title: Mitral valve interstitial Tissue: Myxomatous P2 prolapse of the mitral valve  vs. Control

status: Public on Jan 29 2018

city: Memphis

first: Shannon

last: McKinney-Freeman

state: TN

address: 262 Danny Thomas Place

department: Hematology

country: USA

institute: St. Jude Children's Research Hospital

summary:
Aim: Test the hypothesis that 5HT receptors (5HTRs) signaling contributes to MVP pathophysiology.
Methods and results: MV RNA was used for microarray analysis of MVP patients versus control, highlighting genes that indicate the involvement of 5HTR pathways and extracellular matrix remodeling in MVP. These canine MVP leaflets (N=5/group) showed 5HTR2B upregulation.
Conclusion: In humans, MVP is associated with an upregulation in 5HTR2B expression and increased 5HT receptor signaling in the leaflets. 5HTR signaling is involved not only in previously reported 5HTrelated valvulopathies, but it is also involved in the pathological remodeling of MVP.

overall_design: Two-condition experiment, 4 MVP patients vs. 4 controls. 3 replicates per sample.

first: Kathryn

middle: H

last: Driesbaugh

first: Emanuela

last: Branchetti

first: Juan

middle: B

last: Grau

first: Samuel

middle: J

last: Keeney

first: Kimberly

last: Glass

first: Mark

middle: A

last: Oyama

first: Nancy

last: Rioux

first: Salma

last: Ayoub

first: Michael

middle: S

last: Sacks

first: John

last: Quackenbush

first: Robert

last: Levy

first: Giovanni

last: Ferrari


title: PAX3-FOXO1 regulated microRNAs contribute to the pathogenesis of alveolar rhabdomyosarcoma

status: Public on Jan 26 2018

first: Yong-Dong

last: Wang

address: 262 Danny Thomas Pl, MS1135

summary: Interrogation of microRNA expression and regulation by PAX3-FOXO1 in Fusion-Positive Rhabdomyosarcoma.

overall_design: MicroRNA expression in RMS cell lines, patient-derived xenografts, and cell lines with forced expression of PAX3-FOXO1 and inducible shRNA knockdown of PAX3-FOXO1.

middle: E

last: Hatley

first: Jason

last: Hanna


title: Modulation of the gastrointestinal microbiota normalizes the systemic inflammation and islet immunocyte recruitment capacity associated with autoimmune diabetes (in Biobreeding rats) [RatPBMC_D30HCD-ABS]

status: Public on Jan 23 2018

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

summary:
The incidence of Type 1 diabetes (T1D), a T-cell mediated autoimmunity that targets the insulin secreting β-cells, has significantly increased, suggesting greater environmental pressure.  In studies of T1D families and the BioBreeding rat model, we have identified a peripheral innate inflammatory state that is associated with diabetes susceptibility, consistent with pattern recognition receptor (PRR) ligation, but independent of disease progression.  Here, compared to control strains, islets of spontaneously diabetic BB DRlyp/lyp and nondiatetic BB DR+/+ weanlings provided a standard cereal diet were found to temporally express a proinflammatory transcriptional program consistent with microbial antigen exposure that included numerous cytokines/chemokines.  Dependence of this proinflammatory phenotype on the diet and gastrointestinal microbiota was investigated by transitioning DR+/+ weanlings to a hydrolyzed casein diet (HCD) or treating them with antibiotics to respectively alter or reduce PRR ligand exposure.
Sequencing of the bacterial 16S rRNA gene revealed that these treatments significantly altered the ileal and cecal microbiota, resulting in increases in the Firmicutes:Bacteriodetes ratio, and abundances of lactobacilli and butyrate producing genera.  Both treatments partially normalized the peripheral inflammatory state, reducing plasma cytokine, chemokine and TLR-4 activity levels.  The proinflammatory islet transcriptome was more extensively normalized by HCD and immune-fluorescent staining revealed reductions in β-cell chemokine expression.  HCD and antibiotic treatment did not normalize BB rat PBMC hyper-responsiveness to ex vivo mitogen stimulation.  Combined, these studies link islet-level T1D susceptibility in BB rats to a genetically controlled innate inflammatory state that is influenced by environmental determinants encompassing the diet and the intestinal microbiota.

overall_design: The induction of gene expression was accomplished by culturing the PBMCs of healthy day180 Brown Norway(BN) donor rats for 6 h at 37°C in 5% CO2 and stimulated with a 20% a) Autologous day180 BN plasma (4 samples), b) day30 DR HCD plasma (4 samples), c) day30 DR ND plasma (4 samples), d) day30 DR B/S plasma (4 samples), and e) day30 F+/+ ND plasma (4 samples). Gene expression profile of F+/+, DR HCD, and DR B/S were compared to those of age matched DR+/+ ND.

first: Angela

middle: M

last: Henschel

first: Susanne

last: Cabrera

first: Mary

last: Kaldunski

first: Shuang

last: Jia

first: Rhonda

last: Geoffrey

middle: F

last: Roethle

first: Vy

last: Lam

first: Xujing

first: Nita

last: Salzman


title: Molecular heterogeneity of multinodular hepatocellular carcinoma [gene expression]

status: Public on Jan 28 2018

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary:
Genome-wide gene expression profiles of multiple hepatocellular carcinoma tumors and non-tumor liver tissues from the same patients.
Introduction: Hepatocellular Carcinoma (HCC) is the second cause of cancer-related death worldwide. Understanding tumor heterogeneity is relevant for the pathogenesis and treatment of this neoplasm. Particularly, whether multinodular tumors result from intrahepatic metastasis (IM or clonal tumors) or de novo cancers (synchronic tumors) have direct implications in treatment decisionmaking for resection and transplantation. We aimed to assess the genomic heterogeneity of multifocal HCC using single-nucleotide polymorphism (SNP) and gene expression analyses.  Methods: Among 544 HCC patients consecutively transplanted at Mount Sinai Hospital between 1990- 2007, we selected 18 patients with a total of 42 multinodular tumors (2-3 non-satellite foci HCCs) for this molecular study. Formalin-fixed blocks were collected for each tumor along with corresponding clinico-pathological data. SNP array and gene expression profiling was generated. Clonality was defined by measuring the similarity of genome-wide copy number variation (CNV) profiles between two nodules. Unsupervised hierarchical clustering based on gene expression data was performed to measure genetic proximity between each tumor. Prediction of previously published signatures was performed using Nearest Template Prediction (NTP). Association of clonality with clinic-pathological parameters was assessed.  Results: A total of 42 tumors have been analyzed (10 patients- 2 tumors; 8- 3 tumors). Most patients were male (17/18, 95%) with median age of 53-yr-old (range 39–67), HCV (10/18, 56%) or HBV infection (6/18, 33%). Median tumor size was 3 cm (range 1.5-6.5), satellites were present in 3 (17%) and vascular invasion in 11 patients (61%), respectively. CNV profiles predicted clonal tumors in 38% (6/16) and non-clonality in 62% of cases (10/16). CNV profiles of the remaining 2 cases were not informative. Clonal tumors were significantly associated with HCV infected patients (5/6 vs 3/10, p=0.007), whereas all HBV-induced HCC were synchronic tumors (0/6 vs 6/10, p=0.03). Furthermore, clonal tumors were significantly associated with presence of satellites and shorter time-torecurrence. Assessment of genetic proximity based on gene expression revealed that each clonal tumor showed proximity to its paired tumor and clustered around the same node (6/6,100%) as opposed to non-clonal (2/9,22%). When exploring molecular subclasses within clonal tumors (intrahepatic metastases), while half of them retained the molecular fingerprint, the other half switch to more aggressive subclasses. Conversely, all non-clonal tumors within the same patient belonged to distinct molecular subclasses.  Conclusion: Multinodular HCCs undergoing transplantation are molecularly heterogeneous. Using CNV profiling we identified clonal multinodular tumors (true intrahepatic metastasis) in 40% of cases and de novo tumors in 60%. Clonal tumors were significantly associated with HCV infection, satellites and recurrence. Genetic proximity was observed in clonal tumors, but molecular subclasses prediction revealed that intrahepatic metastases share more aggressive subclasses in half of cases.

overall_design: Genome-wide gene expression profiling of macrodissected FFPE HCC tumor and adjacent non-tumor liver tissues.

first: Daniela

last: Sia

first: Andrew

middle: N

last: Harrington

first: Josep

last: Llovet


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and smyd4 mutant zebrafish cardiac transcriptomes

status: Public on Jan 25 2018

city: Shanghai

first: deyong

last: xiao

address: Room 308, Mingdao building, Research Center For Birth Defects, School of Basic Medical Sciences,  Fudan University, 130 Dongan Road, Shanghai , China

country: China

institute: Fudan university

type: Expression profiling by high throughput sequencing

summary: Heart tissue mRNA profiles of  50 wild-type (WT) and  50 homozygous smyd4 mutant zebrafish embryos  at 72-hpf created by CRISPR/Cas9 were generated by deep sequencing.

overall_design: Heart mRNA profiles of 72-hpf  wild type (WT) and smdy4 mutant zebrafish were generated by deep sequencing using illumina

first: Deyong

last: Xiao

first: Duan

last: Ma


title: Expression data from developing zebrafish embryos treated with pesticides and 11-ketotestosterone

status: Public on Jan 30 2018

city: Farmington

first: Mara

middle: H.

last: O'Brien

state: CT

address: 263 Farmington Ave.

department: Craniofacial Sciences

institute: University of Connecticut Health Center

summary: During critical periods the developing organism is particularly sensitive to exposure to bioactive environmental contaminants. Our objective was to test p,p’-DDE and dieldrin in a zebrafish whole embryo model in order to identify potential endocrine disrupting activity during development.

overall_design: Zebrafish embryos were collected and raised in egg water until treatment at 72-96 hours post fertilization

first: Adam

middle: C

last: Gower

first: Ian

middle: P

last: Callard


title: Expression profiling of human valve interstitial and endothelial cells and the effect of BMP and TGFB signaling

city: Darlinghurst

first: Joshua

last: Ho

state: NSW

address: Lowy Packer Building

country: Australia

institute: Victor Chang Cardiac Research Institute

summary: Microarray gene expression profiling of the minimally cultured human heart valve interstitial and endothelial cells with and without treatment with BMP4 and TGFB3 signaling molecules

overall_design: We collected heart valve tissues from explanted non-diseased heart valve from pediatric patients undergoing heart transplant. Valve interstitial cells (VICs) and valve endothelial cells (VECs) were harvested and expanded in a culturing system for a few passages. These cells either treated with BMP4 or TGFb3 signaling agonists or untreated (control) and incubated for 8 hours before used for microarray profiling experiments. The goal is to identify (1) the gene expression signatures associated with human heart valve interstitial and endothelial cells, and (2) the effect of BMP and TGFb signaling signaling on these cells, especially with regard to promoting/inhibiting the endothelial-mesenchymal transformation (EMT) program.

first: Ahmed

last: Bayoumi

middle: W


title: Molecular heterogeneity of multinodular hepatocellular carcinoma

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

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

overall_design: Refer to individual Series


title: Expression of Adipocyte/Macrophage Fatty Acid Binding Protein in Tumor Associated Macrophages Promotes Breast Cancer Progression

status: Public on Jan 27 2018

city: Minneapolis

first: Ying

last: Zhang

state: MN

address: 117 Pleasant St S.E.

department: Minnesota Supercomputing Institute

institute: University of Minnesota

summary: Identification of A-FABP as a new functional marker for pro-tumor associated macrophages.

overall_design: Using tumor/macrophages co-culutre experiments to investigate the molecular mechanisms by which A-FABP expression in macrophages promotes tumor progression.

first: Jiaqing

last: Hao

first: Li

last: Bing


title: microRNA expression in sham and ovariectomy (OVX) mice femur tissue

first: Jingyu

last: Zhao

address: 320 Yueyang Road

institute: Zhaojingyu, Huang Mingjian

summary: To search for the role of microRNAs in postmenopausal osteoporosis, we used an experimental ovariectomized (OVX) mice moldel. We operated ovariectomy in 3-month-old C57BL/6 mice and collected the femurs after 6months to perform miRNA microarray analysis to identify dysregulated microRNAs.

overall_design: Two groups were accessed by by miRNA microarray (wt-sham and wt-OVX), and each sample was mixed with four mice tissue.

first: J

first: M

last: Huang


title: Gene expression profiling of immune response genes and epigenetic modification factors in melioidosis patients

city: colombo

first: Aruna Dharshan

last: De Silva

address: Kandawala Road, Ratmalana

country: Sri Lanka

institute: Kotelawala Defense University

summary: The study population consisted of 30 melioidosis cases, 10 healthy controls and 10 sepsis cases caused by other pathogens. Total RNA was extracted from peripheral blood mononuclear cells (PBMC’s) of study subjects. Gene expression profiles of 25 gene targets including 19 immune response genes and 6 epigenetic factors were analyzed by real time quantitative polymerase chain reaction (RT-qPCR).

overall_design: qPCR gene expression profiling of melioidosis patients compared to other sepsis cases and healthy controls

first: Shivankari

last: Krishnananthasivam


title: Apoptosis-associated transcriptome profiles in peripheral blood leukocytes from healthy volunteers

status: Public on Jan 31 2018

city: Nizhny Novgorod

first: Dmitry

last: Knyazev

address: Malaya Yamskaya, 71

country: Russia

institute: I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology

summary: Refer to the SuperSeries

overall_design: This series is the set of microarray measurements of transcriptome profiles in peripheral blood leukocytes from healthy volunteers for identifying potentially clinically relevant  mRNAs. The set is intended for comparisons with the acute stage groups and the reconvalescent groups presented in the other series in the superseries. The splicing-sensitive microarray (platform GPL23086) covers 221 genes, each microarray encompasses 4 identical probe-containing areas. Blood samples obtained from 6 healthy volunteers were included in the series.

first: Nikolay

last: Sakharnov

first: Leonid

last: Solntsev

first: Oleg

last: Utkin


title: Expression analysis of response to external status of ammonium in rice roots.

status: Public on Jan 24 2018

city: Tsukuba

first: Mitsuhiro

last: Obara

state: Ibaraki

address: Ohwashi 1-1

country: Japan

institute: JIRCAS

summary: Nitrogen is major nutrient for plant growth. Two forms for inorganic nitrogen are available for plant, ammonium and nitrate. External status of them affects largely plant growth and production. Generally, root is a sole organ to uptake nitrogen. Hence, identifying regulatory genes depend on nitrogen status in roots is important to improve sustainable production or rice. To isolate the candidate gene, array experiments were performed. Consequently, we isolated genes which showed marked accumulation in deficient and sufficient concentrations of ammonium in roots.

overall_design: Rice Oligo DNA Microrray 4X44K RAP-DB (Agilent Technologies) was used in this research. Total RNA was extracted from roots of Koshihikari grown for 10 days in 0.005 and 1 mM NH4Cl with RNeasy Plant Kit (QIAGEN) in accordance with recommend protocol. We performed four biological replicate for both treatments. Before array analyses, RNA integrity was confirmed with Agilent 2100 Bioanalyzer. Array analysis was performed in accordance with recommend protocol as follow. Total RNA (100ng) was labeled with Cy3 using Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies). Cy-labeled cRNA (0.00165 mg) was fragmented for 30 min at 60 degree and the hybridized for 17 hrs at 65 degree with gentle shaking (10 rpm) using Gene Expression Hybridization Kit (Agilent Technologies). Following, the arrays were washed using Gene Expression Wash Buffers Pack (Agilent Technologies) and then scanned using a scanner, Agilent DNA Microarray Scanner (G2565CA). For data processing, Agilent Feature Extraction software was used for delineation and measurement of the signal, normalization of intensity, and measurement of local background at individual spot in accordance with the manufacturer’s instructions.


title: Enhancer invasion shapes MYCN dependent transcriptional amplification in neuroblastoma [ARRAY]

city: Boston

first: James

last: Bradner

state: MA

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: In neuroblastoma, amplification of the oncogenic basic helix-loop-helix (bHLH) transcription factor (TF) MYCN is the defining prognosticator of high-risk disease, occurs in one-third of neuroblastoma, and drastically reduces overall survival rates1,2. As a proto-oncogene, targeted MYCN overexpression in peripheral neural crest is sufficient to initiate disease in mouse models3. In MYCN amplified neuroblastoma, elevated expression of the factor is crucial to maintain tumor stemness4,5 and is associated with increased proliferation and aberrant cell cycle progression, as these tumors lack the ability to arrest in G1 in response to irradiation6-9. MYCN down-regulation broadly reverses these oncogenic phenotypes in a variety of neuroblastoma models10-12 and recent thereapeutic strategies to indirectly target MYCN production or protein stability have reduced tumor growth in vivo13-15. These observations motivate an investigation of MYCN binding in MYCN amplified tumors as it remains fundamentally unclear how elevated levels of the factor occupy the genome and alter transcriptional programs in neuroblastoma. Here we present the first dynamic chromatin and transcriptional landscape of direct MYCN perturbation in neuroblastoma. We find that at oncogenic levels, MYCN associates with E-box (CANNTG) binding motifs in an affinity dependent manner across most active cis-regulatory promoters and enhancers. MYCN shutdown globally reduces histone acetylation and transcription, consistent with prior descriptions of MYC proteins as non-linear amplifiers of gene expression. We establish that MYCN load at the promoter and proximal enhancers predicts transcriptional responsiveness to MYCN shutdown and that MYCN enhancer binding occurs prominently at the most strongly occupied and down-regulated genes, suggesting a role for these tissue specific elements in predicating MYCN responsive “target” genes. At these invaded enhancers, we identify the lineage specific bHLH TWIST1 as a key collaborator and dependency of oncogenic MYCN. These data suggest that MYCN enhancer invasion helps shape transcriptional amplification of the neuroblastoma gene expression program to promote tumorigenesis.

overall_design: Expression profiling in SKNAS, BE2C, NGP, KELLY, and SHS-Y5Y neuroblastoma cell lines

first: Rhamy

last: Zeid

first: Charles

middle: Y

last: Lin


title: IRE1-mediated downregulation of miR-146a and miR-155 in primary dermal fibroblasts across three TNFRSF1A mutations results in hyperresponsiveness to LPS

city: Birmingham

first: Stephanie

middle: Rose

last: Harrison

address: Mindelson Way

country: United Kingdom

institute: Queen Elizabeth Hospital Birmingham

summary: As part of the above publication, experiments look at fold changes in 380 miRs at baseline in 3 healthy controls and 3 TRAPS patients were analysed.

overall_design: A scientific experiment using RT-qPCR to look at fold change difference in miR expression between HC dermal fibroblasts and TRAPS dermal fibroblasts at baseline (i.e. without any stimulation of the fibroblasts).

first: S

middle: R

first: T

last: Scambler

first: L

last: Ouboussad

first: C

last: Wong

last: Wittmann

last: McDermott

last: Savic


title: Neutral sphingomyelinase 2 (nSMase2)-dependent exosomal transfer of angiogenic microRNAs regulate cancer cell metastasis

city: Tokyo

first: Nobuyoshi

last: Kosaka

address: 5-1-1, Tsukiji, Chuo-ku

department: Research of Molecular Functions and Targets

institute: National Cancer Center

summary: Comparing the expression profiles of exosome and cellular microNRA from cancer cells whose expression of nSMase2 was modified by shRNA or expression vector for overexpression.

overall_design: Collect and isolate the total RNA from exosome or cells. These cells are genetically modified by shRNA or expression vector for overexpression of nSMase2.

first: Takahiro

last: Ochiya


title: Competitive interactions of cancer cells and normal cells via secretory microRNAs

summary: Comparing the microRNA expression profiles from exosome or cell.

overall_design: Exosome or cellular total RNA from cancer cells, PC3M, and normal cells, PNT2, were used.


title: Apoptosis-associated transcriptome changes in peripheral blood leukocytes during CMV antiviral therapy

last: Knyazev

summary: refer to the SuperSeries

overall_design: The splicing-sensitive microarray (platform GPL23086) covers 221 genes, each microarray encompasses 4 identical probe-containing areas. Blood samples obtained from 5 CMV patients during acute mononucleosis and after convalescence were included in the experiment.


title: Effects of formin impairment on gene expression in Arabidopsis seedlings

city: Praha 2

first: Fatima

last: Cvrckova

address: Vinicna 5

department: Experimental Plant Biology

country: Czech Republic

institute: Charles University, Faculty of Science

summary:
Formins (FH2 proteins) are a family of evolutionarily conserved proteins involved in many aspects of cytoskeletal organization and signalling, shown in some cases to participate in transcriptional regulation in metazoans. However, nothing is known about their possible involvement in the regulation of gene expression in angiosperms.
We examined the effects of mutational loss of the main housekeeping Arabidopsis thaliana formin, FH1 ((At3g25500) on global gene expression pattern in 7 days old seedlings and compared them with the effect of treatment with SMIFH2, a broad-spectrum inhibitor of formin function.

overall_design: Four sets of samples (seedling pools) have been analyzed, each with two biologivcal replicates: wild type (wt) seedlings grown for 7 days on soliud media, fh1-1 mutant seedlings grown for 7 days on solid media, wt seedlings grown for 6 days on solid media and 1 day in liquid media, and wt seedlings grown for 6 days on solid media and 1 day in liquid media in the presence of 20 uM SMIFH2.

last: Cvrčková

first: Ampao

last: Rosero

first: Michal

last: Hála

first: Viktor

last: Žárský


title: Analysis of transcriptome of Reaumuria songarica and differentially expressed genes in UV-B stressed plants

city: Lanzhou

first: Ruiqing

last: Zhu

state: Gansu

address: DingxiSouth Road 197

department: Instituye of biology

institute: Gansu Academy of Sciences

summary: Reaumuria soongorica (Pall.) Maxim., a typical species of desert plant, presents excellent tolerability to adverse environment. Until yet, little is known about the molecular mechanisms of stress tolerance in R. soongorica. Herein, we used the RNA-seq to study the transcriptome of R. soongorica leaves

overall_design: The experiment was arranged with two groups (untreated,and UV-B radiation treated)


title: Molecular heterogeneity of multinodular hepatocellular carcinoma [genomic DNA copy number]

first: Yujin

last: Hoshida

summary:
Genome-wide DNA copy number profiles of multiple hepatocellular carcinoma tumors and non-tumor liver tissues from the same patients.
Introduction: Hepatocellular Carcinoma (HCC) is the second cause of cancer-related death worldwide. Understanding tumor heterogeneity is relevant for the pathogenesis and treatment of this neoplasm. Particularly, whether multinodular tumors result from intrahepatic metastasis (IM or clonal tumors) or de novo cancers (synchronic tumors) have direct implications in treatment decisionmaking for resection and transplantation. We aimed to assess the genomic heterogeneity of multifocal HCC using single-nucleotide polymorphism (SNP) and gene expression analyses.  Methods: Among 544 HCC patients consecutively transplanted at Mount Sinai Hospital between 1990- 2007, we selected 18 patients with a total of 42 multinodular tumors (2-3 non-satellite foci HCCs) for this molecular study. Formalin-fixed blocks were collected for each tumor along with corresponding clinico-pathological data. SNP array and gene expression profiling was generated. Clonality was defined by measuring the similarity of genome-wide copy number variation (CNV) profiles between two nodules. Unsupervised hierarchical clustering based on gene expression data was performed to measure genetic proximity between each tumor. Prediction of previously published signatures was performed using Nearest Template Prediction (NTP). Association of clonality with clinic-pathological parameters was assessed.  Results: A total of 42 tumors have been analyzed (10 patients- 2 tumors; 8- 3 tumors). Most patients were male (17/18, 95%) with median age of 53-yr-old (range 39–67), HCV (10/18, 56%) or HBV infection (6/18, 33%). Median tumor size was 3 cm (range 1.5-6.5), satellites were present in 3 (17%) and vascular invasion in 11 patients (61%), respectively. CNV profiles predicted clonal tumors in 38% (6/16) and non-clonality in 62% of cases (10/16). CNV profiles of the remaining 2 cases were not informative. Clonal tumors were significantly associated with HCV infected patients (5/6 vs 3/10, p=0.007), whereas all HBV-induced HCC were synchronic tumors (0/6 vs 6/10, p=0.03). Furthermore, clonal tumors were significantly associated with presence of satellites and shorter time-torecurrence. Assessment of genetic proximity based on gene expression revealed that each clonal tumor showed proximity to its paired tumor and clustered around the same node (6/6,100%) as opposed to non-clonal (2/9,22%). When exploring molecular subclasses within clonal tumors (intrahepatic metastases), while half of them retained the molecular fingerprint, the other half switch to more aggressive subclasses. Conversely, all non-clonal tumors within the same patient belonged to distinct molecular subclasses.  Conclusion: Multinodular HCCs undergoing transplantation are molecularly heterogeneous. Using CNV profiling we identified clonal multinodular tumors (true intrahepatic metastasis) in 40% of cases and de novo tumors in 60%. Clonal tumors were significantly associated with HCV infection, satellites and recurrence. Genetic proximity was observed in clonal tumors, but molecular subclasses prediction revealed that intrahepatic metastases share more aggressive subclasses in half of cases.

overall_design: Genome-wide DNA copy number profiling of macrodissected FFPE HCC tumor and adjacent non-tumor liver tissues.

first: Daniela

last: Sia

first: Andrew

last: Harrington

first: Josep

last: Llovet


title: Modulation of the gastrointestinal microbiota normalizes the systemic inflammation and islet immunocyte recruitment capacity associated with autoimmune diabetes (in Biobreeding rats)

first: Martin

last: Hessner


title: Therapeutic effects of telomerase in mice with pulmonary fibrosis induced by damage to the lungs and short telomeres

status: Public on Jan 22 2018

city: Madrid

first: Gonzalo

last: Gomez-Lopez

state: Madrid

address: Calle Melchor Fdez Almagro 3

department: Structural Biology

country: Spain

institute: CNIO

summary: In our previous study, mice with pulmonary fibrosis induced by a bleomycin insult in the context of short telomeres develop pulmonary fibrosis. By using AAV9 vectors carrying the telomerase Tert gene to treat those mice, we explore the possibility of telomerase gene therapy as a possible treatment for IPF patients carrying short telomeres. To further understand gene expression changes undergoing in ATII cells upon telomerase activation, we isolated ATII cells from pulmonary fibrosis Tert-treated and empty vector-treated lungs at 1 week after AAV9 inoculation by FACS.

overall_design: Mice with pulmonary fibrosis were treated with either AAV9-Tert or empty vector and were sacrificed 1 week post-virus inoculation. ATII cells were sorted by FACS from mouse lungs of both groups AAV9-Tert and AAV9-empty vector.

first: Juan

last: Povedano

first: Paula

last: Martinez

first: Maria

last: Blasco


title: Transcriptomic profile in the liver of rats treated with the chemopreventive butyrate-containing structured lipids.

city: Jefferson

first: Aline

last: de Conti

state: Arkansas

address: 3900 NCTR Road

department: Biochmical Toxicology

institute: FDA-NCTR

summary: It is widely believed that the prevention of cancer is the most promising strategy for reducing both cancer incidence and cancer-related mortality. Dietary bioactive components have been found to modulate many dysregulated molecular pathways associated with the development of cancer. Epidemiological and pre-clinical data suggest that sodium butyrate and its derivatives possess chemopreventive properties. Specifically, the butyrate-containing structured lipid (STL) presented strong chemopreventive proprieties in experimental hepatocarcinogenesis. To determine the mechanistic basis, the hepatic transcriptomic profiles in rats submitted to a classic “resistant hepatocyte” model of hepatocarcinogenesis and treated with butyrate-containing STL were evaluated. A total of 1583 genes were found to be differentially expressed in the livers of rats treated with butyrate-containing STL. Pathways analysis of the differentially expressed genes demonstrated a strong enrichment in genes involved in epithelial mesenchymal transition, vasculogenesis, and cell proliferation. In conclusion, tumor-suppressing activity of butyrate containing STLs is associated with its ability to regulated major hepatocarcinogenesis-related pathways at early stages of rat liver carcinogenesis.

overall_design: Transcriptomic profile in the liver of rats treated with butyrate-containing structured lipid (n=4). Age-matched control samples were also analyzed (n=4).

first: Volodymyr

last: Tryndyak

first: Renato

last: Heidor

first: Fernando

last: Moreno

first: Igor

last: Pogribny


title: Change expression of genes in iron chelation and deficient conditions

city: Setagayaku

first: horofumi

last: INOUE

address: 1-1-1 Sakuragaoka

institute: Tokyo University of Agriculture

summary: Firstly, cell senescence and anti-oxidant genes were down-regulated by iron deficient mice and iron-specific chelator deferoxamine (DFO) using a DNA microarray. Our data suggested that down-regulation of anti-oxidant genes and cell senescence gene induced oxidative stress in iron-deficient and -specific chelated condition.

overall_design: FAO cells (rat liver cell lines) were untreated or treated with iron chelator, DFO for 24 h (n=3, respectively). Mice in the CTL (n=6) and ID groups (n=6) were fed AIN-93G diet with or without iron for 4 weeks. Rat liver cells and FAO cells were extracted total RNA and hybridization on Agilent microarrays.

first: Hirofumi

last: Inoue

first: Mariko

last: Uehara


title: Exosomal miR - 21  causes neurotoxicity via TLR7 signaling in SIV neurological disease.

city: Omaha,

first: Sowmya

middle: V

last: Yelamanchili

state: NE

address: 985800 Nebraska Medical Center - DRC 1 3008

department: Pharmacology and Experimental Neuroscience

institute: University of Nebraska Medical center

type: Non-coding RNA profiling by high throughput sequencing

summary: Exosomes from the brains of rhesus macaques were isolated and characterized, both with and without simian immunodeficiency virus (SIV) induced central nervous system (CNS) disease. Small RNA sequencing revealed that exosomes from the brains of animals with CNS disease contained significantly increased miR-21, a microRNA we have previously shown to be significantly increased in both SIV and HIV induced CNS disease. In addition to neurons in the brain, macrophage/microglial cells/nodules also express miR-21 during SIV induced CNS disease. In vitro culture of macrophages revealed that miR-21 is released into exosomes, and exosomes from macrophage cultures produced from WT, but not miR-21-/- KO, animals are neurotoxic. We find this neurotoxicity is dependent upon exosome carriage of miR-21, and mutation of the sequence within miR-21 predicted to bind TLR7 eliminates this neurotoxicity. Indeed exosomal miR-21 activates TLR7 in a reporter cell line, and the neurotoxicity of exosomal miR-21 is dependent upon TLR7, as neurons isolated from TLR7-/- KO mice are protected from neurotoxicity. Finally, we show that exosomes isolated from the brains of monkeys with SIV induced CNS disease both activate TLR7 and are neurotoxic when compared to exosomes from control animals.

overall_design: Exosomes were isolated from n=4 SIV infected without encepholitis, n=4 SIV infected with encepholitis, and n=3 control Macaca mulatta.

first: Howard

last: Fox


title: Modulation of the gastrointestinal microbiota normalizes the systemic inflammation and islet immunocyte recruitment capacity associated with autoimmune diabetes (in Biobreeding rats) [RatIslet_Longitudinal]

city: Milwaukee

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

summary:
The incidence of Type 1 diabetes (T1D), a T-cell mediated autoimmunity that targets the insulin secreting β-cells, has significantly increased, suggesting greater environmental pressure.  In studies of T1D families and the BioBreeding rat model, we have identified a peripheral innate inflammatory state that is associated with diabetes susceptibility, consistent with pattern recognition receptor (PRR) ligation, but independent of disease progression.  Here, compared to control strains, islets of spontaneously diabetic BB DRlyp/lyp and nondiatetic BB DR+/+ weanlings provided a standard cereal diet were found to temporally express a proinflammatory transcriptional program consistent with microbial antigen exposure that included numerous cytokines/chemokines.  Dependence of this proinflammatory phenotype on the diet and gastrointestinal microbiota was investigated by transitioning DR+/+ weanlings to a hydrolyzed casein diet (HCD) or treating them with antibiotics to respectively alter or reduce PRR ligand exposure.
Sequencing of the bacterial 16S rRNA gene revealed that these treatments significantly altered the ileal and cecal microbiota, resulting in increases in the Firmicutes:Bacteriodetes ratio, and abundances of lactobacilli and butyrate producing genera.  Both treatments partially normalized the peripheral inflammatory state, reducing plasma cytokine, chemokine and TLR-4 activity levels.  The proinflammatory islet transcriptome was more extensively normalized by HCD and immune-fluorescent staining revealed reductions in β-cell chemokine expression.  HCD and antibiotic treatment did not normalize BB rat PBMC hyper-responsiveness to ex vivo mitogen stimulation.  Combined, these studies link islet-level T1D susceptibility in BB rats to a genetically controlled innate inflammatory state that is influenced by environmental determinants encompassing the diet and the intestinal microbiota.

overall_design: In order to investigate T1D susceptibility at the target tissue level, we longitudinally examined the islet transcriptomes of using RNA pools of DRlyp/lyp, DR+/+, Flyp/lyp, and F+/+ rats provided normal cereal chow (n=6-8 rats per pool, technical triplicates were conducted at experimental condition).  The study design encompassed day 20 (weaning), day 30 (prior to histological detection of Ccl11 expression by BB rat β-cells), day 40 (prior to insulitis in DRlyp/lyp rats), and day 50 (after insulitis but prior to diabetes onset in DRlyp/lyp rats). Unsupervised PCA found the islet transcriptomes of young and old rats were highly distinct, and the longitudinal data set for each stain was analyzed with STEM (Short Time Series Expression Miner).

first: Angela

last: Henschel

first: Susanne

last: Cabrera

first: Mary

last: Kaldunski

first: Shuang

last: Jia

first: Rhonda

last: Geoffrey

first: Mark

last: Roethle

first: Vy

last: Lam

first: Xujing

last: Wang

first: Nita

middle: H

last: Salzman


title: Epigenetic regulation of macrophage cholesterol efflux and atherogenesis by a long noncoding RNA

city: Los Angeles

first: Tamer

last: Sallam

state: CA

address: 675 Charles E Young

institute: UCLA

summary:
In this work we show that the LXR target lncRNA MeXis plays an important role in cellular responses to cholesterol overload
In this experiment we use array technology to decipher the contribution of loss of MeXis from mouse primary peritoneal macrophages.

overall_design: Mouse peritoneal macrophages from WT or MeXis null. Each group pooled from 3 separate samples.

first: Marius

last: Jones

first: Brandon

last: Thomas

first: Xiaohui

last: Wu

first: Thomas

last: Gilliland

first: Kevin

last: Qian

first: Ascia

last: Eskin

first: David

last: Casero

first: Zhengyi

last: Zhang

first: Jaspreet

last: Sandhu

last: Salisbury

first: Prashant

last: Rajbhandari

first: Mete

last: Civelek

first: Cynthia

last: Hong

first: Ayaka

last: Ito

first: Xin

last: Liu

first: Bence

last: Daniel

first: Aldons

last: Lusis

first: Julian

last: Whitelegge

first: Laszlo

last: Nagy

first: Antonio

last: Castrillo

first: Stephen

last: Smale

first: Peter

last: Tontonoz


title: The effect of PCN on gene expression in mouse primary hepatocytes

city: Kuopio

first: Jaana

last: Rysae

address: Yliopistonranta 1C

department: School of Pharmacy

country: Finland

institute: University of Eastern Finland

summary: The effect of prototypical pregnane receptor X (PXR) agonist (pregnenolone 16α-carbonitrile) PCN on hepatic gene expression was studied in mice primary hepatocytes.

overall_design: The effect of pregnenolone 16α-carbonitrile (PCN) was studied in male 9-week-old C57BL/6 mouse primary hepatocytes. Cells were treated with 10 μmol/l PCN for 12 h, DMSO was used as a control. Three parallel RNA samples were pooled in both groups. DNA microarrays we used for gene expression profiling.

first: Jukka

last: Hakkola

first: Marcin

last: Buler


title: Proteotoxic stress induced by mRNA mistranslation leads to proteome aggregation and mitochondrial dysfunction in vertebrates.

city: Aveiro

first: Marisa

last: Reverendo

state: Aveiro

address: campus universitário de santiago

department: Biology

country: Portugal

institute: University of Aveiro

summary: Protein misfolding and aggregation deregulate the proteostasis network and are hallmarks of cell degeneration processes associated with aging and human diseases. But how proteome aggregation causes cell degeneration remains controversial due to the lack of suitable methods for controlling proteome aggregation at the cellular and organismal levels. To overcome this limitation, we have generated zebrafish embryos that exhibit protein aggregation due to misincorporation of Serine (Ser) at non-cognate protein sites on a proteome wide scale. These mistranslating embryos display up regulation of the unfolded protein response (UPR) and the ubiquitin proteasome pathway (UPP), increased protein ubiquitination and down-regulation of protein biosynthesis. Proteome damage also induces major disruption of the mitochondrial network, accompanied by mitochondrial and nuclear DNA damage and accumulation of reactive oxygen species (ROS). Taken together, our data highlight important roles of gene translational accuracy in the maintenance of ER homeostasis, DNA damage, mitochondrial function and oxidative stress. We postulate that protein biosynthesis errors (PBE) contribute to proteome aggregation and are a main cause of mitochondrial disruption.

overall_design: Mistranslation induced gene expression was measured at 24hfp zebrafish embryos expressing mutant serine tRNAs. Three different experiments were perfomed for each mutant tRNA.

first: Ana

last: Soares

first: Patrícia

last: Pereira

first: Laura

last: Carreto

first: Manuel

last: Santos


title: Expression profiling of PpNAC1 RNAi Pinus pinaster plantlets

city: Malaga

first: Rafael

last: Cañas

address: Facultad de Ciencias, Campus de Teatinos

department: Biología Molecular y Bioquímica

institute: Universidad de Málaga

summary: The transcriptome of PpNAC1 RNAi Pinus pinaster plantlets (60 days) were analyzed.

overall_design: The samples are from two different PpNAC1 RNAi lines, PN5 and PN9 and were compared to wild type plantlets. Their trasncriptomes were analyzed using one color microarrays.

first: M

middle: B

last: Pascual

first: Blanca

last: Craven-Bartle

first: Concepción

last: Ávila

first: Francisco

last: Cánovas


title: microRNA as a new immune-regulatory agent in breast milk

status: Public on Jan 21 2018

first: Nobuyoshi

last: Kosaka

summary: Finding the miRNA expression profile in human breast milk

overall_design: Collect the total RNA from supernatant of breast milk and hybridized to the Agilent Human miRNA Microarray 2.0 G4470B

first: Takahiro

last: Ochiya

first: Kazunori

last: Sekine

first: Hirohisa

last: Izumi


title: Secreted α-Klotho maintains tissue homeostasis by repressing NOS2-ZIP8-MMP13 catabolic axis

city: MONTPELLIER

first: Paul

last: CHUCHANA

address: 80 rue Augustin Fliche

country: France

institute: CNRS

summary: Progressive loss of tissue homeostasis hallmarks numerous age-related pathologies. By using parabiosic approaches in animal models, recent evidences demonstrate that age-regulated geronic factors such as GDF11 or CCL11 could widely control positively or negatively tissue homeostasis. Here we evaluated the impact of the first identified anti-geronic hormone a-Klotho on tissue homeostasis taken articular cartilage and osteoarthritis (OA) as studying models. We show that a-Klotho is secreted during an in vitro induced chondrogenesis of osteo-chondral stem cells. Expression of a-Klotho is reduced in both cartilage of OA patients compared to healthy donors and in cartilage of OA murine models. Gain and loss of function experiments followed by a genome-wide gene array analysis identified Nos2-Zip8-MMP13 catabolic axis as repressed in OA chondrocytes upon a-Klotho treatment.  Accordingly, intra-articular delivery of secreted a-klotho delays cartilage loss of functions in experimental OA mouse models thus revealing a novel chondroprotective function for this anti-geronic hormone.

overall_design: Gain and loss of function experiments on human primary OA chondrocytes to identify opposite gene expression profiles obtained from chondrocytes treated with 40ng/ml of recombinant a-Klotho normalized to untreated versus SiRNA against Klotho transfected chondrocytes normalized to siRNA control.

first: Espinoza

last: Francisco

last: Chuchana

first: Jean-Marc

last: Brondello


title: Microarray-sequencing of WT and Jam3-null leukemia-initiating cells (LICs)

status: Public on Jan 18 2018

city: Shanghai

first: Xianghua

last: Yi

address: NO.389, Xincun Rd, Putuo distrct

department: pathology

institute: Tongji hospital

summary: To tease apart the downstream signaling triggered by the Jam3-mediated signaling, Microarray-sequencing analyses were conducted with WT and Jam3-null LICs.The gene ontology (GO) analysis showed that JAM3 might mainly be involved in signal transduction and phosphorylation pathways. KEGG further indicated that JAM3 was required for the Wnt signaling and hematopoietic cell lineage.

overall_design: WT and Jam3-null YFP+Mac-1+c-Kit+ LICs were purified by flow cytometry for the extraction of total RNA and subjected to Microarray-sequencing.

first: Jun-Ke

last: Zheng

first: Yaping

last: Zhang


title: Pharmacokinetic, antihypertension and deep sequencing MiRNomes analysis of aorta from SHR fed with EGCG

status: Public on Jan 20 2018

first: Bingjun

last: Qian

address: 800 Dongchuan Road

institute: Shanghai Jiao Tong University

summary: Mechanism (s) of the epigallocatechin-3-gallate (EGCG) as major effective components in green tea regarding the reduction of hypertensive risk might associate with microRNAs (miRNAs). The plasma distribution of EGCG and epigallocatechin (EGC) in Sprague-Dawley rats were analyzed pharmacokinetically and found that they did not distribute well in plasma but widely in tissues, and their plasma deposition best fitted a mono-compartmental model with Cmax (6.65 vs 4.45 μg/mL) and Tmax (15 vs 10 min). Blood pressure monitoring of spontaneously hypertensive rats (SHR) intragastrically administrated with 300 mg/kg BW showed that systolic blood pressure (SBP) decreased to the lowest point by 34.04 mmHg and recovered by 23.39 mmHg after 15 and 30 min of administration, respectively, and it decreased again at 60 min and recovered at time 2 h. Total 150 upregulated and 18 downregulated miRNAs were identified via the deep sequencing and were 1.0 or 0.5 fold to the control group (P<0.01) after EGCG administration. And, hypertension-associated miRNA-126-3p and miRNA-150 were further validated by qRT-PCR. It might help explore novel pathways involving antihypertensive effect of EGCG.

overall_design: Sprague-Dawley (SD) male rats (8 weeks of age) from Shanghai Slac Laboratory Animal Co., Ltd. (Shanghai, China) were housed in cages, and they were maintained under specific pathogen-free conditions with a 12 h light/dark cycle at Center of Experimental Animal, Jiangsu Vocational College of Medicine.Three SHRs were randomly chosen to form three groups, defined as HD group (fed with EGCG at high dose, 300 mg/kg BW), LD group (fed with EGCG at low dose, 30 mg/kg BW) and Control group (fed with 0.7% saline solution). TRIzol reagent (Invitrogen, CA, USA) was used to extract the total RNAs from each sample, and the quality and concentration of the total RNAs in each samples were assessed by Nanodrop (ND-1000) with 260/280 ratio. Then the extracted total RNAs from three samples within each group were mixed in equal amount, and the small RNA libraries were constructed as previously described. Each small RNA library was sequenced in individual lane for 36 cycles using Illumina Genome Analyser II (Illumina, San Diego, CA, USA).

first: Pu

last: Jing


title: RNAseq comparison of HSV-1 KOS vs n199 infected cells

city: Pittsburgh

first: Neal

last: DeLuca

state: PA

address: 450 Technology Dr

institute: Univ. of Pittsburgh

summary: The abundance of HSV mRNAs was determines over 16h of infection in wt (KOS) and n199 (ICP22 mutant) infected cells.  ICP22 is an immediate early gene of HSV that affects gene expression

sample_organism:
Homo sapiens
Human alphaherpesvirus 1

platform_organism:
Homo sapiens
Human alphaherpesvirus 1

overall_design: 2 X 10E6 MRC5 cells were infected at an MOI of 10 PFU/cell.  mRNA was isolated at different times post infection using Ambion RNaqueous-4PCR kit  and quantified using an Agilent Eukaryotic RNA Nano kit and a 2100 bioanalyzer.  Individual samples each with unit barcodes were quantified using an Agilent DNA 7500 chip an a 2100 bioanalyzer.  Pooled multiplexed samples were sequenced at the Tufts University Genomics facility.  The demulitplexed sequence read files were mapped to the HSV strain KOS genome and quantified using CLC Genomics Workbench.

first: Hannah

last: Fox


title: NLRC5 deficiency protects against acute kidney injury in mice by mediating CEACAM1 signaling

status: Public on Jan 19 2018

city: JiNan

first: Li

middle: quan

last: Xin

state: Shandong

address: 44#, Wenhua Xi Road

department: Department of Pharmacology

institute: Shandong University

summary: Although there is significant progress in understanding the structure and function of NLRC5, a member of the NOD like receptor (NLR) family, in the context of MHC class I gene expression, the functions of NLRC5 in innate and adaptive immune responses beyond the regulation of MHC class I genes remain controversial and unresolved. In particular, the role of NLRC5 in the kidney keeps unknown. In this study, we found that NLRC5 was significantly upregulated in the kidney from mice with renal ischemia/reperfusion injury (IRI). NLRC5 deficient (NLRC5-/-) mice significantly ameliorated renal injury as evidenced by decreased serum creatinine levels, improved morphological injuries, and reduced inflammatory responses versus wild type mice. Similar protective effects were also observed in cisplatin-induced acute kidney injury (AKI). Mechanistically, NLRC5 contributed to renal injury by promoting tubular epithelial cell apoptosis and reducing inflammatory responses which is associated with, at least in part, the negative regulation of carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1). To determine the relative contribution of NLRC5 expression by parenchymal cells or leukocytes to renal damage during IRI, we generated bone marrow (BM) chimeric mice. NLRC5-/- mice engrafted with WT hematopoietic cells had significantly lower serum creatinine and less tubular damage than WT mice reconstituted with NLRC5-/- BM, suggesting that NLRC5 signaling in renal parenchymal cells plays the dominant role in mediating renal damage. Collectively, modulation of NLRC5-mediated pathway may have important therapeutic implications for patients with AKI.

overall_design: NLRC5-/- mice and age-matched C57BL/6 wild type (WT) mice were used in this study, We established a bilateral renal ischemia model for 30min and mice were sacrificed after reperfusion at 48h.

first: Quanxin

last: Li

first: Fan


title: Expression data from fetal membranes

city: Ann Arbor

first: Richard

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

summary:
Genome wide expression profiling was used to identify signifnificantly changed genes in fetal membranes after GBS treatment
Genome-wide expression profiles in GBS-inoculated human extraplacental membranes in vitro were used to identify transcriptomic pathways altered by GBS . Using bioinformatics analysis of these expression profiles we aimed to test our hypothesis that GBS activates pathways related to inflammation and premature birth in human extraplacental membranes.

overall_design: RNA was analyzed using membranes obtained from 4 separate women for each condition (GBS treated and controls) and for each timepoint (4, 8 and 24 hours) for a total of 24 total samples.

first: R

first: H

last: Park

first: S

last: Harris

first: M

last: Sartor

first: E

last: Boldenow

last: Loch-Caruso


title: Comparative transcriptomics reveals a conserved Bacterial Adaptive Phage Response (BAPR) to viral predation

city: Leuven

first: Bob

last: Blasdel

state: Vlaams-Brabant

address: Kasteelpark Arenberg 21, bus 2462

country: Belgium

institute: KU Leuven

summary: Intrinsic and acquired defenses against bacteriophages, including Restriction/Modification, CRISPR/Cas, and Toxin/Anti-toxin systems have been intensely studied, with profound scientific impacts.  However, adaptive defenses against phage infection analogous to adaptive resistance to antimicrobials have yet to be described. To identify such mechanisms, we applied an RNAseq-based, comparative transcriptomics approach in different \textit{Pseudomonas aeruginosa} strains after independent infection by a set of divergent virulent bacteriophages. A common host-mediated adaptive stress response to phages was identified that includes the Pseudomonas Quinolone Signal, through which infected cells inform their neighbors of infection, and what may be a resistance mechanism that functions by reducing infection vigor. With host transcriptional machinery left intact, we also observe phage-mediated differential expression caused by phage-specific stresses and molecular mechanisms. These responses suggest the presence of a conserved Bacterial Adaptive Phage Response mechanism as a novel type of host defense mechanism, and which may explain transient forms of phage persistence.

overall_design: Four Phage negative control samples are compared to seven samples representing phage LUZ19, eight samples representing phage YuA, three samples representing phage PEV2, and seven samples representing phage 14-1.

middle: G

first: Pieter-Jan

last: Ceyssens

first: Rob

last: Lavigne


title: Affymetrix OncoScan FFPE Microarray data for Malignant Pleural Mesothelioma Samples

city: Zurich

first: Kathrin

last: Oehl

address: Schmelzbergstrasse 12

country: Switzerland

institute: University Hospital Zurich

summary: For establishing a live-cell biobank of Malignant Pleural Mesothelioma (MPM) samples, cultures of two MPM patients were compared to the original tumor tissue using Affymetrix OncoScan Microarrays for genome-wide CNV and LOH detection.

overall_design: Affymetrix OncoScan FFPE Microarrays were performed according the manufacturer's protocol on DNA extracted from FFPE tissue or primary cell cultures

first: Peter

middle: J

last: Wild


title: Developmental transcriptome of Castanospermum australe seed tissues

status: Public on Jan 17 2018

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

institute: INRA

summary: Seeds of the legume Castanospermum australe are shed at relatively high moisture contents, and to do not acquire desiccation tolerance during their seed development, they are referred to as 'recalcitrant'. To characterize the regulatory pathways and molecular mechnanisms are occur during seed development and to allow for a comparative analysis with seed development of desiccation-tolerant species, cotyledon and embryonic axes were harvested at different stages of development, arbitrarily defined in terms of seed weight (grams) and color. Transcriptomes of 6 stages were analysed using Nimblegen slides: 2.5g - 4.5g - 7.5g - yellow-green (YG) - green (G) - brown (B) for cotyledons (C) and YG, G and B for emrbyonic axes (A)

overall_design: Six-condition experiment, 2.5C/4.5C - 7.5C/YGC - GC/BC - YGC/BC - GA/BA - YGA/BA. Two replicates from each developmental stage were used for dye switch, each time the control was considered as the earlier developmental stage vs the treatment, corresponding to the later developmental stage. A total of four replicates were analysed.

first: Udisha

last: Chathuri

first: David

last: Lalanne

first: Julia

last: Buitink


title: Expression profiling of Cellvibrio japonicus using either glucose or xylan

status: Public on Jan 15 2018

city: Baltimore

first: Jeffrey

middle: G.

last: Gardner

state: MD

address: 1000 Hilltop Circle

department: Department of Biological Sciences

institute: University of Maryland - Baltimore County

summary: Lignocellulose degradation by microbes plays a central role in global carbon cycling, human gut metabolism, and renewable energy technologies While considerable effort has been put into understanding the biochemical aspects of lignocellulose degradation, much less work has been done to understand how these enzymes work in an in vivo context Here, we report a systems level study of xylan degradation in the saprophytic bacterium Cellvibrio japonicus Transcriptome analysis indicated seven genes that encode carbohydrate active enzymes were up-regulated during growth with xylan containing media In-frame deletion analysis of these genes found that only gly43F is critical for utilization of xylo-oligosaccharides, xylan, and arabinoxylan Heterologous expression of gly43F was sufficient for the utilization of xylo-oligosaccharides in Escherichia coli Additional analysis found that the xyn11A, xyn11B, abf43L, abf43K, and abf51A gene products were critical for utilization of arabinoxylan Furthermore, a predicted transporter (CJA_1315) was required for effective utilization of xylan substrates, and we propose this unannotated gene be called xntA (xylan transporter A) Our major findings are 1) C japonicus employs both secreted and surface associated enzymes for xylan degradation, which differs from the strategy used for cellulose degradation, and 2) a single cytoplasmic β-xylosidase is essential for the utilization of xylo-oligosaccharides

overall_design:
One carbon condition (xylan); Two sample points (exponential phase, stationary phase); Data collected in biological triplicate; Total of 6 samples

Please note that glucose-grown sample data is published and thus, available in the previous GEO records [GSE90955; GSM2418311-GSM2418316].


title: Microarray analysis to investigate the global expression of miRNAs in pediatric T1D patients in comparison to non-diabetic controls.

city: Poznan

first: Magdalena

last: Żurawek

address: Strzeszynska 32

country: Poland

institute: Institute of Human Genetics PAS

summary: MicroRNAs (miRNAs) are small non-coding RNAs that target multiple mRNAs and regulate gene expression. The implication of miRNAs in T1D pathogenesis, as potential modulators of immune response genes, remains poorly defined. The aim of this study was to investigate the expression profile of miRNAs in new onset T1D to identify autoimmune associated miRNAs.

overall_design: Total RNA from peripheral blood mononuclear cells of newly diagnosed T1D pediatric patients and age-matched controls was screened for disease-associated miRNAs by a microarray analysis.

last: Zurawek

first: Agnieszka

last: Dzikiewicz-Krawczyk

first: Katarzyna

last: Izykowska

first: Iwona

last: Ziolkowska-Suchanek

first: Bogda

last: Skowronska

first: Maria

last: Czainska

first: Marta

last: Podralska

first: Piotr

last: Fichna

first: Grzegorz

last: Przybylski

first: Jerzy

last: Nowak


title: High miR-34a expression improves response to doxorubicin in diffuse large B-cell lymphoma.

city: Aalborg

first: Julie

middle: Støve

last: Bødker

address: Sdr. Skovvej 15

department: Department of Heamatology

country: Denmark

institute: Aalborg University Hospital

summary: The standard treatment for patients with diffuse large B-cell lymphoma (DLBCL) is the immunochemotherapy-based R-CHOP regimen (rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisolone). Resistance to treatment, intrinsic or acquired, is observed in approximately 40% of patients with DLBCL, who thus require novel interventions to survive. To identify biomarkers for cytotoxic response assessment, microRNAs (miRNAs) associated with doxorubicin sensitivity were determined by combining global miRNA expression profiling with systematic dose-response screens in 15 human DLBCL cell lines. One candidate, miR-34a, was tested in functional in vitro studies and in vivo in a retrospective clinical cohort. High expression of miR-34a was observed in cell lines sensitive to doxorubicin, and upregulation of miR-34a is documented here to increase doxorubicin sensitivity in in vitro lentiviral transduction assays. High expression of miR-34a had a prognostic impact using overall survival as outcome. With risk stratification of DLBCL samples based on resistance gene signatures (REGS), doxorubicin-responsive samples had statistically significant upregulated miR-34a expression. Classification of the DLBCL samples into subset-specific B cell-associated gene signatures (BAGS) revealed differentiation-specific expression of miR-34a. Our data further support FOXP1 as a target of miR-34a, suggesting that downregulation of FOXP1 may sensitize DLBCL cells to doxorubicin. We conclude that miRNAs, in particular miR-34a, may have clinical utility in DLBCL patients as both predictive and prognostic biomarkers.

overall_design: 15 DLBCL cell lines for which microRNA expression was determined with microRNA arrays. 64 DLBCL primary clinical samples; gene expression was determined for 34 samples with Affymetrix GeneChip HG-U133 Plus 2.0 arrays and for 37 patients (7 overlapping) with Affymetrix HuEx 1.0 ST Array.

first: Sara

last: Marques

first: Benyamin

last: Ranjbar

last: Laursen

first: Steffen

last: Falgreen

first: Anders

middle: E

last: Bilgrau

middle: S

first: Laura

middle: K

last: Jørgensen

last: Primo

first: Alexander

last: Schmitz

first: Marianne

last: Ettrup

first: Hans

last: Johnsen

first: Martin

last: Bøgsted

first: Jacob

last: Mikkelsen

first: Karen

last: Dybkær


title: Transcriptional profiling of two drosophila species: Drosophila melanogaster versus Drophila sechellia

city: Sophia Antipolis cedex

first: frederique

last: hilliou

address: 400 route des chappes, BP167

department: SPE

summary: Transcriptional profiling of 3 day old virgin male and female adults  comparing control male Drosophila melanogaster (MDM) versus male D sechellia (MDS) and comparing control female Drosophila melanogaster (FDM) versus female D sechellia (FDS). Goal was to determine why D sechellia is tolerant to octanoïc acid, the major toxic compound  of Morinda citrifolia fruit

sample_organism:
Drosophila melanogaster
Drosophila sechellia

overall_design: Four-condition experiment, MDM vs. MDS adults and FDM vs. FDS adults. Biological replicates: 2 control replicates  for each condition: MDM, MDS, FDM and FDS.

first: Frédérique

last: Hilliou

first: Trang

last: Tran

first: Pascaline

last: Audant

first: Gaëlle

last: Le Goff

first: René

last: Feyereisen


title: RNA-seq of Acinetobacter oleivorans DR1: on hydrogen peroxide

city: seoul

first: BORA

last: SHIN

state: 성북구 안암로

country: South Korea

institute: Korea university

summary: Transcriptional profiling of A. oleivorans DR1 treated low and high level of hydrogen peroxide for 15min .

overall_design: To identify effect of hydrogen peroxide in A. oleivornas DR1, the cells were grown to exponential phase (OD600 ~0.4) and treated 0.1mM/1mM hydrogen peroxide for 15 min.

first: Bora

last: Shin

first: Woojun

last: Park


title: RNA Sequencing  analysis of  transcriptomics to investigate the  bile stress response in L. paracasei L9

city: Beijing

first: Xiayin

last: Ma

address: 17 Qing Hua East Road Hai Dian District

institute: China Agricultural University

summary:
Purpose: To understand the bile salts resistance mechanisms in L. paracasei L9
Methods: Samples from L9 cultured with or without bile salts were sequenced on an  Illumina Hiseq platform. Three independent biological replicates were produced including 6 samples in total.
Results:  Raw data were firstly processed through in-house perl scripts to generate clean data, and then clean date were mapped to the reference genome, getting about 8-10 million total mapped reads per sample.

overall_design: L. paracasei L9 was cultured in MRS medium with 0.13% oxgall,f


status: Public on Jan 12 2018

city: Columbus

first: Sashwati

last: Roy

state: OH

department: Surgery

country: USA

institute: Ohio State University

summary:
Gene Expression in day 3 and day 7 wound macrophages of C57BL/6 mice
Affymetrix GeneChip® Mouse Transcriptome Array 1.0 was used to study Gene Expression in day 3 and day 7 wound macrophages of C57BL/6 mice

overall_design: Wound macrophages of C57BL/6 mice were isolated and gene expression studies were performed

first: Roy

last: Sashwati


title: Expression profiles of Ramularia collo-cygni (strain urug 2) grown on 6 conditions revealed common and different sets of regulated genes

status: Public on Jan 13 2018

city: Freising

first: Ulrich

last: Guldener

state: Bavaria

address: Maximus-von-Imhof-Forum 3

department: Chair of genome-oriented bioinformatics

country: Germany

institute: Technische Universität München

summary: The fungal RNA from 6 different conditions, especially one that mimics the plant environment (Barley Straw Agar –BSagar) was also sequenced to help in one hand the annotation and in other hand to uncover putative gene of interest that might be involved in the pathogenicity or the fungicide resistances for example.

overall_design: Expression analysis of Ramularia collo-cygni (strain urug 2) grown on 6 conditions using RNA-seq

first: Remco

last: Stam

first: Hind

last: Sghyer

last: Münsterkötter

first: Saurabh

last: Pophaly

first: Aurélien

last: Tellier

last: Güldener

first: Ralph

last: Hückelhoven

first: Michael

last: Hess


title: Proximity of oligodendrocytes remodels astrocytes' transcriptome

status: Public on Jan 11 2018

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary: We and other groups doumented that astrocytes modulate migration, maturation and myelin sythesis of oligodendrocytes through release of neurotransmitters, cytokins and other signaling molecules. However, much less is known about on how the oligodendrocytes affects the astrocytes. We compared the transcriptome of cortical astrocytes when cultured alone and co-cultured with non-touching immortalized precursor oligodendrocytes (Oli-neu) in insert systems. Experimental data indicate that the oligodendrocyte-conditioning medium  has a substantial effect on the the gene expression in astrocytes. Moreover, oligodendendrocyte proximity remodels major astrocyte functional pathways.

overall_design: we have used the multiple yellow design in which distinctly labeled samples of biological replicates are cohybridized with the microarray, the similarly labeled distinct conditions were compared and the results averaged for both channels. Thus each raw data file contains raw data for two samples (e.g. C1-2_US83300186_252665513680_S01_GE2_1105_Oct12_1_4.txt contains raw data for both C1 and C2 samples) and dye assignment is indicated in the label field in the corresponding sample records.

middle: A

first: Sanda


title: Beta-catenin in Desmoid Tumors: the role of T41A and S45F mutations on gene expression

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: Desmoids tumors (DTs) are rare mesenchymal infiltrative lesions that exhibit high risk of local recurrence despite surgery with negative margins. Mutations in CTNNB1 gene encoding for β-catenin are typically carried by most sporadic DTs but the evidences in support to the clinical/biological role of these mutations are contrasting. Our work is the first study specifically investigating if mutation type could influence the stability of the β-catenin structure, its affinity for α-catenin, as well as the pattern of gene expression and could in turn guide the behavior of the disease.

overall_design: We selected for this study 33 primary DTs surgically treated at our Institution. All samples had these characteristics: 1) DT diagnosis by an expert pathologist (SP); 2) known CTNNB1 mutational status assessed by direct sequencing as previously described (Colombo et al. Cancer 119; 3696–3702, 2013); 3) availability of the formalin fixed paraffin embedded (FFPE) surgical specimen; 4) availability of RNA amount and quality adequate for molecular analysis. The distribution of mutations was T41A (14 cases), S45F (10 cases), and wt (9 cases).

first: L

first: C

last: Colombo


title: Expression data from human colorectal cancer cell line LoVo

status: Public on Jan 10 2018

city: Nanjing

first: Chenbo

last: Ding

address: No. 87, Dingjiaqiao, Gulou District

country: China

institute: Medical School of Southeast University

summary:
PEAK1 overexpression vector and negative control vector were transiently transfected into LoVo cells, respectively, and named LoVo-PEAK1 and LoVo-control groups.
LoVo cells of different groups were determined to investigate the different expressions of mRNA using a global gene microarray.

overall_design: To construct the HA-PEAK1 overexpression vector, the full-length human PEAK1 gene was amplified from the template PEAK1 cDNA clone. LoVo cells were seeded at 70-80% confluence, and 12 hours later cells were transiently transfected with indicated vectors with Lipofectamine® 3000 according to the manufacturer’s instructions.

first: Guoqiu

last: Wu


title: The NEMO (NF-KB Essential Modulator) Binding Domain (NBD) peptide induces apoptosis in several melan

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

summary: The transcription factor NF-kB is an important regulator of genes involved in inflammation and cell proliferation. Several studies previously showed that NF-kB transcription factor was constitutively activated in melanoma cell lines due to the up regulated activity of inhibitor of NF-kB kinases (IKK). In the present study, we tested the activation of NF-kB pathway following TNF stimulation in 9 melanoma cell lines and the subsequent inhibition after the treatment of a small–molecule IKK inhibitor NDB peptide using Secreated Alkaline Phosphate (SEAP) reporter gene assay. The pro-apoptotic effects induced by NBD peptide treatment were determined by flow cytometry as well as by Western Blot testing of PARP’s cleavage. Our findings showed that NBD peptide was able to block IKK-NFKB pathway in all tested cell lines by inducing apoptosis as confirmed by increased levels of active caspase 3 and PARP cleavage after treatment. Moreover, our finding provides the basis for the development of a novel therapeutic approach targeting NF-kB transcription factor to treat melanoma.

overall_design: Microarray samples were obtained from 9 melanoma cell lines (A375, M14, 397 MEL, UACC 257, SK-MEL 5, UACC62, SK-MEL2, LOX IMVI and SK-MEL28). Reference T-RNA was obtained from 6 normal donor PBMCs.


title: Dysfunction of hepatic regulatory T cells in experimental sclerosing cholangitis is associated with IL-12 signaling

status: Public on Jan 07 2018

city: Hamburg

first: Thomas

last: Streichert

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

department: Institute For Clinical Chemistry / Central Laboratories

institute: University Medical Center Hamburg-Eppendorf

summary: In this study we successfully enriched regulatory T cells (Treg) in the liver using injections with IL-2/IL-2ab complex. Enriched Treg were mainly located in areas of inflammation, but they had no impact on liver inflammation or fibrosis in two different cholangitis mouse models. We found that liver derived Treg had less suppressive capacity compared to splenic derived Treg. We used microarray analysis of IL-2/IL-2ab complex enriched liver and splenic derived regulatory T cells in order to elucidate the organ specific differences. We identified upregulation of IL12 receptor beta 2 on hepatic Treg and could identify IL-12 signalling as key factor for reduced suppressive capacity of regulatory T cells.

overall_design: Regulatory T cells were expanded by repeated injection of IL-2/IL-2Ab complex in vivo. Enriched Treg were isolated from spleen and liver for RNA extraction and hybridization on Affymetrix microarrays.

first: Dorothee

last: Schwinge

first: Christoph

last: Schramm


title: From the morphologic to the transcriptomic characterization of a compromised 3D in vitro model mimicking atopic dermatitis

city: SAINT-VIANCE

first: VINCENT

last: BARRUCHE

state: If applicable (USA / Canada)

address: ZI de la Nau

department: R&D

institute: SILAB

summary: To characterize our compromised reconstructed epidermis at the transcriptomic level, we have employed whole genome microarray expression profiling as a discovery platform to compare genes modification with those known in AD skins. To this purpose,  normal human keratinocytes (NHK) were used to generate RE, treated or not with an inflammatory cocktail (Poly I:C, TNF-α, IL-4 and IL-13). Inflammation and cellular differentiation pathways were analysed and then confirmed by Q-PCR experiments.

overall_design:
Inflammation induced gene expression in reconstructed epidermis was measured 2 days after exposure to inflammatory cocktail or normal medium.  Four independent experiments were performed for each condition (inflamed or normal) using different donors for each experiment.
Contrinuted by: R&D department, SILAB, France


title: Endometrial gene expression in fertile and subfertile cows

city: Aichi-gun

first: Shuichi

last: Matsuyama

address: 94 Hatajiri, Morowa

country: Japan

institute: Nagoya University

summary: In order to clarify the cause of reproductive failure, we conducted global endometrial gene expression analysis in fertile and subfertile cows. Hierarchical cluster analysis with the expression levels of mitochondrial DNA encoded genes was divided these cows into two clusters. One cluster was composed of fertile cows, the other cluster contained subfertile cows, and the expressions of mitochondrial DNA encoded genes in subfertile cows were higher than those in fertile cows

overall_design: To clarify differences in gene expression patterns of the endometrium between fertile and subfertile cows, endometrial biopsy samples were collected from fertile cows (n=6) and subfertile cows (n=5) at day 7 of the estrus cycle. The cows, which became pregnant at ET or AI within 3 times until biopsy and resulted in pregnant at the first ET in the following cycles after biopsy, were used as fertile cows. The subfertile cows were the animals which failed to conceive in three consecutive ET or AI without detectable abnormalities in their genital tracts and with apparently normal estrus cycles before and after biopsy, respectively.

first: Sho

last: Nakamura

first: Shiori

last: Minabe

first: Miki

last: Sakatani

first: Naoki

last: Takenouchi

first: Hisataka

last: Iwata

first: Koji

last: Kimura


title: Gene expression in bovine endometrium at different period after parturition

summary: In order to clarify whether the term after calving is a factor to affect the gene expression in the endometrium of cows, we conducted global endometrial gene expression analysis at different period after parturition. In bovine endometrium between 60.1 ± 4.0 days and 388.9 ± 8.2 days after parturition, the gene expression pattern was similar and the differentially expressed (>2-fold difference, P<0.05) genes were only 4 genes.

overall_design: To clarify the gene expression in bovine endometrium at different period after parturition, 10 female cows were used. The endometrial tissues were collected twice from the same individual on both 42 - 86 (mean 60.1 ± 4.0) days and 343 - 436 (mean 388.9 ± 8.2) days after parturition. During each period, on 7 days after estrus, endometrial tissue of the uterine horn ipsilateral to the corpus luteum was obtained using uterine biopsy forceps.


title: The whole transcriptome expression profiling comparison between the Pin1 knockIn in Hose cells and  Pin1 knockdown in ovarian cancer MCAS and SK-OV-3 cells

status: Public on Jan 04 2018

city: Boston

first: Shu-Wing

last: Ng

state: MA

address: 221 Longwood Avenue

department: Department of Obstetrics, Gynecology and Reproductive Biology

institute: Brigham and Women’s Hospital; Harvard Medical School

summary: To discover the abnormal regulatory role of Pin1 in the ovarian cancer, The Pin1 full cDNA was knockIn (KI) the normal ovarian epithelium (Hose), and parallelly Pin1 was knockdown in the Ovarian cancer cells MCAS and sk-ov-3, and then compared the expression profiles of them to discovery the key features regulated by Pin1.

overall_design: There are  three groups  cells used for this expression profile comparison :  Hose Pin1 KnockIn (KI) and Hose scramble control;  Skov3 Pin1 knockdown (KD) and Scramble control; Mcas Pin1 knockdown and scramble control. The RNA was extracted from well cultured cells using TRIzol reagent, and whole transcriptome gene expression profiling were performed using an Affymetrix Human Gene 1.1 ST  whole transcriptome microarray platform.

first: Shubai

last: Liu


title: Impact of Vitamin D on murine myotubes

status: Public on Jan 08 2018

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

summary: Fully differentiated murine myotubes (C2C12) were treated during 72 hours with either the vehicle, 1 or 10 nM of 1,25 (OH)2-vitamin D3. RNA profiling by microarrays was performed

overall_design: 3 biological replicates for each condition were performed

first: Jerome

last: Salles

first: Sandra

last: Pesenti

first: Emmanuelle

last: Meugnier


title: Profiling of long non-coding RNAs associated with atrial fibrillation in patients with rheumatic heart valvular disease

status: Public on Jan 03 2018

city: Chengdu

first: Peng

state: Sichuan

address: Huimin Road 211#

department: Maize Research Institute

institute: Sichuan Agriculture University

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

summary: To investigate the expression profiles of long non-coding RNAs (lncRNAs) in atrial fibrillation (AF), atrial tissues from 5 AF patients and 5 non-AF patients that were collected for lncRNA expression microarray analyses to explore the role of lncRNA in the pathogenesis of AF.rhythm (SR) patients with rheumatic heart valvular disease,we have employed

overall_design: Five specimens of right auricular dextra were obtained from patients of rheumatic heart valve disease with permanent AF and with SR respectively. Expression profiling of lncRNA and mRNA were performed on SurePrint G3 Human Gene Expression 8x60K v2 Microarray, and the functions of lncRNAs were predicted by gene ontology analysis (GO analysis), kyoto Encyclopedia of Genes and Genomes analysis(KEGG analysis).

first: Gen

last: Zhang

first: Ying


title: Differentially expressed genes in blood of BPD and Normal preterm neonates [miRNA]

status: Public on Jan 05 2018

city: Shanghai

first: cai

last: cheng

address: No. 355, Luding Road

department: Department of neonatology

institute: Shanghai Children’s Hospital, Shanghai Jiao Tong University

summary: Bronchopulmonary dysplasia (BPD) is the major cause of chronic lung disease (CLD) and morbidity in preterm infants, which characterized by impaired pulmonary alveolar development in preterm infants. There is increasing evidence that micro RNA (miRNA) has a close association with the development of pulmonary diseasesincluding lung growth, pulmonary fibrosis, pneumonia, etc. The potential role of miRNA in the pathogenesis of BPD is unclear. This study aims to clarify the role of adrenomedullin (ADM) regulated by miRNA-547-3p during the process of BPD and illustrate the protective effect of ADM involved in preterm infants.We indentified the differential expressed miRNA and their potential target genes, microarray analysis using Agilent Human 4x44K Gene Expression Microarrays v2 and miRCURY LNA™ microRNA Array was performed. The results of miRNA chip were scanned by Axon GenePix 4000B and the signal of probes were read by GenePix Pro 6.0 software. Only the target genes which exist in both two databases and having different expression trend were remained. Thus, miRNA-574-3p and it’s target gene ADM were selected to do the further research in our study. And we verified miRNA-574-3p and ADM expression in BPD premature infants by realtime q-PCR. After the microarray expression analysis, there were 516 probes differential expressed between BPD samples and normal samples. Among them, 510 were up-regulated and 213 were down-regulated. Meanwhile, to the miRNA aspect, there were 37 up-regulated and 44 down-regulated. After text mining, we found ADM was already found play a role in BPD. ADM is an endogenous peptide with potent angiogenic, anti-oxidant, and anti-inflammatory properties. Realtime q-PCR assay results showed that, miRNA-574-3p expression level in blood samples from preterm infants with BPD was significantly decreased, ADM expression level in blood samples from preterm infants with BPD was significantly increased. In our study, we found that up-regulation of ADM regulated by miRNA-574-3p could protect preterm infants with BPD. These data provide novel insights into ADM regulated by miRNA-574-3p which may be shed light on BPD prevention and treatment.

overall_design: The differential expressed genes in in blood of BPD and Normal preterm neonates were measured. Five independent experiments were performed using different donors for each experiment.

first: Xiaohui

last: Gong

first: Jiajun

last: Qiu

first: Li

last: Ma

first: Gang

first: Yunlin

last: Shen

first: Chongbin

last: Yan

first: Cheng

last: Cai


title: Differentially expressed genes in blood of BPD and Normal preterm neonates

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: The long noncoding RNA expression profiles of reticulocytes for hereditary persistence of fetal hemoglobin and β-thalssemia minor with high fetal hemoglobin.

status: Public on Jan 01 2018

city: Nanning

first: Ketong

last: Lai

address: Shuangyong Road

department: Department of Pediatrics

institute: the First Affiliated Hospital of Guangxi Medical University

summary: To explore long noncoding RNA (lncRNA) expression and the biological functions of lncRNAs in fetal hemoglobin (HbF) induction, we surveyed lncRNA and mRNA expression profiles using circulating reticulocytes isolated from individuals with hereditary persistence of fetal hemoglobin (HPFH) and β-thalassaemia minor with high HbF.

overall_design: Reticulocytes were isolated from whole blood of control individuals (n=7) and individuals of HPFH or β-thalssemia minor with high HbF (n=7). All 14 samples were analyzed for lncRNAs and mRNAs expression.

first: Yunyan

last: He


city: Baltimore

first: leslie

last: cope

address: 550 N. Broadway

institute: leslie cope

summary: Heterogeneity of triple-negative breast cancer was examined and compared across morphologic and molecular features

overall_design: Routine pathologic sections of triple negative breast cancer were examined and cases with highly similar morphologic features were selected for immunohistochemical and gene expression array studies. Data in this table summarizes immunohistochemical scores (0 = negative, 1 = positive) and clinical-pathologic characteristics of the breast cancers evaluated by Illumina DASL microarray analysis.

first: Young

last: Bae

first: Edward

last: Gabrielson

first: Leslie

last: Cope


title: Genome-wide expression analyses in Aspergillus fumigatus growing under alkaline zinc-limiting conditions

city: Villamayor

first: Marta

last: Montero-Barrientos

state: Salamanca

address: Río Duero 12

institute: CENIT SUPPORT SYSTEMS

summary: In this study it was investigated the role of ZafA on gene expression at a genome wide scale by comparing the transcriptional profile of a wild-type strain of A. fumigatus with that of a dzafA null strain grown in zinc-limiting media. The analysis of the results indicated that among genes up-regulated under zinc-limiting conditions were those most directly involved in zinc homeostasis such as zafA, that encoded for the ZafA transcriptional regulator of zinc homeostasis, zrfA, zrfB and zrfC that encoded zinc transporters presumably located at the plasma membrane and zrfF that encodes a zinc transporter located presumably at the vacuole membrane. Besides, a gene encoding a putative zinc-metallochaperone that might play a role in the correct folding of certain metalloproteins was also induced under zinc-limiting conditions. In addition, many other genes whose encoding products are either predicted or shown to be related to different metabolic or regulatory processes were also up-regulated under zinc-limiting conditions, including genes related to amino acid metabolism, cell wall biosynthesis, cytoskeletal assembly and reorganization, energy homeostasis, oxidative stress response, ER and vacuolar functions, iron metabolism, vesicular trafficking, lipid and ergosterol metabolism, protein degradation and modification, sulfur metabolism, ribosomal biogenesis and biosynthesis of secondary metabolites.

overall_design: Total RNA will be purified (QIAGEN RNeasy mini Kit cat. 74904) from a wild-type (wt) and a zafA null strain (dzafA) of Aspergillus fumigatus was cultured in the SDN zinc-limiting (-Zn) and zinc replete (+Zn) media at 37ºC for 20 hours with shaking at 200 rpm. The following hibridizations will be performed: (1) wt-Zn versus wt+Zn; (2) dzafA-Zn versus dzafA+Zn and, (3) wt-Zn versus dzafA-Zn

first: José

last: Calera

first: Rocío

last: Vicentefranqueira


title: Roles of Cdc42 and Rac in Bergmann glia during cerebellar corticogenesis (WT_primary_astrocyte)

city: Kobe

first: Takehiko

last: Ueyama

state: Hyogo

address: Rokkodai-cho 1-1, Nada-ku

department: Biosignal Research Center

institute: Kobe university

summary: Bergmann glia (BG) are important in the inward type of radial migration of cerebellar granule neurons (CGNs). However, details regarding the functions of Cdc42 and Rac in BG for radial migration of CGN are unknown. To examine the roles of Cdc42 and Rac in BG during cerebellar corticogenesis, mice with a single deletion of Cdc42 or Rac1 and those with double deletions of Cdc42 and Rac1 under control of the glial fibrillary acidic protein (GFAP) promoter: GFAP-Cre;Cdc42flox/flox (Cdc42-KO), GFAP–Cre;Rac1flox/flox (Rac1-KO), and GFAP-Cre;Cdc42 flox/flox;Rac1flox/flox (Cdc42/Rac1-DKO) mice, were generated. Both Cdc42-KO and Rac1-KO mice, but more obviously Cdc42-KO mice, had disturbed alignment of BG in the Purkinje cell layer (PCL). We found that Cdc42-KO, but not Rac1-KO, induced impaired radial migration of CGNs in the late phase of radial migration, leading to retention of CGNs in the inferior half of the molecular layer (ML). Cdc42-KO, but not Rac1-KO, mice also showed aberrantly aligned Purkinje cells (PCs). These phenotypes were exacerbated in Cdc42/Rac1-DKO mice. Alignment of BG radial fibers in the ML and BG endfeet at the pial surface of the cerebellum evaluated by GFAP staining was disturbed and weak in Cdc42/Rac1-DKO mice, respectively. Our data indicate that that Cdc42 and Rac, but predominantly Cdc42, in BG play important roles during the late phase of radial migration of CGNs. We also report here that Cdc42 is involved in gliophilic migration of CGNs, in contrast to Rac, which is more closely connected to regulating neurophilic migration.

overall_design: The expression levels of mRNAs in primary astrocytes were examined.


title: Gene expression profiles of zebrafish larvae exposed to secondary effluent of a wastewater treatment plant in Tucson, Arizona, USA

city: Singapore

first: Siew Hong

last: Lam

address: #02-01, T-Lab Building, 5A Engineering Drive 1

country: Singapore

institute: National University of Singapore

summary: To investigate gene expression changes in fish by the secondary effluent (directly released to environment) of a waterwater treatment plant in Tucson, Arizona, zebrafish larvae with 5-day exposure to the original (1x) or half (0.5x) concentration of the effluent were analyzed using Agilent  G2519F-026437 Zebrafish Oligo Microarray.

overall_design: Embryos aged 3 h post-fertilisation were exposed to 1x or 0.5x concentration of reconstituted effluent in E3 medium with a maximum of 0.05% DMSO. The control group contained 0.05% (v/v) DMSO in E3 medium only. After five days of exposure, embryos from each well were collected as one replicates. Four replicates of control group and five replicates of treatment group were analyzed.

first: Siew

first: Qiyu

last: Chen


title: Expression data from skin biopsies in patients with systemic sclerosis

status: Public on Jan 02 2018

first: Julio

middle: C

last: Mantero

address: 72 E Concord St

department: Rheumatology

institute: Boston University School of Medicine

summary: We used microarrays to explore gene expression in Systemic Sclerosis patients.

overall_design: Compilation of skin biopsies gene expression from patients with diffuse cutaneous systemic sclerosis and healthy controls.

first: Robert

last: Lafyatis


title: Magnaporthe appressoria: wt vs. bip1 deletion mutant

city: College Station

first: Andrew

last: Tag

address: 3258 TAMU

department: Biology

institute: Texas A&M University

summary:
The identification of genes regulated by the transcription factor Bip1 during appressorial development.
The rice blast fungus Magnaporthe grisea develops melanized appressoria with high turgor pressure that inject the fungus into epidermal host cells. A screen for M. grisea non-pathogenic mutants recovered mutant M763 with reduced penetration efficiency and infectious growth. Complementation analysis identified a gene inactivated in M763 that encodes a novel basic leucine zipper (bZIP) transcription factor named Bip1 (B-ZIP Involved in Pathogenesis1). Deletion of Bip1 by targeted replacement generated non-pathogenic mutants that are unable to infect rice or barley. These mutants develop melanized appressoria that are unable to penetrate intact or wounded host leaves. Bip1 mRNA was detected in fungal spores, appressoria and infected leaves but not in mycelia, while a BIP1:GFP fusion was detected only in nuclei of mature appressoria. Genome wide transcriptome analysis identified 44 genes down regulated in Δbip1:hph appressoria. Most of these genes (77%) are specifically expressed in appressoria and encode enzymes involved in secondary metabolism (11), secreted proteins and enzymes (18) and G-Protein Coupled Receptors (GPCRs) (5). Promoters of BIP1 down-regulated genes share a similar GCN4/bZIP DNA binding motif (TGACTC). Gel shift assays showed that the motifs from 6 of the 7 promoters tested bind to recombinant BIP1 in vitro, including MGG_08381.5 from the ACE1 locus. Mutation of BIP1 binding sites in the MGG_08381.5 promoter significantly reduced its appressorium specific expression. Molecular and biochemical studies confirmed that BIP1 controls the expression of a distinct set of M. grisea genes in the appressorium, revealing a novel regulatory network involved in early stages of fungal infection that activates a diverse gene expression program resulting in a “shock and awe” impact on the plant host.

overall_design: Two condition experiment, wt P1.2 vs. delta bip1 at 24 h post-inoculation on Teflon.  Three biological replicates, four technical replicates per biological replicate consisting of two slides plus two dye-swapped slides.

first: Karine

last: Lambou

first: Jérome

last: Collemare

first: Pierre-Henri

last: Clergeot

first: Crystel

last: Barbisan

first: Phillipe

last: Perret

first: Roland

last: Beffa

first: Terry

last: Thomas

first: Marc-Henri

last: Lebrun


title: MiRNAs expression profiles of nasopharyngeal carcinoma cell line HNE2 following TP53 overexpression

city: Changsha

first: Wei

last: Xiong

state: Hunan

address: 110 Xiangya Road

department: Cancer Research Institute

institute: Central South University

summary: Recent studies have revealed that microRNAs (miRNAs) participate in all steps of cancer initiation and progression by regulating protein coding genes at the post-transcriptional level. MiRNAs are in turn regulated by other genes, forming a complex regulatory network. The regulation networks between the p53 tumor suppressor and miRNAs in nasopharyngeal carcinoma (NPC) remain unclear. The aim of this study was to investigate the regulatory roles of the TP53 gene in regulating miRNA expression profiles in NPC cell line HNE2.

overall_design: p53 induced miRNAs expression in human nasopharyngeal carcinoma cell line HNE2 was measured at 0, 12, 24 and 48 hours after transfected by pCMV-p53 plasmid.

first: Zhaoyang

last: Zeng

first: Zhaojian

last: Gong

first: Fang

first: Qian

last: Yang

first: Yong

first: Xiaoling

last: Li

first: Guiyuan


title: Gene expression profiling of multiple sclerosis pathology identifies early patterns of demyelination surrounding chronic active lesions

city: Amsterdam

first: Inge

last: Huitinga

address: meibergdreef 47

department: Neuroimmunology

country: Netherlands

institute: NIN

summary: In multiple sclerosis (MS), activated microglia and infiltrating macrophages phagocytose myelin focally in (chronic) active lesions. These demyelinating sites expand in time, but at some point turn inactive into a sclerotic scar. To identify molecular mechanisms underlying lesion activity and halt, we analyzed genome-wide gene expression in rim and peri-lesional regions of chronic active and inactive MS lesions, as well as in control tissue. Gene clustering revealed patterns of gene expression specifically associated with MS and with the presumed, subsequent stages of lesion development. Next to genes involved in immune functions, we found regulation of novel genes in and around the rim of chronic active lesions, such as NPY, KANK4, NCAN, TKTL1, and ANO4. Of note, the presence of many foamy macrophages in active rims was accompanied by a congruent upregulation of genes related to lipid binding, such as MSR1, CD68, CXCL16, and OLR1, and lipid uptake, such as CHIT1, GPNMB, and CCL18. Except CCL18, these genes were already upregulated in regions around active MS lesions, showing that such lesions are indeed expanding. In vitro downregulation of the scavenger receptors MSR1 and CXCL16 reduced myelin uptake. In conclusion, this study provides the gene expression profile of different aspects of MS pathology and indicates that early demyelination, mediated by scavenger receptors, is already present in regions around active MS lesions. Genes involved in early demyelination events in regions surrounding chronic active MS lesions might be promising therapeutic targets to stop lesion expansion.

overall_design: Microarray was performed on 7 chronic active MS lesions (PL-NAWM and RIM), 8 inactive MS lesions (PL-NAWM and RIM), and white matter (WM) of 10 control donors were included in this study. In total 40 samples were included. Experimental RNA and reference pool RNA input was used for linear amplification and fluorescent labeling

first: Debbie

last: Hendrickx

first: Jackelien

last: vanScheppingen

first: Marlijn

last: vanderPoel

first: Koen

last: Bossers

first: Karianne

last: Schuurman

first: Corbert

last: vanEden

first: Elly

middle: M

last: Hol

first: Jorg

last: Hamann


title: Thorax irradiation of Non-Human Primates induces persistent gene expression changes in blood cells.

city: New York

first: Shanaz

middle: Adi

last: Ghandhi

state: NY

address: 630, W 168th street

department: Center for Radiological Research

institute: Columbia University Medical Center

summary:
In the current study, we investigated the gene expression response of blood cells of non-human primates that were whole thorax irradiated with a 10.1 Gy total dose. Partial irradiation of the NHP in the upper half of the body allows study of late radiation lung injury while avoiding acute respiratory syndromes related to hematopoietic and gastrointestinal injury.  In this study, we report gene expression changes in the peripheral blood, an easily biopsied tissue, up to a month after radiation injury to the lungs.
We isolated total RNA from peripheral blood at 3 days before irradiation, and then from the same animals on days 2, 5 and 30 after irradiation. Using Agilent Human Whole Genome microarrays, we identified 1187 genes that were significantly differentially expressed across the 30-day time course of this study. We identified common biological functions affected that persisted across the 30-day study, such as immune response. Response to oxygen-containing compounds and bacterial molecules were implicated by the gene expression changes at both the earliest day 2 and last, day 30 time-point   and suggest that although cells are being recycled through the body in a 30-day time course after exposure to irradiation, the damage to blood cells and immunity, specifically the response to infections might persist throughout the study .

overall_design: Radiation induced gene expression was measured at 2, 5 and 30 days after partial (upper) body irradiation. There were 5 replicates in this study.

first: Sally

last: Amundson


title: Omeprazole regulate gastric cancer microenvironment by regulate exosomes associated miRNA

city: Tianjin

first: Xu-wen

last: Guan

state: Tianjin

address: Huanhuxi Road, Tiyuanbei, Hexi District

institute: Tianjin Medical University

summary: Exosomal miRNAs have emerged as microcommunicators of pathologic conditions including cancer where they educate the tumor microenvironment in favor of metastasis. We purified exosomes from the medium of SCG-7901 cells which was treated by 80ug/ml omeprazole 24h and was analysed by Aglient human microarray.

overall_design: SGC-7901 cells was treated with omeprazole at 80ug/ml for 24h, and PBS was used as control. And the medium of SGC-7901 cells were collected and the exosomes were isolated by ExoQuick-TC exosome precipitation solution. Then the miRNA involved in exosomes was isolated by the total RNA purification Kit.Next the miRNA was analysised by microarry.

first: Ding-zhi

last: Huang


title: Differentially expressed genes in blood of BPD and Normal preterm neonates [mRNA]

first: cai

last: cheng

first: Xiaohui

first: Jiajun

last: Qiu

first: Li

last: Ma

first: Gang

first: Yunlin

last: Shen

first: Chongbin

last: Yan

first: Cheng

last: Cai