title: Effect of Foxd1 knockdown in the reprogramming process

city: Barcelona

first: Miki

last: Ebisuya

address: PRBB Building, C/ Dr. Aiguader, 88

department: EMBL Barcelona

institute: EMBL

summary: It remains unclear how the ectopic expression of defined transcription factors induces dynamic changes in gene expression profiles that establish a pluripotent state during direct cell reprogramming. In the present study, we first identified a temporal gene expression program during the reprogramming process. Promoter analyses then predicted the role of two forkhead box transcription factors, Foxd1 and Foxo1, as mediators of the gene expression program. Knockdown of Foxd1 or Foxo1 reduced the number of induced pluripotent stem cells (iPSCs). The knockout of Foxd1 prevented the downstream transcription program, including the expression of reprogramming marker genes. Interestingly, the expression level of Foxd1 was also transiently increased in a small population of cells in the middle stage of reprogramming. The presence or absence of Foxd1 expression in this stage was correlated with a future cell fate as iPSCs or non-reprogrammed cells. These results suggest that Foxd1 is a mediator and indicator of the successful progression of the gene expression program in cell reprogramming.

overall_design: Mouse embryonic fibroblasts (MEFs) of Foxd1+/+, Foxd1+/- or Foxd1-/- were infected with retroviruses encoding the three transcription factors (Oct4, Sox2 and Klf4) at day 0 and sampled at day 8.

first: Makito

last: Koga

first: Mitsuhiro

last: Matsuda

first: Teruhisa

last: Kawamura

first: Takahiro

last: Sogo

first: Asako

last: Shigeno

first: Eisuke

last: Nishida


title: Inducible expression of MyoD directly mediates myogenic conversion of human induced pluripotent stem cells (iPSCs) derived from Duchenne muscular dystrophy (DMD).

status: Public on Jan 09 2014

city: San Diego

first: Dave

last: Robbins

state: CA

address: 3535 General Atomics Court Ste. 200

country: USA

institute: Fate Therapeutics

summary: Genome-wide gene expression analysis of MyoD-infected DMD-specific iPSCs (GM05112-M5.1) on days 0 (untreated), day 3 and day 8 post Dox treatment, human primary myoblasts (undifferentiated and as differentiated myotubes), and undifferentiated iPSCs from healthy donors (iPSCs-1 and iPSCs-2).

overall_design: DMD-specific iPSCs were infected with lentivirus expressing MyoD under the control of Tet-inducible promoter and another lentivirus expressing the transactivator. To initiate myogenic differentiation,  iPSCs were treated with 1µg/ml Dox. RNA was isolated 0, 3 and 8 days later and gene expression analysis was performed.

first: Ramzey

last: Abujarour

first: D

middle: L

first: Peter

last: Flynn


title: Inhibition of TGFβ Signaling Increases Direct Conversion of Fibroblasts to Induced Cardiomyocytes

status: Public on Jan 14 2014

city: Philadelphia

first: John

last: Gearhart

state: PA

address: 3400 Civic Center Blvd, Building 421, 9-121 Smilow Center for Translational Research

department: Dept of Cell and Developmental Biology, Institute for Regenerative Medicine

institute: University of Pennsylvania

summary: Recent studies have been successful at utilizing ectopic expression of transcription factors to generate induced cardiomyocytes (iCMs) from fibroblasts, albeit at a low frequency in vitro.  This work investigates the influence of small molecules that have been previously reported to improve differentiation to cardiomyocytes as well as reprogramming to iPSCs in conjunction with ectopic expression of the transcription factors Hand2, Nkx2.5, Gata4, Mef2C, and Tbx5 on the conversion to functional iCMs.  We utilized a reporter system in which the calcium indicator GCaMP is driven by the cardiac Troponin T promoter to quantify iCM yield.  The TGFβ inhibitor, SB431542 (SB), was identified as a small molecule capable of increasing the conversion of both mouse embryonic fibroblasts and adult cardiac fibroblasts to iCMs up to ~5 fold.  Further characterization revealed that inhibition of TGFβ by SB early in the reprogramming process led to the greatest increase in conversion of fibroblasts to iCMs in a dose-responsive manner.  Global transcriptional analysis at Day 3 post-induction of the transcription factors revealed an increased expression of genes associated with the development of cardiac muscle in the presence of SB compared to the vehicle control.  Incorporation of SB in the reprogramming process increases the efficiency of iCM generation, one of the major goals necessary to enable the use of iCMs for discovery-based applications and for the clinic.

overall_design: Mouse embryonic fibroblasts (MEFs) and adult mouse cardiac fibroblasts (CFs) were transfected with an empty vector (0F) or the combination of  Hand2, Nkx2.5, Gata4, Mef2C, and Tbx5 (5F).  Samples were exposed to the vehicle control (D, DMSO), SB431542 (SB, 0.5 uM MEF, 5 uM CF), or TGFb1 (T, 2 ng/mL) during culture.  Transcription factor expression was induced at Day 0 and samples were isolated at Day 3 post-induction.

first: Jamie

last: Ifkovits

first: Russell

middle: C

last: Addis

first: Johnathan

middle: A

last: Epstein

middle: D


title: Gene expression profiling in the reprogramming process

status: Public on Jan 11 2014

country: Spain

overall_design: Mouse embryonic fibroblasts (MEFs) were infected with retroviruses encoding the four transcription factors (Oct4, Sox2, Klf4 and c-Myc), three factors (Oct4, Sox2 and Klf4) or GFP (control) at day 0 and sampled at day 1, 2, 3, 4, 5, 6, 8, 10, 12.


title: The NEWEST trial

status: Public on Jan 08 2014

city: Hørsholm

first: Thomas

last: Jensen

address: Venlighedsvej 1

department: lab

country: Denmark

institute: MPI

summary:
The NEWEST (Neoadjuvant Endocrine Therapy for Women with  Estrogen-Sensitive Tumours) trial compared the clinical and biological  activity of fulvestrant 500 mg vs 250 mg in the neoadjuvant setting.  In this multi-centre phase II study, post-menopausal women with  operable, locally advanced (T2, 3, 4b; N0-3; M0) ER-positive breast  tumours were randomised to receive neoadjuvant treatment with either  dose of fulvestrant for 16 weeks before surgery.
Tumour core biopsies  were obtained at baseline, 4 weeks and at surgery for assessment of  changes in biomarker expression.  Tumour volumes were measured by 3-D  ultrasound at the same timepoints.  In this trial, the percentage of  patients who showed a reduction in tumour volume or stabilisation of  disease (using RECIST criteria) after treatment with fulvestrant 500  mg was 36% (26 out of 69 patients).  Therefore, within a population of  endocrine-therapy naive patients whose tumours were confirmed as being  ER-positive at the time of study entry, there is a subgroup who gained  particular clinical benefit from fulvestrant treatment.  These  clinical response data together with the availability of biological  response information and frozen tumour tissue from participants makes  the NEWEST trial an attractive setting in which to investigate the  potential of new markers of response to fulvestrant.

overall_design: 42 samples

first: Steen

last: Knudsen

first: Anker

last: Hansen

first: Wiktor

last: Mazin

first: Justin

last: Lindemann

first: Naomi

last: Laing

first: Elizabeth

last: Anderson


title: UNRAVELING A NOVEL TRANSCRIPTION FACTOR CODE INDUCTIVE FOR THE HUMAN ARTERIAL-SPECIFIC ENDOTHELIAL CELL SIGNATURE

status: Public on Jan 07 2014

city: Pamplona

first: Xabier

last: Agirre

state: Navarra

address: Pio XII, 55

department: Oncology

institute: CIMA

summary: Endothelial cells (EC) lining arteries and veins have distinct molecular and functional signatures. The (epi)genetic regulatory mechanisms underlying this heterogeneity in human EC are incompletely understood. Using genome-wide microarray screening we established a specific fingerprint of freshly isolated arterial (HUAEC) and venous EC (HUVEC) from human umbilical cord comprising 64 arterial and 12 venous genes, representing distinct functions and pathways. Among the arterial genes were 8 transcription factors, including HEY2, a downstream target of Notch signaling and the current ‘golden standard’ pathway for arterial EC specification. Short-term culture of HUAEC or HUVEC abrogated differential gene expression resulting in a default state. Erasure of arterial gene expression was at least in part due to loss of canonical Notch activity and HEY2 expression. Notably, nCounter analysis revealed that restoring HEY2 expression or Delta-like 4 (Dll4)-induced Notch signaling in cultured HUVEC or HUAEC only partially reinstated the arterial EC gene signature while combined overexpression of the 8 transcription factors restored this fingerprint much more robustly. Each transcription factor had a different impact on gene regulation, with some stimulating only few and others boosting a large proportion of arterial genes. Interestingly, although there was some overlap and cross-regulation, the transcription factors largely complemented each other in regulating the arterial EC gene profile. Thus, our study showed that Notch signaling determines only part of the arterial EC signature and identified additional novel and complementary transcriptional players in the complex regulation of human arteriovenous EC identity

overall_design: To identify an arteriovenous (AV)  fingerprint in human endothelial cells (EC) across different vascular beds, we used microarrays on RNA from 38 EC samples corresponding to 6 cultured human arterial-EC types (hepatic artery EC or HHAEC, N=3; aorta EC or HAEC, N=2; coronary artery EC or HCAEC, N=2; iliac artery EC or HIAEC, N=2; pulmonary artery EC or HPAEC, N=3; and umbilical artery EC or HUAEC-C, N=5), 4 cultured human venous-EC types (hepatic vein EC or HHVEC, N=3; iliac vein EC or HIVEC, N=3; pulmonary vein EC or HPVEC, N=2; and umbilical vein EC or HUVEC-C, N=5), freshly isolated HUAEC (HUAEC-F, N=4) and freshly isolated HUVEC (HUVEC-F, N=4). Due to the difficulty to obtain biopsies from healthy donors, we did not have access to freshly isolated aEC or vEC matched for all cultured EC types.

last: Aranguren

first: Victor

last: Segura

first: Alberto

last: Pascual-Montano

first: Felipe

last: Prósper

first: Aernout

last: Luttun


title: White Matter transcriptome in chronic alcoholism

status: Public on Jan 04 2014

city: Sydney

first: Greg

middle: Trevor

last: Sutherland

state: NSW

address: Room 502A, Blackburn Building  D06

department: Pathology

country: Australia

institute: University of Sydney

summary:
Chronic alcohol consumption can lead to alchohol-related brain damage (ARBD). Despite the well known acute effects of alcohol the mechanism responsible for chronic brain damage is largely unknown. Pathologically the major change is the loss of white matter while neuronal loss is mild and restricted to a few areas such as the prefrontal cortex. In order to improve our understanding of ARBD pathogenesis we used microarrays to explore the white matter transcriptome of alcoholics and controls.
Our results suggest that hepatic encephalopathy, along with two confounders, gray matter contamination and low RNA quality, are major drivers of gene expression in ARBD. All three exceeded the effects of alcohol itself. In particular, low quality RNA samples were characterized by an upregulation of protein translation machinery while hepatic encephalopathy was associated with a downregulation of mitochondrial energy metabolism pathways. The findings in HE alcoholics are consistent with the metabolic acidosis seen in this condition. In contrast non-HE alcoholics had widespread but only subtle changes in gene expression in their white matter.

overall_design: The initial cohort was compromised of four alcoholics without hepatic encephalopathy (non-HE alcoholics), three alcoholics with HE (HE alcoholics) and three neurologically normal controls. For each indvidual frozen white matter was sampled in the superior frontal gyrus (prefrontal cortex) and the precentral gyrus (motor cortex). These two cortices experience either moderate (prefrontal cortex) or no neuronal loss (motor cortex) with alcohol-related brain damage. Each white matter sample was divided in two before RNA was extracted  to give two 'biological' repeats and a total of 40 samples. Subsequently eight duplicates were removed due to their gray matter contamination or low RNA quality to leave a 32-sample cohort (23 alcoholic (including eight with HE ) and nine control samples.

middle: T

first: Donna

last: Sheedy

first: Pam

middle: J

last: Sheahan

first: Warren

last: Kaplan

first: Jillian

last: Kril


title: COUP-TFII regulates human endometrial stromal genes involved in inflammation

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: Although the function of COUP-TFII in uterine decidualization has been described in mice, its role in the human uterus remains unknown.To interrogate the role of COUP-TFII in human endometrial function, we utilized a siRNA-mediated loss of function approach in primary human endometrial stromal cells.

overall_design:
Primary human endometrial stromal cells (HESCs), coup-TFII siRNA group and control group
Two group comparison

first: Francesco

last: DeMayo

first: Xilong

last: Li

first: Yiqun

last: Zhang


title: A probiotics strain attenuating the effects of aspirin in the gut

city: Odawara

first: Kimiko

last: Amafuji

state: Kanagawa

address: 540 Naruda

country: Japan

institute: Meiji Co., Ltd.

summary:
Transcriptome analysis of partially degraded and fragmented RNA samples from mus musculus gut
Global gene expression profiling has shown the gut transcripts changes through administration of aspirin while probiotics strain administration beforehand attenuates the effect more than teprenone.

overall_design: We analyzed five groups of mice gut using the Affymetrix Mouse Gene 1.0 ST platform. Array data was processed by Affymetrix Exon Array Computational Tool. No techinical replicates were performed.

first: Misato

last: Soeda

first: Yoshiko

last: Honme

first: Minehiko

last: Yokoyama


title: RSK2 is a modulator of craniofacial development

status: Public on Jan 13 2014

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

country: France

institute: IGBMC

summary: The RSK2 gene is responsible for Coffin-Lowry syndrome, an X-linked monogenic disease associating severe learning deficit andassociated to typical facial and digital abnormalities and skeletal changes. Craniofacial and dental anomalies encountered in this rare disease have been poorly characterized.

overall_design: In this study we explore, through X-Ray microtomographic analysis, the variable craniofacial dysmorphism and dental anomalies present in Rsk2 knockout mice, an animal model of Coffin-Lowry syndrome, as well as in triple Rsk1,2,3 knockout mutants. We report in these mutants the occurrence of a surpernumerary tooth mesial to the first molar. This highly penetrant phenotype is considered as a remnant of evolutionary lost teeth. This possibly leads to the significant reduction of the maxillary diastema. Abnormalities of molar shape were almost restricted to the mesial part of both upper and lower first molars (M1). We also report an expression analysis of the four Rsk genes (Rsk1, 2, 3 and 4) at various stages of odontogenesis in wild-type (WT) mice. Rsk2 was mainly expressed in the mesenchymal, neural crest derived compartment, correlating with proliferative areas of the developing teeth and consistent with a biological function of RSK2 in cell cycle control and cell growth, which when invalidated could be responsible for the dental phenotype. In an attempt to unravel the molecular pathways involved in the genesis of these dental defects, we performed a comparative transcriptomic (DNA microarray) analysis of mandibular wild-type versus Rsk2-/Y molars, and further demonstrated a misregulation of selected genes, using a Rsk2 shRNA knock-down strategy in molar tooth germs cultured in vitro.

first: Virginie

last: Laugel-Haushalter

first: Marie

last: Paschaki

first: Pauline

last: Marangoni

first: Coralie

last: Pilgram

first: Arnaud

last: Langer

first: Thibaut

last: Kuntz

first: Julie

last: Demassue

first: Supawich

last: Morkmued

first: Philippe

last: Choquet

first: André

last: Constantinesco

first: Fabien

last: Bornert

first: Matthieu

last: Schmittbuhl

first: Solange

last: Pannetier

first: Laurent

last: Viriot

last: Hanauer

first: Pascal

last: Dollé

first: Agnès

last: Bloch-Zupan


title: Tissue macrophage subsets derived from regenerating muscle

status: Public on Jan 02 2014

city: Debrecen

first: Szilard

last: Poliska

address: Egyetem ter 1.

department: Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

summary:
Muscle injury was elicited by cardiotoxin injection into the tibialis anterior muscle. Macrophages were isolated 2 days post-injury from the regenerating muscle.
We used microarray to obtain global gene expression data of muscle-derived tissue macrophage subsets.

overall_design: Tissue macrophages were collected from regenerating muscle samples of three animals, Ly6C+ F4/80low and Ly6C- F4/80high macrophage subsets were sorted. The global gene expression patterns of distinct macrophage subsets were analyzed on Affymetrix microarrays.

first: Tamas

last: Varga

first: Rémi

last: Mounier

first: Peter

last: Gogolak

first: Bénédicte

last: Chazaud

first: Laszlo

last: Nagy


title: Expression data in splenic DC subsets in wild type and Xbp1 deficient mice

status: Public on Jan 01 2014

city: Ghent

first: Sophie

last: Janssens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: University of Ghent-VIB

summary:
Xbp1 is a major transcription factor in the unfolded protein response. To uncover its function in DCs we generated a conditional KO for Xbp1 in dendritic cells. We here compare the expression of mRNAs in two different splenic DC subpopulations, CD8a and CD11b DCs in both WT and KO mice.
Reference: Inositol-requiring enzyme 1-alpha regulates CD8a dendritic cell function via regulated mRNA decay. Osorio et al, Nature Immunology (2014)

overall_design: Primary DC subsets were isolated and sorted from spleens from 3 different WT or CD11c-cre Xbp-1fl/fl mice. RNA was isolated, converted to cDNA and then hybridised on Affymetrix GeneChip Mouse Gene 1.0 ST Arrays (GPL6246).

first: Fabiola

last: Osorio

first: Simon

last: Tavernier

first: Eik

last: Hoffman

first: Yvan

last: Saeys

first: Liesbet

last: Martens

first: Jessica

last: Vetters

first: Iris

last: Delrue

first: Riet

last: De Rycke

first: Eef

last: Parthoens

last: Poulliot

first: Takao

last: Iwawaki

first: Bart

middle: N

last: Lambrecht


title: Isolation of human skeletal muscle precursor cells by fluorescence-activated cell sorting.

city: Boston

first: Amy

last: Wagers

state: MA

address: 1 Joslin Place

department: Islet Cell and Regenerative Biology

institute: Joslin Diabetes Center

summary:
Novel fluorescence-activated cell sorting (FACS) strategies to prospectively purify functionally distinct cell populations from the human myofiber-associated (hMFA) cell compartment, including human Skeletal Muscle Precursor cells (hSMPs):
HSMPs, identified as CD45-Mac1-GlyA-CD31-CD34-CD56intITGA7hi hMFA cells, are highly enriched for cells expressing the satellite cell marker PAX7 and show efficient myogenic and lack adipogenic capacity.
CD45-CD11b-GlyA-CD31-CD34+ hMFA cells (CD34+ cells) do not express PAX7, lack myogenic and exhibit adipogenic activity.

overall_design: We used Affymetrix Human Genome U133 Plus 2.0 microarrays to gain deeper insights into the molecular underpinnings functionally and phenotypically discrete human myofiber-associated cell subsets.

first: Alessandra

last: Castiglioni

first: Simone

last: Hettmer

first: Tata

last: Rao


title: Exposure of human A549 and THP-1 cells and mouse J774 cells to single walled carbon nanotubes

status: Public on Jan 03 2014

city: Aarhus

first: Christiane

last: Beer

address: Bartholinsalle 2

department: Department of Public Health

institute: Aarhus University

summary:
The microarray investigations were part of a toxicological investigation of the effect of exposure to single-walled carbon nanotubes (SWCNTs) to macrophages and non-phagocytotic cells
The results of this study are accepted for publication in Toxicological Research with the title: The toxic effects of single-wall carbon nanotubes are linked to the phagocytic ability of cells

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Cell lines were treated for 24 hours either with water (vehicle control) or SWCNTs for 24 hours and the toxic effects were investigated including gene expression changes by affymetrix microarrays.

first: Rasmus

last: Foldbjerg

first: Eveline

middle: S

last: Irving


title: Gene expression profiles of ovarian cancer cells by inhibiting Hh signaling

status: Public on Jan 15 2014

city: NANCAHNG

first: Shiwen

last: Luo

state: JiangXi

address: 17 Yong Wai street

department: Center for experimental medicine

country: China

institute: The Frist Affiliated Hospital of Nanchang University

summary: Analysis of  gene expression levels in response to inhibition of Hh signaling in ovarian cancer cells using a cDNA microarray technique. Results suggest that  208 genes (50.5%) were up-regulated and 204 gene (49.5%) were down-regulated after GANT61 treatment.The focal adhesion and ECM-receptor interaction cross-talk in SKOV3 cells after treatment with GANT61, and the expression change of “focal adhesion” related genes play an important role in the processes of response to GANT61-treatment.

overall_design: SKOV3 cells were treated with GANT61 (20 μM for 60 hr) and control vehicle DMSO, respectively.

first: Libin

last: Deng


title: WNV- and JEV-infected adult mouse brain

city: Aurora

first: Tzu Lip

last: Phang

state: CO

address: 12700 East 19th Avenue

department: Medicine

institute: University of Colorado, Denver

summary: Flaviviruses, particularly Japanese encephalitis virus (JEV) and West Nile virus (WNV), are important causes of virus-induced central nervous system (CNS) disease in humans. We used microarray analysis to identify cellular genes that are differentially regulated following infection of the brain with JEV (P3) or WNV (New York 99). Gene expression data for these flaviviruses was compared to that induced following infection of the brain with reovirus (Type 3 Dearing), an unrelated neurotropic virus. Although several studies have described gene expression changes following virus infection of the brain, this report is the first to directly compare large-scale gene expression data from different viruses. We found that a large number of genes were up-regulated in common to infections with all 3 viruses (fold change > 2, P < 0.001), including genes associated with interferon signaling, the immune system, inflammation and cell death/survival signaling. In addition, genes associated with glutamate signaling were down-regulated in common to infections with all 3 viruses (fold change > 2, P < 0.001). These genes may serve broad spectrum therapeutic targets for virus-induced CNS disease. A distinct set of genes were up-regulated following flavivirus-infection, but not following infection with reovirus. These genes were associated with tRNA charging and may serve as therapeutic targets for flavivirus-induce CNS disease.

overall_design: Gene expression in the brain following WNV or JEV infection. WNV- or JEV-infected (N=3) vs. mock-infected (N=3) mouse brain.

first: Penny

last: Clarke


title: Distinct DNA methylation patterns of cognitive impairment and Trisomy 21 in Down Syndrome

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

summary: The presence of an extra whole or part of chromosome 21 in people with Down syndrome (DS) is associated with multiple neurological changes, including pathological aging that often meets the criteria for Alzheimer’s Disease (AD). While the mechanism underlying these changes is unknown, it has been hypothesized that the presence of the amyloid precursor protein (APP) on chromosome 21 may contribute to the  phenotype. Genome-wide DNA methylation abnormalities have been shown in neural tissue of patients with AD, and cells may respond to changes in gene dosage with altered DNA methylation. We therefore examined whole-genome DNA methylation in buccal epithelial cells of adults with DS to determine whether patterns of DNA methylation correlated with DS and/or cognitive impairment. In addition we examined DNA methylation at the APP gene itself, to see whether there were changes in DNA methylation in this population. Using the Illumina 450K Human Methylation Array, we examined more than 485,000 CpG sites distributed across the genome in buccal epithelial cells. We found 297 CpGs to be differentially methylated between the groups, including 26 genes that were represented by more than one CpG. In addition, we found 331 probes that were correlated with cognitive function including 23 genes represented by more than one probe. We found no enrichment on chromosome 21 and targeted analysis of the APP gene revealed weak evidence for epigenetic impacts related to the AD phenotype. Overall, our results indicate that both Trisomy 21 and cognitive impairment are associated with distinct patterns of DNA methylation.

overall_design: This cohort consist of genomic DNA extracted from 20 buccal swabs, bisulphite converted and hybridized to the Illumina Infinium HumanMethylation450 Beadchip for genome wide DNA methylation profiling.

first: Meaghan

last: Jones

first: Pau

last: Farre

first: Lisa

middle: M

last: McEwen

first: Julia

last: MacIsaac

first: Kim

last: Watt

first: Sarah

last: Neumann

first: Eldon

last: Emberly

first: Max

last: Cynader

first: Naznin

last: Virji-Babul


title: T helper lymphocyte- and monocyte-specific type I interferon (IFN) signatures in autoimmunity and viral infection.

status: Public on Jan 06 2014

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

summary: This study demonstrates quantitative and qualitative differences between type I IFN signatures in autoimmunity and viral infection using purified CD4pos T cells and CD16pos- and CD16neg-monocyte subsets. We were able to discriminate between cell-specific viral response signatures and the pathogenically amplified IFN signatures observed in autoimmunity. The differences were of both a qualitative and quantitative nature, as the signatures in the patients with SLE were characterized by much more complexly compiled gene patterns with increased absolute gene expression levels.

overall_design: Collection of cells from Systemic Lupus Erythematosus (SLE) patients: For CD4pos T cells, six patients with SLE (average age: 29.0 +/- 7.6) and four normal healthy donors (ND; 24.8 +/- 0.5) were recruited. For CD16neg monocytes, four patients with SLE (26.5 +/- 1.7) and four NDs (24.8 +/- 0.5) were recruited. For CD16pos monocytes, four patients with SLE (26.5 +/- 1.7) and three NDs (24.7 +/- 0.6) were recruited. All patients and NDs were female. The same NDs were examined before and after immunisation with yellow fever vaccine (YFV).  Collection of cells from yellow-fever vaccinated individuals: ND were immunised with a vaccine against the wild-type YF virus, which is a single-stranded RNA virus without adjuvants. This vaccine consists of a live but attenuated strain of the yellow fever virus (YFV-17D). Based on its vaccination-associated clinical and serological manifestations, this immunisation can be regarded as a real viral infection. A total of 50 ml peripheral blood was taken 7 days after immunisation, when sufficient numbers of CD19pos/CD27high plasmablasts were detected by flow cytometry.  Cell sorting: A total of 50 ml peripheral blood was collected in Vacutainer heparin tubes and erythrocytes were lysed in EL buffer. Subsequently, granulocytes were depleted using CD15-conjugated microbeads (MACS). The CD15-depleted fraction was stained with a CD14-fluorescein isothiocyanate (FITC) antibody, a CD16-APC-Cy7 antibody, a CD3-Vioblue antibody and a CD4-FITC antibody. Using a FACSAria cell sorter, CD4pos T cells, CD16neg monocytes and CD16pos monocytes were isolated with purities and viabilities of >97%. After sorting, the cells were immediately lysed with RLT buffer and frozen at -70 °C. Total RNA was isolated using an RNeasy mini kit, and quality control was ensured by Bioanalyser measurements.Total RNA was extracted using the RNeasy Mini kit. The integrity and amount of isolated RNA was assessed for each sample using an Agilent 2100 Bioanalyzer and a NanoDrop ND-1000 spectrophotometer. Biotinylated complementary RNA (cRNA) was synthesized from 100 ng total RNA, using reagents as recommended in the technical manual from Affymetrix. Fifteen micrograms of fragmented cRNA of each sample were hybridized to HG-U133 plus 2.0 arrays. Hybridization was performed according to procedure 2 as described in the technical manual. Finally, the arrays were scanned with a GeneChip Scanner 3000 using the GCOS software. All relevant GCOS data of quality checked microarrays were analyzed with High Performance Chip Data Analysis (HPCDA, unpublished), using the BioRetis database (www.bioretis-analysis.de), as described and validated previously.

first: Chieko

last: Kyogoku

first: Biljana

last: Smiljanovic

first: Joachim

middle: R

last: Grün

first: Robert

last: Biesen

first: Ursula

last: Schulte-Wrede

first: Thomas

last: Häupl

first: Falk

last: Hiepe

first: Tobias

last: Alexander

first: Andreas

last: Radbruch

last: Grützkau


title: Parsing the roles of transcription factors Gata4 and Gata6 in adult cardiac hypertrophic responses

city: Cincinnati

first: Bruce

last: Aronow

state: OH

address: 240 Albert Sabin Way

department: Biomedical Informatics, Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

summary:
Cardiac hypertrophy is regulated by the zinc finger-containing DNA binding factors Gata4 and Gata6, both of which are required to mount a productive growth response of the adult heart.  To determine if Gata4 and Gata6 are redundant or have non-overlapping roles, we performed cardiomyocyte-specific conditional gene deletions for Gata4 and Gata6 in conjunction with reciprocal replacement with a transgene encoding either Gata4 or Gata6, during the pressure overload response.  We determined that Gata4 and Gata6 play a redundant and dosage-sensitive role in programming the hypertrophic growth response itself following pressure overload stimulation. However, non-redundant functions were identified as functional decompensation induced by either Gata4 or Gata6 deletion was not rescued by the reciprocal transgene, and only Gata4 heart-specific deletion produced a reduction in capillary density after pressure overload.  Gene expression profiling from hearts of these gene-deleted mice showed both overlapping and unique transcriptional codes, with Gata4 exhibiting the strongest impact. These results indicate that Gata4 and Gata6 play a dosage-dependent and semi-redundant role in programming cardiac hypertrophy, but that each has a unique role in maintaining cardiac homeostasis and adaptation to injury that cannot be compensated by the other.
Microarray-bassed gene expression profiling identified overlapping, distinct, and quantitatively/differentially regulated classes of Gata4 or Gata6 regulated genes.

overall_design: To determine if Gata4 and Gata6 are redundant or have non-overlapping roles in programming  cardiac hypertrophic responses and adaptation to stress or injury, we performed cardiomyocyte-specific conditional gene deletions for Gata4 and Gata6 in conjunction with reciprocal replacement with a transgene encoding either Gata4 or Gata6, during the pressure overload response.

first: Jop

middle: H

last: Van Berlo

first: Jeffrey

last: Molkentin


title: Expression data from hepatitis E virus inoculated PLC/PRF/5 cells

city: Beijing

first: Feng

last: Zhang

address: Tiantan xili 2# NIFDC

institute: National Institutre for Food and Drug Control

summary:
Hepatitis E virus (HEV) is an important causative pathogen of acute hepatitis. Because of the absence of an in vitro culture system for HEV, research has been greatly impeded. And interaction between HEV and host cells was mainly studied by tansfection/transinfection system, such as Adeno virus transinfection system. We developed an in vitro culture system for HEV in PLC/PRF/5 cells. With this in vitro culture system, we studied the gene expression profile change by HEV infection.
Using a microarray assay, we analysed genes of PLC/PRF/5 cells, whose transcription level could be changed by HEV infection.

overall_design: Five flasks of PLC/PRF/5 cells inoculated with HEV were used as test sample, and five flasks inoculated with serum-free DMEM/199 medium were used as control samples. Both test and control flasks were cultured under the same conditions. Sixty days after inoculation, the test and control flasks was resolved with Trizol and analysed with Affymetrix HG-U133 Plus 2 array.


title: Transcription factor Achaete-Scute homologue 2 initiates T follicular helper cell development [array]

city: Bethesda

first: Lai

last: Wei

state: MD

address: 10 Center Dr. Room 2B47

institute: NIH/NEI/NCCAM

summary: In immune responses, activated T cells migrate to B cell follicles and develop to T follicular helper (Tfh) cells, a new subset of CD4+ T cells specialized in providing help to B lymphocytes in the induction of germinal centers 1-3. Although Bcl6 has been shown to be essential in Tfh cell function, it may not regulate the initial migration of T cells 4 or the induction of Tfh program as exampled by CXCR5 upregulation 5. Here, we show that the Achaete-Scute homologue 2 (Ascl2) gene that encodes a basic helix-loop-helix (bHLH) transcription factor 6, is selectively upregulated in its expression in Tfh cells. Ectopic expression of Ascl2 uniquely upregulates CXCR5 but not Bcl6 and downregulates CCR7 expression in T cells in vitro and accelerates T cell migration to the follicles and Tfh cell development in vivo. Combined transcriptome profiling and genome-wide occupancy analysis indicate that Ascl2 directly regulates Tfh-related genes while inhibits expression of Th1 and Th17 genes. Acute deletion of Ascl2 as well as blockade of its function with the Id3 protein in peripheral CD4+ T cells results in a failure in Tfh cell development and the germinal center response. Conversely, mutation of Id3, known to cause antibody-mediated autoimmunity, greatly enhances Tfh cell generation. Thus, Ascl2 critically and directly initiates Tfh cell development.

overall_design: Decide gene expression patterns of CD4+ T cells with overexpressed Ascl2 or Tfh cells

first: Xindong

last: Liu

first: Xiaowei

last: Yan

first: Chen

last: Dong


title: Expression data from human oral epithelial cell line

city: Davis

first: Michael

last: George

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

summary:
A majority of individuals infected with human immunodeficiency virus (HIV) have inadequate access to antiretroviral therapy and ultimately develop debilitating oral infections that often correlate with disease progression.  Our study evaluates the impact of chronic exposure to the pro-inflammatory cytokine, interferon gamma, on the growth and barrier functions of the oral epithelium.
Microarrays were used to characterize changes in gene expression in the TR146 oral epithelial cell line that occur in response to constitutive exposure to interferon gamma in the growth media.

overall_design: TR146 epithelial cells were grown to confluence in two 6-well culture plates in the presence (plate 1) or absence (plate 2) of interferon gamma and used for RNA extraction and hybridization on Affymetrix microarrays.


title: Gene array analysis of clear cell renal cell carcinoma tissue versus matched normal kidney tissue

city: Jacksonville

first: John

last: Copland

state: Florida

address: 4500 San Pablo Rd

department: Cancer Research

institute: The Mayo Clinic, Jacksonville FL

summary: Currently there is a lack of effective therapies which result in long-term durable response for patients presenting with advanced and metastatic clear cell renal cell carcinoma (ccRCC). This is due in part to a lack of molecular factors which can be targeted pharmacologically. In order to identify novel tumor-specific targets, we performed high throughput gene array analysis screening numerous patient ccRCC tumor tissues across all stages of disease, and compared their gene expression levels to matched normal kidney. Our results identify a number of genes which demonstrate tumor-specific overexpression, and may present as novel targets for therapy.

overall_design: Patient tissue samples were sorted into disease stages based on pathology reports. RNA was extracted from flash frozen patient tumor and normal samples. Gene array analysis was performed, and resulting expression levels were compared between normal and tumor samples.

first: Christina

last: von Roemeling

first: Christopher

last: Kolbert

first: Han

middle: W

last: Tun


title: Effects of BRD4 inhibition in AML

first: Kapil

last: Bhalla

address: 1400 Holcombe Blvd., Unit 428

institute: MD Anderson Cancer Center

summary: The BET (bromodomain and extra terminal) protein family members including BRD4 bind to acetylated lysines on histones and regulate the expression of important oncogenes, e.g., MYC and BCL2. Here we demonstrate the sensitizing effects of the histone hyperacetylation inducing pan-histone deacetylase inhibitor (HDI) panobinostat (PS) on human AML blast progenitor cells (BPCs) to the BET protein inhibitor JQ1. Treatment with JQ1 but not its inactive enantiomer (R-JQ1) was highly lethal against AML BPCs expressing mutant NPM1c+ with or without co-expression of FLT3-ITD, or AML expressing MLL fusion oncoprotein. JQ1 treatment reduced binding of BRD4 and RNA polymerase II to the DNA of MYC and BCL2, and reduced their levels in the AML cells. Co-treatment with JQ1 and the HDAC inhibitor panobinostat (PS) synergistically induced apoptosis of the AML BPCs, but not of normal CD34+ hematopoietic progenitor cells. This was associated with greater attenuation of MYC and BCL2, while increasing p21, BIM and cleaved PARP levels in the AML BPCs. Co-treatment with JQ1 and PS significantly improved the survival of the NOD/SCID mice engrafted with OCI-AML3 or MOLM13 cells (p < 0.01). These findings highlight co-treatment with a BRD4 antagonist and an HDI as a potentially efficacious therapy of AML.

overall_design: Two samples were analyzed (untreated cells, cells treated with JQ1)


title: Transcription profiling reveals potential mechanisms of dysbiosis in the oral microbiome of rhesus macaques with chronic untreated SIV infection

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

sample_organism:
Macaca mulatta
Homo sapiens

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: Refer to individual Series


title: Gene expression data from high grade serous ovarian cancer

city: Kingston

first: Madhuri

last: Koti

state: Ontario

address: Botterell Hall, Stuart Street

department: Biomedical and Molecular Sciences

institute: Queen's University

summary: Background: Resistance to platinum-based chemotherapy remains a major impediment in the treatment of serous epithelial ovarian cancer. The objective of this study was to use gene expression profiling to delineate major deregulated pathways and biomarkers associated with the development of intrinsic chemotherapy resistance upon exposure to standard first-line therapy for ovarian cancer.   Methods: The study cohort comprised 28 patients divided into two groups based on their varying sensitivity to first-line chemotherapy using progression free survival (PFS) as a surrogate of response. All 28 patients had advanced stage, high-grade serous ovarian cancer, and were treated with the same standard platinum-based chemotherapy. Twelve patient tumors demonstrating relative resistance to platinum chemotherapy corresponding to shorter PFS (< eight months) were compared to sixteen tumors from platinum-sensitive patients (PFS > eighteen months). Whole transcriptome profiling was performed using a Affymetrix high-resolution microarray platform to permit global comparisons of gene expression profiles between tumors from the resistant group and the sensitive group.   Results: Microarray data analysis revealed a set of 204 discriminating genes possessing expression levels, which could influence differential chemotherapy response between the two groups. Robust statistical testing was then performed which eliminated a dependence on the normalization algorithm employed, producing a restricted list of differentially regulated genes, and which found IGF1 to be the most strongly differentially expressed gene. Pathway analysis, based on the list of 204 genes, revealed enrichment in genes primarily involved in the IGF1/PI3K/NFκB/ERK gene signalling networks.   Conclusions: This study has identified pathway specific prognostic biomarkers possibly underlying a differential chemotherapy response in patients undergoing standard platinum-based treatment of serous epithelial ovarian cancer. Future studies to validate these markers are necessary to apply this knowledge to biomarker-based clinical trials.

overall_design: Total RNA from 12 chemotherapy resistant and 16 sensitive chemotherapy sensitive high-grade serous epithelial ovarian cancer samples was subjected to whole transcriptome profiling using Affymetrix U133 Plus 2.0 arrays

first: Robert

last: Goooding

first: Jeremy

last: Squire


title: mRNA Profiling of Polysome fractions from #483 T-ALL treated with 4EGI-1 or DMSO

city: Hannover

first: Adrian

last: Schwarzer

address: Carl-Neuberg-Str. 1

department: Experimental Hematology

institute: Hannover Medical School

summary: High activation of the PI3K-AKT-mTOR pathway is characteristic for T-cell acute lymphoblastic leukemia (T-ALL). Here we investigated how 4EGI-1, a small inhibitor of cap-dependent translation, induces apoptosis in T-ALL clones displaying hyperactive PI3K-AKT-mTOR signaling.  4EGI-1 treatment  reduced the ribosomal occupancy of transcripts that define the molecular difference between T-ALL blasts and normal thymocytes. These transcripts encoded proteins for the translational machinery, for mitochondrial metabolism as well as oncoproteins such as Cyclin D1, Bcl-2 and c-myc. Therefore, targeting translation initiation proves valuable in situations where mTOR is activated by multiple events.

overall_design: For each biological replicate 5 x 107 #483 T-ALL cells were treated with 100 µM 4EGI-1 or DMSO. After 2 h incubation at 37°C cells were washed in ice-cold PBS containing cycloheximide (0.1 mg/ml), pelleted and resuspended in extraction buffer (20 mM Tris-HCl, pH 8.0, 140 mM KCl, 0.5 mM DTT, 5 mM MgCl2, 0.5 % nonidet-P40, 0.1 mg/ml cycloheximide, 10000 IU/ml dalteparin sodium) and incubated for 5 min on ice. All subsequent steps were carried out in the cold. After centrifugation for 10 min at 12000 x g, 0.4 ml supernatant was layered onto a 12 ml linear sucrose gradient (10 - 50% sucrose [w/v] in extraction buffer without nonidet-P40) and centrifuged at 4 °C in an SW40Ti rotor (Beckman) at 35000 rpm without brake for 120 min. The gradients were harvested and absorbance profiles at 254 nm recorded (type 11 optical unit/UA-6 detector, ISCO). 1 ml fractions were collected and supplied with 0.1 volume of 3 M sodium acetate (pH 5.2) and 1 volume of isopropanol for overnight precipitation at -20 °C. RNA was purified using Nucleospin RNAII tubes (Macherey & Nagel) following the manufacturer´s protocol. For microarray analysis RNA from polysome fractions were pooled, precipitated by adding LiCl to a final concentration of 2 M and resolubilized in 15 µl of RNase-free water. RNA concentrations were determined and the samples were stored at -80 °C.


title: Genome-wide DNA methylation in cervical tissue

city: Örebro

first: Sanja

last: Farkas

address: Södra rosen grevsgatan

department: Laboratory medicine

country: Sweden

institute: Örebro University hospital

summary: The aim of this study was to identify new candidate genes that are differentially methylated in squamous cell carcinoma compared to the DNA samples from cervical intraepithelial neoplasia grade 3 (CIN3) and normal cervical scrapes. The Illumina Infinium Human Methylation 450 K BeadChip method identifies genome-wide DNA methylation changes in CpG islands, CpG shores and shelves.

overall_design: In this study 20 normal cervical samples (HPV negative), 18 samples with CIN3 lesions (HPV positive) and 6 cervical cancer tissues (HPV positive) were included.

first: Nina

last: Milutin-Gašperov

first: Magdalena

last: Grce

first: Torbjörn

middle: K

last: Nilsson


title: Imatinib therapy of chronic myeloid leukemia restores the expression levels of key genes for DNA damage and cell cycle progression

city: Salamanca

first: ROCIO

last: BENITO

address: Campus Unamuno s/n

institute: centro investigacion del cancer

summary: Background: Chronic myeloid leukemia (CML) is a malignant clonal disorder of the hematopoietic system caused by the expression of the BCR/ABL fusion oncogene. It is well known that CML cells are genetically unstable. However, the mechanisms by which these cells acquire genetic alterations are poorly understood. Imatinib mesylate (IM) is the standard therapy for newly diagnosed CML patients. IM targets the oncogenic kinase activity of BCR-ABL. Objective: To study the gene expression profile of BM hematopoietic cells in the same patients with CML before and one month after imatinib therapy. Methods: Samples from patients with CML were analyzed using Affymetrix GeneChip Expression Arrays. Results: A total of 594 differentially expressed genes, most of which (393 genes) were downregulated, as a result of imatinib therapy were observed. Conclusions: The blockade of oncoprotein Bcr-abl by imatinib could cause a decrease in the expression of key DNA repair genes, and cells try to restore the normal gene expression levels required for cell proliferation and chromosomal integrity.

overall_design:
Materials and Methods
Patients
Nine patients with the diagnosis of Ph-positive CML and nine samples from normal donors were analyzed. In all patients bone marrow samples were obtained by bone marrow aspiration. All patients received a daily dose of 400 mg imatinib mesylate (IM). In all patients bone marrow was sampled before IM administration commenced and 4 weeks after the treatment, by which time all cases were in hematological response. In addition, all patients showed a complete cytogenetic response six months after starting therapy. The study was approved by the local research ethics committee and written informed consent was obtained from all patients.
RNA isolation, labeling and microarray hybridization
Total RNA was isolated from bone marrow in Trizol aliquots, following the manufacturer’s instructions, and purified using an RNeasy kit (Qiagen Inc., Valencia, CA). RNA integrity and yield were assessed by determining sample absorbance at 260 and 280 nm and by analysis on the Agilent RNA 6000 Nano LabChip (Agilent Technologies, Inc., Palo Alto, CA).
Microarray assays were performed according to the standard protocol described in the Affymetrix GeneChip Expression Analysis Technical Manual, rev. 3 (http://www.affymetrix.com/support/index.affx). Messenger RNA was amplified and labeled from 5-µg samples, which produced a sufficient yield of cRNA. These samples were fragmented and combined with array hybridization controls (Affymetrix, Santa Clara, CA, USA) in hybridization buffer. 11 µg of cRNA target were then hybridized with the GeneChip HG_U133 Plus 2.0 array (Affymetrix) and scanned with the GeneArray laser scanner (Affymetrix).
Genome-wide expression data analysis
The expression value for each probe set was calculated using RMA-Express software, which uses the robust multi-array average (RMA) algorithm, as previously described [28]. For an initial analysis, gene-filtering methods were applied following the detection calls calculated using the MAS 5.0 algorithm (Affymetrix). Probe sets with absent calls and those showing minimal variation across all samples (maximum-minimum log2 variation <2.5) were filtered out.
The significant analysis of microarrays (SAM) algorithm was used to identify genes with statistically significant differences in expression between classes. All data were permuted over 100 cycles using the two-class (unpaired) and multi-class response format, with no necessity for equal variances. Significant genes were identified on the basis of the lowest false-discovery ratio (FDR), controlling the q-value for the gene list. The FDR was <2% in all class comparisons.
A web-delivered bioinformatics tool set, Ingenuity Pathway Analysis (IPA 5.5; http://www.ingenuity.com), was used to identify functional networks. IPA is a knowledge database generated from peer-reviewed scientific publications. It enables the discovery, visualization and exploration of functional biological networks in gene expression data and delineates the most significant functions in those networks.
Gene-specific real-time PCR
In order to validate the results of the microarray studies, quantitative real-time reverse transcriptase polymerase chain reaction (RT-PCR) was performed at the time of diagnosis and four weeks after imatinib therapy. One microgram of total RNA was subjected to cDNA synthesis, as previously described [29]. Quantification was performed using Fast SYBR-Green Master Mix according to the manufacturer's instructions (Applied Biosystems, Foster City, CA). The expression of the following genes was analyzed: POLE2, FANCD2, PTEN, FOXO3, and ABCB7. The specific primers were designed with Primer Express 3.0 software (Applied Biosystems) and tested for specificity using NCBI's BLAST software. Gene expression was achieved using relative quantitative real-time RT-PCR and the SYBR® Green I. Expression was quantified relative to GAPDH expression by the application of the Pfaffl analysis method.

first: Rocio

last: Benito

first: Eva

last: Lumbreras

first: María

last: Abáigar

first: Norma

last: Gutiérrez

first: Manuel

last: Delgado

first: Cristina

last: Robledo

first: Juan

last: García

first: Ana

middle: E

last: Rodríguez-Vicente

first: Consuelo

last: Cañizo

first: Jesús

last: Hernández


title: Early Mouse Hepatic Stellate Cell Activation

city: Brussels

first: Inge

last: Mannaerts

address: Laarbeeklaan 103

department: Liver Cell Biology Lab

institute: Vrije Universiteit Brussel

summary:
Early during culture of primary mouse HSCs gene expression changes.
These expression alterations can be affected by treating cells with histone deacetylase inhibitor, valproic acid

overall_design:
Primary mouse Hepatic stellate cells were cultured for short periods of time (4-16-64h) in presence or absence of valproic acid.
Gene expression analysis (mouse Gene 1.0 ST arrays according to manufacturer’s manual 701880Rev4 (Affymetrix, Santa Clara, CA)), in vitro stellate cell activation and inhibition of the activation by valproic acid treatment.

first: Ben

last: Schroyen

first: Stefaan

last: Verhulst

first: Leentje

last: Van Lommel

first: Frans

last: Schuit

first: Marc

last: Nyssen

first: Leo

last: van Grunsven


title: Regional difference in gene expression of proliferating human choroidal endothelial cells

status: Public on Dec 31 2013

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

country: United Kingdom

institute: Newcastle University

summary:
To investigate the differences in gene expression between matched human macular and peripheral choroidal endothelial cells (CEC) and matched human macular inner and outer CEC.
The gene expression profiles of the unpassaged cell types were compared using Affymetrix GeneChip arrays.

overall_design: 9 arrays are included. 6mm diameter samples were dissected from 3 regions of the eye: peripheral inner choroid, macular outer choroid and macular inner choroid.  RNA extracts from cells were hybridised to Affymetrix HGU133plus2 arrays in triplicate.

first: Andrew

last: Browning

first: Eugene

middle: P

last: Halligan

first: Elizabeth

last: Stewart

first: Daniel

last: Swan

first: Winfried

last: Amoaku


title: Derivation of Neural Stem Cells from human adult peripheral CD34+ Cells for an Autologous Model of Neuroinflammation

first: Kory

last: Johnson

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: Activated T cells inhibit neurogenesis in adult animal brain and cultured human fetal neural stem cells (NSC). However, the role of inhibition of neurogenesis in human neuroinflammatory diseases is still uncertain because of the difficulty in obtaining adult NSC from patients. Recent developments in cell reprogramming suggest that NSC may be derived directly from adult fibroblasts. We generated NSC from adult human peripheral CD34+ cells by transfecting the cells with Sendai virus constructs containing Sox-2, Oct3/4, C-MyC and Klf-4. The derived NSC could be differentiated to astroglia and action potential firing neurons. Co-culturing NSC with activated autologous T cells or treatment with recombinant granzyme B caused inhibition of neurogenesis as indicated by decreased NSC proliferation and neuronal differentiation. Thus, we have established a unique autologous in vitro model to study the pathophysiology of neuroinflammatory diseases that  has potential for usage in personalized medicine.

overall_design: 11 Human samples from 7 sources representing 4 different cell types: 2 CD34 (CD34+ cells purified from adult peripheral blood), 3 iNS (induced Neural Stem Cells derived directly from CD34+ cells), 2 iNS derived from iPSC (Neural Stem cells differentiated from induced Pluripotent Stem Cells from CD34+ cells), 4 NPC (human primary cultured neural progenitor cells)

first: Tongguang

last: Wang

first: Maria-Chiara

middle: G

last: Monaco

first: Emilie

last: Campanac

first: Elliot

last: Choi

first: Marie

last: Medynets

first: Thao

last: Do

first: Prashant

last: Rao

first: Abdel

last: Elkahloun

first: Gloria

last: Von Geldern

first: Tory

first: Sriram

last: Subramaniam

first: Dax

last: Hoffman

last: Major

first: Avindra

last: Nath


title: Characterization of osteogenic differentiation and gene expression profile of multiple miliary osteoma cutis

city: Oulu

first: Jussi

last: Vuoristo

address: Aapistie 5

department: Biocenter Oulu

country: Finland

institute: University of Oulu

summary: Multiple miliary osteoma cutis (MMOC) is a rare skin disorder characterized by heterotopic ossification in dermis and subcutis. The etiology and disease mechanism is unknown, but earlier data indicates that it seems to be different from other diseases containing heterotopic intramembranous ossification. The purpose of this study was to further investigate the pathogenesis of MMOC by comparing patients’ osteoma affected skin area to their unaffected healthy skin area, as well as to skin from controls. This comparison was made by using osteogenic differentiation studies in cell cultures and by gene expression experiments. Both patient and control dermal fibroblast-like cells were able to differentiate into osteoblast-like matrix mineralizing cells. The differentiation seems to diminish with bone morphogenetic protein (BMP) 4 and 2/7 exposures and seems to correlate with proportion of stem cell associated cell surface marker CD105 positive cells. Microarray analysis revealed altered gene expression patterns between skin samples of patients and controls, as well as between samples taken from different skin areas. BMP receptor II and G-protein α-stimulatory subunit genes were among downregulated and β-catenin among upregulated genes in patient compared to control samples. Genes for homeobox proteins were among downregulated and gene for secreted frizzled related protein 2 among upregulated genes when compared patients’ osteoma area to their unaffected area. Differences in unaffected skin area in patients and controls suggest that the nature of MMOC may be more systemic than previously thought.  Detected differences in separate skin areas may, in turn, provide new information for understanding the localized characteristics of MMOC. BMPs’ inhibitory effect to osteogenic differentiation of human dermal fibroblast-like cells may provide a new perspective to the clinical use of BMPs.

overall_design: Skin biopsies were taken from three patients and two controls for RNA extraction and hybridization on Affymetrix microarrays.

first: Riina

last: Myllylä

first: Kirsi-Maria

last: Haapasaari

first: Riitta

last: Palatsi

first: Päivi

last: Hägg

first: Tiina

last: Hurskainen

first: Petri

last: Lehenkari

first: Juha

last: Tuukkanen


title: mRNA and microRNA profile in colon cancer [mRNA data]

city: Tampa

first: Dung-Tsa

last: Chen

state: FL

address: 12902 Magnolia Drive

department: Biostatistics and Bioinformatics

institute: Moffitt Cancer Center

summary: Compariosn of mRNA and miRNA profile in colon cancer

overall_design: mRNA was extracted from  colon tissues for microarray analysis

first: Timothy

last: Yeatman


title: Expression data from endothelial cells sorted from breast cancer cells MDA-MB231 as compared with normal endothelial cells

city: Doha

first: Najeeb

last: Halabi

address: Education City

country: Qatar

institute: Weill Cornell Medicine in Qatar

summary: We studied the crosstalk between tumor and endothelial cells to explore the role of tumor microenvironment on cancer growth and progression.  As part of our investigation, we showed that contact-dependent interaction of endothelial cells with breast tumor cells triggered the differential expression of a large number of genes in endothelium.

overall_design:
Endothelial and MDA-MB231 cells were co-cultured together under serum- cytokine-free environment for 5 days followed by sorting endothelial cells and extracting RNA for microarray analysis. All conditions were made in triplicate.  Endothelial cells were obtained using the methods described in Seandel M. & Butler J.M., 2008.
WCMC-Q Genomics Core

first: Pegah

last: Ghiabi

first: Arash

last: Rafii


title: miR-483 overexpression in human sarcoma cell line MHH-ES-1.

city: Charlestown

first: Mingzhu

last: Liu

address: 149 13th street

institute: MGH cancer center

summary: miRNA abnormalities are increasingly relevent to cancer development, We used microarrays to detail the global programme of gene expression upon miR-483 overexpression in sarcoma cell line MHH-ES-1.

overall_design: MHH-ES-1 cells were transfected with miR-483-5p, -3p or scrambled control mimics and then harvested 48 hours after to isolate total RNAs using Trizol reagent (Invitrogen). Total RNA was converted to cRNA probes using the BioArray High Yield Transcript Labeling Kit (ENZO diagnostics), and hybridized to Affymetrix GeneChip human HG-U133ver2+ 3’-mRNA expression microarray chips using protocol EukGEs2v4 on the GeneChip Fluidic Station.

first: Anna

last: Roth

first: Min

last: Yu

first: Robert

last: Morris

first: Francesca

last: Bersani

first: Miguel

last: Rivera

first: Jun

last: Lu

first: Shobha

last: Vasudevan

first: Sridhar

last: Ramaswamy

first: Shyamala

last: Maheswaran

first: Sven

last: Diederichs

first: Daniel

last: Haber


title: Gene expression analysis in the hippocampus of SUMO1 and SUMO2 transgenic mice

city: Munich

first: Moritz

last: Rossner

address: Nussbaumstr. 7

department: Psychiatry

summary:
Transgenic mouse lines that express His6-SUMO1 and His6-SUMO2 under the control of the neuron specific Thy1.2 promoter were generated and characterized.
The effect of increased levels of SUMO1 and -2 at the level of  gene expression in the hippocampus was studied.

overall_design: Pooled (left and right) hippocampi were dissected from adult littermate wild-type control (WT1) and SUMO1 and WT2 and SUMO2 transgenic animals (n=3) and subjected to RNA expression analysis.

first: Maylin

last: Tirard


title: β-catenin target genes in colorectal carcinoma cell lines with deregulated Wnt/β-catenin signaling

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

institute: Ludwig-Maximilian University

summary:
To validate the suitability of two commonly used colorectal cancer cell lines, DLD1 and SW480, as model systems to study colorectal carcinogenesis, we treated these cell lines with β-catenin siRNA and identified β-catenin target genes using DNA microarrays. The list of identified target genes was compared to previously published β-catenin target genes found in the PubMed and the GEO databases.
Based on the large number of β-catenin target genes found to be similarly regulated in DLD1, SW480 and LS174T as well as the large overlap with confirmed β-catenin target genes, we conclude that DLD1 and SW480 colon carcinoma cell lines are suitable model systems to study β-catenin regulated genes and signaling pathways

overall_design: 12 arrays (2 cell lines, 2 treatments, 3 biological replicates)

first: Andreas

last: Herbst

first: Vindi

last: Jurinovic

first: Susanne

last: Thieme

first: Helmut

last: Blum

first: Frank

last: Kolligs


title: Expression data from murine Hemophagocytes (HPCs) versus resting splenic macrophages

city: BETHESDA

first: Scott

last: Canna

department: MIIB

institute: NIAMS

summary:
Hemophagocytes are activated macrophages seen morphologically to have engulfed other hematopoietic cells. Their function is unknown. Attempts to induce these cells in vitro or purify them ex vivo have been unsuccessful.
We isolated HPCs and resting splenic macrophages by laser capture microdissection. RNA was isolated from captured cells and microarray performed to compare the activation state of HPCs versus resting splenic macrophages.

overall_design: We treated WT mice with PBS or CpG1826 and an IL-10receptor blocking antibody. Cells were captured from splenic touch preps on PEN-coated slides, RNA isolated by WT-Ovation One-Direct Amplification System and assayed on Affymetrix mouse gene ST 1.0 chips.

first: Patricia

last: Costa-Reis

first: William

last: Bernal

first: Kathleen

last: Sullivan

first: Michele

last: Paessler

first: Edward

last: Behrens


title: Analysis of expression and epigenetic changes in human colorectal cancer and matching mucosa tissues

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

type: Methylation profiling by genome tiling array

type: Genome binding/occupancy profiling by genome tiling array


title: Expression data for 4 colon tumor (Duke's stage II) /matching mucosa tissue pairs

summary: Analysis of expression changes between colon tumors (Duke's stage II) and matching colon mucosa tissues using Affymetrix GeneChip® Human Gene 2.0 ST arrays.

overall_design: All experiments were performed simultaneously for matching tissue samples.

first: Maria

last: Hahn

first: Arthur

middle: X

last: Li

first: Richard

last: Yang

first: Yong

last: Jiang

first: Raymond

middle: F

last: Schinazi

first: David

last: Drew

last: Rosenberg

first: Gerd

last: Pfeifer


title: Genes involved in cholestatic intestinal injury

city: Baltimore

first: Susan

last: Dorsey

address: 655 West Lombard Street

department: School of Nursing

institute: University of Maryland Baltimore

summary:
In this study, we examined C57BL/6J and AJ mice who received either sham surgery or cholestatic intestinal injury.
Mice were anesthetized by inhaled isoflurane anesthesia. The abdomen was clipped and then prepared in sterile fashion with 70% ethyl-ethanol followed by betadine. A transverse upper abdominal incision was performed. The CBD was dissected away from the portal vein and was ligated near its junction with the duodenum using aneurysm clips engineered with a precisely standardized opening/closing mechanism. The abdominal wall was then closed in a two-layer fashion using absorbable sutures. Sham-operated mice were treated identically but without dissection or ligation of the CBD.

overall_design: Male AJ and C57BL6J mice, 8 weeks of age, were randomly assigned to surgery or sham (n=3 microarrays per strain/condition).

first: Samuel

last: Alaish


title: Sustained expression of cyclin D1 or cyclin D1/KE in mouse mammary gland

city: PHILADELPHIA

first: Adam

last: Ertel

address: 233 S 10TH ST

department: Cancer Biology

institute: Thomas Jefferson University

summary:
Analysis of mammary glands from tet-inducible(rtTA) transgenic mice expressing cyclin D1 using Affymetrix Mouse Gene 1.0 ST GeneChip arrays. MMTV-rtTA transgenic mice (MMTV-Mouse Mammary Tumor Virus promoter) were cross-mated to  cyclin D1 transgenic mice under control of tet operon. 8-week-old tetracycline-inducible cyclin D1/rtTA bi-transgenic pregnant female mice (12 days postcoitus) were treated with doxycycline through drinking water supplementation at a final concentration of 2 mg/ml. Control mice were rtTA transgenics alone and treated in the same manner. After 7 days of doxycycline treatment, the mice were sacrificed and mammary glands taken for RNA isolation. Results provide insight into the in vivo gene expression pattern regulated by cyclin D1 through acute induction.
Analysis of mammary glands from MMTV-cyclin D1/WT and MMTV-cyclin D1/KE using Affymetrix Mouse 430A v2.0 GeneChip arrays. Cyclin D1 point mutant, cyclin D1/KE K112E (K112E) contains a lysine to glutamine substitution at amino acid position 112. cyclin D1. The cyclin D1/KE mutant fails to induce cyclin D1-dependent kinase activity. Female MFD1, MFD1-KE, and WT mice were monitored twice weekly, up to 760 days, for the development of palpable tumors. Those developing palpable tumors were sacrificed within a week of tumor detection. Tumors were dissected and portions snap frozen for RNA isolation. Results provide insight into the in vivo gene expression pattern regulated by cyclin D1 that is kinase independent.

overall_design: Two separate control mice were positive for MMTV-rtTA transgene compared to 3 separate cyclin D1/rtTA bitransgenic female mice and 3 separate cyclin D1 KE mutant/rtTA bitransgenic female mice (Mouse Gene 1.0 ST arrays).  Three separate control WT FvBmice were compared to three MMTV-cyclin D1/WT and 3 MMTV-cyclin D1/KE  mice (Mouse 430A v2.0 arrays).

last: Pestell

first: Mathew

middle: C

last: Casimiro

first: Zuoren

last: Yu


title: Transcriptional response to Smarcb1 re-expression in murine derived Smarcb1 deficient p53 null tumors

city: jerusalem

first: jonatan

last: darr

address: mavo qidda

department: cellulal and developmental biology

country: Israel

institute: huji

summary:
SMARCB1 (Snf5/Ini1/Baf47) is a potent tumor suppressor, the loss of which serves as the diagnostic feature in Malignant Rhabdoid Tumors (MRT) and Atypical Teratoid/Rhabdoid Tumors (AT/RT), two highly aggressive forms of pediatric neoplasms. Here, we restore Smarcb1 expression in cells derived from Smarcb1-deficient tumors which developed in Smarcb1-heterozygous p53-/- mice.
Profiling Smarcb1 dependent gene expression we find genes which are dependent on Smarcb1 expression to be enriched for ECM and cell adhesion functions. We identify Igfbp7, which is related to the insulin-like growth factor binding proteins family, as a downstream target of Smarcb1 transcriptional activity, and show that re-introduction of Igfbp7 alone can hinder tumor development.

overall_design: Two cancer cell lines, 167 and 365, derived from Smarcb1-deficient tumors which developed in Smarcb1-heterozygous p53-/- mice were re-infected with a retro-viral vector for Smarcb1 re-expression or an empty retro-viral vector as control. Total-RNA was collected 3 days post infection so as to enrich for direct targets of Smarcb1 transcriptionaly regulated genes

first: Amir

last: Eden

first: Jonatan

last: Darr


title: Genome-wide analysis of RNAs translationally regulated upon BRCA1 depletion in human mammary epithelial cells

city: LYON

first: Estelle

last: DACHEUX

address: 28 rue Laennec

institute: Centre de Recherche en Cancérologie de Lyon

summary:
Loss of function of the tumor suppressor BRCA1 (Breast Cancer 1) protein is responsible for numerous familial and sporadic breast cancers. We previously identified PABP1 as a novel BRCA1 partner and showed that BRCA1 modulates translation through its interaction with PABP1. We showed that the global translation was diminished in BRCA1-depleted cells and increased in BRCA1-overexpressing cells. Our findings raised the question whether BRCA1 affects translation of all cytoplasmic cellular mRNAs or whether it specifically targets a subset of mRNAs.
In the present study, we investigated which mRNAs are regulated by BRCA1 using a microarray analysis of polysome-associated RNAs from BRCA1-depleted MCF7 cells, a human breast cancer cell line.

overall_design: We isolated mRNAs from the high-molecular-weight polysomes (fractions 12 to 18) and total cellular cytoplasmic mRNAs from the cytoplasmic fraction of MCF7 cells transiently expressing either siRNA directed against BRCA1 or control siRNA. Since we were interested in identifying the mRNAs that were translationally regulated by BRCA1, we determined the relative translatability of each mRNA. The relative translatability of an mRNA was determined by normalizing the change in abundance in polysomal mRNA to the change in abundance in total cytoplasmic mRNA for each mRNA.

last: Dacheux

first: Nicole

middle: D

last: Venezia

first: Nicolas

last: Nazaret

first: Séverine

last: Croze

first: Catherine

last: Rey

first: Joel

last: Lachuer


title: Expression data from TGF-beta-treated human ovarian fibroblasts

city: Houston

first: Tsz-Lun

last: Yeung

address: 1515 Holcombe Blvd. Unit 1362

department: Gynecologic Oncology and Reproductive Medicine

institute: University of Texas MD Anderson Cancer Center

summary: Advanced ovarian cancer is the most lethal gynecologic malignancy in the United States. Ovarian cancer cells are known to have diminished response to TGF-beta, but it remains unclear whether TGF-beta can modulate ovarian cancer cell growth in an indirect manner through cancer-associated fibroblasts (CAFs). Using transcriptome profiling analyses on TGF-beta-treated ovarian fibroblasts, we identified a TGF-beta-responsive gene signature in ovarian fibroblasts. Identifying TGF-beta-regulated genes in the ovarian microenvironment helps in understanding the role of TGF-beta in ovarian cancer progression.

overall_design: The human telomerase-immortalized ovarian fibroblast line NOF151 was treated with 5ng/mL of either TGF-beta-1 or TGF-beta-2. Total RNA was isolated from control samples and TGF-beta-treated fibroblasts samples at 48 hours post-treatment, followed by cDNA synthesis, IVT and biotin labeling. Samples were then hybridized onto Affymetrix Human Genome U133 Plus 2.0 microarrays. For each treatment group, three independent samples were prepared for the microarray experiment.

first: Tsz

middle: L

first: Sze

last: Leung

last: Mok


title: Gene expression profile of human monocytes stimulated with all-trans retinoic acid (ATRA) or 1,25a-dihydroxyvitamin D3 (1,25D3)

city: Los Angeles

first: Philip

middle: T.

last: Liu

address: 615 Charles E Young Drive South, 410 OHRC

department: Department of Orthopaedic Surgery

institute: University of California at Los Angeles

summary: A role for vitamin A in host defense against Mycobacterium tuberculosis has been suggested through epidemiological and in vitro studies; however, the antimicrobial mechanism is unclear.  Here, we demonstrate that vitamin A mediates host defense through regulation of cellular cholesterol content.  Comparison of monocytes stimulated with all-trans retinoic acid (ATRA) or 1,25-dihydroxyvitamin D3, the biologically active forms of vitamin A and vitamin D respectively, indicates that ATRA and 1,25D3 induce mechanistically distinct antimicrobial activities.  Gene expression profiling reveals that ATRA but not 1,25D3 triggers a lipid metabolism and efflux pathway, including expression of lysosomal lipid transport gene NPC2.  ATRA-induced decrease in total cellular cholesterol content, subcellular lipid reorganization, lysosomal acidification and antimicrobial activity are all dependent upon expression of NPC2.  Finally, the addition of HIV-protease inhibitors known to inhibit cholesterol efflux, Ritonavir and Nelfinavir, blocked both ATRA-induced cholesterol decrease as well as antimicrobial activity.  Taken together, these results suggest that the vitamin A-mediated host defense mechanism against M. tuberculosis requires regulation of cellular cholesterol.

overall_design: Monocytes derived from four independent healthy blood donors that were stimulated with control (CTRL), ATRA or 1,25D3 at 10-8M for 18 hours.

first: Matthew

last: Wheelwright

first: Elliot

last: Kim

first: Avelino

last: DeLeon

first: Stephan

last: Krutzik

middle: T


title: Gene expression from NMuMG cells overexpressing major satellite treated with TGFbeta

city: Barcelona

first: Sandra

last: Peiró

address: Aiguader 88

department: Programa de Recerca en Càncer

institute: IMIM-Hospital del Mar

summary:
Although heterochromatin is enriched with repressive traits, it is also actively transcribed, giving rise to large amounts of non-coding RNAs. Although these RNAs are responsible for the formation and maintenance of heterochromatin, little is known about how their transcription is regulated. Here we show that the Snail1 transcription factor represses pericentromeric transcription, acting through the H3K4 deaminase LOXL2. Since Snail1 plays a key role in the epithelial to mesenchymal transition (EMT), we analyzed the regulation of mouse heterochromatin transcription in this process. At the onset of EMT, one of the major structural heterochromatin proteins, HP1a, is transiently released from heterochromatin foci in a Snail1/LOXL2–dependent manner during EMT, concomitantly with a down-regulation of major satellite transcription. Global transcriptome analysis indicated that ectopic expression of heterochromatin transcripts affects the transcription profile of EMT-related genes. Additionally, preventing the down-regulation of major satellite transcripts compromised the migratory and invasive behavior of mesenchymal cells. We propose that Snail1 regulates heterochromatin transcription through the histone-modifying enzyme, LOXL2, thus creating the favorable transcriptional state necessary for completing EMT.

Keywords: Expression Profiling by array

overall_design: We analyzed 2 arrays from each condition: Control and Major treated 8 hours with TGFbeta

first: Peiro

last: Sandra


title: Expression Analysis of Macrodactyly

city: Boston

first: Frank

last: Lau

address: 185 Cambridge St - CPZN 4500

institute: Center for Regenerative Medicine

summary: Macrodactyly is a rare family of congenital disorders characterized by the diffuse enlargement of 1 or more digits. To date, no genes or loci have been implicated in the development of macrodactyly.  In this study, we performed the first transcriptional profiling of macrodactyly tissue.

overall_design: RNA was isolated from tissue samples from 4 macrodactyly patients and hybridized to Affymetrix Human Genome U133 Plus 2.0 Arrays.

first: Brian

middle: I

last: Labow


title: mRNA and microRNA profile in colon cancer

first: Dung-Tsa

last: Chen

type:
Expression profiling by array
Other

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

overall_design: Refer to individual Series


title: Expression data from Versican (VCAN) protein treated ovarian cancer cell line OVCA433

summary: Advanced ovarian cancer is the most lethal gynecologic malignancy in the United States. Currently patients are treated by surgical cytoreductive surgery with the aim of reducing tumor burden to microscopic disease followed by adjuvant combined treatment with a platinum and taxane containing chemotherapy, which affords 80% of patients an initial complete response. However, Abdominal and pelvic recurrence rates are high and response to further chemotherapy is limited.  Attempts at introducing biologic therapeutic agents to improve outcome in this disease are ongoing, while prognostic or predictive biomarkers that can stratify patients for treatment are still lacking. Using transcriptome profiling of microdissected tissue samples from high-grade serous ovarian cancer patients, we identified a cancer associated fibroblast (CAF) specific gene signature. Versican, which encodes a extracellular matrix protein, was one of the identified genes which demonstrated up-regulation in cancer stroma. To investigate the function roles, signaling machanism and the effect of versican treatment on ovarian cancer cells, transcriptome profiling of versican treated OVCA433 high-grade serous ovarian cancer cells was performed.

overall_design: High grade serous ovarian cancer cell line OVCA433 was used. Total RNA was isolated from control samples and versican treated cancer cell samples at 48 hours post-treatment followed by cDNA synthesis, IVT and biotin labeling. Samples were then hybridized onto Affymetrix Human genome U133 plus 2.0 microarrays. For each treatment group, three independent samples were prepared for the microarray experiment.

first: Samuel


title: Expression data from cultured human dermal fibroblasts

status: Public on Dec 28 2013

city: Osaka

first: Kiyoshi

last: Higashi

address: 1-98, Kasugadenaka 3-chome, Konohana-ku

institute: Sumitomo Chemical Co. Ltd.

summary: We used microarrays to identify the molecular targets of a novel small compound HSc025.

overall_design: Fibroblasts were exposed to four different stimulants, DMSO, HSc025, TGF-bata or HSc025 plus TGF-beta.

first: Kayo

last: Sumida


title: Drug efficacy reprogramming against aggressive human prostate cancer

city: Tokyo

first: Shigeru

last: Saito

address: 2-34-17, Jingumae, Shibuya-ku

institute: INFOCOM CORPORATION

summary: We enriched for prostate cancer cells by the selection system used in human iPS purification. Gene expression signature-based chemical prediction enabled us to identify candidate drugs for reverting the EOS (early transposon promoter, OCT4 and SOX2 enhancer) signature with chemoresistance into a chemosensitive phenotype.

overall_design: We compared the gene expression between control and EOS-selected cancer cells.

first: Takeo

last: Kosaka

first: Go

last: Nagamatsu

first: Katsuhisa

last: Horimoto


title: Expression data for nasopharyngeal carcinoma cell line 5-8F stably expressing either LTF gene or empty vector.

status: Public on Dec 26 2013

city: Changsha

first: Jian

last: Ma

state: Hunan

address: 110 Xiangya Road

department: Cancer Research Institute

institute: Central South University

summary: LTF (lactotransferrin, lactoferrin) is a key component of innate immune defense. It has recently been found to have antitumor and antimetastatic activity in different cancers. We previously reported LTF to be the most significantly downregulated gene in nasopharyngeal carcinoma (NPC) specimens relative to normal nasopharyngeal epithelial tissues and it was also negatively associated with the progression and metastasis of NPC. However, the mechanism underlying this remains unclear. In the current study, we performed genome expression profiling analysis using the Affymetrix genome wide microarray system to identify broad scale changes in gene expression associated with LTF gene overexpression in NPC cell line 5-8F.

overall_design: NPC cell line5-8F were transfected with either PIRES empty vector (Clontech) or PIRES-LTF vector by Lipofectamine 2000 (Invitrogen).  Cells stably expressing either LTF or empty vector were generated by selection with growth medium supplemented with 400 μg/mL G418. When cells were growing at 80% confluence, total RNA were extracted and detected by Affymerix GeneChip Human Gene U133 plus2.0.

first: Guiyuan

last: Li


title: Genome-wide parent-of-origin DNA methylation analysis [Methylation450 BeadChip]

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

institute: IDIBELL

summary: Genomic imprinting is a form of epigenetic regulation that results in expression of either the maternally or paternally inherited allele of a subset of genes. Imprinted loci contain differentially methylated regions (DMRs) where cytosine methylation marks one of the parental alleles, providing cis-acting regulatory elements that influence the allelic expression of surrounding genes, however to date the total number of imprinted loci within the human genome is unknown. To characterize known imprinted DMRS and identify novel imprinted loci we have performed whole-genome bisulphite sequencing and high-resolution DNA methylation array analysis of healthy tissues.

overall_design: Sequencing of bisulfite converted DNA and array based analysis of normal tissues, human embryonic stem cells, androgenetic hydatidiform moles and leukocytes from reciprocal genome-wide uniparental disomies.

first: David

last: Monk

first: Kazuhiko

last: Nakabayashi


title: Identification and Validation of Genes with Expression Patterns Inverse to Multiple Metastasis Suppressor Genes in Breast Cancer Cell Lines

status: Public on Dec 27 2013

city: Indianapolis

first: Natascia

last: Marino

state: IN

address: 980 W. Walnut St

department: Medicine

institute: Indiana University

summary:
Metastasis suppressor genes (MSGs) have contributed to an understanding of regulatory pathways unique to the lethal metastatic process. When re-expressed in experimental models, MSGs block cancer spread to, and colonization of distant sites without affecting primary tumor formation. On a single MSG basis, genes have been identified with expression patterns inverse to a MSG, and found to encode functional, druggable signaling pathways. We now hypothesize that common signaling pathways mediate the effects of many MSGs. By gene expression profiling of human MCF7 breast carcinoma cells expressing a scrambled siRNA or siRNAs to each of 19 validated MSGs (NME1, BRMS1, CD82, CDH1, CDH2, CDH11, CASP8, MAP2K4, MAP2K6, MAP2K7, MAPK14, GSN, ARHGDIB, AKAP12, DRG1, CD44, PEBP1, RRM1, KISS1), we identified genes whose expression was significantly opposite to at least five MSGs.
We used microarrays to evaluate the modification in gene expression profile after donregulation of  multiple metastasis suppressors (NME1, BRMS1, CD82, CDH1, CDH2, CDH11, CASP8, MAP2K4, MAP2K6, MAP2K7, MAPK14, GSN, ARHGDIB, AKAP12, DRG1, CD44, PEBP1, RRM1, KISS1) in the breast cancer cell line, MCF7.

overall_design: MCF7 cell line was transfected with siRNA targeting each of 19 metastasis suppressors (NME1, BRMS1, CD82, CDH1, CDH2, CDH11, CASP8, MAP2K4, MAP2K6, MAP2K7, MAPK14, GSN, ARHGDIB, AKAP12, DRG1, CD44, PEBP1, RRM1, KISS1). Two siRNA sequences (siRNA1 and siRNA2) were used for each metastasis suppressor. Two time points (48hr and 96hr) were considered as end of transfection in order to measure early and late effects of the metastasis suppressors downregulation.

first: Joshua

last: Collins

first: Changyu

last: Shen

first: Yesim

last: Gökmen-Polar

first: Chirayu

last: Goswami

first: Natasha

middle: J

last: Caplen

first: Yongzhen

last: Qian

first: George

last: Sledge

first: Patricia

middle: S

last: Steeg


title: Bioinformatics Multivariate Analysis Determined a Set of Phase-Specific Biomarker Candidates in a Novel Mouse Model for Viral Myocarditis

status: Public on Dec 24 2013

city: Osakasayama

first: Seiichi

last: Omura

state: Osaka

address: 377-2 Ohnohigashi

department: Department of Microbiology

institute: Kindai University Faculty of Medicine

summary: Myocarditis is an inflammatory disease in the heart and is mainly caused by viral infections.  Viral myocarditis has been proposed to be divided into three phases; the acute viral phase, the subacute immune phase, and the chronic cardiac remodeling phase.  Although individualized therapy should be applied depending on the phase, no clinical or experimental studies have found biomarkers that distinguish between the three phases of myocarditis.  Theiler’s murine encephalomyelitis virus (TMEV) belongs to the genus Cardiovirus, and can cause myocarditis in susceptible mouse strains.  Using this novel model for viral myocarditis induced with TMEV, we conducted multivariate analysis including echocardiography, serum troponin and viral RNA titration, and microarray for identifying the biomarker candidates that discriminate the three phases.  Using C3H mice infected with TMEV on 4, 7, and 60 days post infection (p.i.), we conducted bioinformatics analyses, including principal component analysis (PCA) of microarray data, since our traditional cardiac and serum assays, including two-way comparison of microarray data, did not lead to the identification of a single biomarker.  PCA separated heart samples clearly between the groups of 4, 7, and 60 days p.i.  Representative genes contributing to the separation were as follows: 4 and 7 days p.i., innate immunity-related genes, such as Irf7, and Cxcl9; 7 and 60 days p.i., acquired immunity-related genes, such as Cd3g and H2-Aa; and cardiac remodeling-related genes, such as Mmp12 and Gpnmb.  Here, sets of molecules, but not a single molecule, identified by the unsupervised PCA, were found to be useful as the phase-specific biomarkers.

overall_design: Five mice were infected with TMEV intraperitoneally and hearvested their hearts on 4, 7, and 60 days post infection, respectively, for RNA isolation and hybridization on Affymetrix microarrays. As the control groups, age-matched uninfected mice were prepared.

first: Ikuo

last: Tsunoda


title: Effect of oocyte-enriched histones Th2a, Th2b, and histone chaperone Npm on mouse iPS cell generation

status: Public on Dec 25 2013

city: Bunkyo-ku

first: Naoko

last: Yokota

state: Tokyo

address: 1-1-1 yayoi

department: Department of Cell and Molecular Biology

institute: The University of Tokyo

summary: Expression of key transcription factors Klf4, Oct3/4, Sox2, and c-Myc (KOSM) in embryonic stem cells can reprogram somatic cells into pluripotent cells. We found that two histone variants, TH2A and TH2B, and histone chaperone Npm enhance the KOSM-dependent generation of induced pluripotent cells (iPSCs) and produce iPSCs only with Klf4 and Oct3/4. To identify directly affected genes by these histone variants during reprogramming, we carried out gene expression profiling of MEFs overexpressing TH2A/TH2B/Npm and TH2A/TH2B deficient MEFs after infection with retroviruses expressing KOSM.

overall_design: A total of 21 Affymetrix Mouse Gene ST array were done for mRNA expression profiling of ES cells, iPS cells induced by Klf4, Oct4, Sox2, and c-Myc (KOSM) or Klf4, Oct4, Th2a, Th2b, and p-Npm (KOBAN), wild-type MEFs infected with retrovirus vectors expressing KOSM, KOSMBAN, or empty vector and Th2a/Th2b-deficient MEFs infected with retrovirus vector expressing KOSM.

first: Toshie

last: Shinagawa

first: Shunsuke

last: Ishii


title: An epigenetic profile of early T-cell development from multipotent progenitors to committed T-cell descendants.

city: basel

first: maria alessandra

last: vigano

department: department of biomedicine

country: Switzerland

institute: university of basel

summary: Using a stromal cell free system, we described the gene expression and two genome wide epigenetic profiles of a unique population of undifferentiated bone marrow cells selectively driven towards the T cell differentiation pathway

overall_design: Undifferentiated bone marrow cells, transduced with NUP98-HOXB4 fusion protein, in vitro expanded with IL6 and SCF represents the hematopoietic stem cells (HSC); when grown in the presence of  DLL4 (Notch1 ligand) and IL7, they are directed towards the T cell lineage (ProT); these in vitro generated ProT cells injected in a Rag2-/- mouse give rise to mature double positive T cells (DP). 2 replica for each population

first: M

middle: A

last: Vigano


title: Platelet-derived growth factor alpha mediates the proliferation of peripheral T-cell lymphoma cells via an autocrine regulatory pathway

city: Bologna

first: Fabio

last: Fuligni

address: Via Massarenti 9

department: Department of Experimental, Diagnostic, and Specialty Medicine Bologna University Medical School

country: Italy

institute: University of Bologna

summary: Identification of the determinants of PDGFRA activity in PTCL/NOS (Peripheral T-cell lymphoma/not otherwise specified) and to elucidate the biological consequences of its activation.

overall_design: We generated GEP from samples of primary PTCL/NOS cells treated or not with imatinib mesylate (see below) as well as from EOL1 cells (3 samples each)

first: Pier

last: Piccaluga

first: Maura

last: Rossi

first: Claudio

last: Agostinelli

first: Francesca

last: Ricci

first: Anna

last: Gazzola

first: Simona

last: Righi

first: Maria

last: Laginestra

first: Manuela

last: Mancini

middle: R

last: Sapienza

first: Amalia

last: De Renzo

last: Tazzari

first: Davide

last: Gibellini

first: Philip

last: Went

first: Francesco

last: Alviano

last: Zinzani

first: Gian

last: Bagnara

first: Giorgio

last: Inghirami

last: Tripodo

first: Stefano

last: Pileri


title: Expression profile of sweat gland label retaining cells (LRCs)

first: Krzysztof

last: Kobielak

state: CA

address: 1425 San Pablo Street

department: Department of Pathology

country: USA

institute: University of Southern California

summary:
We have used the slow cycling property, found in hair follicle stem cells, to look for LRCs in sweat glands as putative stem cells.
Gene expression profiling allowed us to determine the common and unique genes expressed in SG LRCs and non-LRCs. This allowed us to probe for the signaling pathways active in this skin appendage as well as determine potential molecular markers of SG LRCs.

overall_design: Sweat gland label retaining cells (LRCs) and surrounding basal layer cells were isolated from K5TetOffTreH2BGFP mice after a 4 week chase with doxycycline and compared to the basal layer of the sole's epidermis in 2 independent experiments.

first: Yvonne

last: Leung

first: Eve

last: Kandyba

first: Yi-Bu

last: Chen

first: Seth

last: Ruffins


title: Global Target mRNA Specification and Regulation by RNA-Binding Protein ZFP36/Tristetraprolin/TTP [Affymetrix]

city: Aurora

first: Neelanjan

last: Mukherjee

department: BMG/RBI

institute: University of Colorado School of Medicine

summary: Tristetraprolin/ZFP36/TTP and ELAVL1/HuR are two disease-relevant RNA-binding proteins (RBPs) that both interact with AU-rich sequences but have antagonistic roles. While ELAVL1 binding has been profiled in several studies, the precise in vivo binding specificity of ZFP36 has not been investigated on a global scale. We determined ZFP36 binding preferences using cross-linking and immunoprecipitation in human embyonic kidney cells and examined combinatorial regulation of AU-rich elements by ZFP36 and ELAVL1. Among the targets ZFP36 binds and negatively regulates the mRNA of genes encoding proteins necessary for immune function and cancer, and other RBPs. Using partial correlation analysis, we were able to quantify the association between ZFP36 binding sites and differential target RNA abundance from ZFP36 overexpression independent of effects from confounding features, such as 3’ UTR length. We identified thousands of overlapping ZFP36 and ELAVL1 binding sites, in 1,313 genes. ZFP36 preferentially interacts with and regulates AU-rich sequences while ELAVL1 prefers predominantly U- and CU-rich sequences. RNA target specificity identified by global in vivo ZFP36-mRNA interactions were quantitatively similar to previously reported in vitro binding affinities. ZFP36 and ELAVL1 both bind an overlapping spectrum of RNA sequences, yet with differential relative preferences that dictate combinatorial regulatory potential. Our findings and methodology delineate an approach to untangle the in vivo combinatorial regulation by RNA-binding proteins.

overall_design: Five biological replicates for each of the four sample classes -> Parental and EGFP-ZFP36 HEK293 cells treated with either doxycycline or water.

first: Thomas

last: Tuschl

first: Uwe

last: Ohler

first: Perry

last: Blackshear


title: Expression data from P15 mouse testes control and Ikbkap-knockout mice

first: Fu-Jung

last: Lin

address: 200 Longwood Ave.

institute: Harvard Medical School

summary: Ikbkap/Elp1 regulates genes involved in spermatogenesis. Ikbkap deficiency causes male infertility by disrupting meiotic progression. In this dataset, we include the expression data for control and Ikbkap-knockout mouse testis.

overall_design: We analyzed the gene expression in control and Ikbkap-knockout testes using the the Affymetrix MoGene-1_0-st-v1 platform. Three replicates per genotype.

first: Fu

first: Li

last: Shen

first: Chuan

middle: W

last: Jang

first: Pål

middle: O

last: Falnes

first: Yi

last: Zhang


title: Expression data from control and Mbd4 KO CH12 cells that were activated with CIT for 24 hours.

status: Public on Dec 19 2013

city: Chicago

first: Amy

last: Kenter

state: IL

address: 835 South Wolcott E825

department: Microbiology/Immunology

institute: University of Ilinois at Chicago College of Medicine

summary: AID-dependent U/G mismatches in S DNA are converted by BER and MMR DNA pathways into double-stranded breaks that are required for optimal CSR in activated B cells. Deficits in MMR proteins, MSH2, MLH1, and PMS2 result in lower CSR frequencies that are coupled with impaired DSB formation. MBD4 interacts with MLH1 and has been postulated to coordinate mismatch repair of U/G. Deletions of Mbd4 targeting the 5' end of the gene in mice do not affect CSR . However, Mbd4 transcription is complex, with the propensity to create alternative transcripts, including residual transcription leading to to truncated protein expression that complicates ananlysis in these mice. We describe a novel function of MBD4 housed in the C-terminus that is critical for DSB formation, which shares several characteristics with MMR . We conclude that the 3' end of the Mbd4 gene positively contributes to CSR and likely intersects the MMR pathway.

overall_design: 2 independent samples for each control and Mbd4 KO group

first: F

last: Grigera

first: A


title: Circadian Liver Gene Expression in Animals on Normal Chow or High Fat Diet

city: Irvine

first: Kristin

middle: Lynn

last: Eckel-Mahan

address: 360 Sprague Hall

department: Biological Chemistry

institute: UCI

summary: Circadian and metabolic processes are codependent. This experiment was designed to understand how a high fat diet affects circadian gene expression in the liver. Circadian gene expression in the liver is necessary for energy balance.

overall_design: Animals consuming normal chow or high fat diet (60% kcal from fat) for ten weeks were analyzed for circadian gene expression. Livers were harvested from animals every four hours throughout the circadian cycle.

first: K

first: P

last: Sassone-Corsi


title: DLC1 Suppresses Breast Cancer Bone Metastasis

city: Shanghai

first: Guohong

last: Hu

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health

summary: The skeleton is the most common metastasis site of breast cancer cells and the molecular underpinning of this process is incompletely understood. The tumor suppressor gene deleted in liver cancer-1 (DLC1) encodes a multi-domain protein including a RhoGTPase activating protein (RhoGAP) domain and has been reported to suppress the lung colonization of breast cancer cells. However, the role of DLC1 in breast cancer bone metastasis and the importance of RhoGAP-dependent and -independent pathways in this process remain unclear. Here, we showed that DLC1 silencing is linked to enhanced bone-tropism of breast cancer cell lines and poor prognosis of clinical samples.

overall_design: In the study presented here, DLC1 was overexpressed in the SCP2 breast cancer cells, and the control SCP2 and overexpression cells were treated with TGFbeta. Microarray profiling of mRNA levels was performed in the control and overexpression cells with or without TGFbeta treatment.

first: Yufeng

last: Wang


title: Whole genome transcriptional profile of human tissues and cells

first: Fuyuki

last: Miya

address: 35 Shinanomachi, Shinjuku-ku

department: School of Medicine

institute: Keio University

type: Expression profiling by genome tiling array

type: Non-coding RNA profiling by genome tiling array

summary:
We performed tiling array experiments to examine whole genome expression in human tissues. We investigated tissue specificity and association between evolutionary sequence conservation and transcription.

A total of 22 tissues (bone marrow, cerebellum, colon, cortex, fetal brain, heart, kidney, liver, lung, pancreas, prostate, salivary gland, skeletal muscle, small intestine, spinal cord, spleen, stomach, testes, thymus, thyroid, trachea and uterus) and 2 cell lines (HeLa and SH-SY5Y) were examined in 36783546 regions of the Human genome in this study.

Keywords: whole genome transcription, tiling array, non-coding transcripts, tissue specificity

overall_design: Total RNA isolated from Human tissues and cell cultures were labeled and hybridized to the GeneChip Human Tiling 1.0R Array set of 14 chips (24 samples x 14  = 336 chips total) according to the manufacturer's protocol.

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