arrays. We defined a Salivary Exon Core Transcriptome (SECT) with highly similar expression profiles in healthy individuals verified by quantitative PCR. Informatics analysis of SECT provided important mechanistic insight to their potential origin and function. Finally we demonstrated the diagnostic potential of true exon level expression profiling approach with salivary exon biomarkers that accurately discriminated gender in healthy individuals.
Recent studies have demonstrated that discriminatory salivary biomarkers can be readily detected upon the development of systemic diseases such as pancreatic cancer, breast cancer, lung cancer and ovarian cancer. However, the utility of salivary biomarkers for the detection of systemic diseases has been undermined due to the absence of biological and mechanistic rationale why distal diseases from the oral cavity would lead to the development of discriminatory biomarkers in saliva. Here, we examine the hypothesis that pancreatic tumor-derived exosomes are mechanistically involved in the development of pancreatic cancer-discriminatory salivary transcriptomic biomarkers. We first developed a pancreatic cancer mouse model that yielded discriminatory salivary biomarkers by implanting the mouse pancreatic cancer cell line Pan02 into the pancreas of the syngeneic host C57BL/6. The role of pancreatic cancer-derived exosomes in the development of discriminatory salivary biomarkers was then tested by engineered a Pan02 cell line that is suppressed for exosome biogenesis, implanted into the C56BL/6 mouse and examine if the discriminatory salivary biomarker profile was ablated or disrupted. Suppression of exosome biogenesis results in the ablation of discriminatory salivary biomarker development. This study supports that tumor-derived exosomes provide a mechanism in the development of discriminatory biomarkers in saliva and distal systemic diseases.

overall_design: We analyzed saliva from 6 healthy mice and 6 mice with a pancreatic tumor using the Affymetrix Mouse Exon Genome 430 2.0 platform. Array data was processed by dChip. No techinical replicates were performed.

first: C

middle: S

last: Lau

first: N

last: Spielmann

first: Y

middle: L

last: Lin

first: G

last: Eibl

first: D

last: Elashoff

first: W

last: Fang

first: A

last: Moro

first: T

first: S

last: Chiang

last: Chia

middle: T

last: Wong


title: Expression data from intestine of HDAC1 and HDAC2 conditionally mutated mice

status: Public on Jun 08 2013

city: Sherbrooke

first: Martin

last: Lessard

state: Qc

address: 2000 College

department: Sherbrooke Research Centre

country: Canada

institute: Agriculture and AgriFood Canada

summary:
Acetylation and deacetylation of histones and other proteins depend on the opposing activities of histone acetyltransferases and histone deacetylases (HDACs), leading to either positive or negative gene expression changes. The use of HDAC inhibitors (HDACi) has uncovered a role for HDACs in the control of proliferation, apoptosis and inflammation. However, little is known of the roles of specific HDACs in intestinal epithelial cells (IEC). We investigated the consequences of ablating both Hdac1 and Hdac2 in murine IECs gene expression.
HDAC1 and HDAC2 conditionally mutated mice were provided by Dr EN Olson (University of Texas Southwestern Medical Center, Dallas, TX) (Montgomery et al., 2007). Floxed HDAC1 and HDAC2 mice were crossed with villin-Cre transgenic mice to insure specific intestinal epithelial cell gene deletion (Madison et al., 2002).

overall_design: Total RNAs from the colon of three control and three HDAC1/2 IEC-specific knockout mice were isolated with the Rneasy kit (Qiagen, Mississauga, ON, Canada).

first: François

last: Boudreau


title: Integrative investigation on breast cancer in ER, PR and HER2-defined subgroups using mRNA and miRNA expression profiling and cancer core pathway analysis

city: Helsinki

first: Xiaofeng

last: Dai

address: Haartmaninkatu 8 P.O. BOX 700

country: Finland

institute: Helsinki University Central Hospital

summary: Accurate characterization and understanding of the breast cancer subtypes is of crucial clinical importance to the heterogeneity of this disease. Several layers of information, including immunohistochemical markers, mRNA and microRNA expression profiles, and pathway analysis have been used for such purpose in several studies. However, a comprehensively integrative approach is currently missing. This paper provides microRNA and mRNA expression profiles, characterizing four breast tumor subtypes, as defined by four immunohistochemical markers. The defined sets of features were validated in two independent data sets at multiple levels, including unsupervised clustering and supervised classification. Moreover, the gene expression signatures of the tumor subtypes were screened by in-depth analysis of 12 cancer core pathways. We successfully identified and validated a novel breast cancer subtypes gene expression signature composed of 976 mRNAs and 69 miRNAs. Luminal and non-luminal tumors are shown to significantly differ both at the mRNA and miRNA levels. HER2 positive tumors are more closely related to triple negative tumors by mRNA profiling than by miRNA expression. Closely related miRNAs sharing the same targets may exert opposite roles during tumor progression. Besides the core cancer pathways, other pathways such as those controling biomass synthesis are shown to be important to enable the core basal subtype with additional progressive nature compared with the other triple negative tumors. Some therapeutic strategies are proposed for breast cancer treatment, including the combined blockage of MAPK/ERK and PI3K/Pten signalings for tumors with poor clinical outcome, and targeting Wnt and JAK/STAT and/or Hedgehog, depending on tumor subtypes, together with conventional chemotherapy with the purpose of achieving an eradicative outcome. The pathway analysis also reveals that the clinical strategy and pivotal targets need to be tuned according to different tumor subtypes. This study is the first attempt to elucidate breast cancer subtypes by combining microRNA and mRNA expression, immunohistochemical markers, and cancer core pathways. The results can avail the functional studies of the etiology of breast cancer and translated for clinical use given their intrinsic link in terms of immunohistochemistry and survival.

overall_design: This submission consists of microRNA profiles of 115 breast cancer tumors of several subtypes only.

first: Sofia

last: Khan

first: Tuomas

last: Heikkinen

first: Päivi

last: Heikkilä

first: Kristiina

last: Aittomäki

first: Carl

last: Blomgvist

first: Dario

last: Greco

first: Heli

last: Nevanlinna


title: Age-mediated transcriptomic changes in adult mouse substantia nigra

status: Public on May 29 2013

city: Seville

first: Lin

last: Gao

address: Avda Manuel Siurot, Hospital Virgen del Rocío

country: Spain

institute: Instituto de Biomedicina de Sevilla

summary:
Substantia nigra pars compacta (SNpc) is highly sensitive to normal aging and selectively degenerates in Parkinson's disease. Until now, molecular mechanisms behind SNpc aging have not been fully investigated using high throughput techniques.
Here, aging-associated early changes in transcriptome of SNpc were investigated comparing late middle-aged (18 months old) to young (2 months old) mice.

overall_design: Three age groups of C57 wild type mice were used in microarray analysis: young (2 months old), middle aged (10 months old), and late-middle aged (18 months old) mice. Four replicates were included in each age group and each replicate was pooled from 4 mice (4 mice/replicate x 4 replicates x 3 age groups). Total RNA was isolated from SNpc for hybridization on Affymetrix microarrays.

first: María

last: Hidalgo-Figueroa

first: Luis

last: Escudero

first: Juan

last: Díaz-Martín

first: José

last: López-Barneo

first: Alberto

last: Pascual


title: Age-mediated transcriptomic changes in adult mouse brain ventral tegmental area

summary:
Substantia nigra pars compacta (SNpc) is highly sensitive to normal aging and selectively degenerates in Parkinson's disease. However, ventral tegmental area (VTA), a region adjacent to SNpc, is less affected in PD. Until now, molecular mechanisms behind VTA aging have not been fully investigated using high throughput techniques.
Here, aging-associated early changes in transcriptome of VTA were investigated comparing late middle-aged (18 months old) to young (2 months old) mice.

overall_design: Three age groups of C57 wild type mice were used in microarray analysis: young (2 months old), middle aged (10 months old), and late-middle aged (18 months old) mice. Four replicates were included in each age group and each replicate was pooled from 5 mice (5 mice/replicate x 4 replicates x 3 age groups). Total RNA was isolated from VTA for hybridization on Affymetrix microarrays.


title: Gene expression profile of liver from adult and neonatal Balb/c mice after listeriosis

city: Dallas

first: Josiah

last: Hawkins

address: 5323 Harry Hines Boulevard

institute: UT Southwestern

summary:
Expression profiling by microarray was used with a murine listeriosis model to better understand increased susceptibility of preterm neonates to infection.
We used DNA microarray to identify genes that were differentially expressed in liver of adult and neonatal Balb/c mice after listeriosis infection.

overall_design: A murine listeriosis model was established. The methods for culturing and counting the Listeria monocytogenes (strain CNL 85/163) had been described in previous publications. The Listeria was injected intraperitoneally using a 1-mL U-100 insulin syringe with a 30 gauge needle. Doses of Listeria monocytogenes used were based on work by our laboratory showing that similar bacterial colony counts were obtained with 4.2 x 10^5 total Listeria per adult mouse and 150 Listeria per gram for 3 to 5 day old neonatal mice. In neonatal mice, great care was taken to void deep intraperitoneal injection towards the viscera, or across the central abdominal vessels. At specified time points, liver was removed upon animal sacrifice and immediately flash frozen in liquid nitrogen and stored at -80 degrees Centigrade. Three adult mice and three neonatal mice were used at each time point.

first: Seth

first: QingQing

last: Wu

first: Yanxia

last: Wang

first: C

last: Lu


title: Immunoglobulin-like domain receptor 1 mediates fat-stimulated cholecystokinin secretion.

status: Public on May 23 2013

city: Durham

first: Rashmi

last: Chandra

state: NC

address: Research Drive

department: Medicine/GI

institute: Duke University Medical Center

summary: Cholecystokinin (CCK) is a satiety hormone produced by discrete enteroendocrine cells scattered among absorptive cells of the small intestine. CCK is released into blood following a meal; however, the mechanisms inducing hormone secretion are largely unknown. Ingested fat is the major stimulant of CCK secretion. We recently identified a novel member of the lipoprotein remnant receptor family known as immunoglobulin-like domain containing receptor 1 (ILDR1) in intestinal CCK cells and postulated that this receptor conveyed the signal for fat-stimulated CCK secretion. In the intestine, ILDR1 is expressed exclusively in CCK cells. Orogastric administration of fatty acids elevated blood levels of CCK in wild type but not ILDR1-deficient mice, although the CCK secretory response to trypsin inhibitor was retained. The uptake of fluorescently labeled lipoproteins in ILDR1-transfected CHO cells and release of CCK from isolated intestinal cells required a unique combination of fatty acid plus HDL. CCK secretion secondary to ILDR1 activation is associated with increased [Ca2+]i consistent with regulated hormone release. These findings demonstrate that ILDR1 regulates CCK release through a mechanism dependent on fatty acids and lipoproteins and that absorbed fatty acids regulate gastrointestinal hormone secretion.

overall_design: GFP positive cells from CCK-EGFP transgenic mice were isolated by FACS and the expression profile was compared with an equal number of non-fluorescent intestinal cells.

first: Rodger

last: Liddle


title: Hippocampal gene expression profiling of a model of Alzheimer`s Disease upon treatment with the ACE inhibitor captopril

status: Public on May 14 2013

city: Zurich

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

country: Switzerland

institute: ETH Zurich

summary: Extracellular senile plaques of amyloid beta (Abeta) are a pathological hallmark in brain of patients with Alzheimer`s Disease (AD). Abeta is generated by the amyloidogenic processing of the amyloid precursor protein (APP). Concomitant to Abeta load, AD brain is characterized by an increase in protein level and activity of the angiotensin-converting enzyme (ACE). ACE inhibitors are a widely used class of drugs with established benefits for patients with cardiovascular disease. However, the role of ACE and ACE inhibition in the development of Abeta plaques and the process of AD-related neurodegeneration is not clear since ACE was reported to degrade Abeta. To investigate the effect of ACE inhibition on AD-related pathomechanisms, we used Tg2576 mice with neuron-specific expression of APPSwe as AD model. From 12 months of age, substantial Abeta plaque load accumulates in the hippocampus of Tg2576 mice as a brain region, which is highly vulnerable to AD-related neurodegeneration. The effect of central ACE inhibition was studied by treatment of 12 month-old Tg2576 mice for six months with the brain penetrating ACE inhibitor captopril. At an age of 18 months, hippocampal gene expression profiling was performed of captopril-treated Tg2576 mice relative to untreated 18 month-old Tg2576 controls with high Abeta plaque load. As an additional control, we used 12 month-old Tg2576 mice with low Abeta plaque load. Whole genome microarray gene expression profiling revealed gene expression changes induced by the brain-penetrating ACE inhibitor captopril, which could reflect the neuro-regenerative potential of central ACE inhibition.

overall_design: Microarray gene expression profiling was performed of hippocampi isolated from aged, 18 month-old Tg2576 (APPSwe-transgenic) AD mice with high Abeta plaque load relative to age-matched Tg2576 mice, which were treated for 6 months with the centrally active ACE inhibitor captopril. Another study group consisted of 12 month-old Tg2576 mice with low Abeta plaque load. In total, three study groups were analyzed, i.e. (i) 18 month-old untreated Tg2576 mice with high Abeta plaque load, (ii) age-matched Tg2576 mice treated for 6 months with the brain-penetrating ACE inhibitor captopril (20 mg/kg body weight/day in drinking water), and (iii) untreated 12 month-old Tg2576 mice with low Abeta plaque load reflecting the time point when captopril treatment was initiated. Two biological replicates were made of each group, and total hippocampal RNA of four mice was pooled for one gene chip.

first: Said

last: AbdAlla


title: Transcription Factor Foxo1 Controls Memory CD8+ T Cell Responses To Infection [Affymetrix]

status: Public on May 16 2013

first: Willey

last: Liao

state: NY

address: 101 Avenue of the Americas

department: Bioinformatics

institute: New York Genome Center

summary: Memory T cells provide immunity against pathogen reinvasion, but mechanisms of their long-term maintenance is unclear.  Here we show that mice with the deletion of the transcription factor Foxo1 in activated CD8+ T cells had defective secondary but not primary responses to Listeria monocytogenes infection.  Compared to short-lived effector T cells, memory precursor effector T cells expressed higher amounts of Foxo1 that promoted their generation and maintenance.  Gene expression profiling and chromatin immunoprecipitation sequencing experiments revealed the chemokine receptor CCR7 and the transcription factor TCF1 as novel Foxo1-bound target genes with critical functions in memory T cell trafficking and transcriptional regulation.  These findings demonstrate that Foxo1 is selectively incorporated into the genetic program that regulates memory but not effector CD8+ T cell responses to infection.

overall_design: Wild-type and GzmB-cre Foxo1fl/fl CD27hiKLRG1lo OT-I T cells were isolated by FACS sorting at 7 days post LM-OVA infection.  RNA was prepared with the miRNeasy kit according to the manufacturer’s instructions (Qiagen). RNA amplification, labeling and hybridization to Mouse 430 2.0 Array chips (Affymetrix) were carried out at the Genomics Core Facility of Memorial Sloan-Kettering Cancer Center.

first: Myoungjoo

middle: V

last: Kim

first: Weiming

last: Ouyang

first: Will

first: Michael

middle: Q

last: Zhang

first: Ming

middle: O

last: Li


title: Microarray profiling of primary neurons transduced with shRNA for multiple ASD-implicated genes

city: Groton

first: Thomas

last: Lanz

state: CT

address: Eastern Point Rd

department: Multi-Omics & Biomarkers

institute: Pfizer

summary: Austism spectrum disorder (ASD) is a heterogeneous behavioral disease most commonly characterized by severe impairment of social engagement and the presence of repetitive activities. The molecular etiology of ASD is still largely unknown despite a strong genetic component.  Part of the difficulty in turning genetics into disease mechanisms and potentially new therapeutics is the sheer number and diversity of the genes that have been associated with ASD and ASD symptoms.  The goal of this work is to use shRNA-generated models of genetic defects proposed as causative for ASD to identify the common pathways that might explain how they produce a common clinical outcome.  Transcript levels of Mecp2, Mef2a, Mef2d, Fmr1, Nlgn1, Nlgn3, Pten, and Shank3 were knocked-down in mouse primary neuron cultures using shRNA/lentivirus constructs. Whole genome expression analysis was conducted for each of the knock-down cultures as well as a mock-transduced culture and a culture exposed to a lentivirus expressing luciferase.  Gene set enrichment and a causal reasoning engine were employed to indentify pathway level perturbations generated by the transcript knock-down. Quantitation of the shRNA targets confirmed the successful knock-down at the transcript and protein levels of at least 75% for each of the genes.  After subtracting out potential artifacts caused by transfection and viral infection, gene set enrichment and causal reasoning engine analysis showed that a significant number of gene expression changes mapped to pathways associated with neurogenesis, long-term potentiation, and synaptic activity.  This work demonstrates that despite the complex genetic nature of ASD, there are common molecular mechanisms that connect many of the best established autism candidate genes.  By identifying the key regulatory checkpoints in the interlinking transcriptional networks underlying autism, we are better able to discover the ideal points of intervention that provide the broadest efficacy across the diverse population of autism patients.

overall_design: n=4 per group.  Luciferase shRNA used as control group for shRNA to various gene targets.

first: Mathew

last: Pletcher


title: Temporal Gene Expression Patterns in the skin of D6 null and wild type mice after inflammation with the chemical irritant TPA

status: Public on May 28 2013

city: London

first: Helen

last: Baldwin

address: 5 University Street

institute: University College London

summary:
The chemokine decoy receptor D6 internalises and degrades inflammatory CC chemokines enabling resolution of inflammation. In D6 deficient mice (D6 KO), otherwise innocuous cutaneous inflammatory stimuli induce a grossly exaggerated inflammatory response that bears many similarities to human psoriasis. In the present study we have used transcriptomic approaches to define the molecular make up of this response.
The result of such analysis highlights potential roles for a number of cytokines iniating and maintaining psoriasis like pathology. Most compellingly, we provide data indicating a key role for the type I interferon pathway in the emergence of this pathology

overall_design: Backskin of D6 null mice was painted with three successive applications of 50uM TPA (in acetone), 24 hours apart. Control (labelled as day 0 or untreated) were treated with acetone only. After the three successive applications of TPA, pathology was left to develop for 1, 2, 4 or 6 days and backskin was taken for microarray analysis at each of these time points.   To identify differentially expressed genes, comparisons were made between D6 KO and WT mice at each time point (D6 KO vs WT mice at day 0, day 1, day 2, day 4 or day 6).  Significantly differentially expressed genes (p<0.05 according to an unpaired t-test) and up or down regulated more than 3 fold were identified ay each time point and selected for further analysis.

first: Vicky

last: King

last: Jamieson

first: Robert

last: Nibbs

first: José

last: Carballido

first: Marcus

last: Jaritz

first: Antal

last: Rot

first: Gerard

last: Graham


title: Molecular profiling of tumor-specific Th1 cells activated in vivo

status: Public on May 15 2013

city: Oslo

first: Alexandre

last: Corthay

address: Rikshospitalet

department: Department of Biosciences

country: Norway

institute: University of Oslo

summary:
Expression data from mouse tumor-specific CD4+ T cells
The central role of tumor-specific Th1 cells in fighting cancer is becoming increasingly appreciated. However, little is known about how these cells are generated in vivo. Here, we used flow cytometry and gene expression microarrays to characterize the primary activation and Th1 differentiation of naïve tumor-specific CD4+ T cells in a mouse model for cancer immunosurveillance. We took advantage of T cell receptor-transgenic mice where CD4+ T cells recognize a tumor-specific antigen secreted by the major histocompatibility complex (MHC) class II-negative MOPC315 myeloma. Cancer cells were injected subcutaneously and T cell activation was analyzed in draining lymph nodes and at the incipient tumor site at day +8. After activation and migration to the incipient tumor site, tumor-specific CD4+ T cells had 29 up-regulated molecules (CD2, CD5, CD11a, CD18, CD25, CD28, CD44, CD45, CD49d, CD51, CD54, CD69, CD71, CD83, CD86, CD90, CD95, CD102, CD122, CD153, CD166, CD200, CD249, CD254, CD274, CD279, Ly6C, MHC class I, and CCR7) and 5 down-regulated molecules (CD27, CD31, CD45RB, CD62L, and CD126) on the surface.  The activated CD4+ T cells produced interferon , a cytokine consistent with Th1 polarization, and also interleukin 2 (IL-2), IL-3, IL-10, and tumor necrosis factor . Activation of naïve tumor-specific CD4+ T cells in draining lymph node resulted in the up-regulation of 609 genes and down-regulation of 284 genes. Bioinformatics analysis of genes differentially expressed identified functional pathways related to tumor-specific Th1 cell activation. This study may represent a useful resource to guide the development of Th1-based immunotherapy for cancer.

overall_design: TCR-transgenic SCID mice (n = 12-15) were injected s.c. on the flank with 10(5) MOPC315 cells suspended in 250 µl ice-cold growth factor-reduced Matrigel. At day +8, draining axillary LN were dissected out and pooled, single-cell suspensions were made and staining with mAb was carried out. Activated tumor-specific CD4+ GB113+ T cells were sorted by FACSAria (≥ 95% pure) in three independent experiments. Naïve tumor-specific CD4+ control T cells were obtained from pooled LN from naive TCR-transgenic SCID mice and treated identically in two independent experiments.

first: Kristina

last: Berg-Lorvik

first: Ole-Audun

last: Werner-Haabeth

first: Trevor

last: Clancy

first: Bjarne

last: Bogen


title: TH-MYCN Mice with Caspase-8 Deficiency Develop Advanced Neuroblastoma with Bone Marrow Metastasis

status: Public on May 22 2013

city: Memphis

first: David

last: Finkelstein

address: 332 N. Lauderdale St.

institute: St Jude Children's Research Hospital

summary: Neuroblastoma, the most common extracranial pediatric solid tumor, is responsible for 15% of all childhood cancer deaths.  Patients frequently present at diagnosis with metastatic disease, particularly to the bone marrow.  Advances in therapy and understanding of the metastatic process have been limited due in part, to the lack of animal models harboring bone marrow disease.  The widely employed transgenic model, the TH-MYCN mouse, exhibits limited metastasis to this site.  Here we establish the first genetic immunocompetent mouse model for metastatic neuroblastoma with enhanced secondary tumors in the bone marrow.  This model recapitulates two frequent alterations in metastatic neuroblasoma, over-expression of MYCN and loss of caspase-8 expression.  In this model, the mouse caspase-8 gene was deleted in neural crest lineage cells by crossing a TH-Cre transgenic mouse with a caspase-8 conditional knockout mouse. This mouse was then crossed with the neuroblastoma prone TH-MYCN mouse.  While over-expression of MYCN by itself rarely caused bone marrow metastasis (5% average incidence), combining MYCN overexpression and caspase-8 deletion significantly increased bone marrow metastasis (37% average incidence).  Loss of caspase-8 expression did not alter the site, incidence, or latency of the primary tumors.  However, secondary tumors were detected in the bone marrow of these mice as early as week 9-10. The mouse model described in this work is a valuable tool to enhance our understanding of metastatic neuroblastoma and treatment options and underscores the role of caspase-8 in neuroblastoma progression.

overall_design: Survey of spontateous 24 NB tumors and 5 bone marrow samples in wt and transgenic mice.

first: Tal

last: Teitz

first: Madoka

last: Inoue

middle: B

last: Valentine

first: Kejin

last: Zhu

first: Jerold

middle: E

last: Rehg

first: Wei

last: Zhao

first: Yong-Dong

last: Wang

first: Melisa

middle: D

last: Johnson

first: Chrisopher

last: Calabrese

first: Marcelo

last: Rubinstein

first: Razqallah

last: Hakem

first: William

last: Weiss

first: Jill

last: Lahti


title: Adult mucous neck cells from corpus gastric epithelium

city: Houston.

first: Jason

last: Mills

state: T

address: One Baylor Plaza

department: Gastroenterology, Medicine

summary: In this experiment, mucous neck cells from the gastric epithelium of normal, adult C57/B6 mice were laser-capture microdissected to determine gene expression in neck cells relative to pit cells, parietal cells, and zymogenic cells, whose expression profiles were previously deposited in GEO.

overall_design: In this screening experiment, only a single replicate Mouse Genome 430 2.0 GeneChip was generated from laser-capture microdissected cells in the neck region of the gastric unit (identified by positive staining with AlexaFluor-488-GS-II lectin positivity and/or position in the middle of the gastric unit with low labeling with E-cadherin and seconndary Alexafluor-488). RNA was purified by PicoPure kit, RNA integrity verified on Agilent Bioanalyzer, and total RNA pooled from multiple dissections and multiple mice to make ~100 ng RNA, which was then amplirifed, labeled, and fragmented (by Arctureus RiboAmp HS kit followed by the RNA Amplification and Labeling Kit from Enzo Life Sciences). Biotinylated cRNA probes were hybridized to the GeneChips. Given the inevitable contamination of the RNA with RNA from parietal cells, this GeneChip is used only in comparisons with laser-captured parietal cells described in GSE5018 as a baseline reference.

first: Won

last: Huh


title: Expression data of mouse embryo brain

status: Public on May 10 2013

city: Toyama

first: Seiji

last: Yamamoto

state: Toayma

address: 2630 Sugitani

department: Department of Pathology

institute: University of Toyama

summary:
Wheather hematopoietic cells contribute to angiogenesis in developing brain, we utilized macrophage deficient mouse embryo.
We used microarrays to detect down-regulated genes in KO embryo brain.

overall_design: KO and WT mouse E10.5 embryo brains were collected for RNA extraction and hybridization on Affymetrix microarrays.

first: Erika

last: Azuma


title: Expression data from GPR15+CD4+ and GPR15-CD4+ T cells in LILP

status: Public on May 09 2013

city: New York

first: Dan

last: Littman

address: 540 First Avenue, SKI 2-17

institute: NYU School of Medicine

summary:
GPR15 is an orphan G-protein coupled receptor and its expression is abundant among T cells in the large intestine lamina propria.
We used microarrays to examine charateristics of GPR15- vs GPR15+ CD4+ T cells in LILP and identified distinct classes of up-regulated genes in GPR15+ CD4+ T cells.

overall_design: We have generated GFP knock-in mice in GPR15 locus and used GFP as a maker for GPR15 expression. In heterozygous mice, GPR15+CD4+ T cells and GPR15-CD4-T cells were sorted and RNA was prepared from them.

first: Sangwon

last: Kim


title: Expression data from c-Myc+ Notch1 T-ALL initiating cells

first: Bryan

last: King

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

summary: Missense FBXW7 mutations are prevalent in various tumors, including T-cell acute lymphoblastic leukemia (T-ALL). To study the effects of such lesions, we generated animals carrying regulatable Fbxw7 mutant alleles. We show here that these mutations specifically bolster cancer-initiating cell activity in collaboration with Notch1 oncogenes, but spare normal hematopoietic stem cell function. We were also able to show that FBXW7 mutations specifically affect the ubiquitylation and half-life of c-Myc protein, a key T-ALL oncogene. Using animals carrying c-Myc fusion alleles, we connected Fbxw7 function to c-Myc abundance and correlated c-Myc expression to leukemia-initiating activity.

overall_design: Three independent Notch1 T-ALL were derived on c-Myc-GFP background and sorted from the spleen of leukemic mice on the basis of GFP expression for RNA extraction and hybridization on Affymetrix microarrays

first: Iannis

last: Aifantis


title: Comparison of gene expression in NOD versus B6 splenic B cell subsets.

city: Concord

first: Pablo

last: Silveira

state: NSW

address: Gate 3 Hospital Rd, Concord Hospital

country: Australia

institute: ANZAC Research Institute

summary: NOD mice are an inbred strain that display enhanced MZ B cell differentiation from an early age. Interestingly, several lines of evidence implicate MZ B cells in this strain as important contributors to the T cell mediated beta cell destruction associated with the development of type 1 diabetes (T1D). In order to develop a better understanding of the underlying causes for augmented MZ B cell production in NOD mice, we obtained the transcriptional profiles of FO and MZ subsets and TR precursors from NOD mice and compared them to those of the B6 strain.

overall_design: Red cell depleted splenocyte suspensions from from eight pooled NOD or B6 mice were stained with biotinylated anti-CD3ε (145-2C11) and CD11b (M1/70, BD Biosciences) antibodies followed by anti-biotin Microbeads (Miltenyi Biotec, Bergisch Gladbach, Germany). Separation of unlabeled B cells from samples was achieved to a >93% purity (as determined by flow cytometry) by negative depletion with an autoMACS cell sorter (Miltenyi Biotec). These cells were then stained with a cocktail of: non-stimulatory Affinipure goat anti-mouse-IgM-FITC Fab fragments from Jackson Immunoresearch; anti-CD21/35-PE (7G6), anti-CD24-biotin (30-F1; with streptavidin-PerCP secondary), B220-APC-Cy7 (RA36B2) from BD Biosciences; anti-CD93-APC (AA4.1), anti-CD23-PE-Cy7 (B3B4) from eBiosciences. T1, T2FO, T3, FO, T2MZ and MZ subsets were then separated with a FACSAria Cell Sorter (BD Biosciences). This process was repeated in an independent experiment in order to generate a duplicate sample of each B cell subset from NOD and B6 mice. Labelled cRNA from B cell samples were hybridized to Mouse Genome 430 2.0 Arrays.

middle: A


title: Age-mediated transcriptomic changes in adult mouse substantia nigra and ventral tegmental area

first: Lin

last: Gao

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

overall_design: Refer to individual Series

first: María

last: Hidalgo-Figueroa

first: Luis

last: Escudero

first: Juan

last: Díaz-Martín

first: José

last: López-Barneo

first: Alberto

last: Pascual


title: Stage-specific regulation of reprogramming to iPSCs by Wnt signaling and Tcf proteins

status: Public on May 01 2013

first: Kathrin

last: Plath

address: 615 Charles E. Young Drive South

summary: Wnt signaling is intrinsic to mouse embryonic stem cell self-renewal. Therefore it is surprising that reprogramming of somatic cells to induced pluripotent stem cells (iPSCs) is not strongly enhanced by Wnt signaling. Here, we demonstrate that active Wnt signaling inhibits the early stage of reprogramming to iPSCs, while it is required and even stimulating during the late stage. Mechanistically, this biphasic effect of Wnt signaling is accompanied by a change in the requirement of all four of its transcriptional effectors: Tcf1, Lef1, Tcf3, and Tcf4. For example, Tcf3 and Tcf4 are stimulatory early but inhibitory late in the reprogramming process. Accordingly, ectopic expression of Tcf3 early in reprogramming combined with its loss-of-function late enables efficient reprogramming in the absence of ectopic Sox2. Together, our data indicate that the step-wise process of reprogramming to iPSCs is critically dependent on the stage-specific control and action of all four Tcfs and Wnt signaling.

overall_design:
For genome wide expression analysis:
A. Tcf3 wt and ko OSK iPS cells were analyzed (ko was performed from 2 different cell lines).
B. Tcf3 ko OCK iPS cells were analyzed (2 different cell lines)
C. Tcf3 wt and ko OCK reprogramming timecourse was analyzed at the indicated days after the beginning of the reprogramming.
D. OCK partial iPS cell clone treated with control siRNA or 2 independent Tcf3 siRNA and RNA were analyzed 48hr after siRNA treatment.

first: Ritchie

last: Ho

first: Bernadett

last: Papp

first: Jackson

last: Hoffman

first: Bradley

last: Merrill


title: Ectopic expression of AP4 in human colorectal cancer cells DLD-1 for different times

city: Munich

first: Rene

last: Jackstadt

address: Thalkirchnerstrasse 36

country: Germany

institute: Ludwigs maximilians University Munich

summary: To characterize the transcriptome of the transcription factor AP4 DLD-1 cells were infected with AP4 coding viruses for different periods of time. Adenovirus amplification and purification was performed as previously described (He et al., 1998). The minimal amount of virus needed to reach more than 90% infection efficiency was determined by monitoring GFP signals with fluorescence microscopy. DLD-1 cells were infected in serum-free medium with adenovirus for 3 hours. After removal an equal amount of medium containing 20% FBS was added.

overall_design: This study contains 17 Samples with different conditions/samples: Triplicates of non-infected cells as a control, triplicates of infections with an AP4 coding viruses harvested after 12, 24 and 48 hours and, as an additional control, a triplicate of cells infected with a GFP expressing virus harvested after 24 hours and unicates harvested after 12 and 48 hours.

first: H

last: Hermeking

first: R


title: Gene expression data for three mouse auditory brainstem nuclei at two times of development

city: Lausanne

first: Nicolas

last: Michalski

address: AI 2104 (Bâtiment AI) Station 19

department: BMI

institute: EPFL

summary: Genome-wide gene expression was obtained in three auditory brainstem nuclei (defined below), at two different ages in mice, postnatal day (P)3 and P14. The primary aim was to identify genes which are differentially expressed between the medial nucleus of the trapezoid body (MNTB) and the superior olive (LSO), at both age groups.

overall_design: Tissue samples from the ventral cochlear nucleus (VCN), the medial nucleus of the trapezoid body (MNTB) and the lateral superior olive (LSO) were collected from 200 μm thick fresh transverse mouse brainstem slices prepared with a vibratome tissue slicer. Individual brainstem nuclei were dissected out with fine forceps under optical control with a binocular. For each nucleus (VCN, MNTB, and LSO), the tissue from six male C57Bl6 mice at postnatal day (P) 3, and from three male C57Bl6 mice at P14 was pooled. The RNA was isolated with the RNeasy Micro kit (Qiagen); RNA samples were amplified using a WT ovation Pico RNA amplification (Nugen, CA, USA). The cDNA was hybridized onto mouse Affymetrix microarrays 430 2.0 (Affymetrix, Santa Clara, USA).

first: Le

last: Xiao

first: Elin

last: Kronander

first: Enida

last: Gjoni

first: Christel

last: Genoud

first: Graham

last: Knott

first: Ralf

last: Schneggenburger


title: Dicer deficiency reveals microRNAs predicted to control gene expression in developing adrenal cortex

city: Detroit

first: Katherine

last: Gurdziel

state: MI

address: 275 E. Hancock

institute: Wayne State University

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


title: MYCN and HDAC2 cooperate to repress miR-183 signaling in neuroblastoma.

city: Heidelberg

first: Marco

last: Lodrini

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center

summary: MYCN is a master regulator controlling many processes necessary for tumor cell survival. Here, we unravel a microRNA network that causes tumor suppressive effects in MYCN-amplified neuroblastoma cells. In profiling studies, histone deacetylase (HDAC) inhibitor treatment most strongly induced miR-183. Enforced miR-183 expression triggered apoptosis, and inhibited anchorage-independent colony formation in vitro and xenograft growth in mice. Furthermore, the mechanism of miR-183 induction was found to contribute to the cell death phenotype induced by HDAC inhibitors. Experiments to identify the HDAC(s) involved in miR-183 transcriptional regulation showed that HDAC2 depletion induced miR-183. HDAC2 overexpression reduced miR-183 levels and counteracted the induction caused by HDAC2 depletion or HDAC inhibitor treatment. MYCN was found to recruit HDAC2 in the same complexes to the miR-183 promoter, and HDAC2 depletion enhanced promoter-associated histone H4 pan-acetylation, suggesting epigenetic changes preceded transcriptional activation. These data reveal miR-183 tumor suppressive properties in neuroblastoma that are jointly repressed by MYCN and HDAC2, and suggest a novel way to bypass MYCN function.

overall_design: BE(2)-C neuroblastoma cells were treated with the pan-HDACi HC-toxin (20 nM) or solvent control (methanol) for 24 h in three replicates, respectively.Total RNA was isolated using miRNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. RNA was eluted in water. The quality of total RNA was checked by gel analysis using the total RNA Nanochip assay on an Agilent 2100 Bioanalyzer.

first: Ina

last: Oehme

first: Christina

last: Schroeder

first: Till

last: Milde

first: Marie

last: Schier

first: Annette

last: Kopp-Schneider

first: Johannes

middle: H

last: Schulte

first: Matthias

last: Fischer

first: Katleen

last: De Preter

first: Filip

last: Pattyn

first: Mirco

last: Castoldi

first: Martina

middle: U

last: Muckenthaler

first: Andreas

last: Kulozik

first: Frank

last: Westermann

first: Olaf

last: Witt

first: Hedwig

last: Deubzer


title: Transcriptomic modulation by adenosine 2A receptors in normal and endotoxemic myocardium

city: Gold Coast

first: Kevin

middle: John

last: Ashton

state: QLD

address: University Drive

department: Health Sciences & Medicine

institute: Bond University

summary: Analysis of venticular myocardium from adenosine 2A receptors (A2AR) knockouts following LPS stimulation. Results provide insight into the molecular components of A2AR mediated protection, but also reveal pathogenetic components of endotoxemic myocarditis as a result of LPS exposure. These findings demonstrate that intrinsic A2AR activity exerts limited transcriptional effects in unstressed heart, modifying G-coupled cAMP/PKA signal paths. LPS-dependent injury and dysfunction is associated with profound up-regulation of inflammatory/immune processes, fibrotic and cell death paths, and NF-kB, Erk/MAPK and JAK/Stat signaling, with shifts in multiple determinants of cardiac contraction and survival. Intrinsic A2AR activity modulates key aspects of these inflammatory responses, involving MAPK, JAK/Stat and NF-kB signaling

overall_design: Total RNA obtained from adenosine 2A receptor knockout or wild-type murine ventricular myocardium that were treated for 24 hours with either saline or lipopolysaccharide (n=4/group).

first: Melissa

last: Reichelt

first: S

last: Mustafa

first: Bunyen

last: Teng

first: Catherine

last: Ledent

first: Lea

last: Delbridge

first: Polly

last: Hofmann

first: R

middle: R

last: Morrison

first: John

middle: P

last: Headrick


title: Transcriptome analysis of CD16/CD62L neutrophil subsets during human experimental endotoxemia

city: Nijmegen

first: Stan

middle: de

last: Kleijn

address: Kapittelweg 29

department: Laboratory of pediatric infectious diseases

country: Netherlands

institute: Radboud University Nijmegen Medical Centre

summary:
During systemic inflammation, different neutrophil subsets are mobilized to the blood circulation. These neutrophil subsets can be distinguished from normal circulating neutrophils (CD16bright/CD62Lbright) based on either an immature CD16dim/CD62Lbright or a CD16bright/CD62Ldim phenotype. Interestingly, the latter neutrophil subset is known to suppress lymphocyte proliferation ex vivo, but the underlying mechanism is largely unknown.
We performed transcriptome analysis on the different neutrophil subsets to identify changes that are relevant for their functions. Neutrophil subsets were isolated by FACS sorting from the blood of healthy volunteers who were administered a single dose of lipopolysaccharide (LPS). The transcriptome was determined by microarray. The mobilized neutrophil subsets were characterized by specific transcriptome profiles reflecting their phase in neutrophil lifespan. Interestingly, the CD16bright/CD62Ldim suppressive neutrophils showed an interferon-induced transcriptome profile. This was confirmed by stimulation of peripheral neutrophils with IFNgamma. These cells acquired the capacity to suppress lymphocyte proliferation through the expression of programmed death ligand 1 (PD-L1).
These data demonstrate that the suppressive phenotype of the neutrophil subset is induced by IFNgamma. Specific stimulation of neutrophils might have a pivotal role in regulating lymphocyte-mediated inflammation and autoimmune disease.

overall_design: After LPS infusion, blood was taken at t=0 and t=4 hours. Neutrophils were FACS sorted based on CD16 and CD62L expression. Gene expression of neutrophil subsets was assessed relative to t=0 as control.

last: de Kleijn

first: J

last: Langereis


title: MLL regulated genes in LSK/CD48- hematopoietic stem cells

status: Public on May 24 2013

city: Hanover

first: Erika

middle: Louiez

last: Artinger

state: New Hampshire

address: 725 Remsen

department: Genetics

institute: Dartmouth Medical School

summary:
The histone methyltransferase mixed lineage leukemia (MLL) is essential to maintain hematopoietic stem cells and is a leukemia protooncogene. Although Hox genes are well-characterized targets of MLL and MLL fusion oncoproteins, the range of Mll-regulated genes in normal hematopoietic cells remains unknown. Here we identify and characterize part of the Mll-transcriptional network in hematopoietic stem cells with an integrated approach by using conditional loss-of-function models, genomewide expression analyses, chromatin immunoprecipitation, and functional rescue assays. The Mll-dependent transcriptional network extends well beyond the previously appreciated Hox targets, is comprised of many characterized regulators of self-renewal, and contains target genes that are both dependent and independent of the MLL cofactor, Menin. Interestingly, Prdm16 emerged as a target gene that is uniquely effective at partially rescuing Mll-deficient hematopoietic stem and progenitor cells. This work highlights the tissue-specific nature of regulatory networks under the control of MLL/Trithorax family members and provides insight into the distinctions between the participation of MLL in normal hematopoiesis and in leukemia.
We used microarrays to determine the gene expression profiles of HSCs upon conditional deletion of Mll.

overall_design: LSK/CD48- HSCs were sorted from 5 pI:pC injected MllF/F control mice or 5 pI:pC injected Mx1-cre;MllF/F mice 6 days after the initial injection. Total RNA was purified from 1,500 to 10,000 sorted cells, amplified, labeled, fragmented and hybridized to GeneChip Mouse Genome 430 2.0 arrays from Affymetrix.

first: Patricia

last: Ernst


title: Gene expression profiling of IR-/-, IGF-1R-/- (dKO) newborn epidermis.

status: Public on May 18 2013

city: Koln

first: Mehmet

middle: Deniz

last: Akyuz

state: NRW

address: Robert Koch Str.21

department: Dermatology

institute: Uni-Klinik Koln

summary: Analysis of newborn mouse epidermis lacking the expression of Insulin receptor (IR) and Insulin like growth factor 1 receptor (IGF-1R). Results show that IR/IGF-1R signalling control epidermal morphogenesis.

overall_design: RNA was isolated from newborn mouse epidermis.Gene expression profiling was on on Affymetrix 430-2.0 platform.

last: Akyüz

first: Carien

middle: M

last: Niessen


title: MicroRNA profiling of human neural stem cells

city: Daejeon

first: Sungsoo

last: Kang

address: 111 Gwahangno, Yuseong-gu

department: KOBIC

country: South Korea

institute: KRIBB

type: Non-coding RNA profiling by high throughput sequencing

summary: To investigate global changes of miRNA profiles upon differentiation of human neural stem cells, we applied massively parallel sequencing (MPS) technology to an immortalized neural stem cell (HB1.F3) and its differentiated cell (F3.Olig2) lines. We identified 339 known miRNAs, out of which 170 miRNAs are up-regulated in F3.Olig2, while only 59 miRNAs in HB1.F3. We also identified 150 novel miRNA candidates.

overall_design: Sequencing miRNAs from an immortalized neural stem cell (HB1.F3) and its differentiated cell (F3.Olig2) lines

first: Sung-Min

last: Ahn

first: Deokhoon

last: Kim

first: Yong

middle: S

last: Lee

first: Sang-Yoon

first: Woo-Yeon

first: Seung

first: Richard

middle: J

last: Simpson

first: Namshin

first: Bonghee


title: Transcriptional regulation of germinal center B and plasma cell fates by dynamical control of IRF4 (expression)

status: Public on May 04 2013

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

summary: Temporal analysis of B cell activation in vitro using CD40L and IL-2/4/5 cytokines in wild type Irf4+/+ B cells or in mutant Irf4-/- B cells harboring a tet-inducible allele of Irf4. IRF4 expression was restored, or not, in the Irf4-/- background by culturing in the presence of low or high concentrations of doxycycline. The results provide insight in the role of IRF4 expression levels in coordinating different programs of B cell differentiation.

overall_design: Resting mature peripheral primary B cells were enriched from the spleens of Irf4+/+ or Irf4-inducible mice on the Irf4-/- background. We sought to compare gene expression profiles of wild type and Irf4 mutant B cells in response to mitogens that promote the differentiation of the B cells into plasma cells and cells that have undergone class switch recombination. Day 0 samples represent RNA analysis of unstimulated cells, whereas Day 1 and Day 3 samples represent analysis of stimulated cells in culture. For stimulation, cells were cultured with insect cell purified CD40L and IL-2/4/5 cytokines for the indicated days. In the case of doxycycline-mediated rescue of IRF4 expression, doxycycline was added at predefined low and high concentrations that yield low or high numbers of plasma cells, respectively (see Molecular Systems Biology 7:495). Each replicate represents analysis of B cells from an individual mouse. Of the three replicates in each group, two were performed in parallel and one was performed at a different time. All cells were lysed using Trizol and total RNA was purified according to manufacturer's suggestions. The high quality of the RNA was confirmed using Agilent Bioanalyzer 2100 system. 250ng of RNA was then processed into biotinylated cRNA according to standard procedures and used to hybridize to Affymetrix 430 2.0 arrays. Signal intensities were normalized using the D-Chip algorithm (PM-only model) and the output was used to quantify differential gene expression between groups.

first: Roger

last: Sciammas

first: Kyoko

last: Ochiai

first: Harinder

last: Singh

first: Aaron

last: Dinner


title: Rapid gene expression changes in peripheral blood lymphocytes upon practice of a comprehensive yoga program

status: Public on Apr 22 2013

first: Leonardo

middle: A.

last: Meza-Zepeda

address: Ullernchausseen 70

department: Dept. of Tumor Biology

institute: The Norwegian Radium Hospital

summary: One of the most common integrative medicine (IM) modalities is yoga and related practices. Previous work has shown that yoga may improve wellness in healthy people and have benefits for patients. However, the mechanisms of how yoga may positively affect the mind-body system are largely unknown. Here we have assessed possible rapid changes in global gene expression profiles in the peripheral blood mononuclear cells (PBMCs) in healthy people that practiced either a comprehensive yoga program or a control regimen. The experimental sessions included gentle yoga postures, breathing exercises, and meditation (Sudarshan Kriya and Related Practices – SK&P) compared with a control regimen of a nature walk and listening to relaxing music. We show that the SK&P program has a rapid and significantly greater effect on gene expression in PBMCs compared with the control regimen. These data suggest that yoga and related practices result in rapid gene expression alterations which may be the basis for longer term cell biological and higher level health effects of these practices.

overall_design: Comparison of genome-wide gene expression upon practice of a comprehensive yoga program.

first: Su

last: Qu

first: Solveig

last: Olafsrud

first: Fahri

last: Saatcioglu


title: Genome-wide gene expression profiling revealed a critical role for GATA3 in the maintenance of the Th2 cell identity

status: Public on Apr 19 2013

city: Chiba

first: Atsushi

last: Onodera

address: Chuo-ku Inohana 1-8-1

department: Immunology

institute: Chiba University

summary: Functionally polarized CD4+ T helper (Th) cells such as Th1, Th2 and Th17 cells are central to the regulation of acquired immunity. However, the molecular mechanisms governing the maintenance of the polarized functions of Th cells remain unclear. GATA3, a master regulator of Th2 cell differentiation, initiates the expressions of Th2 cytokine genes and other Th2-specific genes. GATA3 also plays important roles in maintaining Th2 cell function and in continuous chromatin remodeling of Th2 cytokine gene loci. However, it is unclear whether continuous expression of GATA3 is required to maintain the expression of various other Th2-specific genes. In this report, genome-wide DNA gene expression profiling revealed that GATA3 expression is critical for the expression of a certain set of Th2-specific genes. We demonstrated that GATA3 dependency is reduced for some Th2-specific genes in fully developed Th2 cells compared to that observed in effector Th2 cells, whereas it is unchanged for other genes. Moreover, effects of a loss of GATA3 expression in Th2 cells on the expression of cytokine and cytokine receptor genes were examined in detail.  A critical role of GATA3 in the regulation of Th2-specific gene expression is confirmed in in vivo generated antigen-specific memory Th2 cells. Therefore, GATA3 is required for the continuous expression of the majority of Th2-specific genes involved in maintaining the Th2 cell identity.

overall_design: Mock-transfected and GATA3 siRNA-transfected Th2 and Th2-4th cells are profiled for mRNA expression

first: Tetsuya

last: Sasaki

first: Hiroyuki

last: Hosokawa

first: Yukiko

last: Watanabe

first: Shu

last: Horiuchi

first: Junji

last: Yamashita

first: Hitoshi

last: Tanaka

first: Yasumasa

last: Ogawa

first: Yutaka

last: Suzuki

first: Toshinori

last: Nakayama


title: Expression data from virus-specific mouse Th1 and Tfh CD4 T cell subsets after LCMV infection

city: Atlanta

first: Rama

last: Akondy

state: GA

address: 1462 CLifton Rd

department: Emory Vaccine Center

institute: Emory University

summary:
CD4 T follicular helper (Tfh) cells provide the required signals to B cells for germinal center reactions that are necessary for longlived antibody responses. However, it remains unclear whether there are CD4+ memory T cells committed to the Tfh lineage after antigen clearance.
Using adoptive transfer of antigen-specific memory CD4+ subpopulations (based on CXCR5 and Ly6c expression)in the LCMV infection model, we found that there are distinct memory CD4+ T cell populations with commitment to the Tfh and Th1 lineages. Our conclusions are based on gene expression profiles, epigenetic studies and phenotypic and functional analysis. The gene expression profiles of virus-specific CD4 T cell subets at effector and memory stages is presented here.

overall_design: The SMARTA TCR transgenic / adptive transfer system was used to identify and sort subsets of antigen-specific CD4 T cells (based on their expression of Ly6c and CXCR5) elicited after acute infection with  LCMV (Arm).

first: Scott

last: Hale

first: Ben

last: Youngblood

first: Donald

last: Latner

first: Ata

last: Mohammed

first: Lilin

last: Ye

first: Tuoqi

last: Wu

first: Smita

last: Iyer

first: Rafi

last: Ahmed


title: Expression data from mouse SEOC tumors

city: Frederick

first: Ludmila

last: Szabova

state: MD

address: 1050 Boyles Street

department: CAPR

institute: Frederick National Laboratory for Cancer Research

summary: We have developed mouse models for serous epithelial ovarian cancer (SEOC) based on conditional inactivation of p53 and Rb tumor suppression (RB-TS) in combination with or without Brca1/2 following injection of adenovirus expressing Cre recombinase into the ovarian bursa. These models develop metastatic (Stage IV) disease with key histopathological features resembling human SEOC.To determine whether these mouse tumors resemble human SEOC at the molecular level, we conducted global gene expression analysis on 27 ovarian carcinomas and 3 pooled normal ovarian surface epithelium samples (single epithelial layer isolated from ovarian surface by laser capture).

overall_design: RNA was isolated from flash frozen ovarian tumors or from ovarian surface epithelial cells microdissected from frozen sections using PixCell IIe laser capture microdissection instrument.


title: Genome-wide analysis of monocytes and T cells' response to interferon beta

city: Haifa

first: Noa

last: Henig

address: Efron st.

department: Faculty of Medicine

country: Israel

institute: Technion Israel Institute of Technology

summary: The research hypothesis was that the unique expression profile of monocytes in response to Interferon-beta (IFN-β) might be masked by the response profile of the more abundant T cells. The analysis of monocytes response may highlight novel IFN-β functions and pathways that have not been recognized previously. The aim of this study was to characterized the IFN-β transcriptional response in monocytes, a small but influential  cell-subset, using gene expression profile and pathway analysis. The expression profiles of purified human monocytes and T cells pulse with IFN-β overnight were compared, and revealed 276 and 42 Differentially Expressed Genes (DEGs) in monocytes and T cells respectively, with only 5 genes common to both sets. Many of the DEGs detected in monocytes were novel with respect to the recognized IFN-β response, and included genes involved in immune-specific activities, communication between cells, regulation of apoptosis, cell migration, and  protein translation. Network and pathway analysis of the T cells response revealed the familiar immune pathways, response to virus pathways, and IFN canonical pathway. In monocytes, however, we detected along with known IFN-β-related pathways, such as cell migration also pathways that had not been previously described in the context of IFN-β response, such as the High-Mobility Group Box-1 (HMGB1) signaling pathway. However, most DEGs in monocytes did not cluster to specific networks or canonical pathways. The monocyte-specific DEGs and pathways described herein are beyond the current knowledge regarding the biology of the IFN-β response and the differential response to IFN-β of monocytes versus T cells described emphasizes the importance of cell-specific studies for elucidating the spectrum of cytokine-mediated immunomodulation.

overall_design: Monocytes and T lymphocytes were isolated from 3 healthy volunteers. For each sample the expression profile of untreated cells was compared to the profile of IFN-β treated cells, i.e. 4 samples from each donor (2 cell types, with and without treatment), 12 samples total.

first: Nili

last: Avidan

first: Tamar

last: Paperna

first: Ron

middle: Y

last: Pinter

first: Ariel

last: Miller


title: Egr2-dependent expression in T cell anergy

status: Public on Apr 21 2013

first: Yan

last: Zheng

institute: University of Chicago

summary: T cell anergy is one of the mechanisms contributing to peripheral tolerance, particularly in the context of progressively growing tumors and in tolerogenic treatments promoting allograft acceptance.  We recently reported that early growth response gene 2 (Egr2) is a critical transcription factor for the induction of anergy in vitro and in vivo, which was identified based on its ability to regulate the expression of inhibitory signaling molecules diacylglycerol kinase (DGK)-a and -z.  We reasoned that other transcriptional targets of Egr2 might encode additional factors important for T cell anergy and immune regulation.  Thus, we conducted two sets of genome-wide screens: gene expression profiling of wild type versus Egr2-deleted T cells treated under anergizing conditions, and a ChIP-Seq analysis to identify genes that bind Egr2 in anergic cells.  Merging of these data sets revealed 49 targets that are directly regulated by Egr2.  Among these are inhibitory signaling molecules previously reported to contribute to T cell anergy, but unexpectedly, also  cell surface molecules and secreted factors, including lymphocyte-activation gene 3 (Lag3), Class-I-MHC-restricted T cell associated molecule (Crtam), Semaphorin 7A (Sema7A), and chemokine CCL1.  These observations suggest that anergic T cells might not simply be functionally inert, and may have additional functional properties oriented towards other cellular components of the immune system.

overall_design: T cell-specific Egr2 deletion was mediated by use of a Cre-expressing adenovirus and a CAR Tg x Egr2flox/flox mouse in which CAR is expressed exclusively in the T cell compartment from a Lck promoter/CD2 enhancer cassette.  OVA-specific Th1 cell clones were generated from CAR Tg x Egr2flox/flox mice.  CAR Tg x Egr2flox/flox Th1 T cells were infected with an empty (EV) or a Cre-expressing adenovirus.  Upon confirmation of Egr2 deletion by immunoblot, the T cells were left untreated (Control) or anergized (Anergic) by immobilized anti-CD3 for 16 hours, and microarray was conducted after 1 day of rest in culture medium. The microarray analysis was performed three times using three sets of independently manipulated samples

first: Yuanuan

last: Zha

first: Robbert

last: Spaapen

first: Rebecca

last: Mathew

first: Kenneth

last: Barr

first: Albert

last: Bendelac

first: Thomas

middle: F

last: Gajewski


title: The Presomitic Mesoderm (PSM) CREB family transcriptome

status: Public on Apr 27 2013

city: Baltimore

first: Timothy

middle: Peter

last: Lopez

state: Maryland

address: 3520 San Martin Drive

department: Biology

institute: Johns Hopkins University/Carnegie Institution

summary:
Dynamic gene expression in the PSM of vertebrates is critical for the spatial and temporal patterning of somites.
Using microarray analysis, we explored in detail, genes that are differentially regulated upon removal of CREB family function from the mouse PSM.

overall_design: Mouse PSM from R26R^AC/AC (Control) and R26R^AC/AC;T-Cre (Mutant) were harvested for RNA extraction. Nine PSM's from control and mutant genotypes were combined to generate three biological replicates (three PSM's/replicate). Samples were then applied to microarray analysis to identify differentially expressed genes between controls and mutants.

first: T

first: Chen-Ming

last: Fan


title: Genes regulated by the gamma secretase inhibitor in WT and Ikaros deficient DN3 cells

status: Public on Apr 17 2013

city: Illkirch

first: Susan

last: Chan

address: 1, rue Laurent Fries

country: France

institute: IGBMC

summary: Lineage-negative thymocytes were cultured on OP9-DL1 stromal cells for 16h in the presence of DMSO or the gamma secretase inhibitor MRK-003. DN3 cells cells were then sorted and their transcriptome analyzed.

overall_design: 8 samples

first: Philippe

last: Kastner


title: Gene expression in double positive thymocytes from mice with CD4-Cre-mediated deletion of Ikaros

summary: Double positive thymocytes (CD4+CD8+CD3lo) were sorted from 3-4-week old mice from Ikf/f CD4-Cre+  or Ikf/f CD4-Cre- mice (2 mice per genotype) and their transcriptome analyzed.

overall_design: 4 samples


title: Effect of a gamma secretase inhibitor on the T29 cell line

summary: The mouse Ikaros-deficient thymic lymphoma cell line T29 was treated with a gamma-secretase inhibitor or vehicle (DMSO) for 36h and subjected to transcriptome analysis.


title: Ikaros responsive genes in the T29 cell line

summary: The mouse Ikaros-deficient thymic lymphoma cell line T29 was transduced with an empty retrovirus (MigR1) or a retrovirus expressing an fusion proein between Ikaros1 and the ligand binding domain of the estrogen receptor. Cells trreated with ethanol or 4-hydroxy-tamoxyfen (4OHT) for 24h were profiled.

overall_design: We used expression of an inducible ersion of the Ikaros protein in an Ikaros-deficient cell line to identify Ikaros-regulated genes


title: Notch responsive genes in the T29 cell line

summary: The mouse Ikaros-deficient thymic lymphoma cell line T29 was transduced with a retrovirus expressing an fusion protein between a dominant-negative form of Mastermind and the ligand binding domain of the estrogen receptor. Cells trreated with Ethanol or 4-hydroxy-tamoxyfen for 24h were profiled.

overall_design: We used expression of an inducible ersion of the dominant negative Mastermind protein in an Ikaros-deficient cell line to identify Notch-regulated genes


title: Dicer deficiency reveals microRNAs predicted to control gene expression in developing adrenal cortex [array]

first: Katherine

last: Gurdziel

summary: MicroRNAs (miRNAs) are small, endogenous, non-protein coding RNAs that are an important means of post-transcriptional gene regulation. Deletion of Dicer, a key miRNA processing enzyme, is embryonic lethal in mice, and tissue-specific Dicer deletion results in developmental defects. Using a conditional knockout model, we generated mice lacking Dicer in the adrenal cortex. These Dicer knockout (KO) mice exhibited perinatal mortality and failure of the adrenal cortex during late gestation between embryonic day 16.5 (E16.5) and E18.5. Further study of Dicer KO adrenals demonstrated a significant loss of Sf1 expressing cortical cells that was histologically evident as early as E16.5 coincident with an increase in p21 and cleaved-caspase 3 staining in the cortex. However, peripheral cortical proliferation persisted in KO adrenals as assessed by anti-PCNA staining. To further characterize the embryonic adrenals from Dicer KO mice, we performed microarray analyses for both gene expression and miRNA on purified RNA isolated from control and KO adrenals of E15.5 and E16.5 embryos. Consistent with the absence of Dicer and the associated loss of miRNA-mediated mRNA degradation, we observed an up-regulation of a small subset of adrenal transcripts in Dicer KO mice, most notably the transcripts coded by the genes Nr6a1 and Acvr1c. Indeed, several miRNAs, including let-7, miR-34c, and miR-21 that are predicted to target these genes for degradation, were also markedly down-regulated in Dicer KO adrenals. Together these data suggest a role for miRNA mediated regulation of a subset of genes that are essential for normal adrenal growth and homeostasis.

overall_design: Adrenals from control and Dicer KO litter mates were pooled separately from 4 individual litters, resulting in a total of 4 control (cre-) and 4 Dicer KO biological replicates at both E15.5 and E16.5.

middle: T

last: Krill

first: Joanne

last: Heaton

first: Derek

last: Simon

first: Gary

middle: D

last: Hammer


title: Multiple Roles for Steroid Receptor RNA Activator (SRA) in Regulation of Adipogenesis and Insulin Sensitivity

status: Public on May 07 2013

city: Ann Arbor

first: Bin

last: Xu

address: 1150 W. Medical Center Drive

department: Department of Internal Medicine

institute: University of Michigan Medical School

summary: PPARγ is a master transcriptional regulator of adipogenesis. Hence, the identification of PPARγ coactivators should help reveal mechanisms controlling gene expression in adipose tissue development and physiology. We show that the non-coding RNA Steroid receptor RNA Activator, SRA, associates with PPARγ and coactivates PPARγ-dependent reporter gene expression. Overexpression of SRA in ST2 adipocyte precursor cells promotes their differentiation into adipocytes. Conversely, knockdown of endogenous SRA inhibits 3T3-L1 preadipocyte differentiation.  Microarray analysis reveals hundreds of SRA-responsive genes in adipocytes, including genes in cell cycle, insulin and TNFα signaling pathways. Some functions of SRA may involve mechanisms other than coactivation of PPARγ. SRA increases insulin-stimulated glucose uptake in adipocytes. SRA promotes S-phase entry during mitotic clonal expansion, decreases expression of cyclin-dependent kinase inhibiters p21Cip1 and p27Kip1, and increases phosphorylation of Cdk1/Cdc2. SRA also inhibits the TNFα-induced phosphorylation of c-Jun NH2-terminal kinase. In conclusion, SRA enhances adipogenesis and adipocyte function through multiple pathways.

overall_design: Total RNA was isolated from fully differentiated (MDIT day 4) SRA overexpressing (pMSCV-SRA) and control (pMSCV empty vector) ST2 adipocytes, or fully differentiated (MDIT day 8) shSRA knockdown (pSuperior-shSRA) or shControl (pSuperior-shcontrol) 3T3-L1 adipocytes. Genome wide gene expression analysis was performed using Affymetrix mouse genome 430 2.0 arrays. Triplicate samples were analyzed.

first: Isabelle

last: Gerin

first: Hongzhi

last: Miao

first: Dang

middle: V

last: Phan

first: Craig

last: Johnson

first: Ormond

middle: A

last: MacDougald

first: Ronald

last: Koenig


title: Identification of differential expressed genes between P-RPCs, ESC-RPCs and Dkk1 treated ESC-RPCs through genome-wide transcript profiling

status: Public on Apr 16 2013

city: Shanghai

first: Lu

last: Cui

address: 225 South Chongqing road

country: China

institute: Institue of Health Sciences

summary:
Tumor formation constitutes a major obstacle to the clinical application of embryonic stem cells (ESCs). As P-RPCs could successfully integrate into host eyes without development of teratomas or NOG, we sought to identify differentially expressed genes between P-RPCs and ESC-RPCs through genome-wide transcript profiling. Inhibition of Wnt signaling by DKK1 promotes the commitment of ESC-RPCs to more mature retinal cells and reduces the occurrence of NOG to 3%. DKK1-treated ESC-RPCs efficiently integrate to the host retina, form synaptic connections and restore visual function.
Here, we report that further differentiation of ESC-derived neural progenitors into retinal progenitor cells (ESC-RPCs) completely eliminates teratomas in ocular transplantation. However, tumor-like neural overgrowth (NOG) occurs in 61% of transplanted eyes.

overall_design: ESC-RPCs were divided into two groups according to the differentiation stages for RNA extraction and hybridization on Affymetrix microarrays. Normal control ESC-RPCs (N) were represented the homogeneous populations of early stage expression profiles of immature ESC-RPCs. DKK1 treated ESC-RPCs (D) were represented the homogeneous populations of late stage expression profiles of further differetiated mature ESC-RPCs. To sought the pathways involved in the proliferation and oncogenesis of ESC-RPCs, the newborn C57 mice reitinal progenitor cells (R) were applied as negative control. Each group above had three independent biological repeats.

first: Yuan

last: Guan


title: Gene expression in WT and Ikaros-deficient DN3, DN4 and DP thymocyte populations

summary: DN3, DN4 and DP cells were sorted from 3-4 week old WT and mice and subjected to transcriptome analysis

overall_design: Cells from 3 mice were pooled for sorting.


title: Differential Gene Expression and Mitochondrial Dysfunction in Imprinting center deletion (PWS- IC del) Mouse model of Prader-Willi Syndrome

city: Washington

first: Svetlana

last: Ghimbovschi

state: DC

address: 111 Michigan Ave., NW

department: Research Center for Genetic Medicine

institute: Children's National Medical Center

summary:
Prader-Willi syndrome (PWS) is a genetic disorder caused by deficiency of imprinted gene expression from the paternal chromosome 15q11-15q13 and clinically characterized by neonatal hypotonia, short stature, cognitive impairment, hypogonadism, hyperphagia, morbid obesity and diabetes. Previous clinical studies suggest that a defect in energy metabolism may be involved in the pathogenesis of PWS. Assessment of enzyme activities of mitochondrial oxidative phosphorylation (OXPHOS) complexes in the brain, heart, liver and muscle were assessed.
We used microarrays to detail the global programme of gene expression underlyingthe PWS and identified distinct classes of disregulated genes during this process.

overall_design: Skeletal (quadriceps) muscle Vastus Lateralis and whole brain samples from the mutant mice and their wild-type age-matched littermates were analyzed by microarray technology using the Mouse Genome 430 2.0 arrays (Affymetrix).

first: Virginia

last: Kimonis


title: Expression data from peritoneal macrophages

status: Public on Apr 30 2013

city: new haven

first: chen

last: yao

address: 300 cedar street

institute: yale

summary:
Colony Stimulating Factor 1(CSF1) is known to promote osteoclast progenitor survival but its role in regulating osteoclast differentiation and mature osteoclast function are less well understood.
Macrophages have the potential to differentiate into osteoclasts and are also considered as osteoclast precursors. The microarray screen was designed to identify potential CSF1 targets in macrophage and osteoclast lineage.

overall_design: Wild type C57/BL6 mice were treated with 0.2 ml 10 % thioglycolate medium (FTG) / mouse by intra-peritoneal injection. Mice were sacrificed one week after injection followed by intra-peritoneal lavage with 15ml PBS. Macrophages were plated at a density of 1.5×10^6/well in 6-well plates and cultured in α-MEM supplemented with 10% FBS. At 80% confluence, cells were treated with 100ng/ml CSF1 for 12 hours and RNA extracted. Microarray analysis was performed using Affymatrix Mouse Genome 430 2.0 Arrays. Data were analyzed by Gene spring 6.2 software.

first: Gang-qing

last: Yao

first: Karl

last: Insogna


title: The ISWI ATPase Snf2L is required for superovulation and regulates Fgl2 in differentiating mouse granulosa cells

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

summary: We investigate the role of Snf2l in ovaries by characterizing a mouse bearing an inactivating deletion on the ATPase domain of Snf2l (Ex6DEL). Snf2l mutant mice produce significantly fewer eggs than control mice when superovulated. Thus, gonadotropin stimulation leads to a significant deficit in secondary follicles and an increase in abnormal antral follicles. We profiled the expression of granulosa cells from Snf2l WT and Ex6DEL mice treated with pregnant mares' serum gonadotropin followed by human chorionic gonadotropin

overall_design: Granulosa cells from either Snf2l WT or Ex6DEL mice treated with PMSG followed by hCG were collected at 0h and 4h post-hCG.  Each array includes granulosa cells pooled from 5 mice.

first: Barbara

middle: C

last: Vanderhyden

first: Carol

last: Perez-Iratxeta

first: David

last: Pepin


title: Unique pharmacological actions of atypical neuroleptic quetiapine: possible role in cell cycle/fate control

first: Jonathan

last: Pevsner

address: 707 N. Broadway

department: Neurology

institute: Kennedy Krieger Institute

summary:
Quetiapine is an atypical neuroleptic with a pharmacological profile distinct from classic neuroleptics. It is currently approved for treating patients with schizophrenia, major depression and bipolar I disorder. However, its cellular effects remain elusive.
We used microarrays to characterize RNA transcript levels in the brains of mice chronically treated with quetiapine, the neuroleptic haloperidol, or vehicle. We further characterized particular RNA transcripts in cortical cell cultures.

overall_design: Mice were given one of 5 treatments (vehicle, 1 mg/kg haloperidol, 0.3 mg/kg haloperidol, 100 mg/kg quetiapine, 10 mg/kg quetiapine). Pooled tissue samples were used for microarray analysis of gene expression in the frontal cortex (FC) and striatum (STR). Frontal cortex gene targets were subsequently verified with quantitative real-time PCR (qRT-PCR) from the same cohort of mice and an independent cohort.

first: Mari

last: Kondo


title: Gene expression profiling of the tongue in Tgfbr2 mutant mouse models

status: Public on Apr 11 2013

city: Oklahoma City

first: Richard

last: Pelikan

state: Oklahoma

address: 825 NE 13th St

department: Genes & Human Disease Research Program

institute: Oklahoma Medical Research Foundation

summary: The overall goal of this project is to investigate the role of TGF-beta signaling in tongue development in order to study the contribution of cranial neural crest (CNC) cells towards the patterning of cranial mesoderm for proper tongue formation. Here, we conducted gene expression profiling of embryonic tongue tissue from wild type mice as well as those with a neural crest specific conditional inactivation of the Tgfbr2 gene. The latter mice provide a model of microglossia, a common congenital birth defect which is frequently observed with several syndromic conditions.

overall_design: To investigate the mechanism of microglossia resulting from dysfunctional TGF-Beta signaling during muscle development, we analyzed neural crest specific conditional inactivation of Tgfbr2 in mice (Tgfbr2fl/fl;Wnt1-Cre). We performed microarray analyses of tongue tissue of Tgfbr2fl/fl;Wnt1-Cre mutant mice and Tgfbr2fl/fl control mice at embryonic day E14.5 (n=3 per genotype) to examine the genes regulated by Tgf-beta during tongue muscle development.

first: Jun-ichi

last: Iwata

first: Akiko

last: Suzuki

first: Yang

last: Chai


title: Expression profile of CXCR6 Hi T cells or CXCR6 Lo helper T cells in CD45Rb Hi tranfer model mice

status: Public on Apr 09 2013

city: Toyama

first: yukihiro

last: furusawa

address: Kurokawa

institute: Toyama Prefectural University

summary:
To identify the role of chemokine receptor in inflammation of colon, we isolated CD3+CD4+ helper T cells harboring CXCR6 from colonic lamina propria of mice
We used microarrays to identify the differentially expressed genes between CXCR6Hi Tcells and CXCR6Lo Tcells

overall_design: CXCR6 Hi or CXCR6 Lo T cells were isolated from colonic lamina propria for RNA extraction and hybridization on Affymetrix microarrays.

first: Daisule

last: Takahashi

first: Koji

last: Hase

first: Yuuki

last: Obata

first: Yukihiro

last: Furusawa


title: Let-7 represses Nr6a1 and a mid-gestation developmental program in adult fibroblasts [3p arrays]

status: Public on Apr 10 2013

city: Cambridge

first: A

last: Bhutkar

state: MA

address: 77 Massachusetts Avenue

institute: MIT

summary: MicroRNAs (miRNAs) are critical to proliferation, differentiation, and development. Here, we characterize gene expression in murine Dicer-null adult mesenchymal stem cell lines, a fibroblast cell type.  Loss of Dicer leads to de-repression of let-7 targets at levels that exceed 10-100 fold with increases in transcription.  Direct and indirect targets of this miRNA belong to a mid-gestation embryonic program that encompasses known oncofetal genes as well as oncogenes not previously associated with an embryonic state.  Surprisingly, this mid-gestation program represents a distinct period that occurs between the pluripotent state of the inner cell mass at embryonic day 3.5 and the induction of let-7, upon differentiation, at embryonic day 10.5.  Within this mid-gestation program, we characterize the let-7 target Nr6a1, an embryonic transcriptional repressor that regulates gene expression in adult fibroblasts following miRNA loss.  In total, let-7 is required for the continual suppression of embryonic gene expression in adult cells, a mechanism that may underlie its tumor suppressive function.

overall_design: Three dicer heterozygotes and 3 dicer null sarcoma cell lines.

first: Allan

last: Gurtan

first: Arvind

last: Ravi

first: Peter

middle: B

last: Rahl

first: Andrew

last: Bosson

first: Courtney

middle: K

last: JnBaptiste

first: Arjun

first: Charles

last: Whittaker

last: Young

first: Phillip

last: Sharp


title: Study of the association of DNAhsp65 immunotherapy and conventional drugs in experimental tuberculosis

status: Public on Apr 08 2013

city: Ribeirao Preto

first: Rodrigo

middle: Ferracine

last: Rodrigues

address: Avenida bandeirantes 3900

country: Brazil

institute: University of Sao Paulo

summary:
Despite substantial investments, tuberculosis remains one of the biggest challenges in public health.
DNA-immunotherapy is increasingly being suggested as a possibility to assist conventional treatment of tuberculosis. This strategy could allow treatment to be more efficient, faster and with advantages and modulate the host immune response, as demonstrated by our group with DNAhsp65 vaccine (Silva, Bonato et al., Gene Therapy, 2005).
Based on this evidences, we performed a microarray assay to stydy the functional effects of DNAhsp65 immunotherapy associated with conventional chemotherapy in murine experimental tuberculosis.

overall_design:
Briefly, we used a murine model of tuberculosis treatment compost by DNAhsp65 vaccine, or rifampicin and isoniazid or both therapies combined and performed a comprehensive analysis of its effects on gene expression of host’s lung .
Female BALB/c mice,8 weeks old, were inoculated with 1.0 × 10e5 viable bacilli of Mycobacterium tuberculosis H37Rv strain by the intra-tracheal route in a level III bio-safety room facility (day 0). They were segregated in four groups, described below, with three animals each one.
Control – just infected and not treated.
Immunotherapy - Thirty days after challenge, 50 μg of plasmid with DNA-insert (DNAhsp65) was administered by intramuscular injection in 50 μL of 25% saccharose  solution in saline into each quadriceps muscle, in four occasions, and  at 10-days intervals, performing a final dose of 400 μg of plasmid DNAhsp65 per animal. Control infected mice received saline.
Chemotherapy - Thirty days after infection, animals were treated with water solution of isoniazid (25 mg/Kg, Sigma-Aldrich, St. Louis, MO, USA) and rifampicin (20 mg/Kg, Sigma-Aldrich, St. Louis, MO, USA) daily, during 30 days, by gavage. Control infected mice received the same volume of water.
Association - The therapeutical association consists of the both therapeutical approaches, as described above.
Ten days after the end of treatments, mice were killed by cervical dislocation under mild anesthesia, and lungs were removed to RNA extraction.


title: Whole-genome expression data from normal FVB mouse lung tissue, transgenic cyclin E overexpressing (CEO) normal mouse lung tissue, and transgenic CEO lung adenocarcinomas

status: Public on Apr 04 2013

city: Hanover

first: Sarah

last: Freemantle

state: NH

department: Pharmacology and Toxicology

country: USA

institute: Geisel School of Medicine at Dartmouth

summary: FVB mice were engineered to express wild-type human cyclin E under control of the human surfactant C promoter (CEO mice; Ma et al, PNAS 2007).  These mice develop spontaneous lung tumors, which were shown to be adenocarcinoma by histological analysis.  Here we compare whole-genome RNA expression levels between the tumors and normal lung of 4 CEO mice as well as 4 nontransgenic animals.

overall_design: RNA was isolated from the lungs of 4 FVB mice and adjacent normal and tumor tissue from 4 FVB transgenes harboring human surfactant protein C- driven wild-type human cyclin E, all 7-11 months in age.  These samples were divided into 3 groups of four, and  12 independent hybridizations were performed for analysis with Affymetrix GeneChip Mouse 430 2.0 arrays.

first: Alexander

last: Busch


title: A transcriptomic analysis of a Caucasian family cohort of high risks for the metabolic syndrome [HumanWG-6 v3.0]

status: Public on Apr 12 2013

city: Milwaukee

first: Yi

last: Zhang

state: WI

address: 8701 W Watertown Plank Rd

department: Medicine

institute: Medical College of Wisconsin

summary: Metabolic Syndrome (MetS) is a strong predictor for diabetes and cardiovascular disease and is defined by a constellation of phenotypes including increased and adverse body fat distribution, insulin resistance, abnormalities in lipids and lipoproteins, malfunctional cardiovascular performance, and abnormal levels of adipokines and cytokines. We assayed in a subset of our family cohort phentoyped for MetS phentoypes, the genome-wde transcript levels using the Illumina Human WG-6 v3 expression arrays.

overall_design: Genome-wide gene expression was assayed in members of families that originally contribute to linkage signals in a previous genome-wide linkage scans for multiple MetS phenotypes.

first: Jack

middle: W

last: Kent Jr

first: Michael

last: Olivier

first: Diana

last: Cerjak

first: Joanne

middle: E

last: Curran

first: Melanie

last: Carless

first: Harald

middle: H

last: Göring

first: John

last: Blangero

first: Ahmed

last: Kissebah


title: Expression data from proliferating and senescent murine hepatic stellate cells

status: Public on Apr 05 2013

city: New York

first: Amaia

last: Lujambio

state: NY

address: 1275 York Avenue

department: CBG

institute: MSKCC

summary:
The p53 protein is a cell-autonomous tumor suppressor that restricts malignant transformation by triggering cell cycle exit or apoptosis. p53 also promotes cellular senescence, a program that triggers a stable cell cycle arrest and can modify the tissue microenvironment through its effect on cell membrane and secretory proteins. Here we show that specific ablation of p53 in hepatic stellate cells, which undergo a process of proliferation and senescence in the fibrogenic response to liver damage, enhances liver cirrhosis, reduces survival and increases the malignant transformation of adjacent epithelial cells into hepatocellular carcinoma. This p53-dependent senescence program involves the release of secreted proteins which skew macrophages into a tumor-inhibiting M1-state that can eliminate senescent stellate cells. In contrast, p53-deficient stellate cells secrete factors that promote M2 polarization, which is pro-tumorigenic. Our study reveals that p53 can exert a non-cell-autonomous tumor suppressor response and suggests that this occurs, in part, by its ability to influence macrophage polarization.
We used microarrays to detail the global programme of gene expression underlying p53-dependent senescent and identified distinct classes of up-regulated or down-regulated genes during this process.

overall_design: Proliferating and senescent stellate cell pellets were collected RNA extraction and hybridization on Affymetrix microarrays.

first: Leila

last: Akkari

first: Janelle

last: Simon

first: Danielle

last: Grace

first: Zhen

last: Zhao

first: Jessica

last: Bolden

first: Johanna

last: Joyce

first: Valery

last: Krizhanovsky

first: Scott

last: Lowe

first: Vishal

last: Thapar

first: Darjus

last: Tschaharganeh


title: Activity of a stem cell enhancer influences stem cell programs and clinical outcome in leukaemia

first: Weng Khong

last: Lim

state: Cambridgeshire

address: Tennis Court Road

institute: Cambridge Systems Biology Centre

type: Genome binding/occupancy profiling by genome tiling array

summary:
Chip-chip data from primary human AML patient blasts, normal CD34+ HSCs, normal neutrophils and normal T cells with H3K9 and H3K27 antibodies. Gene expression profiling from primary human AML patient blasts and CD34+ normal cells.
Analysis of the chromatin landscape of the ERG locus using H3K9 and H3K27 as markers of euchromatin and heterochromatin respectively. Analysis of ERG expression in AML patients with normal CD34+ HSCs as control.

overall_design: Correlation of the activity of a stem cell enhancer at the ERG locus in AML primary patient blasts with their transcriptome and clinical outcome data.

first: Weng

first: Brian

last: Huntly


title: Expression data from Satb1- and control-transduced LSK Flt3- cells

status: Public on Apr 01 2013

city: Suita

first: Yusuke

last: Satoh

state: Osaka

address: 2-2, Yamada-Oka

department: Department of Hematology and Oncology

institute: Osaka University Graduate School of Medicine

summary: How hematopoietic stem cells (HSCs) produce specific lineages is not well understood. We searched for key factors that direct HSC to lymphopoiesis. Comparing gene expression profiles for HSCs and early lymphoid progenitors revealed that Satb1, a global chromatin regulator, was significantly induced with lymphoid lineage specification. HSCs from Satb1-null mouse were defective in lymphopoietic activity in culture, and failed to reconstitute T-lymphopoiesis in wild-type recipients. Furthermore, Satb1-transduction in HSCs, as well as in embryonic stem cells, robustly promoted their differentiation toward lymphocytes in culture.

overall_design: We prepared RNA samples from control or Satb1-transfected Lin- c-kitHi Sca-1+ Flt3- cells derived from WT mouse bone marrow.

first: Takafumi

last: Yokota