title: Adenine-induced chronic renal failure causes decreased aortic relaxation rate and altered expression of genes involved in excitation-contraction coupling in vascular smooth muscle cells

status: Public on Jul 21 2016

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

summary:
Rats with adenine-induced chronic renal failure (A-CRF) develop a reduction in the rate of relaxation of the thoracic aorta. The primary aim of this study was to elucidate the mechanisms underlying this abnormality. Male Sprague-Dawley rats received either chow containing adenine or were pair-fed with normal chow (controls). After 8-14 weeks arterial functions were analyzed ex vivo using wire myography and the thoracic aorta was analyzed by DNA microarray.
Plasma creatinine levels were elevated ~8-fold in A-CRF rats. The rate of vascular relaxation following wash-out of KCl was reduced in A-CRF rats vs. controls in the thoracic aorta (P<0.01), abdominal aorta (P<0.05), and common carotid artery (P<0.05), but not in the common femoral artery. Endothelial denudation exaggerated the impairment in relaxation of thoracic aortas. Relaxation rates of thoracic aortas increased (P<0.01), but were not normalized, in response to wash-out of KCl with Ca2+-free buffer. Microarray and qRT-PCR analyses revealed altered gene expression levels for a number of genes involved in vascular smooth muscle cell excitation-contraction coupling in aortas of A-CRF rats.
In conclusion, rats with A-CRF show a marked reduction in the rate of relaxation of larger conduit arteries localized proximal to the common femoral artery. This abnormality may be caused by reduced cytosolic Ca2+ clearance in vascular smooth muscle cells secondary to dysregulation of genes involved in excitation-contraction coupling.

overall_design: Microarray expression analysis of thoracic aortas from rats with adenine-induced chronic renal failure

first: Lisa

last: Nguy

first: Emman

last: Shubbar

first: Margareta

last: Jernås

first: Jaana

last: Lundgren

first: Bob

last: Olsson

first: Holger

last: Nilsson

first: Gregor

last: Guron


title: Role of mast cells in pulmonary hypertension with left heart disease

status: Public on Jul 22 2016

city: Toronto

first: Claudia

middle: Chimisso

last: dos Santos

state: ON

address: 30, Bond Street, room 4-011

department: University of Toronto

country: Canada

institute: Saint Michaels Hospital

summary:
Left heart disease (LHD) frequently causes lung vascular remodelling and pulmonary hypertension (PH). Yet, pharmacological treatment for PH in LHD is lacking and its pathophysiological basis remains obscure. We aimed to identify candidate mechanisms of PH in LHD and to test their relevance and therapeutic potential. In rats, LHD was induced by supracoronary aortic banding. Whole genome microarray analyses were performed, candidate genes were confirmed by RT-PCR and Western blots and functional relevance was tested in vivo by genetic and pharmacological strategies. In lungs of LHD rats, mast cell activation was the most prominently upregulated gene ontology cluster. Mast cell gene upregulation was confirmed at RNA and protein levels and remodelled vessels showed perivascular mast cell accumulations. In LHD rats treated with the mast cell stabiliser ketotifen, or in mast cell deficient Ws/Ws rats, PH and vascular remodelling were largely attenuated. Both strategies also reduced PH and vascular remodelling in monocrotaline-induced pulmonary arterial hypertension, suggesting that the role of mast cells extends to noncardiogenic PH. In PH of different aetiologies, mast cells accumulate around pulmonary blood vessels and contribute to vascular remodelling and PH. Mast cells and mast cell-derived mediators may present promising targets for the treatment of PH.

Whole rat genome microarray analyses were performed in lung homogenates of three rats with established PH following supracoronary aortic banding and in three sham-operated controls. Out of a total of 28,000 analysed genes, differential expression defined as 2-fold change with p<0.05 was evident for 120 genes. Of these, 76 were upregulated and 44 downregulated in aortic banding compared with control lungs gene. Enrichment analysis revealed regulation of mast cell specific genes - 13 out of 20 genes were significantly upregulated in aortic banding compared with control lungs. To test for a putative functional role of mast cells in lung vascular remodelling and PH in LHD, we applied a pharmacological approach by treatment of aortic banding rats with the mast cell stabiliser ketotifen. Microarray analysis then compared rats that were treated with untreated.

overall_design:
In brief, congestive heart failure (CHF) was induced in juvenile rats by supracoronary aortic banding and rats were analyzed 9 weeks thereafter when they had established left heart failure with preserved ejection fraction and secondary pulmonary hypertension. Three heart failure rats were untreated, and 3 received the mast cell stabilizer ketotifen (1 mg/kg-1 bodyweight/day-1) with the drinking water. Sham rats underwent the same surgical procedure but without placement of a clip on the supracoronary aorta.
Microarray analyses: Lungs from banded and control rats were excised and total RNA was extracted (Stratagene Absolutely RNA Miniprep Kit; Stratagene, La Jolla, USA). Three µg total RNA from three control and three banded rats each were processed according to the One-Cycle Target Labeling protocol (GeneChip Expression Analysis, Affymetrix, Santa Clara, USA). Before and after amplifications, the total RNA/complementary RNA concentrations were checked with NanoDrop ND-1000 (Thermo Scientific, Wilmington, USA) and quality was controlled (Experion electrophoresis station, BioRad; Hercules, USA). Samples were hybridized to GeneChip® Rat Genome 230 2.0 arrays (Affymetrix; Santa Clara, USA) containing 31,000 probe sets covering 28,000 rat genes.

first: Wolfgang

middle: M

last: Kuebler

first: Sigfried

last: Breitling

middle: C

last: Dos Santos


title: Expression data from kidneys of rats with and without cisplatin treatment

status: Public on Aug 23 2016

city: Wuppertal

first: Heidrun

middle: Christine

last: Ellinger-Ziegelbauer

address: Aprather Weg 18a

country: Germany

institute: Bayer Pharma AG

summary: We investigated  an acute kidney injury (AKI) model in rats induced by cisplatin (Cp) administration. The  cisplatin is widely used since its biochemical and histopathological characteristics are representative of drug-induced AKI in humans. Male Wistar rats were dosed once ip with 0, 1 and 3 mg/kg cisplatin. Tubular necorsis was observed histopathologically in all treated rats and war recovery on day 26. Gene expression profiling of the kidney cortex with microarrays 3, 5, 8, and 26 days after single administration of 3mg/kg Cp revealed a major profile pattern characterized by maximally increased and decreased mRNA levels on day 8, with clear changes already found 3 days after treatment for about half of the mRNAs. The mRNA expression pattern after administration of 1mg/kg Cp was overall similar, yet with a dose-dependent smaller fold-change. In summary we found 274 mRNAs showing significantly altered levels in the kidney of which 162 were increased and 112 decreased, respectively. Functional interpretation of the proteins encoded by these mRNAs revealed induction of a DNA damage response likely caused by the known molecular activity of Cp as DNA alkylating agent. Increased mRNAs associated with apoptosis (encoded by the corresponding genes like B-cell lymphoma 3-encoded protein, Bcl3; mouse double minute 2 homolog, Mdm2; p21/WAF1 also known as cyclin-dependent kinase inhibitor 1), cell cycle regulation (encoded by the corresponding genes like Cyclin-G1, Ccng1; B-cell translocation gene 2, Btg2) and stress response may have partly been induced by the DNA damage, but also by the kidney damage associated with Cp administration. Increased levels of mRNAs indicating regeneration (encoded by the corresponding genes like SPARC- related modular calcium-binding protein 2, Smoc2; Tenascin C, Tnc) and decreased levels of mRNAs coding for proteins related to kidney function, indicating dedifferentiation, are likely related to the observed kidney injury.

overall_design: Male Han Wistar rats (8 weeks old) were randomly grouped (n = 6) and dosed once i.p. with 0, 1 or 3 mg/kg body weight cis-diamminedichloroplatinum (II) (cisplatin; Sigma Aldrich, Germany) diluted in 0.9% saline. For histopathological examination of the kidney and for kidney RNA isolation animals were euthanized on days 3, 5, 8 and 26.

first: Mira

last: Pavkovic

first: Bjoern

last: Riefke


title: Gene expression of non-apoptotic pancreatic acinar cell death with autophagy

status: Public on Jul 16 2016

city: Honjo, Chuo-ku

first: Masaki

last: Ohmuraya

state: Kumamoto

department: Institute of Resource Development and

country: Japan

institute: Kumamoto University

summary: Serine protease inhibitor Kazal type 3 (Spink3) is a trypsin inhibitor in the pancreas. Spink3-/- pancreatic acinar cells are dead with excessive autophagy at birth (p0.5). To prove the role of nonapoptotic cell death with autophagy, we generated by transgenic technology the pancreas of Spink3-/-;XKI/+ mice contained both normal and dying acinar cells with autophagy. In this new mouse model, chronic inflammation occurred in the pancreas, indicating that some signals from nonapoptotic dead cell induce chronic inflammation in the pancreas.

overall_design: All samples were the pancreas at p0.5. Sample 1 and 2 are the pancreas from wild type (Spink3+/+, control) mice. Sample 3 and 4 are the pancreas from Spink3-/-, which all pancreatic acinar cells show induced nonapoptotic cell death with autophagy. Sample 5 and 6 are the pancreas from Spink3-/-XKI/+, about half acinar cells are normal, but other acinar cells show induced nonapoptotic cell death with autophagy.


title: Mouse iPS cells-derived 3D-retinas: Vehicle control- vs. 4-hydroxytamoxifen (4-OHT)-treated 3D-retinas w/o supplements

status: Public on Jul 05 2016

city: Kobe

first: Shin-ichiro

last: Ito

address: 2-2-3 Minatojima-minamimachi, Chuou-ku

institute: RIKEN Center for Developmental Biology

summary: Transcriptional profiling of 3D-retinas differentiated from mouse iPS cells comparing vehicle control with 4-OHT-treated  w/o supplements. 4-OHT is an inverse agonist of estrogen-related receptor beta (ERRβ), a rod-enriched transcription factor responsible for maintenance of rod photoreceptor cells and the treatment induces photoreceptor specific cell death in the 3D-retinas. Goal was to understand the mechanism of protective effects of representative ophthalmic supplements for treating the photoreceptor degeneration.

overall_design: 4-OHT w/o supplements-induced gene expression in the 3D-retinas was measured at DD 25 when the photoreceptor cells started to be degenerated. Four-condition experiment, vehicle control- vs. 5 µM 4-OHT- vs. 5 µM 4-OHT with 400 µM vitamin E- vs. 5 µM 4-OHT with 200 nM lutein-treated 3D-retinas. Biological replicates: each sample has 24 3D-retinas and 1replicate.

first: Akishi

last: Onishi

first: Masayo

last: Takahashi


title: Mouse iPS cells-derived 3D-retinas

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

overall_design: Refer to individual Series


title: Prepartum body condition score and plane of nutrition affect the hepatic transcriptome during the transition period in grazing dairy cows

status: Public on Jun 06 2016

city: Urbana

first: Mario

middle: Pietro Emilio

last: Vailati Riboni

state: IL

address: 1207 W Gregory Dr

department: Animal Science

country: USA

institute: University of Illinois at Urbana-Champaign

summary: A transcriptomic approach was used to evaluate potential interactions between prepartum body condition score (BCS) and feeding management in the weeks before calving on hepatic metabolism during the transition period. Thirty-two mid-lactation grazing dairy cows of mixed age and breed were randomly allocated to one of four treatment groups in a 2 × 2 factorial arrangement: two prepartum BCS categories [4.0 (thin, BCS4) and 5.0 (optimal, BCS5); based on a 10-point scale], and two levels of energy intake during the 3 wk preceding calving (75 and 125% of estimated requirements). Liver samples were obtained at -7, 7, and 28 d relative to parturition and subsequent RNA was hybridized to the Agilent 44K Bovine (V2) Microarray chip. The Dynamic Impact Approach was used for pathway analysis, and Ingenuity Pathway Analysis was used for gene network analysis. The greater number of differentially expressed genes in BCS4 cows in response to prepartum feed allowance indicated that these animals were more responsive to prepartum nutrition management than optimally-conditioned cows. However, independent of prepartum BCS, pathway analysis revealed that prepartal feeding level had a marked effect on carbohydrate, amino acid, lipid, and glycan metabolism. Altered carbohydrate and amino acid metabolism indicated a greater and more prolonged negative energy balance post-calving in BCS5 cows overfed prepartum. This was indicated by opposite effects of pre-calving feeding in in BCS4 compared with BCS5 cows in amino acid, vitamin, and co-factor metabolism. The prepartum feed restriction ameliorated the metabolic adaptation to the new lactation in BCS5 cows, while detrimentally affecting BCS4 cows, which seemed to adapt better when overfed. Moreover, alterations in the glycosaminoglycans synthesis pathway support this idea, indicating better hepatic health status in feed-restricted BCS5 cows and overfed BCS4 animals. IPA network analysis indicated liver damage in feed-restricted thin cows, likely due to metabolic overload. Overall, the data indicate that overfeeding in late-pregnancy should be limited to underconditioned animals, while cow with optimal degree of body condition should be maintained on an energy restricted diet.

overall_design: 150 mixed breed mid-lactation grazing dairy cows were balanced for age, breed, BCS at the time of enrollment, and expected calving date. Cows were randomly allocated to one of six treatment groups (25 cows per group) in a 2 × 3 factorial arrangement: two pre-calving BCS categories (4.0 and 5.0, BCS4 and BCS5; based on a 10-point scale, where 1 is emaciated and 10 obese) and three levels of energy intake during the three wk preceding calving (75, 100, and 125% of estimated requirements). The different groups were obtained by daily manipulation of pasture allowance. A subset of 32 animals with the complete set of biopsies (8 cows in each of four treatment groups) was used for transcriptomic analysis. These were cows with prepartum BCS4 fed to meet 75 (B4F75) or 125 (B4F125) % of requirements, and cows with prepartum BCS5 fed to meet 75 (B5F75) or 125 (B5F125) % of requirements. The intermediate groups in both BCS classes (B4F100 and B5F100) were omitted from the present analysis as feeding to the exact requirements is rarely achievable in field conditions. In practice, multiple factors (e.g., pasture management and allocation, animal competition and social interaction) cause cows being mostly overfed or underfed. Liver tissue was harvested via percutaneous biopsy under local anesthesia at -7, 7, and 28 d relative to parturition.

last: Vailati-Riboni

first: Susan

last: Meier

first: Chris

middle: R

last: Burke

first: Jane

middle: K

last: Kay

first: Murray

middle: D

last: Mitchell

first: Caroline

middle: G

last: Walker

first: Mallory

middle: A

last: Crookenden

first: Axel

last: Heisen

first: Sandra

middle: L

last: Rodriguez-Zas

first: John

last: Roche

first: Juan

middle: J

last: Loor


title: Leukocyte-Specific Protein1 Regulates T Cell Migration in Rheumatoid Arthritis

status: Public on Jun 01 2016

city: Daejeon

first: Ji-Hwan

last: Park

address: 125 Gwahak-ro, Yuseong-gu

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

summary: Copy number variations (CNVs) have been implicated in human diseases. However, it remains unclear how they affect immune dysfunction and autoimmune diseases, including rheumatoid arthritis (RA). Here, we identified a novel LSP1 deletion variant for RA susceptibility located in 11p15.5. We replicated that the copy number of LSP1 is significantly lower in RA patients, which correlates positively with LSP1 protein expression levels. Differentially expressed genes in Lsp1-deficient primary T cells represent cell motility and immune and cytokine responses. Functional assays demonstrated that LSP1, induced by T cell receptor activation, negatively regulates T cell migration by reducing ERK activation in vitro. In mice with T cell-dependent chronic inflammation, loss of Lsp1 promotes migration of T cells into the target tissues as well as draining lymph nodes, exacerbating disease severity. Moreover, RA patients show diminished expression of LSP1 in peripheral T cells with increased migratory capacity, suggesting that the defect in LSP1 signaling lowers the threshold for T cell activation. Our work is the first to demonstrate how CNVs result in immune dysfunction and a disease phenotype. Particularly, our data highlights the importance of LSP1 CNVs and LSP1 insufficiency in the pathogenesis of RA and provides novel insights into the mechanisms underlying T cell migration toward the inflamed synovium in RA.

overall_design: Total RNA was isolated from splenic T cells of Lsp1-deficient and wild-type mice, which were stimulated with anti-CD3/CD28 Abs for 6 hours.

first: Seong-Hye

last: Hwang

first: Daehee

first: Wan-Uk

last: Kim


title: A Potential Role of the Unfolded Protein Response in the Impaired Production and Release of Epinephrine in Recurrent Hypoglycemia

status: Public on Jul 01 2016

city: Valhalla

first: Bistra

last: Nankova

state: NY

address: 95 Grassland Rd

institute: New York Medical College

summary: In order to gain further insight into the molecular mechanism(s) mediating the blunted epinephrine responses following recurrent hypoglycemia we utilized global gene expression profiling approach. Our results indicate the association between defective counterregulation (impaired epinephrine release) and the activation of the unfolded protein response as well as increased neuropeptide signaling, altered ion homeostasis and downregulation of proteins involved in Ca2+-dependent exocytosis of secretory vesicles.

overall_design: We compared the entire transcriptomes during recurrent (defective CRR model, 2RH) and acute hypoglycemia (normal CRR group, 2RS) in the adrenal medulla of normal Sprague-Dawley rats.

first: Juhye

first: Edmund

middle: F

last: La Gamma

first: Todd

last: Estabrook

first: Necla

last: Kudrick

middle: B


title: β-cateinin activation in hair follicle dermal sheath induces ectopic hair outgrowth and skin fibrosis

status: Public on May 31 2016

city: Shanghai

first: Yi

middle: Xin

last: Tao

address: 1954 Huashan Road, Xuhui District, Shanghai (near Guangyuan Road West)

department: Life School

country: China

institute: Shanghai Jiao Tong University

summary: Dermal sheath (DS) shows potent hair inducing capability and high plasticity without leading to immuno rejection. A recent study showed a subset of DS cells, identified as hair follicle (HF) dermal stem cells, can be mobilized to regenerate DS, maintain/supply the cell number of dermal papilla (DP) and modulate hair type. However, it is unclear how Wnt/β-catenin signaling regulates DS cells behaviors. Here we report that activation of β-catenin in DS, to some extent, endows it with hair inducing ability, reprogramming HF epidermal cells to generate new outgrowth. The new formed dermal condensates (DC)/DP lying adjacent the outgrowth derives from DS and/or its progeny, and homeostasis of pre-existing HFs is disturbed. Additionally, progressive skin fibrosis is prominent in hypodermis, where the excessive activated fibroblasts at least partially originate from DS and/or its progeny. Gene expression analysis of purified DS cells revealed that 44% DC signature genes are regulated, most of which are up-regulated. We found elevated expression of several growth factors, including Noggin, Fgf7 and Fgf10, which were previously implicated in HF induction. In summary, we confirm the high plasticity of DS cells by in vivo assays and report a mechanism by which Wnt/β-catenin signaling controls DS cells behaviors.

overall_design: We prospectively isolated control and cΔex3 DS cells (YFP+ve CD34-ve ALP-ve ITGα8-ve cells) from P15 dorsal skins by FACS.

first: Yixin

first: Gang

last: Ma


title: Role of Lamtor1 and mTOR in the polarization of M2 macrophages.

status: Public on May 27 2016

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Bone marrow-derived macrophages differentiated with L929 culture sup. were stimulated with recombinant mouse IL-4.

overall_design: The Cy3-labeled cRNAs were hybridized on Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray (G4852A) in one color experiments, resulting in four individual microarrays.

first: Tetsuya

last: Kimura


title: Identification of Kdm4a, b and c target genes in MLL-AF9 transformed mouse GMPs (L-GMP) [gene expression]

status: Public on Jun 02 2016

city: Copenhagen

first: Karl

last: Agger

address: Ole Maaloes Vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

summary: In this study we identify genes, that are deregulated in Kdm4a, b and c triple knockout L-GMP cells compared WT L-GMP cells.

overall_design: Four MLL-AF9 transformed L-GMP cell lines conditional knockout for Kdm4a, b and c, were derived from leukemic mice.  The cells were treated with 4-hydroxytamoxifen and total RNA was prepared from 0h, 48h and 96h time points.

first: Kristian

last: Helin


title: Effect of a High Phosphorus Diet on Hepatic Gene Expressions in Rat

status: Public on May 18 2016

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

summary: A high phosphorus (HP) diet causes disorders of renal function, bone metabolism, and vascular function. We previously demonstrated that DNA microarray analysis is an appropriate method to comprehensively evaluate the effects of a HP diet on kidney dysfunction such as calcification, fibrillization, and inflammation. We reported that type IIb sodium-dependent phosphate transporter is significantly up-regulated in this context. In the present study, we performed DNA microarray analysis to investigate the effects of a HP diet on the liver, which plays a pivotal role in energy metabolism. DNA microarray analysis was performed with total RNA isolated from the livers of rats fed a control diet (containing 0.3% phosphorus) or a HP diet (containing 1.2% phosphorus). Gene Ontology analysis of differentially expressed genes (DEGs) revealed that the HP diet induced down-regulation of genes involved in hepatic amino acid catabolism and lipogenesis, while genes related to fatty acid β-oxidation process were up-regulated. Although genes related to fatty acid biosynthesis were down-regulated in HP diet-fed rats, genes important for the elongation and desaturation reactions of omega-3 and -6 fatty acids were up-regulated. Concentrations of hepatic arachidonic acid and eicosapentaenoic acid were increased in HP diet-fed rats. These essential fatty acids activate peroxisome proliferator-activated receptor alpha (PPARα), a transcription factor for fatty acid β-oxidation. Evaluation of the upstream regulators of DEGs using Ingenuity Pathway Analysis indicated that PPARα was activated in the livers of HP diet-fed rats. Furthermore, the serum concentration of fibroblast growth factor 21, a hormone secreted from the liver that promotes fatty acid utilization in adipose tissue as a PPARα target gene, was higher (p = 0.054) in HP diet-fed rats than in control diet-fed rats. These data suggest that a HP diet enhances energy expenditure through the utilization of free fatty acids released via lipolysis of white adipose tissue.

overall_design:
Male Wistar rats (4 weeks old) were purchased from Japan SLC Co. (Hamamatsu, Japan) and individually housed in metabolic cages under controlled conditions of 22±1°C and a 12-hour light/dark cycle (lights on from 08:00 to 20:00 daily). Two different diets containing 0.3% phosphorous (control diet) and 1.2% phosphorous (HP diet) were prepared based on the AIN-93G diet (Table 1).9) All rats were fed the control diet for a 7-day acclimatization period. After acclimatization, rats were divided into two groups of similar mean body weight (n = 5 each) and then fed either the control or the HP diet for 24 days. The animals were allowed to eat ad libitum and had free access to water (MilliQ water).The protocol for the animal experiments was approved by the Animal Use Committee of the Faculty of Agriculture at The University of Tokyo.

Please note that the animals used in this study are identical to those used in GSE31973.

first: Sunwoo

last: Chun

first: Takeshi

last: Bamba

first: Tatsuya

last: Suyama

first: Tomoko

last: Ishijima

first: Eiichiro

last: Fukusaki

first: Keiko

last: Abe


title: Motor cortex after C3 lesion

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: Gene expression analysis of motor cortex after spinal C3 lesion

overall_design: Dorsal column wire knife lesions: Adult female Fischer 344 rats weighing 150-200 gm were used. Animals underwent a laminectomy at spinal level C3. Dorsal funiculus lesions were made in the middle of C3 using a Kopf microwire device (Kopf Instruments, Tujunga, CA). After fixation in a spinal stereotaxic unit, a small dural incision was made. The wire knife was lowered into the spinal cord to a depth of 1.1 mm ventral to the dorsal cord surface and 1.1 mm to the left of the midline. The tip of the wireknife was extruded, forming a 2.25 mm-wide arc that was raised to the dorsal surface of the cord. To ensure complete axotomy of the dorsal funiculus, spinal tissue was compressed against the microwire knife surface using a microaspiration pipette until all visible white matter was transected. Cortical microdissection: The forelimb and hindlimb motor cortex were microdisected from rat cortices: Rostral to Bregma: an area from 2.0 to 4.5 mm mediolateral and from 0 to 2 mm anterior-posterior Caudal to Bregma: an area from 2.0 to 3.5 mediolateral and from 0 to 3 mm caudal to Bregma. Only the inferior half of the cortex containing layer V corticospinal motor neurons was sampled in each region.

first: Mark

last: Tuszynski

first: Armin

last: Blesch


title: Tracking the Fragile X Mental Retardation Protein in a Highly Ordered Neuronal RiboNucleoParticles Population: a Link Between Stalled Polyribosomes and RNA Granules

status: Public on Jun 30 2016

city: Quebec

first: Claude

last: Robert

state: Quebec

address: Pavillon Comtois

department: Animal Sciences

institute: Laval University

summary:
Local translation at the synapse plays key roles in neuron development and activity-dependent synaptic plasticity. mRNAs are translocated from the neuronal soma to the distant synapses as compacted ribonucleoparticles referred to as RNA granules. These contain many RNA-binding proteins, including the Fragile X Mental Retardation Protein (FMRP), the absence of which results in Fragile X Syndrome, the most common inherited form of intellectual disability and the leading genetic cause of autism.
Using FMRP as a tracer, we purified a specific population of RNA granules from mouse brain homogenates. Protein composition analyses revealed a strong relationship between polyribosomes and RNA granules. However, the latter have distinct architectural and structural properties, since they are detected as close compact structures as observed by electron microscopy, and converging evidence point to the possibility that these structures emerge from stalled polyribosomes. Time-lapse video microscopy indicated that single granules merge to form cargoes that are transported from the soma to distal locations. Transcriptomic analyses showed that a subset of mRNAs involved in cytoskeleton remodelling and neural development is selectively enriched in RNA granules. One third of the putative mRNA targets described for FMRP appear to be transported in granules and FMRP is more abundant in granules than in polyribosomes. This observation supports a primary role for FMRP in granules biology. Our findings open new avenues for the study of RNA granule dysfunctions in animal models of nervous system disorders, such as Fragile X syndrome.
Fragile X syndrome is the most common form of inherited mental retardation affecting approximately 1 female out of 7000 and 1 male out of 4000 worldwide. The syndrome is due to the silencing of a single gene, the Fragile Mental Retardation 1 (FMR1), that codes for the Fragile X mental retardation protein (FMRP). This protein is highly expressed in brain and controls local protein synthesis essential for neuronal development and maturation as well as the formation of neural circuits. Several studies suggest a role for FMRP in the regulation of mRNA transport along axons and dendrites to distant synaptic locations in structures called RNA granules. Here we report the isolation of a particular subpopulation of these structures and the analysis of their architecture and composition in terms of RNA and protein. Also, using time-lapse video microscopy, we monitored granule transport and fusion throughout neuronal processes. These findings open new avenues for the study of RNA transport dysfunctions in animal models of nervous system disorders.

overall_design: The control or reference structure or subcellular fraction are the neuronal polyribosomes while the experimental or test structure or subcellular fraction are the neuronal granules. Three independant replicates were done for each structure. Microarray hybridization was done using a two-color design in full dye-swap.

first: Rachid

last: El Fatimy

first: Laetitia

last: Davidovic

first: Sandra

last: Tremblay

first: Xavier

last: Jaglin

first: Alain

last: Dury

first: Paul

last: De Koninck

first: Edouard

middle: W

last: Khandjian


title: Transcriptome analysis of tenotomy immobilized rat soleus muscle

status: Public on May 23 2016

city: Ankara

first: Cetin

last: Kocaefe

state: Sihhiye

address: Hacettepe University School of Medicine

department: Dept. of Medical Biology

country: Turkey

institute: Hacettepe University School of Medicine

summary:
Tenotomy is the release of muscle preload that causes abrupt shortening of the muscle and models atrophy and fibrosis without inflammatory response. Fibrosis in the skeletal muscle is known to be triggered by TGF-β, which is activated by mediators of inflammatory events. As these were lacking, tenotomy provided an opportunity to investigate transcriptional events on a background without inflammation. An unbiased look at the transcriptome of tenotomy-immobilized soleus muscle revealed that the majority of the transcriptional changes took place in the first four weeks.
The transcriptome provided clear-cut evidence for the upregulation of collagens and several extracellular matrix components that defined fibrotic remodeling of the skeletal muscle architecture as well as activation of the fibro-adipogenic precursors.

overall_design: Time-course transcriptome analysis of tenotomy immobilized rat soleus samples from Control muscle (n=4) samples and tenotomy immobilized samples of 1 week (n=2) 2 weeks (n=2), 3 weeks (n=1), 4 weeks (n=1), 6 weeks (n=2), 16 weeks (n=1), 22 weeks (n=1) immobilization.


title: Mouse iPS cells-derived 3D-retinas: Vehicle control- vs. 4-hydroxytamoxifen (4-OHT)-treated 3D-retinas

first: Shin-ichiro

last: Ito

summary: Transcriptional profiling of 3D-retinas differentiated from mouse iPS cells comparing vehicle control- with 4-OHT-treated. 4-OHT is an inverse agonist of estrogen-related receptor beta (ERRβ), a rod-enriched transcription factor responsible for maintenance of rod photoreceptor cells and the treatment induces photoreceptor specific cell death in the 3D-retinas. Goal was to understand the mechanism of 4-OHT-induced degeneration of photoreceptor cells in the 3D-retinas.

overall_design: 4-OHT-induced gene expression in the 3D-retinas was measured at DD 26 when the photoreceptor cells were degenerated.  Two-condition experiment, vehicle control- vs. 5 µM 4-OHT-treated 3D-retinas. Biological replicates: each sample has 24 3D-retinas and 1 replicate.

first: Akishi

last: Onishi

first: Masayo

last: Takahashi


title: Jmjd2a and Jmjd2c regulate H3K9me3 and H3K36me3 at H3K4me3 positive TSSs being essential for ESC self-renewal and embryogenesis (microarray)

status: Public on May 09 2016

city: Copenhagen N

first: Marianne

middle: Terndrup

last: Pedersen

department: University of Copenhagen

institute: BRIC

summary: We have characterized the role of the Jmjd2/Kdm4 proteins in embryonic stem cell (ESC) biology, histone methylation and gene regulation. The Jmjd2 proteins are H3K9/H3K36 histone demethylases and three Jmjd2 family members are expressed in ESCs: Jmjd2a/Kdm4a, Jmjd2b/Kdm4b and Jmjd2c/Kdm4c/Gasc1. We find that specifically Jmjd2a and Jmjd2c exert redundant functions, which are essential for ESC self-renewal and early embryonic development. ChIP-seq studies show that Jmjd2a and Jmjd2c both localize to H3K4me3 marked regions, where they have general and widespread roles preventing the accumulation of especially H3K9me3, but also H3K36me3. Jmjd2 catalytic activity is required for ESC maintenance, and increased H3K9me3 levels in knockout ESCs compromise the expression of several Jmjd2a/c targets, including genes that are important for ESC self-renewal. Thus, continual removal of H3K9 promoter methylation by Jmjd2 demethylases represents a novel mechanism ensuring transcriptional competence and stability of the pluripotent cell identity.

overall_design: We generated conditional Jmjd2a;Jmjd2c (2ac) double knockout ESCs (Jmjd2a(f/f);Jmjd2c(f/f);Rosa26::CreERT2) and Jmjd2a:Jmjd2b;Jmjd2c (2abc) triple knockout ESCs (Jmjd2a(f/f);Jmjd2b(f/f);Jmjd2c(f/f);Rosa26::CreERT2). 3 independently established ESC lines of 2ac and 2abc ESCs, respectively, were grown in the absence or presence of OHT leading to activation of the Cre recombinase and subsequent loss of Jmjd2 expression. Upon recovery from the OHT treatment, RNA was extracted for gene expression analyses. ESCs were cultured in 2i serum-free medium.

middle: T

first: Susanne

last: Kooistra


title: epithelia and fibroblasts gene profile in 4NQO induced tongue carcinogenesis

status: Public on May 17 2016

city: Guangzhou

first: Tong

last: Wu

state: Guangdong

address: Zhongshaner Road

institute: Sun Yat-sen University

summary: Nine groups of rat tongue epithelia and submucosal fibroblasts RNA samples respectively, including three from normal control, three from dysplasia, and three from carcinoma (3 rats per group) were collected for gene microarray hybridization.

overall_design: Significant fold changes among genes were determined by taking the ratio of the expression between dysplasia group and carcinoma group versus normal group in epithelia and fibroblasts cells


title: Deletion of nuoG in recombinant BCG vaccine against TB

status: Public on May 03 2016

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: The current tuberculosis vaccine, Bacillus Calmette-Guérin (BCG), provides insufficient protection. We deleted the NADH dehydrogenase 1 subunit G (nuoG) gene from BCG ΔureC::hly, the most advanced live vaccine candidate in clinical development. Removal of nuoG enhanced co-localisation of LC3 to bacteria in human host cells. BCG ΔureC::hly ΔnuoG vaccination was safer than BCG and improved efficacy of BCG ΔureC::hly by reducing tuberculosis load in murine lungs 1000-fold.

overall_design: Microarray experiments were performed as single-color hybridizations on Agilent SurePrint G3 catalog whole genome mouse 8x60K microarrays (Agilent-028005) according to supplier's recommendations. In total 48 samples were analyzed. Uninfected and M.bovis BCG SSI samples were used as control and reference samples.

first: Martin

last: Gengenbacher

first: Natalie

last: Nieuwenhuizen

first: Hans

first: Stefan

middle: H

last: Kaufmann


title: Common Handling Procedures Conducted in Preclinical Safety Studies Results in Minimal Hepatic Gene Expression Changes in Sprague-Dawley Rats

status: Public on May 05 2016

city: Seattle

first: Kai

last: Lau

address: 1201 Amgen Court West

institute: Amgen Inc.

summary: Gene expression profiling has been used as a tool to gain mechanistic understanding of adverse effects in response to compound exposure.  However, little is known about how the common handling procedures of experimental animals during a preclinical study alter their baseline gene expression.  We report on gene expression changes in the livers of female Sprague-Dawley rats following common handling procedures.  Insight on baseline gene expression changes obtained in this study will allow us to evaluate how these changes may affect interpretation of gene expression profiles following compound exposure.  Rats were divided into three groups (n = 10 per group): one group was not subjected to handling procedures, euthanized on day 2, and served as controls for both handled groups.  Animals in the other two groups were weighed, subjected to restraint in Broome restrainers, and administered water via oral gavage daily for 1 or 4 days with tail vein blood collections at 1, 2, 4, and 8 hours postdose on days 1 and 4 followed by euthanasia on day 2 or 5.  Significantly altered genes were identified in livers of animals following 1 or 4 days of handling when compared to the unhandled animals.  Gene changes in animals handled for 4 days were similar to those handled for 1 day, suggesting a lack of habituation.  The altered genes were primarily immune function related genes. These findings, along with a correlating increase in corticosterone levels suggest that common handling procedures may cause a minor immune system perturbance.

overall_design: Female Sprague Dawley rats were divided into three groups (n = 10 per group) based on body weights. The control group was not subjected to handling procedures. Animals in the other two groups were weighed, restrained with Broome restrainers which consisted of removing the animal from their home cage, recording body weight, restraining for dose administration and then returning the animal to its home cage.  Dose administration consisted of water via oral gavage daily for 1 day or 4 days with tail vein blood collections at 1, 2, 4, and 8 hours postdose on days 1 or 4.

first: Yudong

last: He

first: Christine

middle: M

last: Karbowski

first: Jon

last: Werner

first: Nancy

last: Everds

first: Chris

last: Di Palma

first: Yuan

last: Chen

first: Marnie

last: Higgins-Garn

first: Sandra

last: Tran

first: Cynthia

last: Afshari

first: Hisham

last: Hamadeh


title: Targeting biliary cancer desmoplasia in culture

city: Jacksonville

first: Catherine

last: Dumur

state: FL

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

summary: To more closely reproduce key cellular and stromal features of the desmoplastic reaction of cholangiocarcinoma in vitro, we developed a novel 3-dimensional culture modeling of cancer and stromal cells as a strategy for targeted therapies

overall_design: Cellular, molecular, and functional characterization of different cancer-associated fibroblastic (CAF) and cholangiocarcinoma cell strains isolated from orthotopic tumors arising from bile duct inoculation of spontaneously-transformed rat cholangiocytes (BDEsp cells) in Fischer 344 young adult male rats.

first: Alphonse

last: Sirica

middle: I


title: Flow activated cell sorting and genome-wide analysis of hybrids cells (RFP+YFP+) and non-hybrid cells (RFP+)

status: Public on Apr 30 2016

city: Barcelona

first: Wassim

last: Altarche Xifro

address: Dr Aiguader 88

country: Spain

institute: Centre for Genomic Regulation (CRG)

summary:
Cellular functions in mouse and human tissues can be restored after fusion of bone marrow (BM)-derived cells with a variety of somatic cells. Here, after transplantation of hematopoietic stem and progenitor cells (HSPCs) in the substantia nigra pars compacta (SNpc) of two different mouse models of Parkinson’s disease, we significantly ameliorated the dopaminergic neuron loss and function. We show fusion of transplanted HSPCs with neurons and with glial cells in the ventral midbrain of Parkinson’s disease mice. Interestingly, the hybrids can undergo reprogramming in vivo and survived up to 4 weeks after transplantation, while acquiring features of mature astroglia. These newly generated astroglia produced Wnt1 and were essential for functional rescue of the dopaminergic neurons. Our data suggest that glial-derived hybrids produced upon fusion of transplanted HSPCs in the SNpc can rescue the Parkinson’s disease phenotype via a niche-mediated effect, and can be exploited as an efficient cell-therapy approach.
To further investigate the reprogrammed phenotype of the hybrids genome-wide, we analyzed the transcriptome of the RFP+YFP+ fused cells compared to the RFP+ unfused cells using microarrays in the R26Y, GFAP-Cre and FoxA2-Cre models

overall_design: HSPCs were unilaterally grafted at day 3 after the last MPTP intraperitoneal injection in mice. One week after transplantation in the midbrain MPTP, cells were dissociated and FACS sorted. We FACS-sorted RFP+YFP+ fused and RFP+ unfused cells (obtained after transplanting HSPCsCre/RFP in MPTP-treated R26Y, HSPCsR26Y in MPTP-treated GFAP-Cre or in MPTP-treated FoxA2-Cre mice) and analyzed their transcriptome profile by microarray analysis

first: Maria

middle: P

last: Cosma

last: Xifro


title: Whole genome analysis of iron oxide nanoparticles treated mensenchymal stem cells

status: Public on Apr 27 2016

city: Nanjing

first: Qiwei

last: Wang

address: NO.87 Dingjiaqiao

institute: Southeast University

summary: To determine the cellular effect of iron oxide nanoparticles on MSC, we performed gene expression microarray assay to explore more intensive molecular basis.

overall_design: Human bone marrow-derived mesenchymal were treated by iron oxide nanoparticles at final concentration 100 μg/mL for 7 days, then gene expression microarray analysis were employed.


title: Gene expression in liver of interleukin-18 knockout mice at 6 and 12 weeks of age

status: Public on Apr 12 2016

first: Daisuke

last: Okuzaki

summary: Interleukin-18 knockout mice had metabolic syndromes after 24 weeks of age. We examined gene expression profiles in mice liver using genome-wide microarray technology, and compared gene expression profiles between wild-type and interleukin-18 knockout mice. To verify responsible molecules involved in metabolic syndromes such as obesity, we compared the gene expression levels at 6 and 12 weeks of age, and picked up them whose expression was more than 2-fold increase or less than 1/2-fold decrease.

overall_design: The mouse whole livers derived from wild type and interleukin-18 knockout mice at 6 and 12 weeks of age were examined. Each strain was run in triplicate.

first: Kyosuke

last: Yamanishi


title: Gene expression analysis of primitive erythroid progenitors from 5-FU-treated WT and ESAM-KO mice.

status: Public on Apr 26 2016

summary: To determine the molecular mechanisms involved in the compromised erythropoiesis of ESAM-KO mice, Lin- FCgRII/III-/Lo CD41Lo c-Kit+ Sca1- endoglin+ CD150+ cells, which contain mostly BFU-E and CFU-E, were sorted from 5-FU-treated WT and ESAM-KO mice, and were subjected to microarray analyses.

overall_design: Microarray analyses of primitive erythroid progenitors from 5-FU-treated WT and ESAM-KO mice was performed as 1 color experiment.

first: Takao

last: Sudo

first: Takafumi

last: Yokota

first: Yuzuru

last: Kanakura


title: High-confidence Coding and Noncoding Transcriptome Maps

status: Public on Apr 01 2017

city: Seoul

first: Jin-Wu

last: Nam

address: Seongdong-Gu Hangdang-dong

department: Department of Life Science

institute: Hanyang University

type: Expression profiling by high throughput sequencing

summary: The advent of high-throughput RNA sequencing (RNA-seq) has led to the discovery of unprecedentedly immense transcriptomes encoded by eukaryotic genomes. However, the transcriptome maps are still incomplete partly because they were mostly reconstructed based on RNA-seq reads that lack their orientations (known as unstranded reads) and certain boundary information. Methods to expand the usability of unstranded RNA-seq data by predetermining the orientation of the reads and precisely determining the boundaries of assembled transcripts could significantly benefit the quality of the resulting transcriptome maps. Here, we present a high-performing transcriptome assembly pipeline, called CAFE, that significantly improves the original assemblies, respectively assembled with stranded and/or unstranded RNA-seq data, by orienting unstranded reads using the maximum likelihood estimation and by integrating information about transcription start sites and cleavage and polyadenylation sites. Applying large-scale transcriptomic data comprising 230 billion RNA-seq reads from the ENCODE, Human BodyMap Projects, The Cancer Genome Atlas, and GTEx, CAFE enabled us to predict the directions of about 220 billion unstranded reads, which led to the construction of more accurate transcriptome maps, comparable to the manually curated map, and a comprehensive lncRNA catalogue that includes thousands of novel lncRNAs. Our pipeline should not only help to build comprehensive, precise transcriptome maps from complex genomes but also to expand the universe of non-coding genomes.

sample_organism:
Homo sapiens
Mus musculus

overall_design:
The direction of unstranded reads (from ENCODE, Human BodyMap Projects, GTEx and TCGA  as well as from HeLa and mES cells) were predicted using k-order Markov chain models (kMC) generating a read with a predicted direction (RPD) and were used to assemble transcriptome maps (BIGTranscriptome). Those transcriptome maps were next used for quantification of RPDs.

The following sites contain the bam files for this study:
http://big.hanyang.ac.kr/downloads/datasets/RPDs/
All individual paths to the Sample bam files are listed in the attached metadata sheet.

first: JW

first: BH

last: You

first: SH

last: Yoon


title: Targeted activation of CREB in reactive astrocytes is neuroprotective in focal acute cortical injury.

city: Bellaterra

first: Luis

last: Pardo

state: Barcelona

address: Campus UAB Edificio M

institute: Universitat Autónoma de Barcelona

summary: Transcriptome profiling of mice overexpressing a constitutively active form of CREB in astrocytes (VP16-CREB) vs WT mice, both in normal conditions and after a focal cryolesion (C) in the parietal cortex. Goal is to determine which astrocytic genes are responsible for the neuroprotection we observed in VP16-CREB mice after injury.

overall_design: Four group experiment. Loop design in which each sample was hybridized four times, and balanced with respect to the use of Cy3 and Cy5 in the samples. Biological replicates: WT: 6 replicates; T: 5 replicates; WTC: 5 replicates; TC: 6 replicates

first: Agatha

last: Schlüter


title: Gfi1, a transcriptional repressor, inhibits the induction of the T helper type 1 programme in activated CD4 T cells

status: Public on Apr 11 2016

city: Toon

first: Junpei

last: Suzuki

address: Shitukawa

department: Graduate School of Medicine

institute: Ehime University

summary: The transcriptional repressor Gfi1 promotes Th2 cell development and inhibits Th17 and inducible regulatory T cell differentiation.  However, the contribution of Gfi1 to Th1 cell differentiation and Th1-type immune responses has not been clarified yet.  We herein demonstrate that Gfi1 inhibits the activation of Th1 program in CD4 T cells.  The activated Gfi1-deficient naïve CD4 T cells spontaneously develop into Th1 cells in an IL-12- and IFN-g-independent manner.  The increased in vivo Th1-type immune response in Gfi1-deficient mice is confirmed using murine model of nickel allergy and delayed-type hypersensitivity.  The expressions of Th1-related transcription factors including Tbx21, Eomes, Atf3, Runx1, Runx2 and Runx3 are increased in Gfi1-deficient activated CD4 T cells.  Tbx21, Eomes and Runx2 are identified as candidates for direct target of Gfi1.  Gfi1 binds to the Tbx21, Eomes and Runx2 gene loci and represses histone H3K4 methylation levels.  Together, these findings establish a novel role of Gfi1 in inhibiting Th1 cell differentiation and Th1-type immune response.

overall_design: Gene expression in WT and Gfi1-dficient CD4 T cells

first: Masakatsu

last: Yamashita


title: mRNA profile between 1/3 partial hepatectomy (PH) and 2/3 PH at 24 hours

status: Public on Apr 08 2016

city: Hangzhou

first: Zhikun

last: Liu

address: Qingchun Road 79#

institute: Zhejiang University

summary: Six rats underwent partial hepatectomy (PH) (3, 1/3PH; 3, 2/3PH). The total mRNA of three rats each group were pooled and compared by microarray to selected the mRNA which differs between between 2/3PH with robust DNA replication and 1/3PH with a minimal replicative response.

first: X

last: Xu

first: Z


title: Mouse Liver Raly knockdown

status: Public on Mar 31 2016

first: Peter

last: Tontonoz

address: 675 Charles E Young

department: Pathology

summary: Effects of Raly knockdown on hepatic gene expression

overall_design: Mouse livers treated with adenoshRaly or control

first: Tamer

last: Sallam


title: Gene Expression of brain cortex microvessels in two rat models of acute liver failure (ALF)

status: Public on Apr 05 2016

first: Teresa

last: García-Lezana

address: Paseo de la Vall d'hebron 119-129

institute: Vall d'Hebron Research Institute

summary:
Evaluation of early transcriptional changes in blood brain barrier genes involved in the patogenesis of brain edema associated with ALF.
Two different well stablished rat models were analyzed: Portacaval anastomosis plus hepatic artery ligation and portacaval anastomosis plus total hepatectomy.

overall_design:
ALF was induced by portocaval anastomosis (PCA) and 24 hours after the surgery animals underwent hepatic artery ligation (HAL) or total hepatectomy (HEP). Sham rats were subjected to a fictitious two-step surgery.
Between 8 and 12 hours after the last surgery rats were euthanized by decapitation, to avoid anesthetic effects, and cortical microvessels isolated.

first: Lluis

last: Palenzuela

first: Jordi

last: Romero-Gimenez

first: Laia

last: Chavarria

last: Garcia-Lezana

first: Marc

last: Oria


title: Mouse Hepatocytes +/- GW

summary: Identification of novel LXR target genes

overall_design: Primary mouse hepatocytes were isolated from Bl6 mice and plated on 6 well plates. Cells serum starved and treated with statin/MVA followed by overnight adminstration of DMSO or LXR agonist GW3965. Total RNA isolation using TRIZOL and Qiagen Column.


title: Y. pestis exposed to various concentrations of ciprofloxacin for various time points (treated/nontreated analysis in each array).

status: Public on Mar 30 2016

city: Ness-Ziona

first: Ida

last: Steinberger-Levy

address: P.O. box 19

country: Israel

institute: IIBR

summary: Cultures of Y. pestis Kimberley53 virulent strain were exposed to different concentrations of ciprofloxacin (including 0.016 µg/ml representing the strains' MIC value) for various time periods. Total RNA samples were extructed and used for cRNA synthesis and labelling (using Cy3-CTP for the treated samples and Cy5-CTP for the non-treated sample  in one biological experiment and  dye swap for the 2nd replicate of independent biological experiment). 8 Labeled cRNA samples were hybridized to custom made Agilent 8x15K slide (each slide represent 1 time point). Goal: Identifing alterations in gene expression profile which correlates with the ciprofloxacin induced growth inhibition. Those altered mRNA transcrips will be used as a markers for the development of rapid molecular Antibiotic Susceptibility Test.

overall_design: Y. perstis  exposed to 0.001, 0.016, 0.5 and 4 µg/ml ciprofloxacin, compared to growth control (non treated) sample, for 3 time periods (45, 90 and 120 min.). Two independent biological replicates were performed. Extracted total RNA were used for cRNA synthesis and labeling with Cy3/Cy5-CTP, hybridized to Agilent custom-made 8x15K slide format.

first: Ohad

last: Shifman

first: Anat

last: Zvi

first: Naomi

last: Ariel

first: Adi

last: Beth-Din

first: Ofir

last: Israeli

first: David

last: Gur

first: Moshe

last: Aftalion

first: Sharon

last: Maoz

first: Raphael

last: Ber


title: Mouse Liver LeXis overexpression

first: Peter

last: Tontonoz

summary: Consequences of hepatic Lexis overexpression

overall_design: Mouse livers treated with AdLeXis or AdGFP

last: Sallam


title: s-SHIP expression identifies a subset of murine basal prostate cells as neonatal stem cells

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

summary: Isolation of prostate stem cells is crucial for understanding their biology during normal development and tumorigenesis. In this aim, we used a transgenic mouse model expressing GFP from the stem cell-specific s-SHIP promoter to mark putative stem cells during postnatal prostate development. We showed that cells identified by s-SHIP/GFP expression are present transiently during early prostate development and localize to the basal cell layer of the epithelium. These prostate s-SHIP/GFP-positive cells represent a subpopulation of the lineage-negative / CD24-positive / Sca-1-positive / CD49f-positive (LSC) cells and are capable of self–renewal together with enhanced growth potential in sphere–forming assay in vitro, a phenotype consistent with that of a prostate stem cell population. Transplantation assays of these prostate GFP-positive cells demonstrate reconstitution of prostate ducts containing both basal and luminal cells in renal grafts. Altogether, these results demonstrate that s-SHIP promoter expression is a new marker for neonatal basal prostate cells exhibiting stem cell properties that enables prostate stem cells in situ identification and isolation via a single consistent parameter. Since the GFP-positive cell population is a small subset of basal LSC cells and is most responsible for stem-like activity, we performed transcriptional profiling of GFP-negative LSC and GFP-positive LSC cells to distinguish a basal cell profile from a tissue stem cell profile.

overall_design: Prostate tissue was collected from 6-day-old male mice, minced into small fragment, digested with 200 U/ml collagenase IA–S (Sigma; C5894) in Dulbecco’s modified Eagles medium (DME, Gibco) supplemented with 10% fetal bovine serum (FBS, Hyclone) (DME-10% FBS) at 37°C for 60 min with gentle agitation. The digested cells were filtered through a 40-μm cell strainer (BD Biosciences) washed, and resuspended in DME-10% FBS., filtered and labeled with antibodies against lineage (Ter119, CD31, CD45), CD49f and Sca-1 cell surface markers (Affymetrix ebiosciences). Labeled cells were analyzed and the GFP-negative LSC and GFP-positive-LSC populations were sorted by FACS. For each cell population, 3 independent samples were collected and analysed.

first: Guillaume

last: Brocqueville

first: Roland

last: Bourette


title: Expression data from adult male Sprague Dawley rat liver, investigating how pomegranate skin extract prevents non alcoholic fatty liver diseases

status: Public on Feb 01 2016

city: Beijing

first: yujie

last: shi

address: No.5 building No.5 Road Dijin

institute: Nestle research center- Beijing hub

summary:
Pomegranate skin extract could prevent fatty liver due to high fat diet in adult male Sprague Dawley rat. There are 3 groups of rats, feeding chow diet, high fat diet and high fat diet combined with pomegrante skin extract. After 8 weeks feeding, high fat diet group developped fatty liver but the other two groups still have healthy liver.
We used microarrays to detail the global programme of gene expression underlying the fatty liver development and preventive effect of pomegranate skin extract on fatty liver.

overall_design: There are 3 treatment groups and 6 replicates for each group. The 3 treatment groups are control group feeding chow diet, high fat group feeding high fat diet and PE group feeding high fat diet and pomegranate skin extract. Rat livers were collecteded for RNA extraction and hybridization on Affymetrix microarrays.

first: Yujie

last: Shi


title: 5-HT2A and 5-HT2C receptors as hypothalamic targets of developmental programming in male rats

status: Public on Feb 25 2016

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

summary: Though obesity is a global epidemic, the physiological mechanisms involved are little understood. Recent advances reveal that susceptibility to obesity can be programmed by maternal and neonatal nutrition. Specifically, a maternal low protein diet during pregnancy causes decreased intrauterine growth, rapid postnatal catch-up growth and increased risk for diet-induced obesity. Given that the synthesis of the neurotransmitter 5-hydroxytryptamine (5-HT) is nutritionally regulated and 5-HT is a trophic factor, we hypothesized that maternal diet influences fetal 5-HT exposure, which then influences central appetite network development and the subsequent efficacy of 5-HT to control energy balance in later life. Consistent with our hypothesis, pregnant low protein fed rat mothers exhibited elevated serum 5-HT, which was also evident in the placenta and fetal brains at E16.5. This increase was associated with reduced hypothalamic expression of 5-HT2CR - the primary 5-HT receptor influencing appetite. As expected, reduced 5-HT2CR expression was associated with impaired sensitivity to 5-HT-mediated appetite suppression. 5-HT primarily achieves effects on appetite via 5-HT2CR stimulation of pro-opiomelanocortin (POMC) peptides within the arcuate nucleus of the hypothalamus (ARC). We reveal that 5-HT2ARs are also anatomically positioned to influence the activity of ARC POMC and that 5-HT2AR mRNA is increased in the hypothalamus of in utero growth restricted offspring that underwent rapid postnatal catch-up growth. Furthermore, these animals are more sensitive to 5-HT2AR agonist-induced appetite suppression. These findings may not only reveal a 5-HT-mediated mechanism underlying programming of obesity susceptibility but also provide a promising means to correct it, via a 5-HT2AR agonist treatment.

overall_design: The study was carried out using male Wistar rats (Rattus norvegicus). On postnatal day 3, two experimental groups of offspring were established: controls (offspring of control dams) and recuperated (offspring of dams fed a low-protein diet (8% protein, w/v), but nursed by control dams. The animals were fed with standard chow until 3 months of age where the brains were collected for transcriptomic profiling

middle: Y

first: Malgorzata

last: Martin

first: Giles

middle: S

last: Yeo

first: Sue

last: O'zanne


title: Maternal Obesity is Associated with Ovarian Inflammation and Up-regulation of Early Growth Response Factor (Egr)-1

status: Public on Jan 31 2016

city: Little Rock

first: Aline

last: Andres

state: Arkansas

address: 15 Children's Way

institute: Arkansas Children's Nutrition Center

summary: Maternal obesity during the pre-implantation period leads to a pro-inflammatory milieu in the ovaries. We conducted a global transcriptomic profiling in ovaries from TEN fed rats during  the pre-implantation period.   Microarray analysis revealed that obesity lead to  increased expression of genes related to inflammation, decreased glucose transporters, and dysregulation of ovarian function-related genes in the ovaries. Our results suggest maternal obesity led to an up-regulation of inflammatory genes and Egr-1 protien expression in peri-implantation ovarian tissue, and a concurrent down-regulation of glucose transporters mRNA and AKT and PI3K protein levels.

overall_design: Lean vs. overfed ovaries

first: Meghan

last: Ruebel

first: Kartik

last: Shankar

first: Dana

last: Gaddy

first: Forrest

last: Lindsey

first: Thomas

last: Badger


title: low and high aerobic capacity rats exposed to cigarette smoke, lung tissue

status: Public on Feb 15 2016

first: Joseph

last: Szustakowski

state: MA

address: 220 Massachusetts Avenue

institute: Novartis Institutes for Biomedical Research

summary: Low aerobic exercise capacity increases susceptibility to smoking-induced   inflammation and tissue damage

overall_design: 38 animals total: 12 HCR Smoke, 12 LCR Smoke, 7 HCR sham, 7 LCR sham

first: John

last: Gounaride

first: Matthew

last: Thomas

first: Abigail

last: Morris

first: Win-Yan

last: Wan

first: Bailin

last: Zhang

first: Cliff

last: Battram

last: Everatt

first: Danielle

last: Fletcher

first: Paul

last: Whittaker

first: Erik

last: Sassaman

first: Erica

last: Hirsch

first: Lauren

middle: G

last: Koch

first: Steven

last: Britton

first: Christopher

last: Stevenson


title: Effects of dual agonist of GLP1 and GCGR on animal model of NAS (MCD diet) and hepatic regeneration

status: Public on Feb 23 2016

city: MADRID

last: VALDECANTOS

state: MADRID

address: C/ARTURO DUPERIER, 4

institute: IIB ALBERTO SOLS

summary: The genomic analysis of liver from mice fed with standard or methyl and choline deficient (MCD) diet and treated with dual agonist of GLP1R/GCGR during two weeks before 70% partial hepatectomy (PH) and after 2 weeks PH resulted in a set of genes regulated by diet and other set regulated differentially by treatment in MCD treated animals. These genes are apparently responsible for the reversion and prevention of NAS and improvement in hepatic regeneration induced by drug treatment

overall_design: All microarray analyses were performed with RNA samples obtained from four independent liver from animals with different diet and drug treatmens.

first: M

last: Valdecantos

first: Virginia

last: Pardo

first: Angela


title: Transcriptional changes in sensory ganglion associated with primary afferent collateral sprouting in spared dermatome model

status: Public on Mar 01 2016

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary:
Primary afferent collateral sprouting (PACS) is a process whereby non-injured primary afferent neurons respond to some stimulus by extending new branches from existing axons. In the model used here (spared dermatome), the intact sensory neurons respond to the denervation of adjacent areas of skin by sprouting new axon branches into that adjacent denervated territory. Neurons of both the central and peripheral nervous systems undergo this process, which contributes to both adaptive and maladaptive plasticity. Investigations of gene expression changes associated with PACS can provide a better understanding of the molecular mechanisms controlling this process. Consequently, it can be used to develop treatment for spinal cord injury to promote functional recovery.
In this study, we sought to identify gene expression changes in PACS using 20 Affymetrix Rat Genome 230 2.0 microarrays. The experiments were designed to discover global gene expression changes in non-injured DRG neurons undergoing PACS. T11 DRG neurons remained intact and undergo PACS after the cutaneous nerves of the adjacent segments (T9, T10, T12, and T13) were injured and regeneration of those injured nerves prevented by ligation. Thus, the T9, T10, T12, and T13 dermatomes were denervated, but the T11 dermatome remained intact. Axons of the T11dermatome (and thus housed in the T11 dorsal root ganglion (DRG)), extended new branches to innervate the T9, T10, T12, and T13 dermatomes. N.B.: This is NOT a spared root experiment. ALL spinal roots were non-injured. Peripheral nerves were used.

overall_design: A total of 20 Affymetrix Rat Genome 230 2.0 microarrays were analyzed: six naïve controls, seven replicates at day 7 post-surgery (presumed to represent an “initiation phase”), and seven replicates at day 14 post-surgery (presumed to represent a “maintenance phase”). DRGs were NOT pooled onto microarrays. Each animal had its own microarray with T11 DRG sample which underwent 2-round amplification. After quality control analysis, one of the naïve control microarrays was removed from further analysis.

first: Benjamin

last: Harrison

first: Gayathri

last: Venkat

first: James

last: Lamb

first: Cassie

last: Drury

first: Thomas

last: Hutson

first: Mary

last: Bartlett Bunge

first: Lorne

last: Mendell

first: Fred

last: Gage

first: Richard

middle: D

last: Johnson

first: Caitlin

last: Hill

middle: C

first: Lawrence

last: Moon

first: Jeffrey

last: Petruska


title: Muscle mitochondrial stress-induced metabolic adaptations do not require FGF21 action

status: Public on Jan 07 2016

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

summary: Fibroblast growth factor 21 (FGF21) is a key metabolic regulator which was recently discovered as stress-induced myokine and common denominator of muscle mitochondrial disease. However, its precise function and pathophysiological relevance remains unknown. Here we demonstrate that white adipose tissue (WAT) is the major target of muscle mitochondrial stress-induced FGF21. Strikingly, substantial browning and metabolic remodeling of subcutaneous WAT, together with the reduction of circulating triglycerides and cholesterol are fully FGF21 dependent. Unexpectedly and in contrast to prior expectations, we found a negligible role of FGF21 in muscle stress-related improved glycemic control, obesity resistance and hepatic lipid homeostasis. Furthermore, we show that the protective muscle mitohormesis and metabolic stress adaptation does not require FGF21 action. Taken together, our data imply that although FGF21 drives WAT remodeling, this effect and FGF21 as stress hormone per se may not be essential for the adaptive response under muscle mitochondrial stress conditions.

overall_design: Wildtype male mice and FGF21-knockout male mice, together with muscle specific UCP1-transgenic male animals, and double cross of FGF21-KO with UCP1-Tg male mice, were kept on a standardized low fat diet for 40 weeks. After sacrifice, subcutaneous white adipose tisseu (scWAT) was rapidly removed, weighed, and snap frozen in liquid nitrogen and used for RNA isolation and whole genome gene expression microarray hybridisation using Agilent arrays.

first: Mario

last: Ost

first: Inge

last: van der Stelt

first: Susanne

last: Klaus

first: Jaap

last: Keijer


title: Intermittent neonatal hypoxia elicits the upregulation of inflammatory-related genes in the adult rat through long-lasting programming effects

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

summary:
The long-term effects of neonatal intermittent hypoxia (IH), an accepted model of apnea-induced hypoxia, are unclear. We have previously shown lasting “programming” effects on the HPA axis in adult rats exposed to neonatal IH. We hypothesized that neonatal rat exposure to IH will subsequently result in a heightened inflammatory state in the adult.  Rat pups were exposed to normoxia (control) or six cycles of 5% IH or 10% IH over one hour daily from postnatal day 2 – 6.  Plasma samples from blood obtained at 114 days of age were analyzed by assessing the capacity to induce transcription in a healthy peripheral blood mononuclear cell (PBMC) population and read using a high-density microarray.  The analysis of plasma from adult rats previously exposed to neonatal 5% IH vs. 10% IH resulted in 2,579 significantly regulated genes including increased expression of Cxcl1, Cxcl2, Ccl3, Il1a, and Il1b.  We conclude that neonatal exposure to intermittent hypoxia elicits a long-lasting programming effect in the adult resulting in an upregulation of inflammatory-related genes.
Apnea is the most common cause of neonatal hypoxia affecting about 50% of preterm births (30 – 31 weeks), usually due to immature respiratory development.  Upregulation of inflammatory genes and pathways in children 7 – 10 years of age has been shown, and there is a known increased risk of insulin resistance in adulthood when the fetus is exposed to maternal hypoxia, but the mechanism is unclear. The long-term metabolic, endocrine, and immunological effects of neonatal intermittent hypoxia (IH) exposure, an accepted model of apnea-induced hypoxia, have not been thoroughly evaluated. Recent studies in rats have shown that perinatal IH exposure can result in oxidative stress, causing a permanent immune response subsequently resulting in features of diabetes mellitus. We have previously examined adult rats exposed to neonatal intermittent hypoxia and perinatal continuous hypoxia, and have found lasting “programming” effects on the HPA axis. We now assess the long term effects of an accepted model of apnea-induced hypoxia using a validated transcriptional bioassay to study the extracellular milieu of adult rats exposed to neonatal intermittent hypoxia.  We hypothesize that exposure to neonatal intermittent hypoxia will result in an increased inflammatory state in the adult as a result of long-lasting programming.

overall_design: Sprague-Dawley (SD) rat pups were treated with neonatal normoxia (21% O2, control), 5% intermittent hypoxia (IH), or 10% IH on postnatal days (PD) 2-6, daily over 1 hr.  They were reared normally by birth dams and weaned at PD22. Males were allowed to mature and sacrificed at age PD114 after an overnight fast. Whole blood collected by decapitation into tubes with EDTA, and plasma saved for further analysis. Two adult (~180 day) male Brown Norway (BN) rats served as PBMC donors. Cells were incubated with 20% plasma that was either autologous BN (self-control), or one of 3 pools: a) SD normoxic N=8, b) SD 5% IH treated N=5, and c) SD 10% IH N=3.

first: Ashley

middle: L

last: Gehrand

last: Kaldunski

first: Eric

last: Bruder

first: Shuang

last: Jia

first: Marty

first: Hershel

last: Raff


title: Dietary Genistein Prevents Denervation-Induced Muscle Atrophy in Male Rodents via Effects on Estrogen Receptor-α.

status: Public on Jan 23 2016

city: Bunkyo-ku

first: Shinya

last: Aoyama

state: Tokyo

department: Applied Biological Chemistry

institute: University of Tokyo

summary:
Genistein is one of the flabonoids which is included in high concentration in soy and has a high estrogenic activity. Beneficial effects of estrogen or hormone replacement therapy (HRT) on muscle mass or muscle atrophy have been demonstrated. We investigated the preventive effects and underlying mechanisms of genistein intake on denervation-induced muscle atrophy.
Genistein intake significantly suppressed the loss of soleus muscle weight and the denervation-induced up-regulations of FOXO1 protein. The results of a DNA microarray showed that the estrogen receptor (ER) target genes are changed by genistein intake. Genistein suppressed the soleus muscle atrophy, and it was attenuated under the ER antagonist treatment. The administration of an ERα agonist suppressed the denervation-induced muscle atrophy and up-regulation of Atrogin1 gene expression, but the ERβ agonist had no effect.

overall_design: Ten-week-old male Wistar rats were given diets containing 0.05% genistein for 24 days. On day 14, the sciatic nerve in the left leg was severed while the rat's right hind lig was sham-treated. 10 days after denevation, soleus muscles were collected for RNA extraction and hybridization on Affymetrix microarrays. Total RNA extracted extracted from the tissues of each rat from the respective groups (4 groups; Control diet_Sham, Control diet_Denervation, Genistein diet_Sham and Genistein diet_Denervation) were pooled (eight animals per group).

first: Huijuan

first: Kyoko

last: Nakazawa

first: Junki

last: Yamamura

first: Kenji

last: Saito

first: Hisanori

last: Kato


title: Gene expression of APJ deficient endothelial cell

status: Public on Jan 01 2016

city: Suita

first: Hiroyasu

last: Kidoya

address: 3-1 Yamadaoka

department: Research Institute for Microbial Diseases

institute: Osaka university

summary: Molecular pathways regulating the development of arterial and venous endothelial cells (ECs) are now well-established, but control of parallel arterial-venous (A-V) alignment is unclear. We report that arterial-venous alignment in the skin is determined by apelin receptor (APJ) expression in venous ECs.

overall_design: We used microarrays to detail the global programme of gene expression in endothelial cells that has relationship with the deficient of APJ.  Endothelial cells were marked and isolated by Fluorescence-activated cell sorting in Trizol.

first: Nobuyuki

last: Takakura


title: Gene expression in rat ovaries treated with DHT

city: Bonn

first: Dessie

last: Salilew-Wondim

state: NRW

address: Endenicher Allee 15

department: Animal breeding and husbandry group

institute: University of Bonn

summary: Polycystic ovarian syndrome (PCOS) is an endocrine disorder of the reproductive and metabolic axis in women during the reproductive age. In this study, we used a rat model exhibiting reproductive and metabolic abnormalities similar to  human PCOS to unravel the molecular mechanisms underlining this complex syndrome.

overall_design: Female Sprague-Dawley rats were implanted with a silicone capsule continuous-releasing 5α-dehydrotestestrone (DHT) per day for 12 weeks to mimic the hyperandrogenic state in women with PCOS, and the control (CTL) groups received an empty capsule. The animals were euthanized at 15 weeks of age and the ovarian cortex tissues of both groups were used for  transcriptome profile analysis.

first: Qi

last: Wang

first: Dawit

last: Tesfaye

first: Karl

last: Schellander

first: Michael

last: Hoelker

first: MM

last: Hussein

first: Benjamin

middle: K

last: Tsang


title: Development of gene expression signatures for murine bladder: Control vs. UTI89

status: Public on Dec 29 2015

city: Columbus

first: Ashley

middle: R

last: Jackson

state: OH

address: 700 Children's Dr

department: Molecular and Human Genetics

institute: Nationwide Children's Hospital

summary: Antimicrobial peptides (AMPs) serve key proposed roles in defending the urinary tract against invading uropathogens, but individual AMPs bearing greatest responsibility for these functions remain largely unknown.  We identified RegIIIγ as the most transcriptionally upregulated AMP in bladder transcriptomes following uropathogenic Escherichia coli (UPEC) infection.  We confirmed induction of RegIIIγ mRNA during cystitis and pyelonephritis by quantitative RT-PCR.  Immunoblotting demonstrates increased bladder and urinary RegIIIγ protein levels following UPEC infection.  Immunostaining localizes RegIIIγ protein to urothelial cells of infected bladders and kidneys.  Human patients with cystitis and pyelonephritis exhibit increased urine levels of the orthologous HIP/PAP protein.  Recombinant RegIIIγ protein does not demonstrate bactericidal activity toward UPEC in vitro, but does kill Staphylococcus saprophyticus in a dose-dependent manner.  RegIIIγ knockout and control urinary tracts contain comparable bacterial burden following experimental inoculation of UPEC as well as Gram-positive uropathogens. Thus, while RegIIIγ and HIP/PAP expression occurs in human and murine UTI, their specific functions in the urinary tract remain uncertain.

overall_design: Control (Uninfected) Bladder vs. UTI89 Bladders (Infected 2, 6, and 48hrs). Biological replicates: 4 control replicates, 4 infected replicates per timepoint.

first: John

last: Spencer

first: Christina

middle: B

last: Ching

first: Birong

last: Li

first: Martin

last: Vonau

first: Bobby

last: Easterling

first: Jay

last: Kolls

first: Kirk

last: McHugh

first: Brian

last: Becknell


title: Gene expression profiling of Nup98HoxA9 expressing ES cells

status: Public on Jan 04 2016

city: Ibaraki

first: Masahiro

last: Oka

address: 7-6-8 Saito-Asagi

institute: National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN)

summary: To know whether the Nup98-HoxA9 affects global gene expression, we performed DNA microarray analysis using the following four clones: two independent Nup98-HoxA9 ES clones (clone#1 and clone#9), parental ES cells, and HoxA9-Ct ES clone.

overall_design: Two independent Nup98-HoxA9 ES clones (clone#1 and clone#9), and HoxA9-Ct ES clone, was compared with parental ES cells (reference sample).

first: Yoshihiro

last: Yoneda


title: Gene expression profiles of ASK1-deficient adipose tissues

status: Public on Jan 08 2016

city: Tokyo

first: Kazuki

last: Hattori

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

department: Graduate School of Pharmaceutical Sciences

institute: The University of Tokyo

summary: To elucidate the potential function of ASK1 in adipose tissues, microarray analysis was performed using iBAT and eWAT. Tissue samples were collected from 10-week-old male mice, and RNA samples derived from three individuals were pooled to analyze. These data provide novel insights into the physiological functions of ASK1.

first: Hidenori

last: Ichijo


title: Global gene expression profiling of mouse soleus hindlimb muscle following gradual exposure to hypoxia

status: Public on Dec 21 2015

city: Liverpool

first: Peter

last: Davidsen

state: Merseyside

address: Crown Street

institute: University of Liverpool

summary: Young adult C57 mice were exposed to chronic hypoxia for up to 2 weeks. Control mice were maintained under normoxic conditions

overall_design: To capture the temporal effect of reduced oxygen tension on gene regulation, we sampled and gene profiled the soleus hindlimb muscle (n=4) at 4 different time-points (day 0, 3, 7 and 14) following initiation of the gradual hypoxic insult (i.e. the O2 level was gradually lowered to 10% over the first week and kept stable during the second week).

first: Francesco

last: Falciani


title: Macrophage Precursor Cells from the Left Atrial Appendage of the Adult Heart Spontaneously Reprogram  into a C-kit+/CD45- Stem Cell-Like Phenotype [Array analysis]

city: Jerusalem

first: Jussi

last: Leinonen

address: Kiryat Hadassah p.o.b 12000

department: Cardiovascular Research Center, Heart Institute

institute: Hadassah-Hebrew University Medical Center

summary: The developmental origin of the c-kit expressing progenitor cell pool in the adult heart has remained elusive. Recently, it has been discovered that the injured heart is enriched with c-kit+ cells, which also express the hematopoietic marker CD45. In this study, we characterize the phenotype and transcriptome of the c-kit+/CD45+ cell population, originating from the left atrial appendage. These cells are defined as cardiac macrophage progenitors. We also demonstrate that the c-kit+/CD45+ progenitor cell population activates heart development, neural crest and pluripotency associated pathways in vitro, in conjunction with CD45 down-regulation, and acquire a c-kit+/lin- phenotype. This spontaneous reprogramming progresses further to a highly proliferative, partially myogenic phenotype. Our data suggests that c-kit+/lin- cells and cardiac macrophages have a common lineage origin possibly resolving some current conundrums in the field of cardiac regeneration.

overall_design: Two different stem cell types were grown by altering the tissue digestion protocol. To investigate their transcriptional profiles we prepared RNA from two cell sorted replicates per cell type and from two left ventricular biopsy samples as controls.

middle: V

first: Ronen

last: Beeri


title: Retinoic acid signaling coordinates the behavior of multiple cell lineages during cardiac outflow morphogenesis

city: Marseille

first: Heather

last: Etchevers

address: 27 boulevard Jean Moulin

department: INSERM U1251

institute: INSERM/Aix-Marseille Univ

summary: Retinoic acid (RA), the bioactive derivative of vitamin A, is essential for vertebrate heart development. Both excess and reduced RA signaling lead to cardiovascular malformations, particularly affecting the cardiac outflow tract (OFT). The cellular mechanisms underlying the effects of RA signaling during OFT morphogenesis are not fully understood. To address this question, we used transient maternal RA supplementation to rescue the early lethality resulting from inactivation of the murine retinaldehyde dehydrogenase 2 (Raldh2) gene. By embryonic day 13.5, Raldh2-/- hearts exhibited OFT septation defects. Although cardiac neural crest cells (cNCC) were present in OFT cushions of Raldh2-/- mutant embryos, we observed that cNCC were ectopically located in the peripheral region of the endocardial cushions, closer to the myocardium rather than immediately subjacent to the endocardium. Mislocated cNCC were aligned in parallel instead of perpendicular arrays to the endocardial surface within the proximal OFT. Supernumerary mesenchyme was generated both in and ex vivo within the cushions by Raldh2-/- mutant endocardium and found in place of the cNCC in a subendocardial, medial position. Although mislocated and misoriented, mutant cNCC resembled wildtype cells in their compaction density and individually elongated shape. Our data show that RA signaling acts on cNCC orientation relative to the septation plane and position within OFT cushions during septation process. Transcriptomic analysis and pathway-specific readout suggest that up-regulation of the Bmp pathway may be responsible for increased endothelial-to-mesenchymal transition, leading thereby to displacement of cNCC.

overall_design: E10.5 stage embryonic mouse outflow tracts were microdissected. Four pools of four outflow tracts were established for wildtype (WT) and mutant (Raldh2-/-) embryos derived from dams whose food had been supplemented with all-trans-RA (Sigma) directly mixed into powdered food at 0.1 mg/g food and offered between E7.5 and E8.5. Total RNA was extracted using Macherey-Nagel NucleoSpin® RNA columns without on-column DNase digestion.

first: Nicolas

last: El Robrini

first: Stéphane

last: Zaffran

last: Bertrand


title: Differential gene expression in the mesenteric fat among crossbred beef steers with divergent gain and feed intake phenotypes

status: Public on Nov 30 2015

city: Clay Center

first: Amanda

last: Lindholm-Perrry

state: NE

address: State Spur 18D

department: NEMRU

institute: USMARC

summary:
Steer mesenteric fat transcriptome.
Evaluation of the naturally occurring transcriptome variation in mesenteric fat among beef steers with divergent gain and feed intake phenotypes.

overall_design: The transcriptomes of mesenteric fat were examined for expression differences that contribute to cattle feed efficiency.

last: Lindholm-Perry


title: ATM-deficient B cell lymphomas

status: Public on Dec 09 2015

city: Bethesda

first: Louis

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

summary: Ataxia-telangiectasia mutated (ATM) kinase plays a central role in maintaining genomic integrity. In both humans and mice, ATM deficiency is associated with an increased incidence of lymphoid cancers that are primarily T cell in origin. We demonstrate here that when T cells are removed as targets for lymphomagenesis and as mediators of immune surveillance, ATM-deficient mice exclusively develop early onset IgM+ B cell lymphomas that by histology and gene expression profiling resemble the activated B cell-like (ABC) subset of human diffuse large B cell lymphomas (DLBCL). These ATM-deficient B cell tumors show considerable chromosomal instability and a recurrent genomic amplification of a 4.48 Mb region on chromosome 18 that contains Malt1 and is orthologous to a region similarly amplified in human ABC-DLBCL. Further, the amplification of Malt1 in these lymphomas correlates with their dependence on NF-kB, MALT1, and BCR signaling for survival, paralleling human ABC-DLBCL. This study reveals that ATM protects against development of B cell lymphomas that model human ABC-DLBCL and identifies a role for T cells in preventing the emergence of these tumors.

overall_design: We performed gene expression profiling on nine ATMKO.CD3epsilonKO lymphoma cell lines (n=12, 3 technical repeats). We analyzed gene expression of anti-IgM stimulated primary B cells from both ATMKO.CD3epsilonKO (n=7, 5 technical repeats) and ATMWT.CD3epsilonKO mice (n=2), and GC B cells isolated from SRBC-immunized ATMWT mice (n=3, 1 biological repeat and 2 technical repeats). We analyzed gene expression following treatment of two ATMKO.CD3epsilonKO lymphoma cell lines with the BTK inhibitor, PCI-32765, at time points (1, 3, 6, and 24 hours) as compared to time points with vehicle (DMSO) (n=8).


title: Scl-Ab: Exploratory 26-Week Subcutaneous Toxicology Study in the Aged Ovariectomized Female Sprague Dawley Rat with an 18-week Recovery [vertebrae]

status: Public on Jan 06 2016

city: Thousand Oaks

first: Scott

last: Taylor

state: CA

address: One Amgen Center Drive

institute: Amgen Inc.

summary: This study is designed to compare and contrast the temporal and spatial changes in bone formation rates and transcriptional profiles in cortical and cancellous bone cell populations enriched by laser capture microdissection (LCM) in ovariectomized rats administered Scl-Ab by subcutaneous injection for up to 26 consecutive weeks, followed by a recovery period of up to 18 weeks.

overall_design: Six-month-old Sprague-Dawley female rats were OVX, left untreated for 8 weeks. Rats were assigned to three treatment groups using a computerized blocking procedure designed to achieve body weight balance across treatment groups and then divided into three groups and administered by s.c. injection VEH or 3 or 50 mg/kg/wk of a Scl-Ab engineered to be less immunogenic in rats up to d183.  Rats were administered either VEH or 3 or 50 mg/kg of Scl-Ab once weekly by s.c. injection. Up to 15 rats per group were euthanized at d8, 29, 85, and 183. To assess effects following treatment withdrawal, additional groups were maintained through a treatment-free period (TFP) and euthanized at d197 and 267 for VEH and 3 mg/kg groups and at d237 and 309 for VEH and 50 mg/kg groups. To label active bone-forming surfaces and facilitate osteoblast (OB) and lining cell (LC) enrichment during laser capture microdissection (LCM), 10 mg/kg calcein green was administered s.c. 13 and 3 days prior to scheduled euthanasia. At necropsy, the first and second lumbar vertebral (L1 and L2) bodies were isolated for histomorphometry and pQCT analyses, respectively. Cryosection preparation of L3 vertebral body, LCM procedure and validation of cell enrichment, RNA extraction and amplification, TaqMan, and initial microarray analysis was performed. LCM was performed on 4-6 µm cryosections of vertebrae from the first 5 animals per treatment group per timepoint to enrich for OB, LC, and osteocyte (OCy) subpopulations for transcriptional analyses using Affmetrix Rat 230_2 microarrays

first: Michael

last: Ominsky

first: Rong

last: Hu

first: Efrain

last: Pacheco

first: Yudong

last: He

first: Sabina

last: Buntich

first: Cynthia

middle: A

last: Afshari

first: Ian

last: Pyrah

first: Paul

last: Nioi

first: Rogely

middle: W

last: Boyce


title: The Double-Strand Break Landscape of Meiotic Chromosomes Is Shaped by the Paf1 Transcription Elongation Complex in Saccharomyces cerevisiae

status: Public on Dec 02 2015

city: New York

first: Andreas

last: Hochwagen

state: NY

address: 1009 Silver Center 100 Washington Square East

institute: New York University

summary:
Genomic features of DSB re-landscaping in rtf1 mutants.
Histone modification is a critical determinant of frequency and location of double-strand breaks (DSBs), which induce recombination during meiosis. The Set1-dependent histone H3K4 and Dot1-dependent H3K79 methylations play an important role in DSB formations in budding yeast. Both methylations are promoted by the RNA polymerase II associated factor 1 (Paf1) complex, Paf1C. This study addressed a role of the Paf1C component Rtf1, which is critical for H3K4 and H3K79 methylations, for the regulation of meiotic DSB formation. Similar to set1 mutation, rtf1 mutation decreased the occurrence of DSBs in the genome. The rtf1 set1 double mutant exhibited a larger reduction in the levels of DSBs than the frequency of DSBs detected in either of the single mutants; this indicates independent roles of Rtf1 and Set1 in DSB formation. Importantly, the distribution of DSBs along chromosomes in the rtf1 mutant changed in a different manner than the pattern observed in the set1 and set1 dot1 mutants; this was characterized by enhanced DSB formation at some DSB-cold regions. These observations suggest that Rtf1, and, possibly, the Paf1C, determine DSB landscape in the genome, independent of H3K4 methylation.

overall_design: dmc1(WT) and rtf1dmc1 mutants cells were harvested during a synchronous meiotic time course at 0 and 5 hours. Isolated ssDNA was differentially labled for each time point and hybridized to a high density microarray. This experiment was repeated with biological replicates and a dye swap.

first: Meaghan

middle: M

last: Colletti

first: Neem

middle: J

last: Patel


title: Comparison of  testes gene expression in Gipr–/– and Gipr+/+

status: Public on Sep 30 2016

city: Akita

first: Tatsunori

last: Shimizu

address: 1-1-1 Hondo

department: Endocrinology, Diabetes and Geriatric Medicine

institute: Akita University Graduate School of Medicine

summary: The aim is to compare gene expression profiles of Gipr–/– mice testes with those of Gipr+/+ mice testes.

overall_design: Testes from Gipr+/+ 　and Gipr–/–mice (8-week-old, n=3, each genotype) were utilized for the microarray analysis.

first: Yuichiro

last: Yamada


title: miRNA and gene expression profile of microglial cells under oxygen-glucose deprivation

status: Public on Nov 23 2015

city: Shanghai

first: Peng

last: Wang

address: 270 Dong An Road

department: Department of Integrative Oncology

institute: Fudan University Shanghai Cancer Center

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

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

platform_organism:
Rattus norvegicus
synthetic construct

overall_design: Refer to individual Series


title: Gene expression profile of microglial cells under oxygen-glucose deprivation

summary: Migroglia cells were exposed to oxygen-glucose deprivation (OGD) for 3 h. The mRNA was isolated and the expression profiles of OGD-activated cells were compared with the profiles of resting cells.

overall_design: Two samples were analysed. mRNAs that were differentially expressed (increased or decreased in expression by ≥1.5-fold) between the OGD-activated and resting  cells were identified.

first: Li

last: Zhang


title: Expression data from 3 week old Rat liver (F1)

status: Public on Nov 17 2015

first: Yanhong

last: HUANG

address: 1665 Kong Jiang Road

institute: Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicne

summary:
Developmental Origins of Health and Disease Hypothesis (DOHaD) all emphasized that maternal nutrition plays an important role on the growth and development of offspring. More and more attention has been paid on the effect of maternal high fat diet and overnutrition during pregnancy on the susceptibility of offspring metabolic diseases. So we aim to build the rat model of maternal high fat diet which may induce steatohepatitis and change of lipid metabolism in the early life of offspring, and explore their possible mechannisms.And then to investigate the influence of maternal high fat diet on the expression of hepatic metabolic genes in the early life of offspring.
We used microarrays to detail the global program of gene expression underlying fatty acid liver and identified distinc distinct classes of up-regulated and down-regulated genes during this process.

overall_design: Rat liver were selected at 3 week of age for RNA extraction and hybridization on Affymetrix microarrays.We sought to obtain the results we need so we chose the timing of 3 week old (at weaning) offspring in order to emphasize on the possible biochemical mechanisms of maternal effect.

first: Tingting

last: Ye

last: Huang


title: A validated gene regulatory network and GWAS identifies early regulators of T-cell associated diseases (Th1 Th2)

status: Public on Nov 12 2015

city: Linköping

first: Danuta

last: Gawel

address: Garnisonsvägen

country: Sweden

institute: Linköping University

summary: In this work we present an analytical strategy to systematically identify early regulators by combining gene regulatory networks (GRN) with GWAS.  We hypothesized that early regulators in T-cell associated diseases could be found by defining upstream transcription factors (TFs) in T-cell differentiation. Time series expression and DNA methylation profiling of T-cell differentiation identified several upstream TFs, of which TFs involved in Th1/2 differentiation were most enriched for disease associated SNPs identified by GWAS.

overall_design: Naïve CD4+ T cells were isolated from buffy coat of four healthy donors using a naïve CD4+ T cell isolation kit (Miltenyi, Bergisch-Gladbach, Germany). Naïve CD4+ T cells were stimulated with plate-bound anti-CD3 (500 ng/mL), soluble anti-CD28 (500 ng/mL), in the presence of IL-12 (5 ng/mL), IL-2 (10 ng/mL) and anti–IL-4 (5 µg/mL) for Th1, IL-4 (10 ng/mL), IL-2 (10 ng/mL) and anti-IL-12 (5 µg/mL) and anti–IFN-g (5 µg/mL) for Th2. Cells were cultured for six days in Iscove’s modified Dulbecco medium (IMDM) supplemented with 2 mM L-glutamine (PAA Laboratories, Linz, Austria), 10% heat-inactivated FCS (PAA Laboratories, Linz, Austria), 5 µM β–mercaptoethanol (Sigma-Aldrich, St. Louis, Missouri, USA) and 50 ug/mL gentamicin (Sigma-Aldrich, St. Louis, Missouri, USA). Cells were cultured for 6 days and then re-stimulated with plate-bound anti-CD3 and soluble anti-CD28 in the presence of corresponding polarizing cytokines and antibodies for another 2 days (Zhang et al. 2013). RNA was extracted using a miRneasy Mini Kit (Qiagen). The RNA concentrations were analysed with NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies). For the gene expression microarray analysis, The cRNA was prepared using a Low Input QuickAmp Labeling Kit. For Th1 and Th2 cells the gene expression microarray analysis was performed using SurePrint G3 Human Gene Expression 8x60K microarray kit, according to the manufacture’s instruction (Agilent Technologies).

first: Mika

last: Gustafsson

first: Sandra

last: Hellberg

first: Aelita

last: Konstantinell

first: Daniel

last: Eklund

first: Jan

last: Ernerudh

first: Antonio

last: Lentini

first: Robert

last: Liljenström

first: Johan

last: Mellergård

first: Hui

first: Colm

middle: E

last: Nestor

first: Huan

first: Mikael

last: Benson