title: Rapid protein turnover and dynamic mRNA regulation drive the mitosis-meiosis transition in maize germinal cells

city: Shanghai

first: Weihua

last: Tang

address: 300 Fenglin Rd

institute: Shanghai Inst. Plant Phys. & Eco.

summary: Transcriptional profiling of mitotic archesporial cells, early pollen mother cells and pollen mother cells comparing control tapetal cells, pollen, parenchyma cells and seedling. Goal was explain the mitosis/meiosis transition at the molecular level.

overall_design: 7 simple at all: mitotic archesporial cells, early pollen mother cells, pollen mother cells, tapetal cells, pollen, parenchyma cells and seedling

first: T

last: Yuan

first: W

first: J

last: He

first: D

last: Zhang


title: Results of differentially expressed lncRNAs in COPD and healthy smoker using the Arraystar Human LncRNA Microarray

status: Public on Nov 29 2017

city: Kunming

first: Chuntao

last: Li

address: 295, xichang Road, Wuhua district

country: China

institute: The Affiliated First Hospital of Kunming Medical University

summary: A total of 3,359 lncRNAs revealed by microarray analysis have been differentially expressed between the two groups, 1,995 lncRNAs identified to be up-regulated in COPD, whereas 1,364 lncRNAs have been down-regulated. Meanwhile，a total of 3,283 mRNAs have been differentially expressed, 2,589 mRNAs identified to be up-regulated in COPD, whereas 694 mRNAs were down-regulated.

overall_design: Differentially expressed lncRNAs and mRNAs in blood samples from COPD patients(n=3) and healthy controls (n=3) with smoking history by human microarray analysis.  Samples from individual patients were pooled and are represented by a single COPD sample and a single Healthy Smoker sample.

first: Jianqing


title: Time course study of the response to LPS targeting the pig immune response gene networks

status: Public on Nov 30 2017

city: Castanet-Tolosan

first: Nathalie

last: Villa-Vialaneix

address: 24 chemin de Borde-Rouge

department: MIA

country: France

institute: INRA

summary: To explore individual variation in the biological response to a systemic challenge in pigs, we have developed a microarray analysis to study the kinetics of the response to a lipopolysaccharide (LPS) injection measured at 4 time points. LPS is a major component of the outer membrane in gram-negative bacteria. LPS provokes an acute inflammatory syndrome resulting eventually in all kinds of pathophysiological damages. The objective was to identify genes up- or down-regulated during the stress response triggered by LPS in the whole blood.

overall_design: To explore individual variation in the biological response to LPS, whole blood from 30 juvenile Large White pigs (8 weeks of age) was collected at 4 time points ( t = 0, +1 h, +4 h, +24 h) for a total of 120 samples. Each animal was injected in the neck muscles with LPS (E. coli serotype 055:B5, Sigma-Aldrich, Saint Quentin Fallavier, FR) at a dose of 15 µg/kg body weight. All pigs were females and were raised in two batches. Arrays were designed such that all observations of a single individual were kept on the same array, with two individuals (one from each batch) on one array. This design secured the kinetics of the response for each individual and prevented confounding effects between batch and array. After quality control, all 120 samples were kept for normalization and analyses.

first: Elena

last: Terenina

first: Valerie

last: Sautron

first: Pierre

last: Mormede

first: Laurence

last: Liaubet

first: Laure

last: Gress

first: Amelie

last: Sevin-Pujol

first: Claire

last: Naylies

first: Yannick

last: Lippi

first: Pascal

last: Martin


title: Alteration in gene expression levels in glioblastoma cells in response to fractionated irradiation

status: Public on Nov 17 2017

city: Seoul

first: Yongjoon

last: Suh

address: Wangsimni-ro 222, Seongdong-gu

country: South Korea

institute: Hangyang University

summary: Analysis of alteration in gene expression levels in response to irradiation. The aim of this study was to screen genes associated with radioresistance and infiltration of glioblastoma (GBM) cells after radiotherapy. Results provide importance information of the response of GBM cells to ionizing radiation.

overall_design: U87MG GBM cells were irradiated with 2 Gy once, twice (2 Gy/day for two days) or three times (2 Gy/day for three days). Each control counterparts (C1, C2 and C3) were cultured with same time periods. Total RAN was extracted manually using Trizol. Gene expression profiles were determined using Illumina Human HT-12 V.4 BeadChip (Illumina, Inc., San Diego, CA, USA) according to manufacturer’s instructions.

first: Ki-Chun

last: Yoo


title: Lamin A/C ablation in pancreatic acinar cells

city: Ann Arbor

first: Juliana

last: Bragazzi Cunha

state: MI

address: 1137 E Catherine St, MSII, room 7720

department: Molecular & Integrative Physiology

country: USA

institute: University of Michigan

summary: Lamin A/C was ablated in pancreatic acinar cells using Elastase1 driven, Cre-ErT mediated, LoxP recombination, causing excision of exons 10 and 11 of the Lmna gene

overall_design: Total RNA was collected from control and knockout pancreata 6 days after tamoxifen administration

middle: B

last: Cunha

first: Bishr

last: Omary


title: Genome-wide transcriptional profiles of biopsies from the MUCUS trial

status: Public on Nov 11 2017

city: Saint Louis

first: Mei San

last: Tang

state: MO

address: 660 S Euclid, Campus Box 8118

department: Pathology & Immunology

institute: Washington University in St Louis

summary: The MUCUS clinical trial (https://clinicaltrials.gov: NCT01433471) was established to investigate the effect of Trichuris suis ova on ulcerative colitis patients.

overall_design: Colon biopsies were collected from two research subjects (ENR1 and ENR3) over three different time-points.

first: Rowann

last: Bowcutt

first: Martin

middle: J

last: Wolff

first: Uma

last: Mahesh Gundra

first: P'ng

last: Loke


title: Hepatic Gene Expression Profiling of Riboflavin-deficient and Riboflavin-rescued Chicken Embryos at 9, 11, 13 and 15 days of incubation

status: Public on Nov 05 2017

city: Newark

first: Larry

middle: Albert

last: Cogburn

state: DE

address: 531 South College Ave.

department: Animal and Food Sciences

institute: University of Delaware

summary: This study aimed to identify key genes and pathways related to essential functions of riboflavin during the development of chicken embryos.  We used as a unique model a strain of mutant chickens (rd/rd) which is unable to produce a riboflavin-binding protein and lays riboflavin-deficient eggs in which the embryos suddenly die between 13 and 15 days of incubation (e13 and e15, respectively). In these embryos, the diminished activity of flavin-dependent enzymes, particularly those associated with β-oxidation of fatty acid, limits the catabolism of yolk lipids that normally serve as the predominant source of energy required for growth. This malady leads to excessive lipid accumulation in liver and severe hypoglycemia prior to death. This lethal effect can be rescued by an injection of riboflavin just prior to incubation of fertile rd/rd eggs. Microarray-based hepatic transcriptome profiling of riboflavin-deficient (Rf-) and riboflavin-rescue (Rf+) chicken embryos were carried out at 9, 11, 13 and 15 days of incubation. Our microarray analysis identified a dramatic change in gene expression between the Rf- and Rf+ groups on e13 and e15 with 221 and 929 differentially expressed genes (DEGs), respectively. PPAR-gamma, apolipoprotein AV, adipophilin and sterol 14-alpha demethylase were up-regulated, while alpha2 antiplasmin, alpha1 antitrypsin, alpha2 microglobulin, TIP120 and GHRG1 were down-regulated in the Rf- embryos which show an increased lipid accumulation in liver that may be resulted from the disruption in fatty acid beta-oxidation. Genes involved in detoxification, the immune response and blood coagulation were down-regulated, whereas several phosphatase genes were increased. There were no apparent systematic changes in expression of genes associated with the flavin-dependent enzymes, with an exception of an increase in medium chain acyl-CoA dehydrogenase.

overall_design: A reference RNA design was used for microarray hybridizations, where the same reference RNA pool was co-hybridized to each target samples on an microarray. RNA pool was made from an equal amount of high-quality amplified RNA (aRNA), derived from all samples. Reference RNA pool was labeled with Alexa 647 while each of target samples was labeled with Alexa 555.

first: Nares

last: Trakooljul

middle: A


title: Gene expression profiling in prostate cancer cell lines transfected with miR-33a

status: Public on Oct 31 2017

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: In this study, we aimed to investigate the functional roles of miR-33a in PCa.We investigated the relative miR-33a level in normal and tumor prostate samples as well as PCa cell lines. Then, we performed a detailed functional analysis of mir-33a in LNCaP and VCaP PCa cells and evaluated proliferative, invasive and anchorage independent growth potential of cells upon overexpression and knockdown of miR-33a. We next explored the potential direct targets of miR-33a in PCa cells via utilizing gene expression microarray analysis, bioinformatics search, further qRT-PCR, western blot, and luciferase assay confirmation. Our results demonstrated that miR-33a is significantly downregulated in PCa tumor samples and PCa cell lines, pointing its tumor suppressor potential in PCa. Overexpression and knockdown of miR-33a significantly altered the proliferative, invasive and anchorage independent growth potentials of cells through altering the expression of its direct target PIM1. Ectopic induction of MiR-33a expression reversed the impacts of PIM1 overexpression on cellular phenotypes associated with PCa progression. Our results suggest that mir-33a exerts its tumor suppressor potential through targeting its direct target PIM1 and carries crucial roles in PCa tumorigenesis.

overall_design:
Two cell lines, LNCaP and VCaP, with or without forced expression of miR-33a
Multiple group comparison

first: Michael

last: Ittmann

first: Omer

last: Karatas

first: Yiqun

last: Zhang


title: The role of macrophage Socs3 in the pathogenesis of aortic dissection

city: Kurume

first: Hiroki

last: Aoki

state: Fukuoka

address: 67 Asahimachi

department: Cardiovascular Research Institute

country: Japan

institute: Kurume University

summary: Background—Aortic dissection (AD) is a life-threatening medical emergency caused by the abrupt destruction of the intimomedial layer of the aortic walls. As previous studies have reported the involvement of proinflammatory cytokine IL-6 in AD pathogenesis, we investigated the role of Stat3 signaling, a downstream pathway of IL-6 in macrophages in pathogenesis of AD. Methods and Results—We characterized the pathological and molecular events triggered by aortic stress, which can lead to AD. Aortic stress on the suprarenal aorta due to infrarenal aorta stiffening and angiotensin II infusion for 1 week caused focal medial rupture at the branching point of the celiac trunk and superior mesenteric artery. This focal medial rupture in 6 weeks in wild type (WT) mice but progressed to AD in mice with macrophage-specific deletion of Socs3 gene (mSocs3-KO). mSocs3-KO mice showed premature activation of cell proliferation, an inflammatory response, and skewed differentiation of macrophages toward the tissue-destructive phenotype. Concomitantly, they showed aberrant phenotypic modulation of SMCs and TGFβ signaling, which are likely to participate in tissue repair. Human AD samples revealed STAT3 activation in adventitial macrophages adjacent to the site of tissue destruction. Conclusions—These findings suggest that AD development is preceded by focal medial rupture, in which macrophage Socs3 maintains proper inflammatory response and differentiation of SMCs, thus promoting fibrotic healing to prevent tissue destruction and AD development. Understanding the sequence of the pathological and molecular events preceding AD development will help predict and prevent AD development and progression.

overall_design: Gene expressions in suprarenal aorta of mice were analyzed in aortic stress model that was induced by 0.5 M CaCl2 application to infrarenal aorta and continuous infusion of angiotensin II (1 microgram/kg/min). Mice were either wild type (WT) or with macrophage-specific deletion of Socs3 gene (KO). All data were compared to WT aorta without intervention (WT_preOPcontrol).

first: Satoko

last: Ohno-Urabe


title: Identification and characterization of long non-coding RNAs in osteogenic differentiation of human adipose-derived stem cells

status: Public on Nov 01 2017

city: Guangzhou

first: Guangxin

last: Huang

address: No.74 Zhongshan 2nd Road

institute: Sun Yat-sen University

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

summary: To investigate expression profile and potential role of lncRNAs in osteogenic differentiation of human adipose-derived stem cells (ASCs), whole genome lncRNA microarray was employed to identify lncRNAs that differentially expressed during osteogenesis of ASCs. Four individual human ASCs derived from four different donors were induced to differentiate into osteoblast in vitro. Expression profiles of lncRNAs and mRNAs of undifferentiated and osteogenic differentiated ASCs were obtained by microarray and compared. The genes that meet both fold change ≥2.0 and p<0.05 were considered as differentially expressed genes during osteogenic differentiation of human ASCs. Expression of five upregulated lncRNAs (SAA3P, LOC284080, XLOC_001453, XLOC_011980, HHIP-AS1) and five downregulated lncRNAs (XLOC_007489, CTC-564N23.3, XLOC_010397, XLOC_002619, LINC00638) from the microarray were quantified in the same RNA samples by real-time PCR, validating the microarray data.

overall_design: Human ASCs derived from four different donors were induced to differentiate into osteoblast for 14 days. Expression of lncRNAs and mRNAs of four paired undifferentiated and differentiated human ASCs was measured by microarray.

first: Yan

last: Kang

first: Ziji

first: Weiming

last: Liao


title: Differential roles of Dicer1 in sarcomagenesis from aP2-lineage

status: Public on Oct 25 2017

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Dicer1 loss in the aP2-lineage leads to the development of aggressive and highly penetrant angiosarcomas independent of other oncogenes or tumor suppressor loss

overall_design: Comparison of angiosarcoma tumors from aP2-Cre;DicerFlox/- mice to normal aorta and skeletal muscle.

first: Jason

last: Hanna

first: Catherine

last: Drummond

first: Matthew

middle: R

last: Garcia

first: Jonathon

middle: C

last: Go

first: Jerold

middle: E

last: Rehg

first: Mark

last: Hatley


title: Treatment with a DNA methyltransferase inhibitor feminizes zebrafish and induces long-term expression changes in the gonads

city: Barcelona

first: Laia

last: Ribas

address: Passeig Maritim 37-49

country: Spain

institute: Institut de Ciencies del Mar

summary:
The role of epigenetic modifications such as DNA methylation during vertebrate sexual development is far from being clear. Using the zebrafish model, we tested the effects of one of the most common DNA methyltransferase (dnmt) inhibitor, 5-aza-2'-deoxycytidine (5-aza-dC), which is approved for the treatment of acute myeloid leukaemia and is under active investigation for the treatment of solid tumours. Several dose-response experiments were carried out during two periods, including not only the very first days of development (0–6 days post fertilization, dpf), as done in previous studies, but also, and as a novelty, the period of gonadal development (10–30 dpf).
Early treatment with 5-aza-dC altered embryonic development, delayed hatching and increased teratology and mortality, as expected. The most striking result, however, was an increase in the number of females, suggesting that alterations induced by 5-aza-dC treatment can affect sexual development as well. Results were confirmed when treatment coincided with gonadal development. In addition, we also found that the adult gonadal transcriptome of 5-aza-dC-exposed females included significant changes in the expression of key reproduction-related genes (e.g., cyp11a1, esr2b and figla), and that several pro-female related pathways such as the Fanconi anemia or the Wnt signaling pathways were downregulated. Furthermore, an overall inhibition of genes implicated in epigenetic regulatory mechanisms (e.g., dnmt1, dicer, cbx4) was also observed. Taken together, our results indicate that treatment with a DNA methylation inhibitor can also alter the sexual development in zebrafish, with permanent alterations of the adult gonadal transcriptome, at least in females. Our results show the importance of DNA methylation for proper control of sexual development, open new avenues for the potential control of sex ratios in fish (aquaculture, population control), and call attention to possibly hidden long-term effects of dnmt therapy when used, for example, in the treatment of prepuberal children affected by some types of cancer.

overall_design: At 10 days post fertilization, fish were divided in 2.8-liter tanks in static conditions. The 5-aza-CdR effects were studied during gonadal development (10–30 dpf) at a concentration of 75 µM. 5-aza-CdR was added into the water tank and half of the water with the corresponding 5-aza-CdR concentration was changed three times a week during the period of treatment. At 90 dpf fish were sacrified and gonads were dissected and flash frozen. RNA was extracted by Trizol (Sigma) and were hybridized individually in 4x44K Agilent platform (G2519F).

first: Konstantinos

last: Vanezis

first: Marco

last: Imues

first: Francesc

last: Piferrer


title: Transcription rates in S. cerevisiae wild type haploid and polyploid cells as well as in whi5 and cln3 mutant cells using Genomic Run On (GRO)

status: Public on Oct 10 2017

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

summary: We analyzed the effect of the cell volume on transcription rate using the Genomic Run-on assay on polyploid and mutant cells of different cell volumes

overall_design: This study focus on the transcriptional activity of RNA pol II in yeast genes on S. cerevisiae strains with different cell volume grown in YPD to exponential phase and then processed for Genomic Run-On. Home-made macroarrays containing entire ORFs were used. Three replicates of each time point were done. Each replicate has been hybridized on a different macroarray. A single DNA genomic hybridization was done on the same microarrays for normalization. Data were normalized by MAD using the ArrayStat software.

first: Daniel

last: Medina

first: José

last: Pérez-Ortín


title: Right atrial tissue gene expression data from human patients in sinus rhythm (SR) and patients whom post-operative atrial fibrillation (POAF) developed

status: Public on Oct 30 2017

city: Lille

first: Lefebvre

last: Philippe

state: Nord

address: Blvd Pr. J.Leclerc

institute: Inserm

summary:
To identify pathway and mechanism undergoing post operative atrial fibrillation, we check transcriptomic expression of patients with and without post operative atrial fibrillation development and compare up and down regulated genes and their pathways.
Right atrial appendage were obtained from patients undergoing cardiac surgery.

overall_design: Prospective study

first: Xavier

last: Marechal

last: Montaigne

first: Thomas

last: Modine

first: Helene

last: Dehondt

first: Celine

last: Gheeraert

first: Philippe

last: Lefebvre

first: Bart

last: Staels


title: Gene expression profile analysis and identification of the effects triggered by essential sandalwood oil on human skin explants

status: Public on Nov 10 2017

city: Longjumeau

middle: M.

last: BADER

address: 1 chemin de Saulxier

institute: GENEX

summary:
The purpose of the present study was to establish at the molecular level, a genetic profile of the biological activity of essential sandalwood oil from Santalum album, produced under standardized conditions. The model system under investigation is based on living human skin explants. This protocol permits to compare ex vivo the effects of SO at the histological level as well as the changes of gene expression as a function of SO concentration and duration of treatment.
In the present report, Sandalwood oil (S. album) was applied to living human skin explants to evaluate the sustained activity of the oil through gene expression profiling. Transcriptomic analysis showed a number of metabolic pathways and biological activities triggered by treatments previously described for aloe, curcumin and luteolin. No inflammatory responses accompanied the beneficial activities. The most intriguing impact was the natural effect on the retinoic acid (vitamin A) metabolism. Furthermore, we found that mechanisms normally acting in more specialized cell types such as immune cells, adipocytes, nerve cells, or hair follicles were activated in human skin explants in response to sandalwood oil. Thus, the oil may have the potential of further beneficial activities such as its antibacterial activity among other protective mechanisms. These results corroborate at a molecular level the rationale for clinical studies with sandalwood oil and support recent studies of patients with eczema (atopic dermatitis) or acne, which is often accompanied by bacterial growth on skin of Propionibacterium acnes.

overall_design:
The wood was obtained from managed plantations of Santalum album grown in the Kununurra district of Western Australia. The plantations were owned by Santanol. The essential oil was extracted from the rich heartwood of plantation trees that were 15 years old. Oil was obtained through the steam distillation of wood chips loaded into commercial size stainless steel distillation pots. The effluent was cooled and condensed into a collection vessel and the top layer containing the oil was collected. The quality of the oil complies with that set out in ISO 3518/2002 – Oils of Sandalwood (Santalum album L.).
The study was approved by an ethics committee and performed in accordance with the Declaration of Helsinki after the patient had given informed consent. A full-thickness human skin biopsy was obtained after plastic surgery from a healthy female donor (49-year-old Caucasian).    Microarray data were quantified and normalized according to Agilent protocol (GeneExtraction Feature V10.5.5.1), and deposited in the public domain (NCBI PubMed Omnibus ).Subsequently, the fold-change (FC) between treated versus untreated condition was calculated by the following ratios: transcript intensity of treated samples versus transcript intensity of control samples. The selection of genes of interest were identified in sequential steps: a) Controls were considered unchanged if their expression was between 0.8 and 1.25 fold-change at two time points, 9h (early) and 24h (late). b) In order to take into account the effect of the tested product (P), only gene transcripts that were not subjected to modulation caused by the excipient (almond oil) were considered. Therefore, genes with an FC ≥1.25 between excipient and control values (intensities higher than background) in at least two out of three similar conditions (for each permutation between treated samples and controls), were removed.  The remaining genes were then filtered for either FC ≥1.25 and <1.45, and for FC ≥1.45 between P and control values (intensities higher than background) in at least two out of three similar conditions (for each permutation between all treated samples and controls) for either P1 (2%) or P3 (0.4%) at either one (9h or 24h) or both time points. P1 and P3 were chosen based on the histology results.

contributor: GENEX, 1 Chemin de Saulxier, 91160 Longjumeau, FRANCE
contributor: SANTANOL, 17-21 Couslon Way, Canning Vale, WA, 6155, AUSTRALIA

middle: M

last: Bader


title: Myc regulates gene expression in P493-6 cell lines which carry a Myc tet-off system

status: Public on Nov 16 2017

city: Hefei

first: Pengfei

last: Zhang

address: 443 Huang-Shan Road

department: School of Life Sciences

institute: University of Science and Technology of China

summary: In order to study the Myc-regulated gene, we have employed whole genome mRNA/ncRNA microarray expression profiling as a discovery platform to identify genes with the potential to be regulated by Myc. Furthermore, we studied whether some Myc-regulated ncRNAs mediated the function of Myc.

overall_design: Noncoding RNA gene and protein-coding gene expression levels in P493-6 were measured after treated with 1μg/mL doxcycline for 0 or 24 hours. Three independent experiments were performed at each time (0 or 24 hours).

first: Mian

last: Wu

first: Limian

last: Cao


title: Gene expression profiling of Erlotinib sensitive and resistant human non small cell lung cancer (NSCLC) cell lines

status: Public on Sep 23 2017

city: Monterotondo (Roma)

first: Giovina

last: Ruberti

address: Via E. Ramarini, 32

country: Italy

institute: Institute of Cell Biology and Neurobiology, National Research Council

summary: We characterized the gene expression profile of Epithelial Growth Factor Receptor  (EGFR) inhibitor (Erlotinib)-sensitive and resistant human NSCLC cell lines. Total RNA was extracted from the cell lines and expression profiles were studied by Agilent microarray analysis. Wide changes in gene expression profiles occur in the Erlotinib-resistant cell lines when compared with their parental cell lines (HCC827 and HCC4006).

overall_design: Erlotinib-resistant HCC827-  (RA1, RA2, RB1, RB1.1, RB2) and  HCC4006-derived NSCLC were compared to their parental sensitive cell lines. A total of 16 samples were analyzed, two replicates for each cell line. Citation for manuscript describing cell line establishment: Presutti D, Santini S, Cardinali B, Papoff G, Lalli C, Samperna S, Fustaino V, Giannini G, Ruberti G. MET Gene Amplification and MET Receptor Activation Are Not Sufficient to Predict Efficacy of Combined MET and EGFR Inhibitors in EGFR TKI-Resistant NSCLC Cells.  PLoS One. 2015 Nov 18;10(11):e0143333. doi: 10.1371/journal.pone.0143333. eCollection 2015.

first: Valentina

last: Fustaino

first: Beatrice

last: Cardinali

first: Rossella

last: Brandi

first: Dario

last: Presutti

first: Teresa

last: Colombo

first: Giovanni

last: Felici


title: Gene expression analysis of RNAs isolated from WT and ZIP10-depleted human keratinocytes

status: Public on Oct 05 2017

city: Pohang

first: Bhin

last: Jin-hyuk

address: Ji-gok research center, hyoja-dong, Nam-gu

department: Department of Chemical engineering

institute: POSTECH

summary: To reveal the mechanisms by which ZIP10 contributes to keratinocyte differentiation, we used mRNAs isolated from human wild-type (WT) and ZIP10-knockdown (KD) keratinocytes in gene expression microarray analyses

overall_design: Duplicate experiments were performed for WT and ZIP10-KD human keratinocytes. Total RNA was isolated from the WT and ZIP10 KD keratinocytes using Qiazol (Qiagen) following the manufacturer’s protocol

first: Bum-Ho

last: Bin

first: Jinhyuk

last: Bhin


title: Human colon cancer SW480 cells: stably transfected with vector control and LRP16 treated with or without etoposide

status: Public on Sep 22 2017

city: Beijing

first: Xiaolei

last: Li

address: #28 Fuxing Road,

institute: Institute of Basic Medicine, Chinese PLA General Hospita

summary: Transcriptional profiling of human colon cancer SW480 cells comparing control untreated SW480 cells with cells stably transfected with LRP16 treated with or without etoposide (50 μM) for the indicated periods (0,1hour, 3hours).An exploratory microarray analysis was performed with mRNA extracted from clutured SW480 cells transfected with LRP16 or control plasmid that were treated with or without etoposide. Total RNA of colon cancer cells stably transfected with vector control and LRP16 treated with or without etoposide (50 μM) for the indicated periods was isolated and purified using RNeasy Kit (Qiagen, Hilden, Germany). Integrity of RNA was assessed by using an Agilent BioAnalyser 2100 (Agilent Technologies).

overall_design: An exploratory microarray analysis was performed with mRNA extracted from clutured SW480 cells transfected with LRP16 or control plasmid that were treated with or without etoposide. Three independent experiments were performed at each time (0, 1 or 3 hours) using different group cells for each experiment.

first: X

first: Z

first: W

last: Han


title: Mast cells decrease efficacy of anti-angiogenic therapy by secreting matrix-degrading granzyme B

status: Public on Sep 15 2017

city: Hamburg

first: Christian

last: Schulze

address: Falkenried 94

country: Germany

institute: ZMNH

summary: Resistance towards anti-angiogenic therapy (AAT) still represents a substantial clinical challenge. We report here that tumor-infiltrating mast cells (MC) are powerful mediators decreasing efficacy of AAT in mice and cancer patients. They act in a cell-extrinsic manner by secreting granzyme B, which liberates pro-angiogenic mediators from the extracellular matrix. In addition, MC also diminish efficacy of anti-angiogenic agents in a cell-autonomous way, which can be blocked by the mast cell degranulation inhibitor cromolyn. Our findings are relevant in humans because patients harboring higher numbers of MC in their tumors have an inferior outcome after anti-angiogenic treatment in the Gepar Quinto randomized Phase 3 clinical trial. Thus, MC-targeting might represent a novel promising approach to increase efficacy of AAT.

overall_design: Panc02 cells were injected subcutanously into the flanks of C57BL/6J mice. After reaching a tumor volume of 100 mm3, mice were randomized into treatment and control group. The treatment group received 40 mg/kg of the anti-angiogenic anti-VEGFR2 antibody DC101 whereas the other group received a placebo. Mast cells from the peritoneum of tumor bearing mice were isolated by lavage. Mast cells  from cell suspensions of both compartments were purified by FACS-sorting staining for DAPI, CD45, CD11b, CD117, and FceRI.

first: Mark

last: Wroblewski

first: Sonja

last: Loges


title: GPR56/ADGRG1 inhibits Mesenchymal Differentiation and Radioresistance in Glioblastoma

status: Public on Oct 01 2017

first: Nuria

last: de la Iglesia

address: Rossello 153

institute: IDIBAPS

summary: A mesenchymal transition occurs both during natural evolution of glioblastoma (GBM) and in response to therapy. However, the molecular mechanisms underlying mesenchymal differentiation are not well understood. We have found that the adhesion G protein-coupled receptor, GPR56/ADGRG1, inhibits mesenchymal differentiation and radioresistance in glioblastoma stem-like initiating cells (GICs). Here, we have performed microarray analysis of control- versus GPR56 knockdown-GICs to characterize gene expression changes upon GPR56 knockdown and identify a gene expression signature associated to GPR56.

overall_design: To identify a GPR56-associated gene signature we compared the gene expression profile of control- and GPR56 knockdown-GICs by genome-wide microarray analysis. Patient-derived CD44low GICs (control- and GPR56 knockdown-GICs) were cultured under adherent conditions on laminin in serum-free neural stem cell medium (in the presence of bFGF and EGF) at 37°C, 5% CO2 and 5% oxygen. Total RNA was extracted, labeled and hybridized in a SurePrint G3 Human GE 8x60k array (Agilent Technologies). Four paired biological replicates of each control- and GPR56 knockdown-GICs were used.

first: Núria


title: miRNA changes after overexpression of uc.372 in HepG2 cells

first: Jian

address: Dahua Road

institute: Beijing Hospital

summary: To identify putative miRNA targets for uc.372, we overexpressed uc.372 in HepG2 cells and carried out a microarray analysis. A total of 66 miRNAs present in the array demonstrated 1.5-fold upregulation or downregulation of expression upon uc.372 transfection.

overall_design: HepG2 cells were tranfected with ad-uc.372 or ad-NC for 48 h. The RNA was collected and further applied for microarray analysis.

first: Jun

last: Guo

first: Weiwei

last: Fang


title: Gene expression profiles from human splenic Marginal Zone and Naive (Follicular) B cells

status: Public on Oct 14 2017

first: Jordi

last: Sintes

address: Dr Aiguader 88

department: B cell Biology

institute: IMIM

summary:
Splenic Marginal Zone B cells mount innate-like T cell-independent (TI) antibody responses to blood-borne antigens upon receiving activation signals from TACI-engaging factors BAFF and APRIL.
The transcriptome analysis of splenic Marginal Zone (MZ) B cells was performed to verify which transcriptional programs are enhanced in the innate-like MZ B cell subset and to study the involvement of mTOR in MZ B cells activated via TACI.

overall_design: Unstimulated human Marginal Zone and Follicular/Naive B cells were FACSorted from spleens of seven (MZ) and three (FO) adult healthy subjects for RNA isolation and Agilent analysis. Moreover, APRIL (500ng/ml) and Rapamycin (10nM) were used to dissect the involvement of mTOR in the induction of Class Switch Recombination and antibody production in MZ B cells activated through TACI.

first: Andrea

last: Cerutti

first: Maurizio

last: Gentile


title: DNA microarray analysis of human colorectal cancer specimens

status: Public on Sep 08 2017

city: Tsuruoka

first: Kiyotoshi

last: Satoh

state: Yamagata

address: Mizukami 246-2, Kakuganji

department: Institute for Advanced Biosciences

institute: Keio University

summary: Cancer cells alter their metabolism for the production of precursors of macromolecules. However, the control mechanisms underlying this reprogramming are poorly understood. Here, we show that metabolic reprogramming of colorectal cancer is caused chiefly by aberrant MYC expression. Multi-omics-based analyses of paired normal and tumor tissues from 275 patients with colorectal cancer revealed that metabolic alterations occur at the adenoma stage of carcinogenesis, in a manner not associated with specific gene mutations involved in colorectal carcinogenesis. MYC expression induced at least 215 metabolic reactions by changing the expression levels of 121 metabolic genes and 39 transporter genes. Further, MYC negatively regulated the expression of genes involved in mitochondrial biogenesis and maintenance but positively regulated genes involved in DNA and histone methylation. Knockdown of MYC in colorectal cancer cells reset the altered metabolism and suppressed cell growth. Moreover, inhibition of MYC target pyrimidine synthesis genes such as CAD, UMPS and CTPS blocked cell growth, and thus they are potential targets for colorectal cancer therapy.

overall_design: Gene expression in paired normal and tumor tissue specimens from patients with colorectal cancer.

first: Shinichi

last: Yachida

first: Masahiro

last: Sugimoto

first: Minoru

last: Oshima

first: Toshitaka

last: Nakagawa

first: Shintaro

last: Akamoto

first: Keiichi

last: Okano

first: Yasuyuki

last: Suzuki

first: Tomoyoshi

last: Soga


title: Plasma Long Noncoding RNA and mRNA Expression Profile of Crohn’s Disease identified by Microarray

status: Public on Sep 01 2017

city: Hangzhou

first: Xi

last: Jin

address: No.79 Qingchun Road

department: Department of

institute: The First Affilated Hospital, School of Medicine, Zhejiang University

summary: We performed a genome-wide analysis of lncRNA expression to identify novel targets in Crohn's disease (CD). Samples obtained from CD patients and control were analyzed using Arraystar human 8×60K lncRNA/mRNA v3.0 microarrays chips to find differentially expressed lncRNAs and mRNAs; The results were confirmed by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). The differentially expressed lncRNAs and mRNAs were identified through fold-change filtering. Gene ontology (GO) and pathway analyses were performed using standard enrichment computational methods.

overall_design: We performed a genome-wide analysis of lncRNA expression to identify novel targets for the further study of Crohn's disease. 3 CD samples(D1-3) and 3 control samples (C1-3) were obtained .

first: Dong

last: Chen


title: Analysis of globle gene expression changes observed in an in vitro fibroblast model of IPF

status: Public on Sep 07 2017

city: Philadelphia

first: Michael

last: Beers

state: PA

address: 3450 Hamilton Walk

institute: University of Pennsylvania

summary: The activated fibroblast is the putative effector cell for the progressive fibrotic phenotype idiopathic pulmonary fibrosis (IPF). Recent studies investigating global gene expression differences between normal and IPF fibroblasts indicate that changes in gene expression occur in these fibroblasts in culture. Employing a technique that minimizes cellular phenotypic alterations, we characterized the global gene expression changes in pulmonary fibroblasts by comparing both cultured and non-cultured IPF and normal cells. The results revealed dramatic difference between IPF and normal fibroblast as they progressed in culture. While there are significant differences in gene expression between IPF and normal fibroblast at P0, after 3 passages in culture, no statistically significant difference was observed. This study is a comprehensive investigation of gene expression within IPF and normal fibroblasts in culture and sheds light on the efficacy of in vitro models of pulmonary fibroblasts.

overall_design: 24 total pulmonary fibroblast samples were used in this study. These fibroblasts were isolated from 8 lungs with end-stage idiopathic pulmonary fibrosis and 4 normal donors lungs (controls) designated brain dead, non-diseased but not suitable for transplantation. 16 IPF samples included 8 non-cultured (P0) and 8 cultured (P3). 8 normal samples included 4 non-cultured (P0) and 4 cultured (P3). RNA extraction was carried out using Qiagen RNeasy Kit. Experimental/control samples were amplified amino-allylated RNA labeled with Cy5 and Stratagene Reference RNA was amplified and amino-allylated and labeled with Cy3. One round of amplification was carried out using Ambion MessageAmp II kit with amino-allylated UTP according to the protocol of the Duke University Institute for Genome Sciences and Policy. Amplification and amino-allylation of the Stratagene Reference RNA and Hybridization of Reference with all samples were carried out by the Duke Institute for Genomic Sciences and Policy.

first: Luis

last: Luis

first: Margaret

last: Emblom-Callahan

first: Mantej

middle: K

last: Chhina

first: Sarah

last: Bui

first: Rebecca

last: Novak

first: Steven

middle: D

last: Nathan

first: Geraldine

last: Grant


title: Lhx2-regulated genes in early retinal progenitors

city: Baltimore

first: Seth

last: Blackshaw

state: Maryland

address: 733 N Broadway

department: Neuroscience

institute: Johns Hopkins School of Medicine

summary: Eye formation is regulated by a complex network of eye field transcription factors (EFTFs), including LIM-homeodomain gene LHX2. We disrupted LHX2 function at different stages during this process using a conditional knock-out strategy in mice. We find that LHX2 function is required in an ongoing fashion to maintain optic identity across multiple stages, from the formation of the optic vesicle to the differentiation of the neuroretina. At each stage, loss of Lhx2 led to upregulation of a set of molecular markers that are normally expressed in the thalamic eminence and in the anterodorsal hypothalamus in a portion of the optic vesicle or retina. Furthermore, the longer LHX2 function was maintained, the further optic morphogenesis progressed. Early loss of function caused profound mispatterning of the entire telencephalic-optic-hypothalamic field, such that the optic vesicle became mispositioned and appeared to arise from the diencephalic-telencephalic boundary. At subsequent stages, loss of Lhx2 did not affect optic vesicle position but caused arrest of optic cup formation. If Lhx2 was selectively disrupted in the neuroretina from E11.5, the neuroretina showed gross dysmorphology along with aberrant expression of markers specific to the thalamic eminence and anterodorsal hypothalamus. Our findings indicate a continual requirement for LHX2 throughout the early stages of optic development, not only to maintain optic identity by suppressing alternative fates but also to mediate multiple steps of optic morphogenesis. These findings provide new insight into the anophthalmic phenotype of the Lhx2 mutant and reveal novel roles for this transcription factor in eye development.

overall_design: Neuroretina from embryonic day 13.5 mice from ;Lhx2 lox/lox and Chx10-Cre;Lhx2 lox/lox mice were dissescted and analyzed.  Two replicates for each genotype were tested.

first: Jimmy

last: de Melo

first: Thuzar

last: Thein


title: Gene expression analysis in naïve and vaccine (peptide vs. DC) primed pmel-1 CD8 Tcells

status: Public on Aug 31 2017

city: Osaka

first: Koji

last: Nagaoka

address: 377-2 Ohno-Higashi, Osaka-Sayama

department: Department of Immunology

institute: Kindai University Faculty of Medicine

summary: We have shown that DC vaccine is superior to peptide vaccine in terms of priming and expansion of antigen-specific CD8+ T cells. DC vaccine-primed pmel-1 cells displayed better effecter functions than cells by peptide-primed cells in terms of cytokine production and externalization of cytotoxic granules. Furthermore DC vaccine-primed cells were metabolically distinct from peptide-primed cells. To confirm these findings, we performed a microarray analysis using splenic pmel-1 T cells from mice immunized with hgp100 peptide vaccine or DC vaccine. We also used splenic naïve pmel-1 T cells as a control.

overall_design: C57BL/6 mice transferred with pmel-1 splenocytes were treated with hgp100 peptide vaccine or DC vaccine twice on days 0 and 14. On day 28, pmel-1 CD8+ T cells were sorted from harvested splenocytes of immunized mice. Gene expression was measured in naïve pmel-1 CD8+ T cells and sorted pmel-1 CD8+ T cells

first: Kazuhiro

last: Kakimi

first: Hirokazu

last: Matsushita


title: Expression profiling of long noncoding RNAs and mRNAs in human plasma of hypertension patients from South China

status: Public on Aug 01 2017

first: Qinghua

last: Cui

address: 38 Xueyuan Road

institute: Peking University

summary: Long noncoding RNA profile in the plasma of human with hypertension and healthy controls from South China.

overall_design: In the study presented here, we identified the genome-wide expression level of lncRNAs for one hypertension sample and one healthy control sample. Each sample (total RNA) was pooled from the total RNA of fifteen age and gender matched subjects (hypertension patients or healthy controls).

first: Cui

last: Qinghua

first: Geng

last: Bin

first: Cai

last: Jun


title: lncRNA Expression Signatures in Response to Jiangtang Tiaozhi Formular in T2DM with Obesity and Hyperlipidemia

first: Lisha

last: He

address: No 5. Beixiange Street, Xicheng District

department: Endocrine Department

institute: Guang’anmen Hospital, China Academy of Chinese Medical Sciences

summary: In the study, patients with type 2 diabetes with obesity and hyperlipidemia were treated by traditional Chinese medicine Jiangtang Tiaozhi Prescription of 24 weeks, we chosed 6 effective cases, 6 invalid cases and 6 health people  as control to analysis the molecular mechanism of TCM treatment. According to the research of LncRNA microarray, GO analysis, Pathway analysis, we found out the target LncRNAs, as well as their associated mRNAs were contribute to the good outcome of Jiangtang Tiaozhi Formula. Then we expand to 12 cases in each group for qPCR validation.

overall_design: We took 30 serum samples separately from 6health people ,6 effective cases and 6  invalid cases with type 2 diabetes with obesity and hyperlipidemia(including before treatment and after treatment), based on lncRNA expression signatures to and analysised the response to traditional Chinese medicine treatment of Jiangtang Tiaozhi Formular.

first: Song

last: Wang

first: Linhua

last: Zhao

first: Xiaolin

last: Tong


title: Expression profiling of long noncoding RNAs and mRNAs in human plasma of hypertension patients from North China

summary: Long noncoding RNA profile in the plasma of human with hypertension and healthy controls from North China.

overall_design: In the study presented here, we identified the genome-wide expression level of lncRNAs for hypertension healthy control samples from North China. Each sample (total RNA) was pooled from  the total RNA of three age and gender matched subjects (hypertension patients or healthy controls).


title: Expression data from parental B16F0 cells and B16F0 exosomes [MoEx]

status: Public on Jul 31 2017

city: Morgantown

first: David

middle: John

last: Klinke

state: WV

department: Chemical Engineering

institute: West Virginia University

summary:
As a type of secreted membrane vesicle, exosomes are emerging as an important mode of cell-to-cell communication. The objective of this study was to compare the abundance of transcripts present in the parental B16F0 cell to transcripts present in exosomes isolated from B16F0 conditioned media.
Identifying local mechanisms of immunosuppression is a key barrier for expanding the clinical benefit of cancer immunotherapy. While exosomes are emerging as a new mode of intercellular communication, their role in establishing a malignant tissue niche remains unclear. Similar to the sculpting of tumor antigens during oncogenesis, a related hypothesis is that proteins secreted by malignant cells are shaped by somatic evolution. To test this hypothesis, we characterized the biological influence of tumor-derived exosomes on immune cell function. In particular, we analyzed exosomes from three melanoma models: B16F0, a non-immunogenic model of malignant melanoma; Cloudman S91, a model of immunogenic melanoma; and Melan-A, an immortalized melanocyte cell line. Using electron microscopy, exosomes derived from all three cell lines were morphologically similar. The exosomes contained receptors derived from the parent cell as demonstrated by IL12RB2 expression on B16F0 exosomes and intact mRNAs. Furthermore, transcript profiling of B16F0 exosomes and cells suggested that exosomal mRNA is enriched for mRNAs that target immune-related pathways, including Ptpn11 that inhibited T cell proliferation and Dnmt3a that inhibited T cell production of IFN-gamma. Functionally, B16F0 exosomes dose-dependently suppressed cell proliferation and the expression of IL12RB2 in primary CD8+ T cells. In contrast, Cloudman S91 exosomes promoted T cell proliferation and Melan-A exosomes had a negligible effect on primary CD8+ T cells. Collectively, the results are consistent with somatic editing of exosomal payloads and suggest that exosomes establish a density-dependent field effect by altering the activity of immune cells that enter the tumor microenvironment.

overall_design: 8 Total samples were analyzed. Gene transcript abundance was estimated based on the average expression of all core probesets for a gene measured by Affymetrix microarray. The probability of a gene being expressed above background by random chance was estimated using the negative control probesets and a Welch's t-test, where the degrees of freedom were calculated using the Welch-Satterthwaite equation. A p-value of less than 0.01 was used for estimating the distribution of mRNA expression between cells and exosomes while a p-value of less than 1e-9 was used for qRT-PCR validation and pathway enrichment analysis.  The lower p-value incorporates a Bonferroni correction for multiple hypothesis testing.


title: Podocyte-specific JAK2 Overexpression Worsens Diabetic Kidney Disease in Mice

city: Ann Arbor

first: Viji

last: Nair

address: 1152 West Medical Centre Dr.

institute: University of Michigan

summary: Overexpression of glomerular JAK2 mRNA specifically in glomerular podocytes of 129S6 mice led to significant increases in albuminuria, mesangial expansion, glomerulosclerosis, glomerular fibronectin accumulation, and glomerular basement membrane thickening as well as a significant reduction in podocyte density in diabetic mice. Treatment with a specific JAK1/2 inhibitor partly reversed the major phenotypic changes of DKD

overall_design: Glomerular RNA was extracted  using the RNeasy Mini Kit and processed for hybridization on Affymetrix Mouse Gene 2.1 ST chip microarrays

first: Hongyu

last: Zhang

first: Jharna

last: Saha

first: Kevin

last: Atkins

first: Racheal

last: Wallace

first: Jeffrey

last: Hodgin

first: Thomas

middle: L

last: Saunders

first: Edward

middle: H

last: Leiter

first: Martin

middle: G

last: Myers

last: Werner

first: Matthias

last: Kretzler

first: Frank

last: Brosius


title: Deregulation of lncRNAs by Kaposi's sarcoma-associated herpesvirus

status: Public on Jul 12 2017

city: Gainesville

first: Rolf

middle: F

last: Renne

state: FL

address: 2033 Mowry Road

department: Molecular Genetics & Microbiology

institute: University of Florida

summary: Deregulation of host lncRNAs following infection with Kaposi’s sarcoma-associated herpesvirus (KSHV) was assessed. Total RNA was prepared from uninfected TIVE cells (telomerase-immortalized vein endothelial cells), and from TIVE cells latently infected with either wild-type KSHV or with a deletion mutant (Δcluster-KSHV) lacking ten of the twelve KSHV microRNA genes. The RNA was converted to labeled cRNA and used to probe a human lncRNA microarray. The goal was to investigate which host lncRNAs were either up- or down-regulated during latent infection with KSHV, and to determine if deregulation of host lncRNAs was dependent on KSHV miRNAs.

overall_design: One biological replicate of each of mock infected, wtKSHV-infected and Δcluster-KSHV infected cells was used. Three technical replicates were performed for each.

first: Sunantha

last: Sethuraman

first: Lauren

last: Gay

first: Vaibhav

last: Jain

first: Irina

last: Haecker


title: Synergistic Interaction Between the LSD1 Inhibitor T-3775440 and the NEDD8-activating Enzyme Inhibitor Pevonedistat (TAK-924/MLN4924) Promotes Anti-Acute Myeloid Leukemia Effects

status: Public on Jun 30 2017

city: Fujisawa

first: Yoshinori

last: Ishikawa

state: Kanagawa

address: 26-1 Muraoka-Higashi 2-chome

department: Oncology Drug Discovery Unit

institute: Takeda Pharmaceutical Company Ltd.

summary: Lysine-specific demethylase 1A (LSD1) specifically demethylates di- and monomethylated histone H3K4 or K9, resulting in context-dependent transcriptional repression or activation. We previously identified an irreversible LSD1 inhibitor T-3775440, which exerts antileukemic activities in a subset of acute myeloid leukemia (AML) cell lines by inducing cell transdifferentiation. The NEDD8-activating enzyme inhibitor pevonedistat (MLN4924, TAK-924) is an investigational drug with antiproliferative activities in AML, and is also reported to induce cell differentiation. We therefore tested the combination of these two agents in AML models.The combination treatment resulted in synergistic growth inhibition of AML cells, accompanied by enhanced transdifferentiation and suppression of the leukemic stem cell gene signature.

overall_design: Total RNA obtained from cells treated treated with vehicle, 50 nM T-3775440, 1000 nM pevonedistat, or T-3775440 and pevonedistat in combination for 24 h in vitro. Effects of each compound or the combination on AML cells lines were compared that of DMSO-treated control.

first: Kazuhide

last: Nakayama

first: Koji

last: Yamamoto


title: The long noncoding RNA expression profiles of paroxysmal atrial fibrillation identified by microarray analysis

first: Ying

last: Su

address: Tieyi Rd. No.10, Yangfangdian, Haidian district

institute: Capital Medical University affiliated Beijing Shijitan Hospital

summary: The purpose of the present study was to identify aberrantly expressed lncRNAs in pAF and predict their potential functions. We recruited three pAF patients undergoing radiofrequency catheter ablation into our study. Peripheral blood leukocytes (PBL) and coronary sinus blood leukocytes (CSBL) were harvested from pAF patients at the same time during the operation. LncRNAs and mRNAs profiles in leukocytes were detected by microarray between pAF patients and controls. We identified 2095 lncRNAs and 1584 mRNAs differentially expressed between pAF patients and controls. Furthermore, expressions of lncRNAs and mRNAs in leukocytes were also measured between peripheral blood (PB) and coronary sinus blood (CSB). The 866 lncRNAs and 528 mRNAs were shown to be aberrantly expressed between CSBL and PBL in all three pAF patients. Bioinformatic analyses (lncRNA classification and subgroup, gene ontology analysis, pathway analysis and gene co-expression network construction) were performed for differentially expressed lncRNAs and mRNAs. Lastly, we confirmed seven aberrant lncRNAs and five dysregulated mRNAs by qRT-PCR. Our results demonstrated the aberrantly expressed lncRNAs and mRNAs in pAF and these lncRNAs/mRNAs may exert a vital role in pAF biology.

overall_design: To explore the potential involvement of lncRNAs in paroxysmal atrial fibrillation(pAF), we firstly conducted lncRNAs and mRNAs profiling in leukocytes by microarray between pAF patients and controls. Then, expressions of lncRNAs/mRNAs in leukocytes were detected between peripheral blood (PB) and coronary sinus blood (CSB) in all three pAF patients.

first: Yunan

last: Yue

first: Shuixiang

last: Yang


title: Gene expression analysis in wild-type and OsHOX24 rice overexpression line under control and drought stress conditions

status: Public on Jun 12 2017

city: New Delhi

first: Mukesh

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

summary:
Several homeobox genes belonging to HD-ZIP I subfamily are highly induced by drought stress at various developmental stages in rice. To analyze the role of a candidate HD-ZIP I subfamily member, OsHOX24, we constitutively overexpressed it in rice. The physiological analyses revealed that overexpression of OsHOX24 gene reduced drought stress tolerance in transgenic plants as compared to wild-type.
We used microarrays to study the global effect of OsHOX24 overexpression in rice as compared to wild-type under control and drought stress condition.

overall_design: Three-weeks-old light-grown wild-type and transgenic rice seedlings grown under controlled conditions and those subjected to drought stress treatment were used for RNA extraction and hybridization on Affymetrix microarrays. Three biological replicates of each sample were used for microarray analysis. For drought stress treatment (DS), rice seedlings were dried for 3 h between folds of tissue paper at 28±1 degree C, in a culture room. The seedlings kept in water for 3 h, at 28±1 degree C, served as control (seedling).

first: Annapurna

last: Bhattacharjee


title: Aberrantly Expressed Long Non-coding RNAs In CD8+ T Cells Response to Active Tuberculosis

status: Public on May 01 2017

city: weifang

first: yurong

last: fu

address: No.7166, Baotong Xi (Western) Street, Weicheng District, Department of Laboratory Medicine, Shandong Provincial Key Laboratory of Clinical Laboratory Diagnostics, Weifang Medical University

institute: weifang medical universtiy

summary: Dysregulated expression of long noncoding RNAs (lncRNAs) has been demonstrated as being implicated in a variety of human diseases. In the study we aimed to determine lncRNA profile in CD8+ T cells response to active tuberculosis (TB).

overall_design: Thirty-four active TB subjects (ATB group) were 18 male and 16 female between 21 and 60 years of age. They were recruited from Weifang No.2 People’s Hospital. The diagnosis of active TB was based on compatible clinical features, together with the presence of the following microbiological evidence: (i) sputum smear positive, (ii) Mtb culture positive, and/or (iii) PCR positive for Mtb from clinical samples. Patients with other co-existing disease, such as diabetes or cancer, were excluded from the study. Gender- and age-matched 35 healthy individuals (Control group) from the staff of Weifang Medical University were also included in the study as controls. Three samples randomly selected from each group  (male/female=1:2,TT1,TT2 and TT3 for ATB group, CT1,CT2 and CT3 for controls) were used for microarray analysis and all of the samples were applied for further RT-qPCR confirmation.

first: Yurong

last: Fu

first: Enxue

last: Tao

first: Ruifang

last: Li

first: Zhengjun

last: Yi


title: Oxidative damage control in a human (mini-) organ: Nrf2 activation protects against oxidative stress-induced hair growth inhibition

status: Public on Jun 29 2017

city: Sharnbrook

first: Fei Ling

last: Lim

state: Bedfordshire

address: Colworth Science Park

country: United Kingdom

institute: Unilever

summary: The in situ control of redox insult in human organs is of major clinical relevance, yet remains incompletely understood. Activation of Nrf2, the “master regulator” of genes controlling cellular redox homeostasis, is advocated as a therapeutic strategy for diseases with severely impaired redox balance. Yet it remains to be shown whether this strategy is effective in human organs, rather than isolated human cell types. We have therefore explored the role of Nrf2 in a uniquely accessible human (mini-) organ, human scalp hair follicles (HFs), by Microarray analysis of human HFs treated with 20uM sulforaphane for 24hr.

overall_design: Nrf2 induced gene expression changes in human HFs was measured at 24 hours after exposure to 20uM Sulforaphane.  HFs from 3 different donors was treated independently with 20uM Sulforaphane and vehicle control.

first: Iain

last: Haslam

first: Laura

last: Jadkauskaite

first: Imre

last: Szabo

first: Selma

last: Staege

first: Jasper

last: Hesebeck-Brinckmann

first: Gail

last: Jenkins

first: Ranjit

last: Bhogal

first: Fei

first: Nilofer

last: Farjo

first: Bessam

first: Tamas

last: Biro

first: Matthias

last: Schäfer

first: Ralf

last: Paus


title: Endothelial Cells from different anatomical origin have distinct responses during Snail/TGF-β2-mediated Endothelial-Mesenchymal Transition

status: Public on Apr 22 2017

city: Ribeirao Preto

first: Mariana

middle: Tomazini

last: Pinto

state: Sao Paulo

address: Tenente Catao Roxo 2501

country: Brazil

institute: Fundacao Hemocentro de Ribeirao Preto

summary: Endothelial-mesenchymal transition (EndMT) is a complex process, in which differentiated endothelial cells undergo phenotypic transition to mesenchymal cells. Given the diversity of the vascular system in architecture, structure, and embryonic origins, it is not clear if endothelial cells lining different vessels are able to undergo EndMT. Therefore, the aim of this study was to evaluate the molecular and functional changes that occur in different types of endothelial cells after induction of EndMT through overexpression of Snail and TGF-β2. Different types of endothelial cells (human umbilical vein, heart, and lung) have distinct response when induced to undergo EndMT. Coronary artery endothelial cells (HCAEC) induced with combined Snail overexpression plus TGF-β2 treatment promotes a decrease of endothelial markers, an increase of mesenchymal markers and migration. The mechanism that HCAEC undergoing EndMT may be mediated through Notch and non-canonical Wnt signaling pathways. These results provide the foundation for understanding the roles of specific signaling pathways in mediating EndMT in endothelial cells from different anatomical origin.

overall_design: Thirteen samples underwent microarray analysis, as follows: two samples of endothelial cell control, two samples of endothelial cell containing Empty vector, three samples of endothelial cell treated with TGF-β2, three samples of endothelial cell containing SNAIL vector, and three samples of endothelial cell containing SNAIL vector and treated with TGF-β2. The microarray analysis was applied to investigate new genetic targets between control and cells that undergoing EndMT.

middle: T

first: Fernanda

middle: U

last: Melo

first: Tathiane

last: Malta

first: Evandra

middle: S

last: Rodrigues

first: Jessica

last: Plaça

first: Rodrigo

last: Panepucci

first: Dimas

last: Covas

first: Claudia

middle: O

first: Simone

last: Kashima


title: Expression data from mice epididymal adipose tissue

city: Jinan

first: Xiaoyan

last: Yang

address: 107 West Wenhua Road

institute: Shandong University Qilu Hospital

summary:
Visceral white adipose tissue is closed correlated with obesity and metabolic dysfunction.  Epididymal adipose tissue (eWAT) is considered as typical visceral white adipose tissue. Induction of browning of white adipose tissue improves metabolic dysfunction such as insulin resistance. In contrast to mice subcutaneous adipose tissue, visceral fat do not show significant browning under 4°C. However,under physiologically tolerable low temperature visceral adipose tissue can turn brown.
We used microarrays to detail the global programme of gene expression in C57Bl/6 mice epididymal adipose tissue exposed to thermoneutral 30°C, 4°C and temperatures lower than 4°C.

overall_design: Epididymal adipose tissues from mice exposed to 30°C, 4°C, -10°C and -20°C(short for -10°C/-20°C) were selected  for RNA extraction and hybridization on Affymetrix microarrays.Temperature exposure last for 5 weeks, counting in the 4°C adaptation for cold groups. Three samples for each temperature were selected.


title: Glucose sensing by skeletal myocytes couples nutrient signaling to systemic homeostasis

status: Public on Apr 20 2017

first: Zhuoxian

last: Meng

state: Michigan

address: 210 Washtenaw Ave

summary:
Skeletal muscle is a major site of postprandial glucose disposal. Inadequate insulin action in this tissue contributes to hyperglycemia in type 1 and type 2 diabetes. While glucose is known to stimulate insulin secretion by pancreatic b cells, whether it directly engages nutrient-sensing pathways in skeletal muscle to regulate glucose metabolism remains largely unexplored. Here we identified the Baf60c-Deptor-AKT pathway as a target of muscle glucose sensing that augments insulin action in skeletal myocytes. Genetic activation of this pathway improves postprandial glucose disposal in mice, whereas the muscle-specific ablation impaired insulin action and led to glucose intolerance. Mechanistically, glucose triggers a rapid calcium response in myocytes that acts on the class IIa histone deacetylase HDAC5, leading to Baf60c induction and insulin-independent AKT activation. The pathway is engaged by the anti-diabetic drugs sulfonylureas, suggesting that its therapeutic activation may have beneficial effects on glycemic control in diabetes.
We used microarrays to elucidate the role of of Baf60c in transcriptional regulation by glucose in skeletal myocytes.

overall_design: C2C12 myoblasts were transduced with retroviruses expressing shRNAs targeting control or mouse Baf60c, differentiated into myotubes, and treated with 1 mM or 10 mM glucose for 12 h. Then cells were harvested for RNA isolation and microarray hybridization using Affymetrix Mouse Gene ST 2.1 Arrays. Two independent biological replicates for each treatment were included in this study.

first: Zhuo-Xian

first: Jianke

last: Gong

first: Zhimin

last: Chen

first: Jingxia

last: Sun

first: Yuanyuan

last: Xiao

first: Yaqiang

last: Li

first: Jianfeng

last: Liu

first: Shawn

last: Xu

first: Jiandie

last: Lin


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [RE_110915data]

status: Public on Apr 07 2017

city: New York

first: Frederique

last: Ruf-Zamojski

state: NY

address: 1468 Madison Avenue

department: Neurology

institute: Mount Sinai Medical Center

summary: Reproduction requires pulsatile release of hypothalamic gonadotropin-releasing hormone (GnRH), which regulates expression of the pituitary gonadotropins follicle-stimulating hormone (FSH) and luteinizing hormone (LH). Fshb expression shows an inverted U-shaped response to GnRH pulse frequency. Increasing GnRH pulse frequency beyond ~one pulse/2 hours, despite increasing the average GnRH concentration, induces progressively less Fshb. To clarify regulatory mechanisms underlying Fshb gene control, we developed three biologically inspired and topologically distinct mathematical models. The models represent: 1) parallel activation of Fshb inhibitory and stimulatory factors (e.g. inhibin α, VGF), 2) activation of a signaling component with a refractory period (e.g. G protein), and 3) inactivation of a factor needed for Fshb induction (e.g. GDF9). Simulations with all three models recapitulated the Fshb expression levels obtained in standard perifusion experiments at different GnRH pulse frequencies. Notably, simulations altering average concentration, pulse duration and frequency showed that the apparent frequency-dependent pattern of Fshb expression obtained with model 1 actually resulted from variations in average GnRH concentration. In contrast, models 2 and 3 showed “true” frequency sensing. To resolve which components of this GnRH signal induce Fshb, a massively parallel experimental system was developed. Analysis of over 4000 samples in ~40 experiments indicated that, while early genes Egr1 and Fos respond only to variations in GnRH concentration, Fshb induction is sensitive to GnRH pulse frequency changes, whilst maintaining the same average concentration. These results provide a framework for understanding the role of different regulatory factors in modulating the responses of the Fshb gene.

overall_design: 750,000 cells were seeded on each tissue culture-treated coverslip and were grown for two days in DMEM supplemented with 10% FBS. Cells were incubated in DMEM supplemented with 2% charcoal-treated FBS and 20mM HEPES overnight before the pulse experiment. Coverslips were placed in inert coverslip racks and pulse patterns were achieved by moving racks among GnRH, wash and resting solutions in chambers maintained at 37°C in a water bath. The chamber solution in the water bath was DMEM supplemented with 2% charcoal-treated FBS and 20mM HEPES. For each condition/time point, a minimum of 3 biological replicates were collected. Cells were pulsed with a cycle period (T) of either 30 min, 1 h,  2 h or 4 h, a pulse duration of either 2.5 min, 5 min, or 10 min, and a pulse amplitude of either 0.5 nM, 1 nM, or 2 nM GnRH. 'No pulse control' samples were included. ET, elapsed time between starting point (i.e. pulse 1) and time of collection.

first: Hanna

last: Pincas

first: Stuart

middle: C

last: Sealfon


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [111615data]


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [113015data]


title: Blood genome-wide gene expression microarray profiles in female patients with advanced Alzheimer's Disease and healthy controls

status: Public on Apr 14 2017

city: Columbus

first: Haiyan

last: Fu

state: Ohio

address: 700 Children's Dive

department: Center for Gene Therapy

institute: Research Institute at Nationwide Childrens Hospital

summary: To date, little is known regarding the etiology and disease mechanisms of alzheimer’s disease (AD). There is a general urgency for novel approaches to advance AD research.  In this study, we analyzed blood RNA from female patients with advanced AD and matched healthy controls using genome-wide gene expression microarrays. Our data showed significant alterations in 3,944 genes (≥2-fold, FDR≤1%) in AD whole blood, including 2,932 genes that are involved in broad biological functions. Importantly, we observed abnormal transcripts of numerous tissue-specific genes in AD blood involving virtually all tissues, especially the brain. Of altered genes, 157 are known to be essential in neurological functions, such as neuronal plasticity, synaptic transmission and neurogenesis. More importantly, 205 dysregulated genes in AD blood have been linked to neurological disease, including AD/dementia and Parkinson’s disease, and 43 are known to be the causative genes of 42 inherited mental retardation and neurodegenerative diseases. The detected transcriptional abnormalities also support robust inflammation, profound ECM impairments, broad metabolic dysfunction, aberrant oxidative stress, DNA damage and cell death. While the mechanisms are currently unclear, this study demonstrates strong blood-brain correlations in AD. The blood transcriptional profiles reflect the complex neuropathological status in AD, including neuropathological changes and broad somatic impairments. The majority of genes altered in AD blood have not previously been linked to AD. We believe that blood genome-wide transcriptional profiling may provide a powerful and minimally invasive tool for the identification of novel targets beyond Aβ and tauopathy for AD research.

overall_design: Study subjects were all female, including patients with advanced AD (n=9, age 79.3±12.3 years) and age–matched female healthy controls (n=10, age 72.1±13.1 years). Peripheral blood from each study subjects were processed to isolate RNA. The isolated blood RNAs were assayed byt geneome-wide gene expression microarrays using the Sureprint G3 Human Gene Expression 8x60k v2 microarrays (Agilent Technologies, CA)

first: Bartholomew

middle: J

last: Naughton

first: F

last: Duncan

first: Darren

middle: A

last: Murrey

first: Aaron

last: Meadows

first: David

middle: E

last: Newsom

first: Nicoleta

last: Stoicea

first: Peter

last: White

first: Douglas

middle: W

last: Scharre

last: Mccarty


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [111015data]


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [112015data]


title: MicroRNA-155 is upregulated in Hoxa9/Meis1 leukemia inducing cells but is dispensable for in vivo transformation and leukemia development

status: Public on Apr 27 2017

city: Gothenburg

first: Lars

last: Palmqvist

address: Sahlgrenska University Hospital

department: Institute of Biomedicine

country: Sweden

institute: University of Gothenburg

summary: OBJECTIVE: The microRNA miR-155 is upregulated in Hoxa9 and Meis1 leukemia inducing cells (LIC) , and miR-155 accelerates the onset of acute myeloid leukemia (AML) together with Hoxa9 but through largely unknown molecular mechanisms. The impact of  miR-155 on accelerated onset of leukemia in the context of Hoxa9 and Meis1 is also unclear. To further resolve this, we performed a gene expression profiling, in the context of Hoxa9 and Meis1 leukemogenesis with miR-155 knocked out. RESULTS: Gene expression profiling of Hoxa9/Meis1 LIC without miR-155 does not delay the onset of AML and the gene expression changes are small

overall_design: Murine bone marrow cells with or without miR-155 knocked out were transduced with Hoxa9-GFP + Meis1-YFP vectors and harvest for mRNA expression array. Three independent experiments were performed for each of the different conditions included in the study. Cells from were also transplanted into lethally irradiated mice to test for their transforming and leukemic potential.

first: Edith

last: Schneider

first: Anna

last: Staffas

first: Arefeh

last: Rouhi

first: Florian

last: Kuchenbauer


title: Molecular mechanism of the G1 arrest and cellular senescence induced by LEE011, novel CDK4/CDK6 inhibitor, in acute myeloid leukemia cells

status: Public on Jun 13 2017

city: suzhou

first: Jian

last: Pan

address: Jingde road 303

department: Department of Hematology and Oncology

institute: Children's Hospital of Soochow University

summary: Background  CDK4 and CDK6 are frequently over expressed or hyper activated in human cancers. Due to the importance of CDK4/6 activity in cancer cells, CDK4/6 inhibitors have emerged as promising candidates for cancer treatment. LEE011, a novel inhibitor of CDK4/6, until now the molecular function of LEE011 in acute myeloid leukemia is still unknown.   Methods    AML cell growth was assessed by CCK-8 and annexin V/propidium iodide staining followed by flow cytometry detected apoptosis in cell culture. AML cell senescence was assessed by β-Galactosidase Staining, p16INK4a expression and HP1α Staining analysis. Gene expressions of LEE011-treated tumor cells were analyzed using an Arraystar Human LncRNA Array. The Multi Experiment View cluster software analyzed the expression data. Differentially expressed genes from the cluster analyses were imported into the GO and KEGG pathway analysis.  Results   Our studies demonstrated that LEE011 inhibited proliferation of leukemia cells and do not induce apoptosis. Hoechst 33342 staining analysis showed that DNA fragmentation and abnormal nuclear cells was observed after LEE011 treatment. Cell cycle analysis showed in these eight acute leukemia cells, LEE011 induce the cell cycle G1 arrest very significantly, except THP-1 cells. Cell senescence β-Galactosidase Staining analysis, p16INK4a expression and HP1α Staining analysis all showed that LEE011 treatment can induce the cell senescence of AML cells.   LncRNA microarray was used to identify 2083 differently expressed mRNAs and 3224 differentially expressed lncRNAs in LEE011-treated HL-60 cells compared with control group. Molecular function analysis showed that LEE011 induced cellular senescence in leukemia cells partially through down regulation the transcriptional expression of MYBL2.  Conclusions   In this study, we showed for the first time that LEE011 treatment resulted in inhibition of cell proliferation and induction of G1 arrest and cellular senescence in AML cells. LncRNA microarray was used to identify differentially expressed genes and lncRNAs in LEE011-treated HL-60 cells and we demonstrated that LEE011 induce cellular senescence partially through down regulation the expression of MYBL2. These results may provide new insights into the molecular mechanism of LEE011-induced cellular senescence; however, further research will be required to determine the underlying details. Taken together, our findings firstly suggest that LEE011 may act as new candidate’s drug for AML.

overall_design: HL-60 cells were treated with 1uM LEE011 and control group cells were treated with the same volume of DMSO 24 hours later. Human LncRNA Array analysis was performed by KangChen Bio-tech, Shanghai P.R. China.Human LncRNA Array analysis was performed by KangChen Bio-tech, Shanghai P.R. China.  Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. For microarray analysis, Agilent Array platform was employed. The sample preparation and microarray hybridization were performed based on the manufacturer’s standard protocols with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were hybridized onto the Human LncRNA Array v2.0 (8 x 60K, Arraystar). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.  Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.0 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 4 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable LncRNAs and mRNAs expression pattern among samples.

first: Yan-Fang

last: Tao


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [102215data]

first: Frederique

last: Ruf-Zamojski

first: Hanna

last: Pincas

first: Stuart

last: Sealfon


title: Gene Expression profiling in luminal breast cancer cells treated with a novel KDM5 inhibitor, 5-aza-2' Deoxycytidine, or both.

status: Public on Dec 08 2017

first: Benjamin

last: Leadem

state: MD

address: 1650 Orleans St. Suite 541

institute: Johns Hopkins University

summary: Recently, the H3K4 demethylase, KDM5B, was shown to be amplified and overexpressed in luminal breast cancer, suggesting it might constitute a potential cancer therapy target.  Here, we characterize, in breast cancer cells, the molecular effects of a recently developed small-molecule inhibitor of the KDM5 family of proteins, either alone, or in combination with the DNA demethylating agent 5-aza-2’ deoxycytidine (DAC).  To determine the effects of these compounds on global gene expression, we used the Agilend Whole Human Genome 4x44k v2 Microarray.  We found that alone, the KDM5 inhibitor (KDM5i) increased expression of a small number of genes, but when combined with DAC, the drug enhanced the effects of the latter for increasing expression of hundreds of DAC responsive genes.

overall_design: Two-condition experiment, Mock v Treated Cells. Biological replicates: 3.  Total samples: 15

first: Stephen

last: Baylin


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [101915data]


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [093015data]


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [092315data]


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [100815data]

summary: Reproduction requires pulsatile release of hypothalamic GnRH, which regulates expression of the pituitary gonadotropins FSH and luteinizing hormone (LH). Fshb expression shows an inverted U-shaped response to GnRH pulse frequency. Increasing GnRH pulse frequency beyond ~one pulse/2 hours, despite increasing the average GnRH concentration, induces progressively less Fshb. To clarify regulatory mechanisms underlying Fshb gene control, we developed three biologically inspired and topologically distinct mathematical models. The models represent: 1) parallel activation of Fshb inhibitory and stimulatory factors (e.g. inhibin α, VGF), 2) activation of a signaling component with a refractory period (e.g. G protein), and 3) inactivation of a factor needed for Fshb induction (e.g. GDF9). Simulations with all three models recapitulated the Fshb expression levels obtained in standard perifusion experiments at different GnRH pulse frequencies. Notably, simulations altering average concentration, pulse duration and frequency showed that the apparent frequency-dependent pattern of Fshb expression obtained with model 1 actually resulted from variations in average GnRH concentration. In contrast, models 2 and 3 showed “true” frequency sensing. To resolve which components of this GnRH signal induce Fshb, a massively parallel experimental system was developed. Analysis of over 4000 samples in ~40 experiments indicated that, while early genes Egr1 and Fos respond only to variations in GnRH concentration, Fshb induction is sensitive to GnRH pulse frequency changes, whilst maintaining the same average concentration. These results provide a framework for understanding the role of different regulatory factors in modulating the responses of the Fshb gene.


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [091815data]


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [100915data]


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [091015data]


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [082615data]


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [072815data]


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [081115data]


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [071615data]


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [072015data]


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [071015data]


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [061615data]


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [051215data]


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [061015data]


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [042215data]


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [041515data]


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [031615data]


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [030316data]


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [060116data]

overall_design: 750,000 cells were seeded on each tissue culture-treated coverslip and were grown for two days in DMEM supplemented with 10% FBS. Cells were incubated in DMEM supplemented with 2% charcoal-treated FBS and 20mM HEPES overnight before the pulse experiment. Coverslips were placed in inert coverslip racks and pulse patterns were achieved by moving racks among GnRH, wash and resting solutions in chambers maintained at 37°C in a water bath. The chamber solution in the water bath was DMEM supplemented with 2% charcoal-treated FBS and 20mM HEPES. For each condition/time point, a minimum of 3 biological replicates were collected. Cells were pulsed with a cycle period (T) of either 30 min, 1 h, 2 h or 4 h, a pulse duration of either 2.5 min, 5 min, or 10 min, and a pulse amplitude of either 0.5 nM, 1 nM, or 2 nM GnRH. 'No pulse control' samples were included. ET, elapsed time between starting point (i.e. pulse 1) and time of collection.


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [030315data]


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [010416_1data]


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [011416_1data]


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [020116data]


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [010516data]


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [2hFreq_LISAdata]


title: Expression of oxysterol pathway genes in estrogen positive breast carcinomas

status: Public on Apr 06 2017

city: Prague 10

first: Pavel

last: Soucek

address: Srobarova 48

country: Czech Republic

institute: National Institute of Public Health

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

overall_design: Refer to individual Series


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [2hFreq_ReanalysisLISAdata]


title: Expression of oxysterol pathway genes in estrogen positive breast carcinomas-second phase

summary:
Metabolism of anticancer drugs markedly affects their antitumor effects. The major goal of our study was to investigate associations of gene expression of enzymes metabolizing taxanes and/or anthracyclines with therapy response and survival of breast carcinoma patients
The present study investigated transcript levels of key modulators of oxysterol signaling pathway, including oxysterol receptors, metabolic enzymes and transporters in the group of hormone-receptor positive breast carcinoma patients to evaluated potential clinical significance of these genes.

overall_design: Transcript levels of twenty-five selected human genes (oxysterol signaling pathway, oxysterol receptors, metabolic enzymes and transporters) were determined by qPCR in tumor tissue samples from 164 breast carcinoma patients treated by antihormone therapy or antihormone therapy and chemotherapy. EIF2B1, ELF1, and UBB were used as reference genes for data normalization.

first: Alzbeta

last: Kloudova

first: Veronika

last: Brynychova


title: Expression data from C17.2 progenitor cells during neural differentiation for 5 and 10 days with NGF and BDNF

status: Public on Apr 04 2017

city: Stockholm

first: Kristina

last: Attoff

address: Svante Arrhenius väg 16C

institute: Department of neurochemistry, Stockholm University

summary:
We used microarray to study the change in gene expression during differentiation in the C17.2 progenitor cell line. The cells were either undifferentiated or differentiated for 5 or 10 days.
The goal was to identify genes important for differentiation of the C17.2 cell line

overall_design: The C17.2 progenitor cells were isolated either as undifferentiated progenitor cells or differentiated for 5 or 10 days with NGF and BDNF.

first: Jessica

last: Lundqvist


title: Epigenetic Inactivation of the RNA Decapping Enzyme NUDT16 in T-Cell Acute Lymphoblastic leukemia

city: L'Hospitalet de Llobregat

first: Manuel

last: Castro

state: Barcelona

address: Av. Gran Vía de l'Hospitalet 199

department: PEBC

institute: IDIBELL

summary: Human tumors show aberrant RNA profiles that can originate from multiple pathways and mechanisms. One underexplored area is that alterations in RNA decapping, the addition of a 5´-end N7-methyl guanosine (m7G)-cap that is essential for stabilization of the RNA molecule,  could also be involved in the distorted transcript landscape of cancer cells. Herein we show that the RNA editing enzyme NUDT16 undergoes promoter CpG island methylation-associated silencing in T-cell acute lymphoblastic leukemia (T-ALL) cell lines and primary samples.  The restoration of in vitro and in vivo NUDT16 activity highlights the growth inhibitory features of the gene. Most importantly, we identify that the epigenetic loss of NUDT16 in leukemia cells prevents the RNA decay of growth-promoting genes, among them the C-MYC stabilizers FBXO28 and USP37, leading to higher levels of the oncogenic protein.

overall_design: RNA-immunoprecipitation (RIP) of m3G/m7G-capped transcripts in empty vector vs NUDT16 transfected MOLT4 cells with 3 replicates each one.

first: Carmen

last: Anadón

first: Geert

last: van Tetering

last: Martínez-Cardús

first: Alberto

last: Villanueva

first: Catia

last: Moutinho

first: Holger

last: Heyn

first: Sebastian

last: Moran

last: de Moura

first: August

last: Vidal

first: Josep

last: Nomdedeu

first: Sonia

last: Guil

first: Manel

last: Esteller


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [050415data]

first: Frederique

last: Ruf-Zamojski

first: Hanna

last: Pincas

first: Stuart

last: Sealfon


title: Differential gene expression in the adipose tissue of crossbred beef cows with divergent gain after feed restriction and ad libitum feeding studies.

status: Public on Apr 03 2017

city: Clay Center

first: Amanda

middle: K

last: Lindholm-Perrry

state: NE

address: State Spur 18D

department: NEMRU

institute: USMARC

summary:
Beef cow adipose tissue transcriptome
Evaluation of the naturally occurring transcriptome variation among beef cows with divergent gain.

overall_design: The transcriptome of adipose tissue obtained after feed restriction and ad libitun feed were examined for expression differences that contribute to body weight gain.

last: Lindholm-Perry

first: Hannah

last: Cunningham


title: Gene expression altered by high-fructose diet feeding and Chrebp deficiency

status: Public on Mar 21 2017

first: Deqiang

last: Zhang

state: MI

address: 1137 Catherine Street

department: Molecular & Integrative Physiology

institute: University of Michigan

summary:
Epidemiologic and animal studies implicate overconsumption of fructose in the development of non-alcoholic fatty liver disease, but the molecular mechanisms underlying fructose-induced chronic liver diseases remains largely unknown. We present evidence supporting the essential function of the lipogenic transcription factor ChREBP in mediating adaptation response to fructose and protecting against fructose-induced hepatotoxicity. High-fructose diet (HFrD) activates hepatic lipogenesis via a ChREBP-dependent manner in wildtype mice, while inducing steatohepatitis in Chrebp-KO mice. In Chrebp-KO mouse livers, HFrD reduces levels of molecular chaperones and activates the CHOP-dependent unfolded protein response, whereas administration of chemical chaperone or Chop shRNA rescues liver injury. Gene expression profiling revealed elevated expression of cholesterol biosynthesis genes in Chrebp-KO livers after HFrD, in parallel with increased abundance of nuclear SREBP2.
genes expression were compared between livers of wildtype mice fed 70%-fructose-diet v.s. regular chow, and between livers of Chrebp-/- mice v.s. wildtype mice fed 70%-fructose-diet.

overall_design: Micro-array assay was performed with RNA samples pooled from livers of regular chow-fed WT mice (n = 7) vs. HFrD-fed WT mice (n = 7) or from livers of HFrD-fed WT mice (n = 4) vs. HFrD-fed Chrebp-/- mice (n = 6). Both male and female mice are used in all 4 groups.

first: Lei

last: Yin


title: Expression data from miR-27a/b-overexpressing HeLa cells

city: Chuo-ku

first: Mitsuhiro

last: Machitani

state: Tokyo

address: 5-1-1 Tsukiji

institute: National Cancer Center Research Institute

summary:
In infection with an adenovirus, it remains to be clarified whether host miRNAs affect Ad replication. We focused on miR-27 as an miRNA crucial for regulation of Ad infection because miR-27 has been reported to be involved in infection of other viruses, including MCMV and herpesvirus saimiri (HVS).
We used microarrays to detail gene expression profiles in miR-27a/b-overexpressing HeLa cells and demonstarted that expression levels of various genes were down- or up-regulated following transfection with miR-27a/b mimics.

overall_design: Hela cells were transfected with miR-27a/b mimics at 20 nM. After 48 h incubation, the cells were collected and gene expression profiles in the cells were analyzed by microarray analysis.

first: Fuminori

last: Sakurai

first: Hiroyuki

last: Mizuguchi


title: Gene expression profiling of lung cancer serum or health plasma cultured human monocytes-derived dendritic cells

status: Public on Mar 28 2017

city: Hefei

first: Rui

last: Li

state: Anhui

address: Huangshan Road 443, USTC West Campus

department: School of Life Sciences

institute: University of Science and Technology of China

summary: Cancer-induced DC dysfunction plays an important role in the tumor immune escape and cancer development. By using lung cancer patients’ sera, we built an in vitro model of tumor induced DCs dysfunction, and gene expression analysis was performed basing on Operon Human Genome Array-Ready Oligo Set (Version 4.0).

overall_design: Immature MoDCs cultured with two tumor sera pools separately (named as Exp1 and Exp2) or healthy controls were collected. Total RNA were isolated, and aRNA were then synthesized. Gene expression profiling were performed with CY5 (health group) or CY3 (cancer group) labeled aRNA.

first: Weihua

last: Xiao


title: Development of gene expression  for FMDV-infected RAW264.7 cell

status: Public on Mar 15 2017

city: Lanzhou

first: Xiaoying

last: Zhi

state: Gansu

address: Xujiaping 1,Lanzhou,Gansu,China

institute: Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences

summary: To determine whether type O FMDV-infected macrophage can release a variety of cytokines and activate innate immune responses, we have taken systematic functional genomics studies using microarray technology on differences expression gene of  FMDV-infected and FMDV-uninfected mouse monocyte macrophage (RAW264.7 cells). We examined the expression patterns of 39,430 mouse genes probes, using Agilent mouse gene expression microarray. The results showed that 2541 genes were differentially expressed after FMDV infection, with 1207 up-regulated and 1334 down-regulated. Based on our previous data, the differential regulation of genes most associate with innate immune response.

overall_design: The mouse monocyte macrophage cell line RAW264.7 and BHK-21 cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum. O type FMDV was grown in BHK-21 cells for 8h at 37°C. The virus titers were detected using the Reed-Muench method to determine the 50% tissue culture infective dose. The supernatants of infected cells were clarified and stored at −80°C. RAW264.7 cells were infected or uninfected with O type FMDV at MOI of 2 for 1h at 37°C, and then removed the supernatant, washed with phosphate-buﬀered saline (PBS) (pH 7.4), and cultured with complete DMEM for 8h at 37°C.

first: jianliang

last: Lv

first: Yuan

last: Gao


title: Mechanisms underlying FSHβ gene sensitivity to GnRH pulse frequency [011416_2data]


title: Expression of oxysterol pathway genes in estrogen positive breast carcinomas-first phase

first: Pavel

last: Soucek

summary:
Metabolism of anticancer drugs markedly affects their antitumor effects. The major goal of our study was to investigate associations of gene expression of enzymes metabolizing taxanes and/or anthracyclines with therapy response and survival of breast carcinoma patients
The present study investigated differences in transcript levels of key modulators of oxysterol signaling pathway, including oxysterol receptors, metabolic enzymes and transporters in the groups of estrogen receptor positive (ER+) breast carcinomas in comparison to estrogen receptor negative (ER-) ones, and to control non-tumor tissues.

overall_design: Transcript levels of seventy-five selected human genes (oxysterol signaling pathway, oxysterol receptors, metabolic enzymes and transporters) were determined by qPCR in 17 ER+ tumor tissue samples, in 12 ER- samples, and 10 non-tumor tissues. EIF2B1, ELF1, and UBB were used as reference genes for data normalization.

first: Alzbeta

last: Kloudova

first: Veronika

last: Brynychova


title: HCoV-229E infection of the human HuH7 cell line [Experiment A]

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

summary: The aim of the experiment is to identify changes in host gene expression upon infection of HuH7 human hepatoma cells with Human corona virus-229E (HCoV-229E) compared to mock-infected cells. All experiments were performed at 33°C which is required for sufficient viral entry/replication.

overall_design: Single-color hybridizations of RNA from different cell lines, either uninfected or infected with HCoV-229E. Duplicates.

first: Michael

last: Kracht

last: Poppe


title: Time-course of HCoV-229E infection of A549 cells

summary: The aim of the experiment is to identify kinetic changes in host gene expression upon infection of A549 lung epithelial carcinoma cells  with human corona virus HCoV-229E as compared to unifected cells. Negativ controls include infections with heat-inactivated virus. Positive controls include treatment of cells with human IL-1alpha (10ng/ml) for 1h. All experiments have been performed at 33°C which is required for sufficient viral entry/replication.

overall_design: Single-color hybridizations of RNA from HCoV.229E infected A549 cells, time course (16,24,48 h), with time-mathched controls plus two additional controls (untreated and IL1-treated). No replicates.


title: Expression data from E12 mouse lumbar motor neuron subsets

status: Public on Mar 10 2017

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary:
Sonic hedgehog (Shh) signals via Gli transcription factors to direct digit number and identity in the vertebrate limb. We have characterized the Gli-dependent cis-regulatory network through a combination of whole genome ChIP-on-chip and transcriptional profiling of the developing mouse limb.
In this dataset, we include the expression data obtained from dissected mouse forelimbs using a variety of gain- and loss-of-function hedgehog pathway mutants, as well as limbs dissected into responsive (posterior 2/3ds) and non-responsive (anterior 1/3d) Hh tissues. These data are used to obtain 753 genes that are differentially expressed in response to Shh signaling.

overall_design: 6 Total samples were analyzed. We generated the following pairwise comparisons using PowerExpress: medial MN vs lateral MN FDR ≤ x % and a fold-change ≥1.5 were selected.

first: G

last: Haase

first: D

last: Gentien

first: P