title: A Developmental Genomic Analysis of Pax1 and Pax9 in Embryonic Intervertebral Disc Development

status: Public on Aug 25 2017

city: Oxford

first: Tim Xiaoming

last: HU

address: Le Gros Clark Building, South Parks Road

department: Department of Physiology, Anatomy and Genetics

institute: University of Oxford

summary: Pax1 and Pax9 play redundant, synergistic functions in the patterning and differentiation of the sclerotomal cells that give rise to the vertebral bodies and intervertebral discs (IVD) of the axial skeleton. Gene expression profiling of an enriched population of Pax1/Pax9-expressing cells of the embryonic IVD revealed that Pax1 and Pax9 regulate cell proliferation, cartilage development, collagen fibrillogenesis and other processes vital in early IVD morphogenesis. Twenty-nine of the Pax1/Pax9 targets are also associated with axial skeletal defects that phenocopy Pax1/Pax9-deficient mice. Pax1 likely auto-regulates itself and is up-regulated in the absence of Pax9, clarifying how it compensates for the loss of Pax9, while Pax9 is unaffected by the loss of Pax1. Pax1 and Pax9 positively regulate several of the cartilage development genes known to be regulated by the “Sox trio” (Sox5/Sox6/Sox9).

overall_design: 5 different genotypes of Pax1 and Pax9 were analyzed (including WT as control/ reference) in this study. FACS sorted cells were used for microarray analysis, whereby WT strain with EGFP was also generated for comparison. A minimum of 3 biological replicates were used for each genotype.

first: V

last: Sivakamasundari

first: Petra

last: Kraus

first: Wenjie

last: Sun

first: Xiaoming

last: Hu

first: Siew

middle: L

last: Lim

first: Shyam

last: Prabhakar

first: Thomas

last: Lufkin


title: Integration of molecular gene signatures with clinicopathological variables improves staging and outcome prediction of oral cancer.

status: Public on Aug 23 2017

city: Parma

first: Nicoletta

last: Bertani

state: Parma

address: Parco Area delle Scienze, 11/A

department: Life Science

country: Italy

institute: University of Parma

summary: The aim of this study is to identify and validate clinically implementable gene signatures for outcome prediction of patients with oral squamous cell carcinoma.

overall_design: Tumor gene expression profiles of surgical specimen of patients with oral squamous cell carcinoma (OSCC)

first: Silvia

last: Rossi

first: Roberto

last: Perris

first: Enrico

middle: M

last: Silini

first: Tito

last: Poli

first: Dennis

last: te Beest

first: Mark

last: van de Wiel


title: BOBCAT Bronchial biopsy study

city: South San Francisco

last: McCreary

state: California

address: 1 DNA Way, MS 93

department: Bioinformatics

country: USA

institute: Genentech

summary: Clinical subphenotypes of asthma are characterized by pathological, cellular, and molecular heterogeneity of the airway. Gene expression profiling of affected tissues in diseased patients by microarray analysis will provide insight into the molecular heterogeneity and support the development of hypotheses of pathological mechanisms.

overall_design: Bronchial biopsies were taken during bronchcoscopy from severe, uncontrolled asthma patients from the Bronchoscopic Exploratory Research Study of Biomarkers in Corticosteroid-refractory Asthma (BOBCAT) (Jia et al., 2012). RNA (Qiagen AllPrep with on-column DNase treatment) was isolated from these biopsies for gene expression microarray analysis.

first: Tao

last: Huang

first: Meredith

last: Hazen

first: Yonglei

last: Shang

first: Meijuan

last: Zhou

first: Xiumin

last: Wu

first: Donghang

last: Yan

first: Zhonghua

last: Lin

first: Margaret

last: Solon

first: Elizabeth

last: Luis

first: Hai

last: Ngu

first: Yongchang

last: Shi

first: Arna

last: Katewa

first: David

middle: F

last: Choy

first: Nhandini

last: Ramamoorthi

first: Erick

middle: R

last: Castellanos

first: Mercedesz

last: Balazs

first: Min

last: Xu

first: Wyne

last: Lee

first: Marissa

last: Matsumoto

first: Jian

last: Payandeh

first: Joseph

last: Arron

first: Jo-Anne

last: Hongo

first: Jianyong

last: Wang

first: Isidro

last: Hötzel

first: Cary

middle: D

last: Austin

first: Karin

last: Reif


title: The thrombopoietin/MPL axis is activated in the Gata1 low mouse model of myelofibrosis and is associated with a defective RPS14 signature

status: Public on Aug 22 2017

city: Chicago

first: John

last: Crispino

state: IL

address: 303 E Superior

department: Medicine-Hematology/Oncology

institute: Northwestern University

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

overall_design: Refer to individual Series


title: The thrombopoietin/MPL axis is activated in the Gata1 low mouse model of myelofibrosis and is associated with a defective RPS14 signature [BM]

summary: Myelofibrosis (MF) is caused by genetic abnormalities involving the thrombopoietin (TPO)/MPL/JAK2 axis. Furthermore MF patients have elevated serum TPO levels. MF is also associated with reduced GATA1 content in MK suggesting that this abnormality represents a phenotypic modifier. In 2014, Dr. Crispino suggested that in MF abnormal TPO signaling induces a ribosomal deficiency hampering GATA1 mRNA translation in MK.   Support for MK GATA1 deficiency as “phenotypic modifier” in MF was provided by the observation that mice carrying the Gata1low mutation reducing Gata1 transcription in MK develop myelofibrosis. Since reduced RBC half-life subject these mice to continuous “erythroid stress”, we investigated the TPO/Mpl axis in this model.  In Gata1low and wild-type mice, TPO mRNA was expressed by bone marrow (BM), spleen and liver. The greatest expression (by 300-fold) was detected in liver. Gata1low livers expressed TPO mRNA levels 6-fold greater than wild-type livers. TPO protein was detected in BM, spleen, liver and peritoneum washes and plasma. The greatest levels where detected in plasma. Gata1low plasma contained TPO levels 2-fold lower than wild-type plasma, but 2-times greater than plasma from bleed wild-type mice and Mplnull mice with similar thrombocytopenia, suggesting that TPO is overproduced in Gata1low mice.   JAK2 and STAT5 were easily detected in Gata1low BM bur barely detectable in wild-type BM, suggesting that in the former MPL is prompt to signaling activation. Furthermore, Gata1low LSK expressed levels of Mpl mRNA 3-times greater than wild-type cells but expressed cell-surface levels of MPL 2-times lower than wild-type cells and similar to those on LSK from TPO-treated wild-type mice, suggesting that MPL is down-modulated in Gata1low LSK.   The Crispino’s hypothesis that in MF activation of TPO/MPL/JAK2 induces a ribosomal deficiency hampering GATA1 mRNA translation and the realization that this axis is activated in Gata1low mice made us question the original hypothesis that reduced content of GATA1 in Gata1low MK results from deletion of lineage-specific enhancers. Microarray analyses indeed identified that Gata1low BM express a discordant ribosome signature including reduced expression of RPS24 and RPS36A, two genes mutated in Diamond Blackfan Anemia, a disease characterized by inefficient GATA1 mRNA translation. Electron microscopy identified that the cytoplasm of Gata1low MK contained poorly developed endoplasmic reticulum with rare polysomes.   In conclusion, these results validate the Gata1low model as a MF model by indicating that these mice express an activated TPO/MPL axis and an abnormal ribosomal signature which may reduce efficiency of Gata1 mRNA translation.

first: Anna

last: Migliaccio

first: Maria

last: Zingariello


title: The thrombopoietin/MPL axis is activated in the Gata1 low mouse model of myelofibrosis and is associated with a defective RPS14 signature [spleen]


title: Gene expression signatures for five tumor sites of each primary liver cancer patient

status: Public on Aug 15 2017

city: Beijing

first: Lijun

last: Shi

address: 9 Dongdan 3rd Alley, Dongcheng,

department: Department of Etiology and Carcinogenesis

country: China

institute: National Cancer Center/Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: Tumor-infiltrating lymphocytes (TIL) were spatial heterogeneous within a single tumor. To investigate whether the gene expression approach relate to TILs diversity of local tumor region, we have employed whole genome microarray expression profiling as a discovery platform to identify different gene expression pattern of each tumor region from five primary liver cancer patients. To collect information reflecting the molecular phenotype in a more robust manner from the mRNA transcriptome profiling data, the GSVA scores of the GO gene sets provided by the Molecular Signatures Database were calculated for each of the 25 tumor samples to evaluate their activities. Correlation analysis was conducted to evaluate the relationship between the diversity of TCR clones and the activity of gene sets. Ten GO gene sets which obtained the largest correlation coefficient were chose, we found six gene sets were associated with immune response, which suggesting a significant association between diversity of TCR clones and anti-tumor immune response.

overall_design: The mRNA transcriptome profiling of the 25 tumor samples from five PLC patients was conducted using Agilent microarrays, to evaluate the correlation between the TCRβ repertoire diversity of the tumor microenvironment and the local molecular phenotype

first: Yang

last: Zhang


title: Transcriptional profiling of kidneys from ADTKD-UMOD mouse model

status: Public on Aug 18 2017

city: Milano

first: Michela

last: Riba

address: via Olgettina 60

department: COSR, Center for Omics Sciences

institute: IRCCS, Ospdale San Raffaele

summary: To gain insight into autosomal dominant tubulointerstitial kidney disease (ADTKD)-uromodulin (UMOD) pathophysiology, we carried out transcriptional profiling of kidneys from 1- and 2-month-old TgUmodC147W mice, a transgenic model that recapitulates the main features of the disease, and TgUmodwt mice, a matched transgenic control of Umod overexpression. These time points correspond to presymptomatic stages that precede renal dysfunction in TgUmodC147W mice.

overall_design: Total RNA obtained from kidneys of mice at different ages carrying either wild type or mutant Umod transgene.

first: Matteo

last: Trudu

first: Celine

last: Schaeffer

first: Paola

last: Brambilla

first: Filippo

last: Martinelli-Boneschi

first: Luca

last: Rampoldi


title: Ginsenoside Rh2 epigenetically regulates cell-mediated immune pathway to inhibit proliferation of the MCF-7 breast cancer cell

status: Public on Jul 30 2017

city: goyang

first: seungyeon

last: lee

address: dongguk-ro 32

department: life science

country: South Korea

institute: dongguk unversity

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of estrogene receptor postive breast cancer cell line MCF-7, treating Ginsoenoside Rh2. The Illumina Infinium Human Methylation EPIC v1.0 B2 Bead chip was used to obtain DNA methylation profiles across approximately 850,000 CpGs. This profiling indicates that Ginsenoside Rh2 induces epigenetic and cellular changes.

overall_design: Genomic DNA obtained from  MCF-7 treated Ginsenoside Rh2

first: Seungyeon

last: Lee

first: Sunjung

last: Kim


title: Keloid tissue: active keloid lesion vs. adjacent normal skin tissue

status: Public on Jul 01 2017

city: Tokyo

first: Rei

last: Ogawa

address: 1-1-5, Sendagi, Bunkyo-ku

department: Department of Plastic, Reconstructive and Aesthetic Surgery

country: Japan

institute: Nippon Medical School

summary: Transcriptional profiling of active keloid lesion and adjacent control normal skin tissue from human. Each control and lesion sample was derived from a matched individual.

overall_design: Two-condition experiment, active keloid lesion vs. adjacent control normal skin tissue. each condition was available in seven biological replicates.

first: R


title: Transient and permanent changes in DNA methylation patterns in inorganic arsenic-mediated epithelial-to-mesenchymal transition

status: Public on Jun 23 2017

city: Grand Rapids

first: Yvonne

middle: Nsokika

last: Fondufe-Mittendorf

state: MI

address: 333 Bostwick Ave NE

department: Epigenetics

institute: Van Andel Institute

summary: To examine the global impact of iAs on DNA methylation patterns. Genomic DNA was bisulfite converted and analyzed using Infinium MethylationEPIC BeadChip.

overall_design: DNA from NT, iAs-treated, and iAsT-reverse treated cells were bisulfite converted and used for analysis through Illumina Infinium Methylation EPIC BeadChip.

first: Meredith

last: Eckstein

first: Matthew

last: Rea


title: RETINOBLASTOMA MICRORNA LANDSCAPE

status: Public on Jul 10 2017

city: Mexico

first: Blanca

middle: E

last: Castro

state: Mexico City

address: Cuauhtemoc 330

country: Mexico

institute: CMNSXXI

summary: In this work we examined miRNome expression in 12 samples of retinoblastoma. Present miRNAs show the common working machinery with Rb affecting most of pathways considered hallmarks of cancer.

overall_design: 12 Rb from enucleated patients with no chemotherapy history. 5 bilteral and 7 unilateral cases from which 4 are female and 8 male.

last: Castro-Magdonel

first: Veronica

last: Ponce-Castaneda

first: Valentin

middle: N

last: Duran-Figueroa

first: Manuela

last: Orjuela

first: Maria

last: Cabrera-Munoz

first: Stanislaw

last: Sadowinski-Pine

first: Javier

last: Camacho

first: Claudia

middle: A

last: Velazquez-Wong

first: Adda

middle: J

last: Garcia-Chequer

first: Adriana

last: Hernandez-Angeles

last: Orozco


title: Gene expression profile of mouse CD206+F4/80+CD11b+ M2-like macrophages

status: Public on Jun 14 2017

city: Saitama

first: Manabu

last: Shiraishi

address: Omiya

institute: Jichi Medical University

summary: Characterisation of M2-like macrophage in terms of gene expression level. The hypothesis tested in the present study was that M2-like macrophages in myocardial infarction (MI) heart have upregulation of genes relevant to cardiac repair. The results obtained showed tha various tanti-inflammatory and reparative genes were upregulated in M2-like macrophage from MI heart compared to those from intact hearts. M2-like macrophages from the heart (either MI or intact) were distinct from those in the peritoneal cavity.

overall_design: Total RNA obtained from M2-like macrophages from peritoneal cavity, intact heart and myocardial infarction heart.


title: Cyclodextrin treatment leads to atherosclerosis regression by dissolution of cholesterol crystals and LXR activation

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Atherosclerosis is an inflammatory disease linked to elevated blood cholesterol levels. Since cholesterol retention and cholesterol crystals in arterial walls are key pathogenetic factors for atherogenesis, we assessed the therapeutic potential of increasing cholesterol solubility in vivo. Here we show that treatment of murine atherosclerosis with the cyclic oligosaccharide 2-hydroxypropyl-β-cyclodextrin (CD), a compound that solubilizes lipophilic substances, reduced atherosclerotic plaque size, cholesterol crystal (CC) load and promoted plaque regression even under continuing Western diet. CD solubilized CC and promoted cholesterylester and oxysterol production in macrophages leading to liver X receptor-mediated transcriptional reprogramming with increased cholesterol efflux and decreased inflammation. CD treatment may thus be used to increase cholesterol solubility and clearance to prevent or treat atherosclerosis.

overall_design: Bone marrow-derived macrophages (BMDMs) were derived from bone marrow isolated from tibiae and femurs of LXR  -/-  -/- mice on a C57BL/6 background and age matched littermate wild type mice. Bone marrow cells were cultured in DMEM supplemented with 10 % FCS, 10   g/ ml Ciprobay-500 and 40 ng/ ml M-CSF (R&D Systems) for six days. BMDMs were treated for 3h with 200 ug cholesterol crystals per 1 mio. cells or control medium. Subsequently cells were incubated for 6h with 10 mM CD before cell lysis in Trizol (Invitrogen). Samples were stored at -80  C for RNA isolation.

first: S

last: Zimmer

first: A

last: Grebe

first: N

last: Bode

first: D

last: De Nardo

first: L

last: Labzin

first: C

last: Hempel

first: T

last: Kerksiek

first: M

last: Heneka

last: Ulas

first: JL

first: G

last: Nickenig

last: Lütjohann

first: E

last: Latz


title: Effect on bone marrow mesenchymal stromal cells of mouse models of acute myeloid leukemia of different genotypes

city: Houston

first: Zhiqiang

last: Wang

state: Texas

address: 7455 Fannin St.

department: Lymphoma and Myeloma

institute: University of Texas MD Anderson Cancer Center

summary: We found that cells of acute myeloid leukemia (AML) affect the transcriptome of mesenchymal stromal cells (MSC) in bone marrow (BM) involved by AML. Gene expression in BM-MSC of AML-bearing mice differed from that in BM-MSC of control mice; some gene changes were the same across different types of AML produced by well-known fusion oncogenes, while others were specific to certain genotypes. There were notable differences between the effects of tp53 WT and tp53-/- AML with the same oncogene (MLL&FLT3-ITD); these were supported by in vitro experiments in which normal BM-derived MSC were cultured with the same tp53 WT and tp53-/- pair of AML cells.

overall_design: We established syngeneic AML, produced by different known AML fusion oncogenes, in C57BL/6 mice and isolated their BM-MSC. Gene expression profiling was used to compare AML-exposed MSC to those of control mice. BM-derived normal MSC were also cultured in vitro with tp53 WT and tp53-/- AML cells of the same genotype (MLL/ENL+FLT3-ITD).

first: Rodrigo

last: Jacamo

first: Xiaoyang

last: Ling

first: Sonali

last: Sonnylal

first: Wencai

last: Ma

first: Min

last: Zhang

first: Scott

last: Lowe

first: Marina

last: Konopleva

first: Michael

last: Andreeff

first: R

last: Davis


title: Genome-wide analysis of SAK-HV treatment caused hepatic genes expression in ApoE knockout mice

status: Public on Jun 13 2017

first: Donggang

last: Xu

address: Haidian district, Taiping road

institute: Beijing Institute of Basic Medical Sciences

summary: A novel recombinant fusion protein (SAK-HV) significantly decreased the serum levels of both total cholesterol (TC) and triglyceride (TG) in apolipoprotein E-deficient (ApoE-/-) mice with hyperlipemia and remarkably ameliorated hepatic steatosis. Particularly, its lipid-lowering effect was significantly better than that of atorvastatin during the observation period of 2 weeks. We then collected the liver tissues of SAK-HV-treated ApoE-/- mice (n=7) and liver tissues of PBS-treated ApoE-/- mice to make the transcriptome chip, and analyze the lipid-lowering mechanism of SAK-HV in liver of ApoE-/- mice.

overall_design: Total RNA obtained from isolated liver tissue of SAK-HV-treated ApoE-/- mice (n=7,) compared to that of PBS-treated ApoE-/- mice control (n=5). These male mice aged 14 weeks was injected with SAK-HV or PBS via tail vein every other day for 7 times. Their liver tissue was collected 14 days after administration.

first: Chao

first: Dong-gang


title: Severe Uncontrolled Asthma Lung Epithelial Brushing Gene Expression

status: Public on Jun 06 2017

first: David

middle: Fong

last: Choy

state: CA

address: 1 DNA Way

institute: Genentech, Inc.

summary: Transcriptional profiling of lung epithelial brushing mRNA from severe uncontrolled asthmatics

overall_design: Two-condition experiment, mRNA from severe uncontrolled asthma lung epithelial brushings for test channel and Stratagene Universal Human Reference RNA for reference channel.


title: LASSIM -a network inference toolbox for genome-wide mechanistic modeling [Time-series polarization: CD4+ T cells toward Th2]

status: Public on Jun 12 2017

city: Linköping

first: Danuta

last: Gawel

address: Garnisonsvägen

country: Sweden

institute: Linköping University

summary: Recent and ongoing revolutions in measurement technologies imply completely new possibilities for genome research: today, time-resolved, quantitative, and systems-level data are available. Nevertheless, without a corresponding revolution in methods for data analysis, these new data tend to drown researchers and doctors, rather than provide clear and useful insights. Such new methods are developed within the field of systems biology. Systems biology has two main approaches: mechanistically detailed and well-determined simulation models for small subsystems, and more approximative statistical models for the entire genome. However, there are few, if any, methods that combine the strengths of these two approaches. Herein, we present LASSIM, a new simulation-based approach, which can be applied to systems of the size of the entire genome. The superior performance of LASSIM is demonstrated in three examples: i) an example with simulated data shows that unlike traditional large-scale methods, LASSIM correctly identifies the true behavior between measured data-points, ii) LASSIM outperforms the winner of a previous DREAM challenge, the most competitive benchmarking approach available, iii) based on new data from TH2 differentiation, LASSIM identifies a first mechanistic model for the entire genome. The key predictions of this model are typically enriched for DNA bindings, which suggests that most predicted interactions are direct. Moreover, in silico knockdowns were experimentally validated. In summary, LASSIM opens the door to a new type of model-based data analysis: to models that combine the strengths of reliable mechanistic models with truly systems-level data.

overall_design: Total CD4+ T cells were isolated from buffy coat using total CD4+ T cell isolation kit (Miltenyi, Bergisch-Gladbach, Germany). Total CD4+ T cells were polarized in T helper 2 (Th2) condition by stimulation with plate-bound anti-CD3 (500 ng/mL), soluble anti-CD28 (500 ng/mL), in the presence of IL-4 (10 ng/ml), IL-2 (10 ng/mL) and anti-IL-12 (5 ug/mL). Total RNA was extracted from total CD4+ T cells and in vitro polarized Th2 cells collected at 6 hours, 48 hours and 96 hours using a miRneasy Mini Kit (Qiagen, Valencia, CA, USA).  RNA concentrations were analyzed with NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Thermo Fisher Scientific Inc., Waltham, MA, USA). The cRNA was prepared using a LowInput QuickAmp Labeling Kit (Agilent Technologies, Palo Alto, Calif, USA). Gene expression microarray analysis was perfromed using Whole Human Genome Microarray 4x44K  according to the manufacture’s instruction (Agilent Technologies, Palo Alto, Calif).

first: Rasmus

last: Magnusson

first: Mattias

last: Köpsén

first: William

last: Lövfors

first: Mikael

last: Benson

first: Rebecka

last: Jörnsten

first: Jörg

last: Linde

first: Torbjörn

last: Nordling

first: Elin

last: Nyman

first: Sylvie

last: Schulze

first: Colm

last: Nestor

first: Huan

first: Gunnar

last: Cedersund

first: Andreas

last: Tjärnberg

first: Mika

last: Gustafsson


title: Expression data from primary medulloblastoma samples

city: Toronto

first: Florence

middle: M G

last: Cavalli

state: Ontario

address: PGCRL, 686 Bay Street

department: Developmental and Stem Cell

country: Canada

institute: The Hospital for Sick Children

summary: Affimetrix Human Gene 1.1 ST Array profiling of 763 primary medullobalstoma samples used for identification of Medullobastoma subtypes

overall_design: We collected 763 fresh frozen primary medulloblastoma samples for RNA extraction and hybridization on Affimetrix microarrays

first: Marc

last: Remke

first: Michael

last: Taylor


title: Increased expression of Deleted in Malignant Brain Tumors (DMBT1) gene in advanced precancerous gastric lesions in three ethnic populations: effect of modulation on mouse mucous metaplasia in response to H. pylori infection

status: Public on Jun 30 2017

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

summary: Helicobacter pylori infection triggers a cascade of inflammatory stages that may lead to the appearance of non-atrophic gastritis, multifocal atrophic gastritis, intestinal metaplasia, dysplasia, and cancer. Deleted in malignant brain tumors 1 (DMBT1) belongs to the group of secreted scavenger receptor cysteine-rich proteins and is considered to be involved in host defense by binding to pathogens. Recent studies have shown that DMBT1 expression is up-regulated in areas of intestinal metaplasia and in gastric tumors. Here, we examined the role of DMBT1 in the development of inflammatory response and gastric precancerous lesions in Caucasian, African American and Hispanic populations as well as in a mouse model. We found that mucosal DMBT1 expression is significantly increased in individuals with more advanced gastric precancerous lesions. We also show that H. pylori infection of Dmbt1-/- mice results in enhanced gastric inflammation and the development of mucous metaplasia that is accompanied by increased cell proliferative rates and reduced IL-33 expression levels in the inflamed mucosa. Taken together, our data suggest that DMBT1 may be mediating mucosal protection that may reduce the risk of developing gastric precancerous lesions in response to H. pylori infection

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Microarray from gastric tissues of Hispanic individuals with different stages of gastritis (MAG, IM and dysplasia) were analyzed to determine gene sets associated with stage of gastritis. The study was validated by real-time PCR in 3 different ethnic groups (African Americans, Caucasian and Hispanic) and the role of the identified gene was determined in mouse models (C57Bl/6) of H. pylori infection.
Please note that the RT-PCR data is not included in the records.

first: Jone

last: Garay

first: M

middle: B

last: Piazuelo

first: Lizbeth

last: Lopez-Carrillo

first: Yelda

last: Leal

first: Sumana

last: Majumdar

first: Li

last: Li

first: Nataly

last: Cruz-Rodriguez

first: Silvia

last: Serrano-Gomez

first: Carlos

middle: S

last: Busso

first: Barbara

middle: G

last: Schneider

first: Alberto

last: Delgado

first: Luis

last: Bravo

middle: C

last: Camargo

first: Keith

middle: T

last: Wilson

first: Pelayo

last: Correa


title: Study of microRNA associated with telmisartan’s anti-tumor effect in esophageal adenocarcinoma cell line

status: Public on Jun 01 2017

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: The miRNAs expression was markedly altered with the treatment of telmisartan　in vitro and various miRNAs induced by telmisartan also may contribute to tumor growth in vitro.

overall_design: Using a custom microarray platform, we analyzed the expression levels of 2555 human miRNA probes in the OE 19 cell line in vitro that was treated with and without telmisartan.

first: S

last: Fujihara

first: T

last: Masaki


title: LASSIM -a network inference toolbox for genome-wide mechanistic modeling

first: Danuta

last: Gawel

summary: We present LASSIM, which is a toolbox built to build and infer parameters within mechanistic models on a genomic scale. This is made possible due to a property shared across biological systems, namely the existence of a subset of master regulators, here denoted the core system. The introduction of a core system of genes simplifies the inference into small solvable sub-problems, and implies that all main regulatory actions on peripheral genes come from a small set of regulator genes. This separation allows substantial parts of computations to be solved in parallel, i.e. permitting the use of a computer cluster, which substantially reduces the time for the computation to finish.

first: Rasmus

last: Magnusson

first: Guido

middle: P

last: Mariotti

first: Mattias

last: Köpsén

first: William

last: Lövfors

first: Rebecka

last: Jörnsten

first: Jörg

last: Linde

first: Torbjörn

last: Nordling

first: Elin

last: Nyman

first: Sylvie

last: Schulze

first: Colm

last: Nestor

first: Huan

last: Zhang

first: Gunnar

last: Cedersund

first: Mikael

last: Benson

first: Andreas

last: Tjärnberg

first: Mika

last: Gustafsson


title: Gene expression profiling of 10 tumor samples from a GBM patient

first: Lin

last: Feng

address: Panjiayuan nanli 17#

institute: Peiking union medical school

summary: Hypothetically the intratumor genomic heterogeneity has the potential to foster the tumor-infiltrating lymphocytes (TILs) diversity or activity, but no one has directly connected them by simultaneously investigating somatic mutations, TILs diversity and immune response activity. We have performed whole-exome sequencing, immune repertoire sequencing and gene expression profiling analysis simultaneously on ten spatially separated tumor samples obtained from two tumor bulks (the primary tumor and its metastatic offspring) of a glioblastoma multiforme (GBM) patient as well as his peripheral blood. We found that although the multi-region samples from one tumor shared more common mutations than those from different ones, the TIL populations did not. The TILs repertoire diversity was not significantly correlated with and the number of nonsynonymous mutations (Spearman's rank correlation, p = 0.4614), but it was highly related to the local immune status as it showed a significant positive correlation both with the local immune cytolytic activity and its down regulating factors. Furthermore, the tumor region having the highest TILs repertoire diversity was founded to show simultaneous local immune activation and suppression. A 20-gene signature was found to represent such contradictory local immune status. 50 GBM patients were stratified by the expression pattern of this signature in their tumors. Survival analysis suggested most of GBM patients (~80%) might be suffered from the simultaneous local immune activation and suppression status, which was unfavorable to patients’ prognoses (log-rank test, p = 0.012). This finding was validated when the similar analysis applied to the existing TCGA GBM dataset (log-rank test, p = 0.005). Through integration analysis of multi-omics data, we provided new insight into the complex relationship among the characteristics of TILs repertoire, somatic mutation pattern, and immune status.

overall_design: Gene expression profiling analysis was applied to the ten spatially separated tumor samples obtained from two GBM bulks (the primary and its related metastatic site) of a patient.

first: Haipeng

last: Qian

first: Xuexin

last: Yu

first: Kan

last: Liu

first: Manchao

last: Kuang

first: Shujun

last: Cheng

first: Jinghai

last: Wan

first: Xueji

last: Li

first: Kaitai


title: Study of microRNA associated with telmisartan’s anti-tumor effect in esophageal adenocarcinoma

first: Satoshi

last: Kondo

summary: The miRNAs expression was markedly altered with the treatment of telmisartan in vivo and various miRNAs induced by telmisartan also may contribute to tumor growth in vivo.

overall_design: Using a custom microarray platform, we analyzed the expression levels of 2555 human miRNA probes in the tumorous tissues in vivo that was treated with and without telmisartan.

first: S

last: Fujihara

first: T

last: Masaki


title: Genome-wide profiling of the Sox chondrogenic trio at E13.5

status: Public on Jun 10 2017

city: Potsdam

first: Thomas

last: Lufkin

state: NY

address: 8 Clarkson Avenue

department: Biology

institute: Clarkson University

summary:
Transgenic mice tagged with EGFP under the control of the endogenous Sox5, Sox6 and Sox9 promoter were used.
E13.5 transgenic embryos were enriched for the skeletal elements and FACS was used to isolate the Sox5/6/9-expressing cells which were used for comparative expression profiling between wildtype and knockout.

overall_design: Total RNA from sorted cells from Sox9 wildtype (3 biological replicates) and Sox9 chimeric knockout (2 biological replicates) embryos were used for comparative analysis. Each genotype had two technical replicates. Sox6 heterozygotes (4 biological replicates) and Sox5-Sox6 double null (2 biological replicates with 2 technical replicates) embryos at E13.5 were used for comparative analysis.

first: Wenqing

last: Lee

first: Sook

last: Yap


title: Genomic and molecular screenings unveil different mechanisms for acquired resistance to MET inhibitors in lung cancer cells

status: Public on May 23 2017

city: L'Hospitalet del Llobregat

first: Sebastian

last: Moran

state: Barcelona

address: Av. Gran Via de l'Hospitalet, 199-203

department: PEBC

country: Spain

institute: IDIBELL

summary: Acquired resistance (AR) is a major hurdle in lung cancer treatment and it is an important drawback in tyrosine kinase inhibitors (TKIs)-based therapeutics. In this context, it is important to unravel the molecular determinants underlying this phenomenon. Our results show molecularly different clones arising during AR to the MET-TKI, many of them involving sensitivity to erlotinib, which supports the known biological crosstalk between MET and the HER-family of receptors. We have also identified inactivation of NF2 in one of the erlotinib-resistant clones. Collectively our findings evidence that AR promote the expansion of multiple subclonal populations with distinct genetic and molecular characteristics highlighting the importance of considering combinatorial therapeutics when designing strategies for second-line treatments in TKI-treated lung cancer patients.

overall_design: The EBC1 cells, which are sensitive to TKIs against MET, were used to generate multiple clones with AR to a MET-TKI. Whole exome sequencing, RNA sequencing and global DNA methylation analysis were used to scrutinize the genetic and molecular characteristics of the resistant cells.

first: Eva

last: Pros

first: Montse

last: Sanchez-Cespedes


title: Gene expression of U937 miR-194-5p cells untreated and upon epigenetic treatments

status: Public on May 22 2017

city: Naples

first: carmela

last: dell'aversana

address: Pietro Castellino 111

institute: IGB - Institute of Genetics and Biophysics - CNR

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

overall_design: Refer to individual Series


summary: Transcriptional profiling of U937 miR-194-5p (UmiR-194-5p) vs U937 miR-194-5p (UmiR-194-5p) treated with MS275 (SNDX 275;Entinostat) for 24 h at 5uM concetration

overall_design: Different Experimental Conditions: U937 miR-194-5p (UmiR-194-5p) (U937 transfected with miR-194-5p vector) vs UmiR-194-5p (U937 transfected with miR-194-5p vector) treated with MS275 for 24 h at 5uM concetration. Two replicates.

first: Carmela

last: Dell'Aversana


title: A low dose of Δ9-THC improves cognitive functions and synaptogenesis in old mice through an epigenetic mechanism

status: Public on May 08 2017

first: Joachim

last: Schultze

summary: THC, the active ingredient of cannabis has been reported to impair learning and memory in humans and in laboratory animals when administered acutely. Unfortunately, most studies have been performed with young individuals although the activity of the endocannabinoid system changes during the aging process. Here we report that low doses of Δ9-THC (Delta-9-Tetrahydrocannabinol) improves learning and memory in old mice, enhances synaptic density, increases the expression of anti-ageing genes and decreases expression of pro-ageing genes in old but not in young animals. Δ9-THC elicited its beneficial effect through the CB1 receptors and increased histone acetylation was crucial for the long lasting effect. Elevation of the cannabinoid signaling may thus represent an exciting new approach to improve brain functions in old individuals.

overall_design: Three-five male 2- and 12-month-old C57BL/6J mice were chronically treated with 3 mg/kg/day Î”9-tetrahydrocannabinol through subcutaneously implanted osmotic minipump (Alzet, Cupertino, CA, model 1004, delivery speed: 0.11 µl/h) for 28 days. Control animals received vehicle (ethanol: cremophor: saline 1:1:18).  Five days after termination of drug treatment the animals were tested in water-mate test (between day 33 and 41). Animals were sacrificed 5 days after the behavioural tests (day 46) by CO2 inhalation, decapitated and their hippocampi were isolated. The hippocampi were snap frozen in dry ice cooled isopentane and stored at -80C until further processing.

first: A

last: Bilkei-Gorzo

first: O

last: Albayram

middle: M

last: Draffehn

last: Piyanova

first: M

last: Dvir-Ginzberg

last: Ulas

first: I

last: Rácz

first: J

middle: L

last: Zimmer


title: Mutant IDH1 regulates the tumor-associated immune system in gliomas

status: Public on May 21 2017

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

summary: Gliomas harboring mutations in isocitrate dehydrogenase 1/2 (IDH1/2) have the CpG island methylator phenotype (CIMP) and significantly longer patient survival time than wild-type IDH1/2 tumors. Although there are many factors underlying the differences in survival between these two tumor types, immune-related differences in cell content are potentially important contributors. In order to investigate the role of IDH mutations in immune response, we created a syngeneic pair mouse model for mutated IDH1 (mutIDH1) and wild-type IDH1 (wtIDH1) gliomas and demonstrated that muIDH1 mice showed many molecular and clinical similarities to muIDH1 human gliomas, including a 100-fold higher concentration of 2-hydroxygluratate (2-HG), longer survival time, and higher CpG methylation compared to wtIDH1. Also, we showed that IDH1 mutations caused downregulation of leukocyte chemotaxis, resulting in repression of the tumor-associated immune system. Given that significant infiltration of immune cells such as macrophages, microglia, monocytes, and neutrophils is linked to poor prognosis in many cancer types, these reduced immune infiltrates in muIDH1 glioma tumors may contribute in part to the differences in aggressiveness of the two glioma types.

overall_design: Ntva_Ink4a/Arf-/- mice were used to generate mouse gliomas. The genetic backgrounds of tva mice are FVB/N, C57BL6, BALB/C, and 129. To generate wtIDH1- and muIDH1-expressing mouse gliomas, we used the RCAS/tva system as described previously. PDGFa-expressing DF1 cells were mixed with either wtIDH1-shp53- or muIDH1-shp53-expressing DF1 cells. These mixed DF1 cells were injected into Ntva_ Ink4a/Arf-/- mice. Mice were monitored daily until they developed signs of illness, such as lethargy, poor grooming, weight loss, dehydration, macrocephaly, seizure, jumping, and/or paralysis. Whole tumor tissue was used for RNA extraction. Total RNA was extracted from tumor tissues using RNeasy Mini kits (QIAGEN).

first: Nduka

last: Amankulor

first: Youngmi

last: Kim

first: Julia

last: Kargl

first: Frank

last: Szulzewsky

first: Mark

last: Hanke

first: Daciana

middle: H

last: Margineantu

first: Aparna

last: Rao

first: Julio

last: Vazquez

first: Hamid

last: Bolouri

first: Jeff

middle: y

last: Delrow

first: David

last: Hockenbery

first: A.

last: Houghton

first: Eric

last: Holland


title: Gene expression profiling of 50 glioblastoma multiforme tissue samples

city: Beijing

first: Lin

last: Feng

overall_design: 50 GBM samples, corresponding to the microscopic sections containing > 50% tumor cells, obtained from patients operated between September 2005 and June 2009, were used for the expression profiling analysis part of the study.

first: Haipeng

last: Qian

first: Xuexin

last: Yu

first: Kan

last: Liu

first: Manchao

last: Kuang

first: Shujun

last: Cheng

first: Jinghai

last: Wan

first: Xueji

last: Li

first: Kaitai

last: Zhang


title: Lineage specific differentiation is influenced by state of human pluripotency [methylation]

status: Public on Apr 26 2017

city: Hamilton

first: Mickie

last: Bhatia

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

institute: McMaster University

summary: Human pluripotent stem cells (hPSCs) have been reported in naïve and primed states. However, the ability of human PSCs to generate mature cell types is the only imperative property for translational utility. Here, we reveal that the naïve state enhances self-renewal capacity while restricting lineage differentiation in vitro to neural default fate. Gene expression analyses indicate expression of multiple lineage associated transcripts in naïve hPSCs and thus failed to predict biased functional differentiation.  Naïve hPSCs can be converted to primed allowing recovery of multilineage differentiation over long serial passage or immediately through suppression of OCT4 but not NANOG. To this end, we identified chemical inhibitors of OCT4 expression that acutely restore naïve hPSC differentiation. Our study identifies unique cell fate features and critical restrictions in human pluripotent states, and provides an approach to overcome these barriers that harness both efficient naïve hPSC growth whilst maintaining in vitro differentiation capacities essential for hPSC applications.

overall_design: hPSC lines were transduced with shRNA lentiviruses in order to assess the effects of reducing NANOG and OCT4 gene expression on differention in the naïve state.  shRNA expressing cells were sorted and then genomic DNA was extracted in order to assess methylation status.

first: Jong

last: Lee


title: The effect of C/EBPepsilon in differentiated granulocytes: cDNA microarray of C/EBPepsilon knock out mice vs C57BL/6 mice bone marrow cells

status: Public on Jun 02 2017

city: St. John's

first: Touati

last: Benoukraf

state: NL

address: Craig L. Dobbin Genetics Research Centre,

department: Faculty of Medicine, Division of BioMedical Sciences

institute: Memorial University of Newfoundland

summary: To identify target genes of C/EBPepsilon in differentiated granulocytes, total RNA were purified from sorted Gr-1intermediate/Mac-1+ and Gr-1hi/Mac-1+ cells of C/EBPepsilon knock out and C57BL/6 wild type mice using RNeasy Mini Kit (Qiagen). The differences of their expression pattern were compared with Illumina Mouse WG-6v2 Expression Chip platform. Raw Illumina BeadArray data in IDAT format were preprocessed using the open-source Bioconductor package illuminaio with the Illumina array design formation BGX file downloaded from NCBI, GEO accession: GPL6887. Following the preprocessing, the expression data were normalized by applying control background correction, log transformation and inter-quantile normalization using the neqc function from the limma bioconductor package. This allowed us to compare the transcriptomic consequences of C/EBPepsilon in two independent populations.

overall_design: Sorted Gr-1intermediate/Mac-1+ and Gr-1high/Mac-1+ bone marrow cells from C/EBPepsilon knock out and C57BL/6 wild type mice

first: Hyung

last: Suh

first: Tong

last: Yin

first: Qi

last: Cao

first: Jonathan

last: Said

first: Stephen

first: Ricky

last: Lim

first: Henry

last: Yang

first: Pavithra

last: Shyamsunder

first: Vikas

last: Madan

first: H

last: Koeffler


title: Identification of GLI1 direct target genes in human prostate cancer cell line PC3

status: Public on Apr 01 2017

city: Aichi

first: Shingo

last: Inaguma

address: Nagakute

department: Department of Pathology and Promoting Center for Clinical Research

institute: Aichi Medical University School of Medicine

summary:
PC3GLI1ER and PC3ER were established from human prostate cancer cell line PC3. PC3GLI1ER cells express a chimeric transgene composed of an enhanced green fluorescent protein (EGFP)-tagged version of the amino-terminal half of GLI1, fused to the AF2 domain of the mouse estrogen receptor 1(Esr1) cDNA. On the other hand, PC3ER harbor only EGFP-tagged AF2 domain.
To identify GLI1 direct target genes, total RNAs were purified from the cells before and 3 hours after the beta-estradiol (E2) treatment.
Gene expression profiles were analyzed by AGILENT human 4x44 cDNA microarray.

Keywords: Expression profiling by array

overall_design: GLI1 direct target genes were identified in PC3 cells. Gene expression profiles of PC3GLI1ER and PC3ER cells were analyzed by AGILENT human 4x44 cDNA microarray before and 3 hours after treatment of beta-estradiol (E2) at doses of 10nM.

first: Kenji

last: Kasai

first: Hiroshi

last: Ikeda


title: Gene expression profiling upon TPO treatment

city: Cambridge

first: Anthony

last: Green

state: Cambridgeshire

address: Hills Road

department: Department of heamatology

country: United Kingdom

institute: University of Cambridge

summary: JAK2 activation by TPO study and its downstream targets STAT1, STAT3 and STAT5 on Mouse HPC7 stem cells on four time points. The aim is to verify wether a JAK/STAT signalling signature is similar to the age-related functional decline in the haematopoietic system.

overall_design: Total RNA was prepared from TPO-treated HPC7 cells at four time points. Samples were collected at 0h (Serum starved – no TPO), 30 minutes, 1 hour and 4 hours. Three replicates were generated per time point.


title: An In Vitro Versus In Vivo Toxicogenomics Investigation of Pre-natal Exposures to Tobacco Smoke [Epiairway]

status: Public on Apr 03 2017

city: Cardiff

first: Iain

last: Perry

state: South Glamorgan

address: Longwood Drive

department: Wales Gene Park

institute: Cardiff University

summary: Lab-grown human bronchial epithelium model (Epiairway) was exposed to cigarette smoke or filtered air. RNA was harvested from the Epiairway tissue and underwent transcriptomic analysis.

overall_design: Two-condition experiment, Cigarette smoke vs. filtered air. 4 biological replicates for each condition of lab-grown human bronchial epithelium model (Epiairway).

first: Keith

last: Sexton

first: Zoe

last: Prytherch

first: Jason

last: Blum

first: Judith

last: Zelikoff

first: Kelly

last: BeruBe


title: U937 scramble (Usc) vs U937 miR-194-5p (UmiR-194-5p)

first: carmela

last: dell'aversana

summary: Transcriptional profiling of U937 scramble vs U937 miR-194-5p (UmiR-194-5p)

overall_design: Different Experimental Conditions: Usc (U937 transfected with empty vector) vs UmiR-194-5p (U937 transfected with miR-194-5p vector). Two replicates.

first: Carmela

last: Dell'Aversana


title: G-CSF plus AMD3100 mobilization in adult patients with beta-thalassemia results in effective mobilization of CD34+ cells with primitive signatures

status: Public on Apr 28 2017

city: Palermo

first: Flavia

last: Contino

address: Viale delle Scienze, Edificio 16

department: Dpt. of Biological, Chemical and Pharmaceutical Sciences and Technologies

institute: University of Palermo

summary: Successful gene therapy for β-thalassemia requires optimal numbers of autologous gene-transduced hematopoietic progenitors stem cells (HPSC) with high repopulating capacity and mobilization is the optimal approach for achieving this goal. We performed a clinical study to investigate safety and efficacy of G-CSF+AMD3100 mobilization in four adult with β-thalassemia to reach a cell dose of ≥8x106 CD34+cells/Kg and to characterize the CD34+cell populations mobilized before and after plerixafor administration.  The procedure resulted well-tolerated in all patients. Three of the four patients reached the target cell dose or more in single-apheresis collections, even one patient where a significant dose reduction of G-CSF was imposed due to early hyperleukocytosis.   A significant increase in the number of circulating CD34+ cells/µl (12.1± 8.2 fold), and in the frequency of the more primitive CD34+/CD133+/CD38- cells (1.7±0.7 fold) was unanimously observed after AMD3100 addiction.  Intraindividual comparison of gene expression profile of CD34+ cells mobilized with G-CSF versus G-CSF+ AMD3100 highlighted a different expression pattern of genes involved in the processes of HSC/stroma adhesion, homing, cell motility and transcription regulation. Overall, the safety profile, the yield, and the expression of genes that potentially promote superior engraftment depict G-CSF+AMD3100 mobilized HSC as optimal graft source for β-thalassemia gene therapy

overall_design: One experiment performed on purified CD34+ PBPC of the same patient 1  after mobilization with G-CSF + Plerixafor , and after mobilization with G-CSF alone. Universal Human Reference RNA (Stratagene, La Jolla, CA), was used as reference.

first: Salvatore

last: Feo


title: Transgenic Plasmodium falciparum blood stage parasites F12/GDV1-GFP-DD: control (-Shield-1;F12/GDV1-GFP-DDOFF) vs GDV1-overexpressing (+Shield-1;F12/GDV1-GFP-DDON) parasites

status: Public on Mar 02 2017

city: Basel

first: Till

middle: Steffen

last: Voss

address: Socinstrasse 59

department: Medical Parasitology and Infection Biology

country: Switzerland

institute: Swiss Tropical and Public Health Institute

summary: Transcriptional profiling of transgenic P. falciparum blood stage parasites expressing an ectopic copy of GDV1-GFP-DD (F12/GDV1-GFP-DD). The DD (FKBP destabilisation domain) allows for the conditional expression of fusion proteins: DD fusion proteins are rapidly degraded or stably expressed in absence or presence of the stabilising ligand Shield-1, respectively (Banaszynski LA, Chen LC, Maynard-Smith LA, Ooi AG, Wandless TJ. A rapid, reversible, and tunable method to regulate protein function in living cells using synthetic small molecules.Cell. 2006 Sep 8;126(5):995-1004). The goal of this experiment was to identify genes differentially expressed in response to induced GDV1 overexpression.

sample_organism:
Plasmodium falciparum
Plasmodium falciparum 3D7

overall_design: P. falciparum clone F12 parasites carrying the pHcam_GDV1-GFP-DD episome were grown in presence of 4nM WR (F12/GDV1-GFP-DDOFF) or 4nM WR/312nM Shield-1 (F12/GDV1-GFP-DDON). RNA extracted from these samples at seven consecutive time points each was processed for microarray analysis.

first: Michael

last: Filarsky

first: Sabine

last: Fraschka

first: Eilidh

last: Carrington

first: Igor

last: Niederwieser

first: Suzette

last: Moes

first: Paul

last: Jenoe

first: Richard

last: Bartfai


title: The Sin3a/HDAC co-repressor complex cooperates with Nanog in promoting stem cell pluripotency and somatic cell reprogramming [Microarray Expression]

status: Public on Feb 21 2017

city: New York

first: Jianlong

last: Wang

state: New York

department: Department of Medicine

institute: Columbia University Irving Medical Center

summary: Despite the requirement of Sin3a for survival of early embryos and embryonic stem cells (ESCs), mechanistic action of Sin3a in the maintenance and establishment of pluripotency remains unexplored. Here we report the transcriptional regulatory roles of Sin3a in maintaining ESC pluripotency and in reprogramming somatic cells towards full pluripotency. Sin3a/HDAC complex members were enriched in an extended Nanog interactome and exhibited a predominant transcriptional co-activator role at a global level in ESCs. We also established a critical role for Sin3a in efficient reprogramming of somatic cells towards full pluripotency. Nanog and Sin3a co-localize at almost all of their genome-wide targets in pre-iPSCs, and both factors are required to directly induce a synergistic transcriptional program wherein pluripotency genes are activated and reprogramming barrier genes are repressed. Our results, for the first time, establish positive roles of the Sin3a/HDAC complex in the maintenance and establishment of pluripotency.

overall_design: Transcriptome analysis was performed for the pre-iPSCs with Nanog or Sin3a ectopic expression in somatic cell reprogramming

first: Arven

last: Saunders

first: Xin

last: Huang


title: Transcriptional response to conditional over-expression of GDV1 in Plasmodium falciparum 3D7 wild type and F12 mutant parasites


title: Manufacturing Differences Affect Human Bone Marrow Stromal Cell Characteristics and Function: Comparison of Production Methods and Products from Multiple Centers

status: Public on May 15 2017

city: BETHESDA

first: PING

last: JIN

state: MD

address: 9000 ROCKVILLE PIKE

department: DTM

institute: CC/DTM/NIH

summary: Human bone marrow stromal cells (BMSCs, also known as bone marrow-derived mesenchymal stem cells) are manufactured using many different methods, but little is known about the spectrum of manufacturing methods used and their effects on BMSC characteristics and function. Seven centers using, and one developing, Good Manufacturing Practices (GMP) processes were surveyed as to their production methods.  Among the seven centers, all used marrow aspirates as the starting material, but no two centers used the same manufacturing methods. Two to four BMSC lots from each center were compared using global gene expression.  Among the twenty-four BMSC lots from the eight centers intra-center transcriptome variability was low and similar among centers.  Principal component and Unsupervised Hierarchical Clustering analysis separated all the lots from five centers into five distinct clusters.  BMSCs from six of the eight centers were tested for their ability to form bone and support hematopoiesis by in vivo transplantation. Those from all six centers tested formed bone, but the quantity formed was variable highly and BMSCs from only three centers supported hematopoiesis. These results show that differences in manufacturing resulted in variable BMSC characteristics including their ability to form bone and support hematopoiesis.

first: Shutong

last: Liu

first: Luis

last: Fernandez de Castro Diaz

first: Ping

last: Jin

first: Sara

last: Civini

first: Jiaqiang

last: Ren

first: Jo-Anna

last: Reems

first: Jose

last: Cancelas

first: Ramesh

last: Nayak

first: Georgina

last: Shaw

first: Timothy

last: O'Brien

first: David

last: McKenna Jr

first: Myriam

last: Armant

first: Leslie

last: Silberstein

first: Adrian

last: Gee

first: Derek

last: Hei

first: Peiman

last: Hematti

first: Sergei

last: Kuznetsov

first: Pamela

last: Robey

middle: F

last: Stroncek


title: Gene expression macrophages in response to LPS/IFN-g

status: Public on May 01 2017

city: New Haven

first: Yajaira

last: Suarez

state: Connecticut

address: 10 Amistad Street

department: Comparative Medicine

institute: Yale University School of Medicine

summary: Analysis of Bone Marrow derived macrophages (BMDMs) incubated in presence of Lipopolysaccharide (LPS) (10ng/ml) + Interferon -gamma (IFN-g) (20ng/ml) for 8 h vs Mock treated controls

overall_design: Total RNA isolated from Bone Marrow derived macrophages incubated in presence of LPS (10ng/ml) + IFN-g (20ng/ml) for 8 h vs Mock treated controls

first: Yajairam


title: The TGF-b superfamily cytokine GDF15 is a CCN2-regulated autocrine/paracrine factor in the heart

status: Public on Feb 19 2017

city: Oslo

first: Ingvild

middle: Tronstad

last: Moe

address: Sognsvannsveien 20

country: Norway

institute: University of Oslo

summary:
Growth differentiating factor (GDF)15 is a TGFβ superfamily cytokine and a reported biomarker of heart failure. Myocardial expression of GDF15 is increased in heart failure. Yet, the mechanisms that control synthesis and release of GDF15 as well as the autocrine/paracrine functions of GDF15 on fibroblast function is lacking. Thus, the aim of this study was to investigate signaling pathways and functions of GDF15  in cardiac fibroblasts.
Cardiac fibroblasts and cardiac myocytes were isolated from adult C57/BL6 mice, maintained in primary culture and stimulated with recombinant (r)GDF15 or recombinant (r)CCN2. Short-term stimulation (30 minutes) of cardiac fibroblasts demonstrated a GDF15-induced activation of several intracellular signaling pathways including a concentration-dependent increase of phospho-Smad3(Ser423/425) (p<0.05, n=3), phospho-AKT(Ser473) (p<0.05, n=3) and phospho-IκBα(Ser32/36) (p<0.05, n=3) levels. However, rGDF15 did not phosphorylate Smad3(Ser423/425) or IκBα(Ser32/36) in cardiac myocyte. Cardiac fibroblasts exposed to rGDF15 for 48 hours displayed differentiation towards myofibroblasts reflected by increased levels of the differentiation marker α-smooth muscle actin (SMA) similar to cardiac fibroblasts stimulated with TGFβ. The effect of GDF15 on α-SMA was dose-dependent ranging from 500 nM - 20 nM rGDF15 (p<0.05, n=3). Differentiation towards a myofibroblast phenotype in the presence of GDF15 was also supported by higher matrix metalloproteinase (MMP) enzyme activity in the cell culture medium (6±1 fold increase, n=3, p<0.05) and increased expression and release of MMP-3, 9 and 13. Immunoreactive GDF15 was predominantly found in cardiac myocytes. Recombinant CCN2 substantially induced GDF15 expression in cardiac myocytes, but not in cardiac fibroblasts.
In conclusion, our data demonstrate that GDF15 is a paracrine factor in myocardial tissue and specifically regulated by CCN2 in cardiac myocytes. GDF15 has similar effects as TGFβ on fibroblasts by activation of intracellular signaling pathways and differentiation to a myofibroblasts phenotype.

overall_design: Gene expression changes between samples treated with GDF15 or CCN2 and untreated control samples.

first: Håvard

last: Attramadal

first: Geir

last: Florholmen

first: Shakil

last: Ahmed

first: Ole

last: Kaasbøll

first: Else

last: Hagelin


title: Gene Expression Analysis of 4T1 orthotopic tumors in PDGFRb-TK mice

status: Public on Mar 09 2017

city: Houston

first: Valerie

last: LeBleu

state: TX

address: 1881 East Road

institute: MDACC

summary: Analysis of the gene expression level of 4T1 orthotopic tumors in mice with and without pericyte depletion.

overall_design: Total RNA obtained from orthopotic 4T1 tumor with and without pericyte genetic targeting (using PDGFRb-TK mice) at early and late stage of tumor progression, and with anti-Ang2 or IgG (control) antibody treatment.

first: Raghu

last: Kalluri


title: Genome-wide survey prior to head formation reveals new insights into the molecular basis of high temperature stress in tolerant and sensitive broccoli genotypes

status: Public on Apr 08 2017

city: Tainan City

first: Chung-Wen

last: Lin

address: No. 1, University Rd

department: Department of Life Sciences

country: Taiwan

institute: National Cheng Kung University

summary: Warmer temperature is predicted to have negative effects on transition from vegetative to reproductive development in plants. The production of floral head in broccoli (Brassica oleracea var. italica) is dramatically reduced because of the high temperature stress. The broccoli inbred lines that are capable of producing head at high temperature in summer are unique varieties in Taiwan. However, knowledge of signalling pathway during the broccoli head formation under heat stress is limited. In this study, heat-tolerance (HT) and heat-sensitive (HS) broccoli genotypes were used to determine the effects of temperatures on the floral head development. We compared the transcription level of the HT and HS genotypes transcriptome under different temperatures ranging from 15 to 27 C. According to weighted correlation network analysis, the high temperature (27 C) activated calcium signalling pathways and mitogen-activated protein kinase cascades in both HT and HS lines. Noticeably, the genes involved in these pathways were expressed to lower level in HT than those of HS. The expression level of genes coding for heat-shock elements was lower in HT than HS. BoFLC1, a key regulator of flowering initiation, was expressed significantly lower in HT at 22 and 27 C but expressed higher in HS. Other FLC homologues were expressed to similar levels between HT and HS.

overall_design: Combimatrix microarray technology were applied to obtain a general overview of the gene expression in shoot meristem of a tolerant and a sensitive broccoli genotype. We analyzed three temperature (15, 22, and 27 degree C) for each genotype. For each sample we performed three biological replicates.

first: C

first: Y

last: Liu

first: S

last: Fu

last: Yang

first: H

last: Huang


title: Validation of the MethylationEPIC BeadChip for fresh-frozen and formalin-fixed paraffin-embedded tumours (EPIC)

city: Gothenburg

first: Helena

last: Carén

address: Medicinaregatan 1F

institute: Gothenburg University

summary: DNA methylation is the most studied epigenetic modification due to its role in regulating gene expression and aberrations in methylation involved in the pathogenesis of cancer and several diseases. The method of choice to evaluate genome-wide methylation has been the Illumina HumanMethylation450 BeadChip (450K), but it was recently replaced with the MethylationEPIC BeadChip (EPIC). We therefore sought to validate the EPIC array in comparison to the 450K array for both fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) pediatric brain tumors. We also performed analysis on the EPIC array with paired FF and FFPE samples, to adapt to a clinical setting where FFPE is routinely used. Further, we compared two restoration methods, REPLI-g and Infinium, for FFPE-derived DNA on the EPIC array.

overall_design: 9 fresh-frozen (FF) pediatric brain tumor samples (tumors T01-T09) were processed on the Illumina 450K and EPIC array to compare the platforms. 9 formalin-fixed paraffin-embedded (FFPE) samples paired to the FF samples (tumors T01-T09) were analyzed on the EPIC array to assess the correlation between FF and FFPE and thereby the suitability of the array in a clinical setting (FFPE samples). Four of the FFPE samples (tumors T01, T06, T08, T09) were restored with both the REPLI-g and Infinium protocol to enable comparison between the methods. Three FFPE samples (tumors T10-T12), restored with REPLI-g, were analyzed with the 450K as well as the EPIC array to compare the platforms for FFPE samples.

first: Teresia

last: Kling

first: Anna

last: Wenger


title: Mesenchymal Transition in Human Mesothelial Cells In Vitro and Ex Vivo

status: Public on Mar 22 2017

city: Madrid

first: Vicente

last: Ruiz-Carpio

address: Nicolás Cabrera, 1

department: Biología Celular e Inmunologia

institute: Centro de Biología Molecular "Severo Ochoa"

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

overall_design: Refer to individual Series


title: Transcriptional heterogeneity of mast cells and basophils upon activation. [mast cells]

status: Public on Mar 17 2017

city: Chicago

first: Paul

last: Bryce

state: IL

address: 420 E Superior Street

institute: Northwestern University Feinberg School of Medicine

summary: We performed large-scale comparative microarrays of bone marrow -derived mast cells and basophils at rest, upon an adaptive-type action (IgE-crosslinking) or upon innate-type activation (IL-33-activation).

overall_design: A total of 24 samples were evaluated in this microarray study. All treatment groups were analyzed in triplicates. Six different groups of bone marrow-derived mast cells (BMMCs) were analyzed. WT or ST2KO BMMCs were either unstimulated, IgE-activated, or IL-33-stimulated. Similarly, six groups of bone marrow-derived basophils (BMBs) were prepared and analyzed in triplicates.

first: Krishan

middle: D

last: Chhiba

first: Chia-Lin

last: Hsu

first: Sergejs

last: Berdnikovs


status: Public on May 22 2017

city: Naples

first: carmela

last: dell'aversana

address: Pietro Castellino 111

institute: IGB - Institute of Genetics and Biophysics - CNR

summary: Transcriptional profiling of U937 miR-194-5p (UmiR-194-5p) vs U937 miR-194-5p (UmiR-194-5p) treated with SAHA (Vorinostat; suberoylanilide hydroxamic acid) for 24 h at 5uM concetration

overall_design: Different Experimental Conditions: U937 miR-194-5p (UmiR-194-5p) (U937 transfected with miR-194-5p vector) vs UmiR-194-5p (U937 transfected with miR-194-5p vector) treated with SAHA for 24 h at 5uM concetration. Two replicates.

first: Carmela

last: Dell'Aversana


title: Transcriptional heterogeneity of mast cells and basophils upon activation.

middle: J

summary: Mast cells and basophils are developmentally related cells whose activation is a hallmark of allergy. Functionally, mast cells and basophils overlap in their ability to produce several mediators, including histamine and granule proteases, but studies have increasingly demonstrated non-redundant roles. To characterize the transcriptional heterogeneity of mast cells and basophils upon their activation, we performed large-scale comparative microarrays of murine bone marrow–derived mast cells (BMMCs) and basophils (BMBs) at rest, upon an adaptive-type activation (IgE crosslinking), or upon an innate-type activation (IL-33 stimulation). Hierarchical clustering demonstrated that BMMCs and BMBs shared specific activation-associated transcriptional signatures but differed in others, both between cell type and between activation mode. In BMMCs, IgE crosslinking upregulated 785 genes including Egr2, Ccl1, and Fxyd6, while IL-33 stimulation induced 823 genes including Ccl1, Egr2, and Il1b. Focused bioinformatics pathway analysis demonstrated that IgE activation aligned with processes such as oxidative phosphorylation, angiogenesis, and the p53 pathway. The IL-33–activated transcriptome was enriched in genes commonly altered by NF-B in response to TNF, by IL-6 via STAT3, and in response to IFN. Furthermore, BMBs activated via IgE crosslinking selectively induced immune response genes Ccl1, Il3, and Il2 compared to IL-33–stimulated BMBs. Principal-component analysis revealed key cell- and activation-specific clustering. Overall, our data demonstrate that mast cells and basophils have cell- and activation-specific transcriptional responses and suggest that context-specific gene networks and pathways may shape how the immune system responds to allergens and innate cytokines.


title: Transcriptional heterogeneity of mast cells and basophils upon activation. [basophils]


title: Effects of far-infrared rays on normal prostate epithelial cells (PrEC)

status: Public on Mar 14 2017

city: Osaka

first: Hiroki

last: Shima

address: 3-7-41 Nakatsu YAMAMOTO  Bild. 4F. Kitaku

institute: SHIMA Institution for Quantum Medicine

summary: Far-infrared rays activated DNA repair genes in human prostate epithelial cells after 7 or 12 days' exposure to far-infrared rays.  As far-infrared rays emitter, synthetic/natural rubber (RB) was used.

overall_design: Two-condition experiment, RB-treated vs. non-RB-treated cells: 2 reference control without RB, independently grown and harvested. One replicate per array. Channels 1 were exposed to RB.

first: Jun

last: Qiu

first: Yoshie

last: Yoshikawa


title: Identification of GLI1 direct and indirect target genes in human pancreatic cancer cell line Panc-1

first: Shingo

last: Inaguma

summary:
Panc-1GLI1ER and Panc-1ER were established from human pancreatic cancer cell line Panc-1. Panc-1GLI1ER cells express a chimeric transgene composed of an enhanced green fluorescent protein (EGFP)-tagged version of the amino-terminal half of GLI1, fused to the AF2 domain of the mouse estrogen receptor 1(Esr1) cDNA. On the other hand, Panc-1ER harbor only EGFP-tagged AF2 domain.
To identify GLI1 direct target genes, total RNAs were purified from the cells before and 24 hours after the beta-estradiol (E2) treatment.
Gene expression profiles were analyzed by AGILENT human 4x44 cDNA microarray.

Keywords: Expression profiling by genome tiling array

overall_design: GLI1 direct and indirect target genes were identified in Panc-1 cells. Gene expression profiles of Panc-1GLI1ER and Panc-1ER cells were analyzed by AGILENT human 4x44 cDNA microarray before and 24 hours after treatment of beta-estradiol (E2) at doses of 10nM.

first: Kenji

last: Kasai

first: Hiroshi

last: Ikeda


title: Mesenchymal Transition in Human Mesothelial Cells In Vitro and Ex Vivo [Epitheliod vs Non-Epitheliod]

summary: Peritoneal dialysis (PD) is an effective form of renal replacement therapy. A significant proportion of patients who initiate PD suffer from PD-related clinical complications, including peritoneal membrane damage, which may limit the duration of treatment. Mesothelial-to-mesenchymal transition (MMT) significantly contributes to the peritoneal dysfunction related to PD. Hence, we analyzed the genetic reprograming of the MMT-process with the aim to identify new biomarkers that may be tested in PD-patients. Microarray analysis revealed a partial overlapping of MMT induced in vitro and MMT of effluent-derived mesothelial cells (ex vivo), and that MMT, both in vitro and ex vivo, is mainly a repression process being higher the number of genes that are down-regulated than those that are induced. According to cellular morphology and the number of altered genes and pathways, the MMT ex vivo could be subdivided into two stages: early/epitheliod and advanced/non-epitheliod. We could demonstrate by RT-PCR array analysis that a number of genes differentially expressed in effluent-derived non-epitheliod cells also showed significant differential expression when comparing standard versus low-GDP PD fluids. Among the secreted proteins that are up-regulated along the MMT process thrombospondin-1 (TSP1), collagen-13 (COL13), vascular endothelial growth factor A (VEGFA), and gremlin-1 (GREM1) were selected to be measured in PD effluents. TSP1, COL13 and VEGFA, but not GREM1, showed significant differences between early and advanced stages of MMT, and their expression were associated with high peritoneal transport status. The results establish a proof of concept about the feasibility of MMT-associated secreted proteins as biomarkers in PD.

overall_design: Two approach: in vitro model, with two-condition experiment, HPMC vs. HPMC treated with TGF-β1 and IL-1β; ex vivo model, with three-condition experiment, HPMC vs. Epithelioid HPMC and HPMC vs. Non-Epithelioid HPMC. Biological samples: in vitro model, two control samples and two treated cells samples; ex vivo model, 1 control sample, 8 Non-Epithelioid samples and 9 Epithelioid samples. This series contains the HPMC vs. Epithelioid HPMC and HPMC vs. Non-Epithelioid HPMC.samples.

first: Manuel

last: López-Cabrera

first: Pilar

last: Sandoval

first: Pedro

last: Botías

first: Jesús

last: García-Cantalejo


title: An In Vitro Versus In Vivo Toxicogenomics Investigation of Pre-natal Exposures to Tobacco Smoke

first: Iain

middle: A

last: Perry


title: Transcriptome profiling of vascular tissues in Angiotensin II-dependent hypertension in vivo

status: Public on Feb 20 2017

city: Kraków

first: Mateusz

last: Siedliński

address: Skarbowa 1

country: Poland

institute: Jagiellonian University Medical College

summary: We hypothesized that angiotensin II (AngII) affects transcriptome in the vasculature in a region-specific manner, which may help to identify genes causally related to the development of AngII-induced hypertension. This work was supported by the National Science Centre grant (decision no. DEC-2012/07/D/NZ4/00644).

overall_design: Transcriptome of thoracic aorta, abdominal aorta and mesenteric arteries was profiled in C57BL/6J wild-type hypertensive mice infused with AngII (490 ng/kg/min) for 2 weeks and control mice using Illumina WG-6 v2.0 chip.

last: Siedlinski

first: Tomasz

last: Guzik


title: Microarray analysis of CD9high and CD9low progenitors isolated from adipose tissue

status: Public on Mar 28 2017

city: paris

first: veronique

last: PELLOUX

address: 50-52 bld Vincent Auriol

department: UMR 1166 eq 6

country: France

institute: INSERM


title: MicroRNAs circulate in the hemolymph of Drosophila and accumulate relative to tissue microRNAs in an age-dependent manner [miRNA]

status: Public on Feb 09 2017

city: Elk Grove

first: joseph

last: dhahbi

state: ca

address: 9700 West Taron Drive

department: Medical Education

institute: California Northstate University College of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: In mammals, extracellular miRNAs circulate in biofluids as stable entities that are secreted by normal and diseased tissues, and can enter cells and regulate gene expression. Drosophila melanogaster is a proven system for the study human diseases. They have an open circulatory system in which hemolymph (HL) circulates in direct contact with all internal organs, in a manner analogous to vertebrate blood plasma. Here we show using deep sequencing that Drosophila HL contains RNase resistant, circulating miRNAs (HL-miRNAs). Limited subsets of body tissue miRNAs (BT-miRNAs) accumulated in HL, suggesting they may be specifically released from cells or particularly stable in HL. Alternatively, they might arise from specific cells such as hemocytes, in intimate contact with HL. Young and old flies accumulated unique populations HL-miRNAs, suggesting their accumulation is responsive to the physiological status of the fly. These HL-miRNAs may function in flies similarly to the miRNAs circulating in mammalian biofluids. The discovery of these HL-miRNAs will provide a new venue for health and disease-related research in Drosophila.

overall_design:
Examination of miRNA levels in hemolymph and body tissues of young and old Drosophila melanogaster.

Fastq file files are not available for this record due to loss after a hard drive crash. Each sample contains a supplementary FASTA file with trimmed read sequences.

first: J

last: Dhahbi


title: The gene expression of HCC cells and HCC cells knocked down TMED3

city: shanghai

first: hao

last: zhen

address: The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, 225 Changhai Road, Shanghai 200438, China

summary: We report that TMED3 was up-regulated in HCC and portal vein tumor thrombus. Gene microarray analysis TMED3-knockdown cells and normal HCC cell.

overall_design: Knocked down TMED3 by virus in HCC cells

first: Hao

last: Zheng


title: Identification of GLI1 direct and indirect target genes in human prostate cancer cell line PC3

status: Public on Apr 01 2017

city: Aichi

address: Nagakute

institute: Aichi Medical University School of Medicine

summary:
PC3GLI1ER and PC3ER were established from human prostate cancer cell line PC3. PC3GLI1ER cells express a chimeric transgene composed of an enhanced green fluorescent protein (EGFP)-tagged version of the amino-terminal half of GLI1, fused to the AF2 domain of the mouse estrogen receptor 1(Esr1) cDNA. On the other hand, PC3ER harbor only EGFP-tagged AF2 domain.
To identify GLI1 direct target genes, total RNAs were purified from the cells before and 24 hours after the beta-estradiol (E2) treatment.
Gene expression profiles were analyzed by AGILENT human 4x44 cDNA microarray.

Keywords: Expression profiling by array

overall_design: GLI1 direct and indirect target genes were identified in PC3 cells. Gene expression profiles of PC3GLI1ER and PC3ER cells were analyzed by AGILENT human 4x44 cDNA microarray before and 24 hours after treatment of beta-estradiol (E2) at doses of 10nM.


title: Sixty Glioblastoma Multiforme (GBM) samples obtained from surgical excision with OS and PFS

status: Public on Feb 11 2017

city: Harbin

first: Xuexin

last: Yu

address: Xuefu Road

department: College of Bioinformatics Science and Technology

institute: Harbin Medical University

summary: To further development of our gene expression signature for survival prediction, we conducted expression profiles of GBM patient samples.

overall_design: Sixty GBM samples with overall survival (OS) and progression-free survival (PFS) information were obtained during surgical resection from Tian Tan Hospital from 2008 to 2010.

first: Shujun

last: Cheng


title: Microarray analysis of CD9high and CD9low progenitors isolated from epididymal adipose from lean C3H/HeOuJ mice

summary: Obesity-induced white adipose tissue (WAT) fibrosis is believed to accelerate WAT dysfunction. However, the cellular origin of WAT fibrosis remains unclear. We showed that adipocyte platelet-derived growth factor receptor-a-positive (PDGFRa+) progenitors adopt a fibrogenic phenotype in obese C3H/HeOuJ (C3H) mice prone to visceral WAT fibrosis. Two progenitor populations could be distinguished in the epididymal white adipose tissue (EpiWAT) of lean C3H mice, based on CD9 expression. In the fibrotic EpiWAT of obese C3H animals, the PDGFRa+CD9low subset is almost completely lost while the density of PDGFRa+CD9high progenitor markedly increase. To further gain insight into the functional differences between the CD9high and CD9low progenitor subsets, we performed transcriptomic profiling of FACS-sorted progenitor populations isolated from EpiWAT of lean C3H mice.

overall_design: EpiWAT from 3-month-old C3H mice was digested with collagenase. CD9high and CD9low progenitors from the stromal vascular fraction were FACS-sorted with CD45- CD31- Gp38+ PDGFRa+ CD9high and CD45- CD31- Gp38+ PDGFRa+ CD9high. Total RNA was amplified and labeled using Ovation Pico WTA System V2 (NuGEN) and Encore BiotinIL Module (NuGEN) kits according to the manufacturer’s protocol.

first: Genevieve

last: Marcelin

first: Veronique

last: Pelloux

first: Karine

last: Clement


title: Whole Genome microarray analysis BMDMs from cmo (Pstpip2 functional knockout), cmo IL1R+/-, and cmo IL-1R-/- mice.

status: Public on Mar 01 2017

city: Iowa City

first: Polly

last: Ferguson

state: IA

address: 25 South Grand Ave

department: Pediatrics

institute: University of Iowa

summary:
Because the cmo mouse (model of human CRMO) is protected from disease on an IL1R-/- background, a gene expression microarray experiment was performed to determine which genes are potentially involved in the pathogenesis of disease in the context of the absence of IL1R activity.
RNA was extracted from cultured bone marrow-derived macrophages from the three mouse strains and analyzed for differential gene expression.

overall_design: RNA from three mice was used for the three different strains (cmo, cmo IL1R+/-, IL1R-/-), for a total of 9 samples.

first: Allison

last: Cox


title: Transgenic Plasmodium falciparum blood stage parasites 3D7/GDV1-GFP-DD: control (-Shield-1;3D7/GDV1-GFP-DDOFF) vs GDV1-overexpressing (+Shield-1;3D7/GDV1-GFP-DDON) parasites

status: Public on Mar 02 2017

city: Basel

first: Till

last: Voss

address: Socinstrasse 59

institute: Swiss Tropical and Public Health Institute

summary: Transcriptional profiling of transgenic P. falciparum blood stage parasites expressing an ectopic copy of GDV1-GFP-DD (3D7/GDV1-GFP-DD). The DD (FKBP destabilisation domain) allows for the conditional expression of fusion proteins: DD fusion proteins are rapidly degraded or stably expressed in absence or presence of the stabilising ligand Shield-1, respectively (Banaszynski LA, Chen LC, Maynard-Smith LA, Ooi AG, Wandless TJ. A rapid, reversible, and tunable method to regulate protein function in living cells using synthetic small molecules.Cell. 2006 Sep 8;126(5):995-1004). The goal of this experiment was to identify genes differentially expressed in response to induced GDV1 overexpression.

overall_design: P. falciparum strain 3D7 parasites carrying the pHcam_GDV1-GFP-DD episome were grown in presence of 4nM WR (3D7/GDV1-GFP-DDOFF) or 4nM WR/312nM Shield-1 (3D7/GDV1-GFP-DDON). RNA extracted from these samples at seven consecutive time points each was processed for microarray analysis.

first: Michael

last: Filarsky

first: Sabine

last: Fraschka

first: Eilidh

last: Carrington

first: Igor

last: Niederwieser

first: Suzette

last: Moes

first: Paul

last: Jenoe

first: Richard

last: Bartfai


title: Expression profiling of primary oral cavity squamous cell carcinoma (OSCC)

status: Public on Aug 10 2017

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

type:
Expression profiling by array
Third-party reanalysis

summary: Gene expression profiling of 66 HPV-negative OSCC primary tumor was performed to identify gene expression that is related to lymph node metastasis and poor prognosis. These gene expression profiles were combined in silico with gene expression profiles of 84 OSCC primary tumors retrieved from GSE30788.

overall_design: Dual-color experiment of 66 samples combined with a reanalysis of 84 samples from GSE30788

first: Steven

last: Mes

first: Dennis

last: te Beest

first: Wessel

last: van Wieringen

first: Elisabeth

last: Bloemena

first: Arjen

last: Brink

first: François

last: Rustenburg

last: van Diest

first: C

middle: R

last: Leemans

first: Mark

last: van de Wiel

first: Ruud

last: Brakenhoff


title: Development of colorectal cancer gene expression signatures from expression profiles of embryonic development, precancer progression and cancer samples

city: Beijing

first: Kaitai

last: Zhang

state: Beijing

address: NO. 17, Pan Jiayuan South, Chao Yang District

department: Department of Etiology and Carcinogenesis

institute: Peking Union Medical College & Cancer Institute (Hospital), Chinese Academy of Medical Sciences

summary: To further development of our gene expression signature for survival prediction, we conducted expression profiles of embryonic development, precancer progression and cancer samples.

overall_design: Developing colon was obtained from 20 cases of abortion in Maternal & Child Health Care Hospital of Hai Dian between 2007 and 2009. The samples included whole embryos (WE) at 3 to 5 postovulatory weeks (PWs), early embryonic colons (EEC) at 8 to 10 PWs and middle embryonic colons (MEC) at 14 to 22 PWs.Normal colorectal mucosae samples were collected from patients with hemorrhoids who received surgical excision in the Department of Colon and Rectal Surgery of Beijing Shi Ji Tan Hospital between 2009 and 2010. Fifty two CRC samples with overall survival (OS) information were obtained as surgically excised specimens from Zhe Jiang University School of Medicine. Colonoscopy biopsy samples, including colorectal adenomas and adenocarcinomas were obtained from the Department of Endoscopy, Cancer Hospital, Chinese Academy of Medical Sciences, between 2008 and 2011.

first: An

last: Ning

first: Zhang

last: Kaitai


title: Genomic, epigenomic, and transcriptomic profiling towards identifying omics-features and specific biomarkers that distinguish uterine leiomyosarcoma and leiomyoma at molecular levels (expression)

city: Fukuoka

first: Tomoko

last: Miyata

state: Fukuoka

address: 3-1-1 Maedashi, Higashi-ku

department: Gynecology and Obstetrics

institute: Kyushu University

summary: Uterine leiomyosarcoma (LMS) is the worst malignancy among the gynecologic cancers. Uterine leiomyoma (LM) is a benign tumor of myometrial origin and is the most common among women of childbearing age. Because the symptoms of women with LMS such as abnormal vaginal bleeding, palpable pelvic mass, and pelvic pain resemble with those of women with LM, it is difficult to preoperatively distinguish LMS and LM only by ultrasound and pelvic MRI. While histopathological diagnosis after hysterectomy is the current major means to distinguish them postoperatively, unusual histologic variants of LM tend to be misdiagnosed as LMS. Furthermore, the low incidence of LMS has been preventing elucidating its causal mechanisms and developing effective diagnoses and treatments. Therefore, development of molecular diagnosis as an alternative or confirmatory means helps diagnosing LMS more accurately. We adopted omics-based technologies to identify genome-wide features to distinguish LMS from LM, and revealed that copy-number, gene expression, and DNA methylation profiles successfully distinguished between these tumors. LMS was found to possess features typically observed in malignant solid tumors, such as extensive chromosomal abnormalities, overexpression of cell cycle –related genes, and hypomethylation spreading through large genomic regions as well as frequent hypermethylation at polycomb group target gene and cadherin gene loci. We also identified candidate expression and DNA methylation markers, which will help establishing diagnostic tests using conventional quantitative assays. While the identified omics-signatures and certain markers specific to LMS need to be further validated in larger numbers of LM and LMS samples, our results demonstrate the practical feasibility of establishing a postoperative diagnostic test to distinguish LMS from LM with high accuracy, and also suggest the future possibility of developing preoperative and non-invasive diagnostic methods.

overall_design: Gene expression data of human normal uterine myometrium (3 samples), human uterine leiomyoma (3 samples), human uterine leiomyosarcoma (3 samples), and three cell lines of human uterine leiomyosarcoma (SKN, SK-UT-1, SK-UT-1B) were generated with Whole Human Genome Microarray Kit, 4x44K (Agilent).

first: Kazuhiko

last: Nakabayashi


title: Gene coexpression network and community detection analyses of CA3 trascriptome reveal distinct pathogenic and compensatory pathways in early and late onset febrile forms of temporal lobe epilepsy

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

country: Brazil

institute: Faculdade de Medicina da Universidade de Sao Paulo

summary: Prolonged febrile seizures history (FH) in early childhood is associated with refractory temporal lobe epilepsy (RTLE). FH-RTLE patients may have early (E, before 4 YOA) or late (L, mid-adolescence, early adult life) disease onset.  In order to investigate molecular mechanisms underlying E and L forms we compared  differentially expressed (DE) and complete (CO) transcriptional networks from hippocampal CA3 explants obtained from E and L patients.

overall_design: CA3 transcriptomic profiles of early and late onset febrile forms of temporal lobe epilepsy were compared in order to identify differentially expressed transcripts.

first: Silvia

middle: Y

last: Bando

first: Fernanda

middle: B

last: Bertonha

first: Priscila

last: Iamashita

first: Filipi

middle: N

last: Silva

first: Luciano

last: Costa

first: Alexandre

middle: V

first: Luiz

last: Castro

first: Wen

last: Hung-Tzu


title: Gene expression analysis of Lgr5-GFP-expressing cells in the adult mammary gland

status: Public on Feb 01 2017

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Epigenetics and Development Division

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

summary: The aim of this study is to identify genes that are differentially expressed in basal cell populations with different levels of Lgr5 gene expression. Samples were isolated from adult mouse mammary glands.

overall_design: Total RNA was isolated and up to 125 ng of total RNA per sample was labelled and hybridized to the Illumina MouseWG-6 v2.0 expression BeadChip platform. Three replicate samples were analysed for each population (Lgr5+ basal, Lgr5- basal, luminal).

first: Nai

last: Fu

middle: E

first: Geoffrey

last: Lindeman

first: Jane

last: Visvader


title: Effect of IL-7 on CD4+ T cell and Th9 cells

status: Public on Feb 06 2017

city: CLEVELAND

first: ENGUANG

last: BI

state: OH

address: 9500 EUCLID AVE

department: CANCER BIOLOGY

country: USA

institute: CLEVELAND CLINIC LERNER RESEARCH INSTITUTE

summary: We found that IL-7 pretreatment enhanced Th9 differentiation. To clarify the underlying mechanisms, we examine the gene expression profiles of CD4+ T cell and Th9 cells with or without IL-7 pretreatment. In Th9 cells, we found that Th9 related genes were greatly increased in IL-7 Th9 group, which demonstrated an enhanced Th9 differentiation.  In CD4+ T cells, we found that IL-7 treatment resulted in a global gene expression change especially on chromatin remodeling related genes, which facilitated the entry of transcriptional factor to the Il9 promoter region and promoted Il9 transcription.

overall_design: Total RNA obtained from naïve CD4+ T cells or Th9 cells from C57BL/6 mice with or without IL-7 treatment; For CD4+ T cells, IL-7 treated for 0h, 6h or 24h. For Th9 cells, naïve CD4+ T cells were treated for 48h and then cultured for 3 days under Th9 condittion.

first: Enguang

last: Bi

first: Qing

last: Yi


title: Comparative transcriptomics reveals gain of proliferative capacity in addition to tumor-promoting mechanisms by tumor-associated macrophages in murine chronic lymphatic leukemia

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Tumor-associated macrophages (TAM) are a major component of the tumor microenvironment linked to reduced survival in most tumor entities. Using comparative transcriptomics between macrophages derived from spleen and bone marrow at pre-leukemic and leukemic state, we revealed profound re-programming of macrophages during leukemogenesis neither associated with M1-like nor M2-like macrophage programs. Instead, major transcriptional changes were linked to gain of proliferative capacity and loss of phagocytic mechanisms which we experimentally validated in vivo in mice and in vitro in humans. Using Mif-/- mice as a model for reduced tumor burden and prolonged survival of leukemic mice, we demonstrate that transcriptional programs in TAM are further shaped by such environmental factors enhancing tumorigenic effects. Comparative transcriptomics of macrophages within the same tissue at pre-malignant and malignant state lead to the identification of important macrophage-mediated suppressive mechanisms that can form a basis for the development of novel cancer diagnostics and therapeutics.

overall_design: F4/80 macrophages were isolated by FACS-sorting from bone marrow or spleen either prior leukemia or during leukemia in Eµ-TCL1 transgenic mice. In some experiments F4/80+ macrophages were isolated from Mif-/- mice.  After the sort, cells were immediately lysed in Trizol (Invitrogen) before storage at -80°C for RNA isolation.

first: C

last: Pallasch

first: T

last: Ulas

first: N

last: Reinart

first: J

last: Schwamb

first: V

last: Ristovska

first: M

last: Beyer

last: Mallmann

first: L

last: Heukamp

first: S

last: Schmidt

last: Hallek M


title: Gene expression profiling of prostate infiltrating hematopoietic cells in TRAMP mice subjected to immunotherapy

status: Public on Jan 23 2017

city: Milano

first: Michela

last: Riba

address: via Olgettina 60

department: COSR, Center for Omics Sciences

country: Italy

institute: IRCCS, Ospdale San Raffaele

summary: Goal of the analysis was to identify the mechansisms accounting fo the synergy of T cells redirected to the tumor associated large T antigen and T cells redirected to the Uty minor histocompatibility antigen

overall_design: Gene expression profiling on CD45+ cells isolated from the prostate of mice treated with Allo/Y, Tumor or Tumor+Allo/Y ACT at one week after T cell transfer, the time of acute prostate infiltration. Samples recovered from mice treated with the combined Tumor+Allo/Y ACT and sacrificed after 28 days were also included in the experimental design to take into account changes occurring over time. Three mice per group were used.

first: Tabea

last: Sturmheit

first: Anna

last: Mondino


title: Gene expression analysis of the liver of MAT1A WT and MAT1A KO mice treated with placebo or SAMe during 8 weeks

status: Public on Feb 02 2017

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

institute: CIC bioGUNE

summary: Methionine adenosyltransferase (MAT) enzymes generate SAMe (S-adenosylmethionine), the main biological methyl donor. There are two MAT encoding genes in mammals (Mat1a and Mat2a), which show different activities and cellular distribution. Mat1a encodes the enzyme mainly expressed in normal liver. Mat1a ablation in mice results in the spontaneous development of non-alcoholic steatohepatitis (NASH). We observed that SAMe depletion in Mat1a KO mice had three main effects on hepatic lipid metabolism: 1) impaired TG (triglyceride) export via VLDL; 2) impaired mitochondrial FA (fatty acid) oxidation (as evidenced by membrane depolarization, downregulation of Phb1 (prohibitin 1, a mitochondrial chaperone protein) and Mcj/Dnajc15 (endogenous mitochondrial repressor of respiratory chain), and accumulation of long-chain acylcarnitines); and 3) increased FA uptake. The convergence of these three factors induced TG accumulation in LD (lipid droplets). LD expansion confronts hepatocytes with a high demand of PC (phosphatidylcholine) molecules to cover the LD surface since other phospholipids, such as PE (phosphatidylethanolamine), cannot stabilize LD and prevent coalescence. In Mat1a KO this situation is aggravated, since SAMe-dependent PC synthesis via PE methylation is decreased, the PC/PE ratio reduced and mitochondrial FA oxidation impaired. To put a brake to this drain of PC molecules to LD, FA are rerouted in Mat1a KO mice liver to other catabolic (endoplasmic reticulum and peroxisome oxidation) and biosynthetic (ceramides synthesis) pathways, causing oxidative stress, inflammation and fibrosis. SAMe treatment for two months in 8-9 month old Mat1a KO mice ameliorated mitochondrial dysfunction (reduces membrane depolarization, improves Phb1 and Mcj expression, and increases SAMe transport to mitochondria) improving FA oxidation efficiency (FA and acylcarnitine levels decrease), which results in a drastic reduction in TG accumulation. SAMe treatment in Mat1a KO mice resulted in more PC available for proper membrane function, improving liver lipid homeostasis, histology (H&E, Sudan red, Sirius red) and liver injury (ALT, AST).

overall_design: Genome-wide changes in gene Expression in MAT1A WT and KO mice treated or not with SAMe were generated by microarray gene expression arrays.

first: José

last: Mato


title: Whole genome transcriptional profile of PyMT/SIRT6 vs PyMT mammary tumors

status: Public on Jan 20 2017

city: Verona

first: Mirco

last: Galiè

address: via Le Grazie, 8

department: Neuroscience, Biomedicine and Movement Sciences

institute: University of Verona

summary: We compared the transcriptional profile of mammary tumors spontaneously developed in PyMT transgenic mice either bearing or not additional copies of the endogeneous SIRT6 gene.

overall_design: We crossed genetically-engineered mice overexpressing functionally competent SIRT6 protein (Sirt6BAC mice) (Anderson et al., 2015) to PyMT mice. PyMT-transgenic females either bearing Sirt6BAC allele or wild-type were sacrified at 12 weeks of age. Mammary tumors spontaneously developd in these mice were excised and subject to micorarray analysis.


title: TGF-beta/atRA induced Tregs express a selected set of microRNAs involved in the repression of transcripts related to Th17 differentiation [mRNA]

city: Ribeirao Preto

first: Rodrigo

middle: Alexandre

last: Panepucci

state: São Paulo

address: R. Tenente Catao Roxo, 2501

institute: Regional Blood Center of Ribeirâo Preto (FUNDHERP, HC-FMRP-USP)

summary: Regulatory T cells (Tregs) are essential regulators of immune tolerance. In light of its potential therapeutic use, in conditions involving transplant rejection and autoimmune disorders, understanding the mechanisms involved in the polarization between inflammatory and regulatory cells is of great importance. Although several studies have shown that atRA and TGF-β can inhibit the polarization of naïve T cells into inflammatory Th17 cells, favoring the generation of stable FOXP3 expressing iTregs, the exact regulatory mechanisms involved are not fully understood. Increasing evidences have suggested several roles for microRNAs in the development and function of different types of T helper cells; however, the roles of individual microRNAs in Tregs function and development are largely unexplored. Here, we explored how atRA may post-transcriptionally regulate distinct signaling pathways, through the induction of specific microRNAs, controlling the balance between Th17 and T regulatory cells. For this, CD4+CD25-CD45RA+ naïve T cells were immunomagnetically isolated from umbilical cord blood and activated with anti-human CD2/CD3/CD28 beads in the presence of IL-2 alone (CD4Med) or with the addition of TGF-β and atRA (CD4TGF/atRA). Immunophenotyping by flow cytometry, whole genome mRNAs and microRNAs profiling and functional characterizations were performed. We report the generation of highly suppressive CD4+CD25hiCD127-FOXP3+ iTregs in the CD4TGF/atRA condition, that exclusively express a set of microRNAs predicted to target important signaling pathways, including PI3K/Akt, mTOR, Toll-Like Receptor, and IL-6/Jak/Stat. Accordingly, percentages of IL-17 and STAT3 expressing cells were strikingly reduced in CD4TGF/atRA condition. Microarray and qPCR results showed that the expression of IL6R, IL6ST, JAK1 and STAT3 (heavily targeted by identified miRs) are all downregulated in CD4TGF/atRA, as compared to CD4med and naïve T cells. Finally, we show that selected synthetic mimics (namely, miR-23a, -30a, -636 and -1299) are able to knockdown IL6R and IL6ST transcript levels, functionally inhibiting IL-17 expression and favoring the generation of FOXP3+ cells. Our work adds novel evidences supporting the central roles played by microRNAs in the post-transcriptional regulation of major pathways involved in the generation and function of regulatory T cells.

overall_design: In order to identify potential microRNA/mRNA regulatory mechanisms involved in the specific roles of TGF-β and atRA in the generation of iTregs, we evaluated and compared the microRNA and mRNA expression profiles of fleshly isolated umbilical cord blood (UCB) naïve T cells and of cells activated with anti-human CD2/CD3/CD28 beads in the presence of IL-2 alone (CD4Med) or with the addition of TGF-β and atRA (CD4TGF/atRA). Microarray profiling was performed for freshly isolated naïve T cells and the corresponding CD4TGF/atRA and CD4Med cells, derived in culture, from three UCB samples (totaling 9 microarray profiles).

first: Josiane

middle: L

last: Schiavinato

last: Haddad

first: Felipe

last: Saldanha-Araujo

first: João

last: Baiochi

first: Amélia

middle: G

last: Araújo

first: Priscila

last: Scheucher

first: Dimas

middle: T

last: Covas

first: Marco

last: Zago