title: Identification of genes regulated by H19 in cornea epithelium

status: Public on Apr 28 2016

city: Irvine

first: Bogi

last: Andersen

state: CA

address: 839 Health Sciences Dr.

department: Medicine

institute: University of California, Irvine

summary: To understand the gene-regulatory role of H19 in corneal epithelial cells and to explore whether  CLIM activation of H19 might account for non-cell proliferation effects of CLIM, we used siRNA to knock down H19 in primary human corneal epithelial cells. Microarray gene expression analysis revealed that 1,249 genes are down regulated 1.5 fold or more by siH19 compared to scramble control, and that 944 genes are up regulated

overall_design: H19 was knocked down with siRNA in triplicate to compare with a mismatch control, also in triplicate; RNA was isolated and microarray analysis performed to assess the effect of H19 knockdown on gene expression in corneal epithelial cells.

first: Rachel

last: Herndon Klein


title: Reconstructing gene regulatory networks of tumorigenesis [genex]

status: Public on May 13 2016

city: Illkirch; Strasbourg

first: Valeriya

last: Malysheva

address: 1 rue Laurent Fries

country: France

institute: IGBMC

summary: The mechanistic links between transcription factors and the epigenetic landscape, which coordinate the deregulation of gene networks during cell transformation are largely unknown. We used an isogenic model of stepwise tumorigenic transformation of human primary cells to monitor the progressive deregulation of gene networks upon immortalization and oncogene-induced transformation. By combining transcriptome and epigenome data for each step during transformation and by integrating transcription factor (TF) - target gene associations, we identified 142 Tfs and 24 chromatin remodelers/modifiers (CRMs), which are preferentially associated with specific co-expression paths that originate from deregulated gene programming during tumorigenesis. These Tfs are involved in the regulation of divers processes, including cell differentiation, immune response and establishment/modification of the epigenome. Unexpectedly, the analysis of chromatin state dynamics revealed patterns that distinguish groups of genes, which are not only co-regulated but also functionally related. Further decortication of TF targets enabled us to define potential key regulators of cell transformation, which are engaged in RNA metabolism and chromatin remodelling. Our study suggests a direct implication of CRMs in oncogene-induced tumorigenesis and identifies new CRMs involved in this process. This is the first comprehensive view of gene regulatory networks that are altered during the process of stepwise human cellular tumorigenesis in a virtually isogenic system.

overall_design: Transcriptional activity in BJEL and BJELM cells has been evaluated  and compared with that found in BJ cells; 2 biological replicates per cell line

first: Marco

middle: A

last: Mendoza-Parra

first: Mohamed

last: Ashick

last: Saleem

first: Hinrich

last: Gronemeyer


title: Identification of aging-associated gene expression signatures that precede intestinal tumorigenesis [human]

status: Public on May 03 2016

city: Kyoto

first: Yoshihisa

last: Okuchi

state: Kyoto

address: Yoshida Konoe-cho, Sakyo-ku

department: Department of Pathology and Biology of Diseases

country: Japan

institute: Kyoto university

summary: Aging-associated gene expression alterations have been implicated in various cancers including colorectal cancer. We examined aging-associated gene expression signatures that precede intestinal tumorigenesis using surgical specimens of Japanese FAP patients.

overall_design: We analyzed normal intestinal mucosae located more than 2 cm away from the adenomas (n = 3), normal intestinal mucosae adjacent to adenomas (within 5 mm) (n = 3), and intestinal adenomas (n = 3) from human FAP patients using the Affymetrix Human Gene 1.0 ST platform. Array data was processed by Affymetrix GeneChip Command Console, Expression Console, and Transcriptome Analysis Console software.

first: Y

first: M

last: Imajo

last: Matsuda


title: Gene expression profiling in paired human hepatocellular carcinoma and liver parenchyma biopsies and normal liver biopsies.

status: Public on May 01 2016

city: Basel

first: Zuzanna

last: Makowska

address: Hebelstrasse 20

department: Biomedicine

country: Switzerland

institute: University of Basel

summary: Hepatocellular carcinoma (HCC) is a heterogeneous disease, and despite considerable research efforts, no molecular classification of HCC has been introduced in clinical practice. The existing molecular classification systems were established using resected tumors, which introduces a selection bias towards patients without liver cirrhosis and with early stage HCCs. So far, these classification systems have not been validated in liver biopsy specimens from tumors diagnosed at intermediate and late stages. We generated and analyzed expression profiles from 60 HCC biopsies from an unselected patient population with all tumor stages. Unbiased clustering identified 3 HCC classes. Class membership correlated with survival, tumor size, and with Edmondson and BCLC stage. Most biopsy specimens could be assigned to the classes of published classification systems, demonstrating that gene expression profiles obtained from patients with early stage disease are preserved in all stages of HCC. When a reference set of healthy liver samples was integrated in the analysis, we observed that the differentially regulated genes up- or down-regulated in a given class relative to other classes were actually dysregulated in the same direction in all HCCs, with quantitative rather than qualitative differences between the molecular subclasses. With the exception of a subset of samples with a definitive β-catenin gene signature, biological pathway analysis could not identify class specific pathways reflecting the activation of distinct oncogenic programs. Our results suggest that gene expression profiling of HCC biopsies has limited potential to direct therapies that target specific driver pathways, but can identify subgroups of patients with different prognosis.

overall_design: 60 biopsy pairs from hepatocellular carcinoma patients (1 biopsy of the tumor and 1 biopsy of the non-tumor liver from each patient), 5 normal liver biopsies

first: Markus

middle: H

last: Heim


title: Virograms for prediction of predisposition to asthma exacerbation

city: Tucson

first: Haiquan

last: Li

state: AZ

address: 1657 E Helen Street

country: USA

institute: University of Arizona

summary:
Background: Clinical transcriptomics of peripheral blood mononuclear cells (PBMC) are coming into focus as a surrogate approach for prognosis, diagnosis, biomarker discovery and examination disease mechanisms. However, bioassays paired with transcriptomic analytic tools are yet to be developed and made available at point of care. Harnessing personal dynamic genomic responses to tailor patient asthma treatment or prevent disease exacerbations remain unmet medical needs.
Method: We developed a rhinovirus-stimulated peripheral blood based-assay (virogram assay) coupled with single-subject analytics (N-of-1-patwhays) to capture dynamic genome-wide expression and dysregulated pathways to retrospectively predict childhood asthma exacerbation. We hypothesized that some genomic factors might predispose any given individual, healthy or asthmatic, to a set of similar transcriptional responses to rhinovirus stimulation. We first generated a classifier from paired sample microarrays, control and stimulated PBMC from healthy subjects and applied this classifier on the transcriptomic analysis of control and HRV-stimulated PBMC samples (virogram assay) from children with asthma.
Results: The analysis of the different genomic responses of single-subject paired PBMC samples (HRV-stimulated and control) derived from healthy individuals (external dataset) enabled the discovery of dysregulated pathways related to acquired immunity, epigenetics and morphogenesis. The classifier built on these results and applied on the transcriptional analysis derived from the virogram assay predicted that the risk of asthma exacerbation among asthmatic subjects with an accuracy of 70%.
Conclusion: We provide evidence that clinical prognosis can be predicted with a PBMC based-bioassay aligned with adequate single-subject analytics to assess dynamic transcriptomic response to specific disease-associated stimuli.

overall_design:
Virogram assay of rhinovirus-stimulated PBMC samples and microarra
Prepherial blood mononuclear cells (PBMCs) were isolated from blood samples collected from the 23 pediatric asthma subjects enrolled in the extension study following their participation in TREXA and BADGER clinical trials. Based on exacerbation status, the pediatric asthma subjects were classified in two groups: 11 subjects coded as no exacerbation (NE) for those that did not receive oral corticosteroids during the year of the study and (ii) 12 subjects coded as recurrent exacerbation (RE) for those that received two or more courses of oral corticosteroids during the year of the study. None of the 23 asthma patients received steroids during the month prior to the extension study when blood samples were collected for PMBCs. Each individual’s PBMCs are divided into two cultures, non-stimulated (PBMC control) and stimulated with human rhinovirus (PBMC stimulated) at 37°C in 5% CO2 for 24 hours. Paired PBMCs samples from each subject were harvested separately for RNA extraction. A total of 46 samples (23 pairs) were assessed for RNA quality, then amplified, tagged, and hybridized on Affymetrix Human Gene 1.0 ST microarrays according to standard operating procedures.

Microarray datasets and gene expression processing
Robust Multiple-array Average (RMA) normalization was applied on each patient data independently (2 paired samples at a time, to avoid bias in the single-patient experiments) using Affymetrix Power Tools (APT).

first: Vincent

last: Gardeux

first: Ikbel

last: Achour

first: Anthony

last: Bosco

first: Jianrong

first: Marylyn

middle: J

last: Halonen

first: Daniel

middle: D

last: Jackson

first: Fernando

last: Martinez

first: Yves

last: Lussier


title: A stage-specific induction system reveals that the oncogenic fusion protein in synovial sarcoma, SS18-SSX, is a cellular context-dependent epigenetic modifier

status: Public on Apr 13 2016

city: kyoto

first: Junya

last: Toguchida

address: 53 kawahara-cho, shogoin

department: Center for iPS Cell Research and Application(CiRA)

institute: Kyoto University

summary: We analyzed the effects of cellular context on the function of the synovial sarcoma-specific fusion protein, SS18-SSX, using human pluripotent stem cells containing the drug-inducible SS18-SSX gene. To investigate the cell-type-dependent effecfts of SS18-SSX, we performed gene expression profiling experiments.

overall_design: Comparison of global gene expressions of hPSCs, hPSC-NCCs, and hPSC-MSCs with or without the inductuion of SS18-SSX2

first: J


title: MondoA mediates in vivo aggressiveness of common ALL and may serve as a T cell immunotherapy target

status: Public on Apr 30 2016

city: Berlin

first: Guenther

middle: HS

last: Richter

address: Augustenburger Platz 1

department: Department of Pediatrics, Division of Oncology and Hematology

country: Germany

institute: Charité - Universitätsmedizin Berlin

summary: Oncogene addiction provides ideal targets for immunotherapy. We previously showed that the high expression of the conserved transcription factor MondoA mediates glucose consumption and stemness of a cALL cell line. We now report the expression of MondoA (MLXIP) in cALL compared to other malignancies, its role in malignancy of cALL in vivo, downstream pathways and correlation with relapse risk. Given the non-accessibility of transcription factors by drugs or chimeric antigen receptor transgenic T cells, we assessed the targetability of MondoA by allo-restricted, peptide-specific T cells. We found MondoA to be most highly expressed in pediatric cALL. MondoA knock down (KD) in cALL cell lines and their subsequent analysis in xenograft mice reduced the number of leukemic blasts in blood, marrow and spleen. Spleen size and weight normalized in mice after MondoA KD. Consistent with these data, MondoA overexpression correlated with relapse risk in cALL patients, as its expression was 63% higher in the very high-risk group relative to the non-high-risk group. Transcriptomic profiling of cALL cell lines after MondoA KD revealed an induction of aerobic glycolysis switch genes and hypoxia-response by MondoA. Indeed, MondoA appeared to be required for HIF1A protein stabilization. Therapeutically, MondoA-derived peptide antigens and HLA-A*02:01+ cALL lines were successfully recognized and killed by specific, allo-restricted CD8+ T cells. In conclusion, our findings demonstrate that MondoA maintains leukemic burden and aggressiveness of cALL in vivo possibly by modulating metabolic and hypoxia stress response. Moreover, we identified MondoA as a promising target for immunotherapy of cALL.

overall_design: cALL leukemic cell lines Nalm6, 697 and Reh were lentivirally infected with inducible MLXIP-specific shRNA and control shRNA. Infected cells were treated for 48h with 1µg/ml doxycycline for specific shRNA induction. RNA from treated cells was isolated with Trizol and subjected to microarray analysis onto human Gene 1.0 ST arrays following the Affymetrix protocol.

first: Günther

first: Alexandra

last: Sipol

first: Thorsten

last: Buch

first: Stefan

last: Burdach


title: Transcription in a Jurkat cell model of T cell memory

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

country: Australia

institute: University of Canberra

summary: Adaptive immune responses to infection result in the formation of memory T cells that respond more rapidly and robustly to reinfections, providing the basis of the immunological memory targeted by vaccines. Underlying the enhanced responsiveness of memory cells is their ability to rapidly up-regulate the transcription of key effector genes at a higher level compared to naïve cells (termed transcriptional memory). While transcriptionally permissive histone modifications are known to provide chromatin structures that facilitate transcriptional memory, the molecular mechanisms that underpin this process still remain elusive. Here we investigate the transcriptional response of the Jurkat T cell line to stimulation with PMA and Ionomycin and determine if this response differs in cells that have seen stimuli previously.

overall_design: 4 different treatments

first: Jasmine

first: Sudha

last: Rao


title: Effect of vitamin D on gene expression in human alveolar type II cells

status: Public on Apr 07 2016

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

summary: To test whether vitamin D has a functionally important effect upon primary alveolar epithelial type II cells we used gene expression microarray to identify genes that are regulated by 25-dihydroxyvitamin D in adult alveolar type II cells.

overall_design: Alveolar type II (ATII) cells were obtained from lung resection tissue specimens of 4 adults. 0.5 Million cells were seeded onto 24 well plates in DCCM-1 (Biological Industries Ltd. Kibbutz Beit-Haemek, Israel) media supplemented with 10% fetal calf serum (FCS).  The cells were cultured for 48 hours in vitro before treating with 100nmol/l of 1, 25-dihydroxyvitamin D in medium containing 0.1% FCS for further 24 hours. Before stimulation with  1, 25-dihydroxyvitamin D for 24 hours, cells were serum starved overnight (0.1% FCS). ATII cells without vitamin D treatment were used as control.

first: Vijay

middle: K

last: D'Souza

first: David

middle: R

last: Thickett


title: Expression data in human oral mucosa fibroblasts (hOFs), dermal fibroblasts, and hOFs-derived iPS cells

status: Public on Apr 21 2016

city: Tokushima

first: Keiko

last: Miyoshi

address: 3-18-15 Kuramoto-cho

department: Department of Molecular Biology

institute: The University of Tokushima Graduate School, Institute of Health Biosciences

summary:
To define the characteristics of human oral mucosa fibroblasts (hOFs), we analyzed the gene expression of hOFs compared with that of human dermal fibroblasts (hDFs), and that of hOF-derived induced pluripotent stem cells (hOF-iPSCs).
In this dataset, we found that 5,738 probes and 5672 probes were differently expressed in hOFs and hDFs respectively, compared with those in hOF-iPSCs at more than 2-fold levels. In contrast, only 434 probes are differently expressed between hOFs and hDFs.

overall_design: Total 9 samples (i.e., 3 samples in each group; hOFs, hDFs, and hOF-iPSCs) were analyzed. The average data from 3 samples in each group were calculated, and used for pairwise comparisons with GeneSpring software; hOFs vs. hDFs, hOFs vs. hOF-iPSCs, hDFs vs. hOF-iPSCs.

first: Takafumi

last: Noma

first: Hideaki

last: Horikawa


title: Effects of Oct1 inhibition  in AR signaling

status: Public on Apr 01 2016

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

institute: Tokyo Metropolitan Institute of Gerontology

summary:
Prostate cancer is the most common cancer in men and AR downstream signalings promote prostate cancer cell proliferation. Oct1 is an AR interacting partner and regulates the transcriptional activity of AR.
In order to investigate the Oct1 function in prostate cancer cells, we performed gene expression in AR-positive prostate cancer cell lines after siOct1 or pyrrole-imidazole (PI) polyamide targeting Oct1-binding treatment. We also treated cells with vehicle or androgen to analyze the effects of Oct1 on AR function.

overall_design: Observation of androgen dependent gene expression changes after treatment with siOct1 or polyamide targeting Oct1 with microarray.

first: K

first: S

last: Inoue


title: p53 and 5hmC in gene regulation

city: Atlanta

first: Peng

last: Jin

state: GA

address: Whitehead Research Building, 615 Michael Street

department: Department of Human Genetics

institute: Emory University School of Medicine

summary: p53 is one of the most frequently mutated genes in human cancers, which could regulate multiple target genes involved in a widespread of cellular processes. The regulation of DNA methylation dynamics is critical for maintaining genome stability and proper gene expression. Recently a family of Ten-Eleven-Translocation (TET) proteins has been shown to possess the enzymatic activity to oxidize 5mC to 5hmC, and contribute to DNA demethylation. Here we explore the relationship between p53 binding, 5hmC modification and gene activation using human p53-deficient cells (H1299).

overall_design: H1299 Cells with and without p53

first: Dahua

last: Chen


title: Gene expression analysis of coronal pulp and apical pulp complexes

status: Public on Mar 31 2016

city: Seoul

first: Seong-Oh

last: Kim

address: 250 Seongsanno, Seodaemun-gu

department: Pediatric dentistry

country: South Korea

institute: Yonsei University College of Dentistry

summary:
We performed this study to compare the gene expression pattern between coronal pulp and apical pulp complex
There were no studies about gene expression of apical pulp complex tissue before. So We performed this study to confirm the gene expression of apical pulp complex tissues.

overall_design:
Coronal pulp tissues were collected from 11 healthy subjects. Gene expression profiles were conducted using cDNA microarray analysis.
Apical pulp complex tissues were collected from 18 healthy subjects. Gene expression profiles were conducted using cDNA microarray analysis.

first: Je-Seon

last: Song


title: Genome wide comparison of the inducible transcriptomes of CAR, PXR and PPARα in primary human hepatocytes

status: Public on Mar 24 2016

city: Stuttgart

first: Ulrich

middle: M.

last: Zanger

address: Auerbachstr. 112

institute: Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology

summary:
To identify the CAR-, PXR- and PPARα-specific genome-wide expression changes, hepatocyte cultures from six individual donors were treated with the prototypical ligands for
CAR (CITCO), PXR (rifampicin) and PPARα (WY14,643) as well as DMSO (vehicle control). Afterwards, the mRNA expression in these samples was determined utilizing Affymetrix® microarrays.

overall_design: Primary human hepatocytes (PHH) from 6 donors were treated for 24 h with 10µM of rifampicin, 50µM of WY14,643, 1µM of CITCO and 0.1% of DMSO (vehicle).

first: Benjamin

last: Kandel

first: Maria

last: Thomas

first: Georg

last: Damm

first: Stefan

last: Winter

first: Daniel

last: Seehofer

first: Oliver

last: Burk

first: Matthias

last: Schwab

middle: M


title: Analysis of White Adipose Tissue Gene Expression Reveals CREB1 Pathway Altered in Huntington's Disease.

status: Public on Mar 20 2016

city: Lund

last: Björkqvist

state: Skåne

address: Sölvegatan 17

department: Experimental Medical Sciences

country: Sweden

institute: Lund University

summary:
We investigated gene expression signatures in subcutaneous adipose tissue obtained from control subjects, premanifest HD gene carriers and manifest HD subjects with the aim to identify gene expression changes and signalling pathway alterations in adipose tissue relevant to HD.
Gene expression was assessed using Affymetrix GeneChip® Human Gene 1.0 ST Array. Target genes were technically validated using real-time quantitative PCR and the expression signature was validated in an independent subject cohort.

overall_design: 20 subcutaneous white adipose tissue samples were analyzed by affymetrix: 7 control samples; 8 premanifest HD samples; 5 stage II/III HD samples.

first: Andrew

middle: C

last: McCourt

first: Jennifer

last: Parker

first: Edina

last: Silajdžić

first: Salman

last: Haider

first: Huma

last: Sethi

first: Sarah

last: Tabrizi

first: Thomas

middle: T

last: Warner


title: Tonic stretch of human lung cells

status: Public on Apr 12 2016

city: Boston

first: Alvin

middle: T.

last: Kho

state: MA

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

summary: We profiled the transcriptomes of 4 human lung cell types that were subjected to control (non-stretch) and 30% tonic stretch conditions for 4 hours and 24 hours.

overall_design:
Total RNA extracted from cells under control (time-matched) or 30% stretch conditions (4 hours or 24 hours) performed in technical replicate experiments.
human lung alveolar A549 cells, human lung bronchoepithelial 16HBE14o- cells, human fetal lung fibroblasts CCL-153, human juvenile lung fibroblasts CCL-151

last: Tschumperlin

first: Francis

last: Boudreault


title: Effects of Systemically Administered Hydrocortisone on the Human Immunome

status: Public on Mar 14 2016

city: Bethesda

first: Yuri

last: Kotliarov

state: MD

address: 4 Memorial Dr., room 134

department: CHI

institute: NHLBI

summary:
Corticosteroids have been prescribed for decades to modulate inflammation, yet there is a paucity of data on their effects in humans.  We examined the changes in cellular and molecular immune system parameters, or “immunome,” in 20 volunteers at baseline, and after intravenous hydrocortisone (HC) administered at moderate (250 mg) and low (50 mg) doses, to provide insight into how corticosteroids exert their effects.
We observed declines in specific B and T cell subsets, and an increase in natural killer cell subsets  4-8 hours after HC.  Whole transcriptome profiling revealed a gene expression signature that preceded lymphocyte population changes. We observed decreases in inflammatory cytokines after HC administration. Our study provides insights into the effects of corticosteroids on the human immunome.

overall_design: According to CHI protocols 11-H-0092, 18 healthy volunteers were administered a single dose of intravenous (IV) hydrocortisone at either 50 mg or 250 mg concentrations. PBMC samples were collected immediately prior to receiving the drug (0 hours), then after 1, 4, 8, 12, and 24 hours.

first: Matthew

last: Olnes

first: Angelique

last: Biancotto

first: Foo

last: Cheung

first: Jinguo

last: Chen

first: Rongye

last: Shi

first: Huizhi

last: Zhou

first: Ena

last: Wang

first: John

middle: S

last: Tsang

first: Robert

last: Nussenblatt


title: Reversal of Flow-Direction is A Critical Mechanical Stimulus for Full Activation of Endothelial Arteriogenesis Signaling Pathways

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

summary: This study characterizes the response of primary human endothelial cells (human umbilical vein endothelial cells, HUVECs) to the relative shear stress changes that occur during the initiation of arteriogenesis at the entrance regions to a collateral artery network. HUVECs were preconditioned to a baseline level of unidirectional shear of 15 dynes/cm2 for 24 hours. After 24 hours preconditioning, HUVECs were subjected to an arteriogenic stimulus that mimics the shear stress changes observed in the opposing entrance regions into a collateral artery network. The arteriogenic stimulus consisted of a 100% step wise increase in shear stress magnitude to a unidirectional 30 dynes/cm2 in either the same or opposite direction of the preconditioned shear stress. This simulates either the feeding entrance to the collateral artery circuit or the region that drains into the vasculature downstream of an obstruction in a major artery, respectively. In vivo analysis of collateral growth in the mouse hindlimb showed enhanced outward remodeling in the re-entrant (direction reversing) region that reconnects to the downstream arterial tree, suggesting reversal of shear stress direction as a key enhancer of arteriogenesis. Transcriptional profiling using microarray techniques identified that the reversal of shear stress direction, but not an increase in shear stress alone, yielded a broad-based enhancement of the mechanotransduction pathways necessary for the induction of arteriogenesis.

overall_design: Human umbilical vein endothelial cells (HUVECs) were preconditioned to a unidirectional clockwise shear stress of 15 dynes/cm2 for 24 hours. An acute increase in shear stress magnitude to 30 dynes/cm2 in either a clockwise (non-reversed) or counter-clockwise (reversed) direction was applied for 6 hours. An additional preconditioned control culture was maintained under a unidirectional clockwise shear stress of 15 dynes/cm2 and harvested at the same time point, 6 hours post-conditioning. Each condition of reversed, non-reversed, and control was performed in tandem from the same starting cell culture as one replicate. The total experiment consisted of four replicates. Gene transcription was then assessed using microarray expression analysis.

first: Joshua

last: Meisner

middle: L

last: Heuslein

first: Richard

last: Price


title: Molecular Characterization of Dieldrin in the Zebrafish (Danio rerio) Hypothalamus

status: Public on Mar 07 2016

city: Saint John

first: Andrew

last: Cowie

state: New Brunswick

address: 100 Tucker Park Rd.

department: Biochemistry and Molecular Biology

country: Canada

institute: Dalhousie University

summary: Dieldrin is a legacy pesticide that has multiple modes of action (MOA) that include being an estrogen receptor agonist, GABA receptor antagonist, and a chemical that disrupts mitochondrial function.  There is also evidence that dieldrin exposure is significantly associated with an increased risk for neurodegeneration in humans. The objective of this thesis was to clarify the effects of dieldrin in the hypothalamus, the major neuroendocrine region of the brain, in the zebrafish (Danio rerio). Zebrafish were fed pellets containing 0.03, 0.15, or 1.8 µg/g dieldrin for 21 days and a global gene expression analysis was performed to characterize cellular processes and pathways affected by dieldrin.

overall_design: Reproductive adult zebrafish (4-6 months of age) were obtained from Mirdo Inc. (Montréal, QC, Canada).  Zebrafish were housed at the Canadian Rivers Institute (Saint John, NB, Canada) in 20 L tanks.  After an acclimation period of 3 weeks, zebrafish were divided into 9 tanks per experimental group giving a total of 36 tanks, each with active carbon within the tank as an extra precaution to minimize any exposure to water-borne dieldrin.  Five fish were added to each tank, with the goal of maintaining a 3 to 2 female to male sex ratio.  Zebrafish in designated tanks were fed 0.065 g of the control or one of the three contaminated feeds twice a day representing a daily intake of 0.13 g (approximately 4% of fish body weight per tank).  Feeding took place at 10 am and 4 pm each day.

first: Kathleena

last: Sarty

first: Angella

last: Mercer

first: Jin

last: Koh

first: Harold

last: Taukilus

first: Karen

last: Kidd

first: Chris

last: Martyniuk


title: Expression data from serum-starved human umbilical vein endothelial cells that have been treated with scrambled (scr) or Map4k4 siRNA to knock down genes of interest 48 hours prior to harvest

city: worcester

first: Michael

last: Czech

address: 373 plantation st

department: PMM

institute: UMASS Medical Scool

summary:
We identified that knocking down Map4k4 in endothelial cells affected genes associated with the cell cycle, mitosis, and inflammatory genes.
We used microarrays to identify genes of interest that are differentially expressed after the addition of scrambled or Map4k4 siRNA.

overall_design: HUVECs were treated with scrambled or siMap4k4. 24 hours later, cells were serum starved overnight. Cells were prepared with this protocol on three different occasions, and total RNA was isolated to provide three biological replicates per sample.

first: Rachel

last: Roth Flach

first: Juerg

last: Straubhaar

first: Sarah

last: Nicoloro


title: A possible role of miRNAs as predictive markers for the recurrence of hepatocellular carcinoma after liver transplantation

status: Public on Mar 01 2016

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

summary:
Background and aims: Liver transplantation (LT) is the most radical treatment for hepatocellular carcinoma (HCC) with high rates of long-term survival, but tumor recurrence after LT is an unresolved problem. The aim of our study was to identify predictive markers for tumor recurrence after liver transplantation.

Methods: In a retrospective single-center study, we included all patients with LT for HCC in our institution (01/2007-12/2012). Beside demographic data, we analyzed course, bridging therapies, Serum-AFP, time point of tumor recurrence, as well as the correlation of imaging and histopathology of our recipients. Additionally, we performed a microarray analysis to identify different miRNA profiles of patients with and without HCC recurrence after LT. Single assay stem-loop real-time PCR (Q-RT-PCR) was used for validation of the results.

Results: During the study period, we performed 92 LT in patients with HCC (22 women, 70 men). Twenty-two (23.9%) patients developed a recurrent HCC after LT. Our subgroup with tumor recurrence after LT, presented with a mean disease-free survival of 10 months (3-55 months) and an overall survival of 25.5 months (4-77 months). Milan criteria, AFP levels and pathologic grading had an influence on the tumor recurrence. Performing miRNA analysis, we could identify significant upregulation of 8 miRNAs and downregulation of another 5 miRNAs in patients with tumor recurrence. Consecutively, array data were successfully validated using Q-RT-PCR. Multivariate Cox regression, ROC analysis and Kaplan-Meier showed that a score consisting of two miRNAs and Milan criteria are an independent predictor for tumor recurrence-free survival.

Conclusions: Despite careful selection of patients, an early recurrence of HCC after LT cannot be avoided completely. Reliable prognostic markers related to tumor biology are still missing. Analysis and validation of specific miRNAs combined with radiological parameters might lead to a promising strategy for the prediction of tumor recurrence, but prospective studies have to follow.

overall_design: 8 macrodissected hepatocellular carcinoma (recurrent HCC) and 10 macrodissected hepatocellular carcinoma (non-recurrent HCC).

first: Jan

last: Peveling-Oberhag


title: Global transcriptome abnormalities of the eutopic endometrium from women with adenomyosis

status: Public on Mar 03 2016

city: San Francisco

first: Linda

middle: C.

last: Giudice

address: 499 Illinois St., Sixth Floor

department: Center for Reproductive Health at Mission Bay

institute: UC San Francisco

summary: Abstract:     Objective: Adenomyosis is a clinical disorder defined by the presence of endometrial glands and stroma within the myometrium, the pathogenesis of which is poorly understood. We postulate that dysregulation of genes and pathways in eutopic endometrium may predispose to ectopic implantation. No study, to our knowledge, has examined the global transcriptome of isolated eutopic endometrium from women with clinically significant adenomyosis.  Design: Laboratory-based study with full IRB approval and consents.  Material and Methods: Endometrial sampling was performed on hysterectomy specimens (proliferative phase) from symptomatic women with pathologically-confirmed diffuse adenomyosis (n=3). Controls (n=5) were normo-ovulatory subjects without adenomyosis. All subjects were free from leiomyoma, endometriosis, and hormonal exposures. Isolated purified total RNA was subjected to microarray analysis using the Gene 1.0 ST Affymetrix platform. Data were analyzed with GeneSpring and Ingenuity Pathway analysis. Validation of several genes was undertaken by QRT-PCR.  Results: Comparison of transcriptomes of proliferative endometrium from women with and without adenomyosis revealed 140 up-regulated and 884 down-regulated genes in samples from women with adenomyosis compared to controls. Highly differentially expressed genes include those involved in regulation of apoptopsis, steroid hormone responsiveness, and proteins involved in extracellular matrix remodeling, as well as microRNAs of unknown significance. Affected canonical pathways included eukaryotic initiation factor 2 signaling, oxidative phosphorylation, mitochondrial dysfunction, estrogen receptor signaling, and mTOR signaling.  Conclusions: The eutopic endometrium in patients with adenomyosis has fundamental abnormalities that may predispose to invasion and survival beyond the myometrial interface.  Key Words: adenomyosis, endometrium, microarray, microRNA, endometriosis, apoptosis, signaling.  Abstract:     Objective: Adenomyosis is a clinical disorder defined by the presence of endometrial glands and stroma within the myometrium, the pathogenesis of which is poorly understood. We postulate that dysregulation of genes and pathways in eutopic endometrium may predispose to ectopic implantation. No study, to our knowledge, has examined the global transcriptome of isolated eutopic endometrium from women with clinically significant adenomyosis.  Design: Laboratory-based study with full IRB approval and consents.  Material and Methods: Endometrial sampling was performed on hysterectomy specimens (proliferative phase) from symptomatic women with pathologically-confirmed diffuse adenomyosis (n=3). Controls (n=5) were normo-ovulatory subjects without adenomyosis. All subjects were free from leiomyoma, endometriosis, and hormonal exposures. Isolated purified total RNA was subjected to microarray analysis using the Gene 1.0 ST Affymetrix platform. Data were analyzed with GeneSpring and Ingenuity Pathway analysis. Validation of several genes was undertaken by QRT-PCR.  Results: Comparison of transcriptomes of proliferative endometrium from women with and without adenomyosis revealed 140 up-regulated and 884 down-regulated genes in samples from women with adenomyosis compared to controls. Highly differentially expressed genes include those involved in regulation of apoptopsis, steroid hormone responsiveness, and proteins involved in extracellular matrix remodeling, as well as microRNAs of unknown significance. Affected canonical pathways included eukaryotic initiation factor 2 signaling, oxidative phosphorylation, mitochondrial dysfunction, estrogen receptor signaling, and mTOR signaling.  Conclusions: The eutopic endometrium in patients with adenomyosis has fundamental abnormalities that may predispose to invasion and survival beyond the myometrial interface.  Key Words: adenomyosis, endometrium, microarray, microRNA, endometriosis, apoptosis, signaling.

overall_design: A total of 8 samples were used and analyzed by disease state. Endometrial samples  from hysterectomy specimens in proliferative phase of menstrual cycle from symptomatic women with pathologically-confirmed diffuse adenomyosis were compared with endometrial samples from  normo-ovulatory healthy subjects with no endometrial or uterine pathology.

first: Christopher

middle: N

last: Herndon

first: Lusine

last: Aghajanova

first: Shaina

last: Balayan

first: David

middle: W

last: Erikson

first: Fatima

last: Barragan

first: Gabriel

last: Goldfein

first: Shannon

last: Hawkins


title: Expression data of soybean accessions under different phosphorus treatments

status: Public on Mar 08 2016

city: Nanjing

first: Qing

last: Wang

address: No.1 Weigang

country: China

institute: Nanjing Agricultural University

summary:
Phosphorus is one of the most important macronutrients that is required for plant growth and development. However, stress under low-P conditions has become a limiting factor that affects crop yields and qualities. Plants have developed strategies to cope with this, while few genes associated with low-P tolerance have been identified in soybean.
We used microarrays to detail the global programme of gene expression under different phosphorus treatments of two soybean accessions CD and YH with different phosphorus efficiency.

overall_design: The roots and leaves of a low-P-tolerant accession and a low-P-sensitive accession were harvested after 10 days of hydroponics under different P treatments, each with three biological replicates.Then microarray chips were performed on the 24 samples. We sought to identify genes associated with low-P stress. To that end, we analyzed the differently expressed genes between different P treatments, different accessions and different tissues.

first: Jiao

first: Yuming

last: Yang

first: Wenkai

last: Du

first: Dan

last: Zhang

first: Hao

last: Cheng

first: Deyue

last: Yu


title: Expression data from CD34+/CD71- cells following knockdown of HSPA9

status: Public on Feb 23 2016

first: Matt

last: Walter

address: 4940 parkview

department: oncology

institute: washington university in st.louis school of medicine

summary: Knockdown of HSPA9 causes a dose-dependent decrease in erythroid maturation of CD34+ cells differentiated in culture. Due to differences in the degree of differentiation, a more homogeneous population was selected for using FACS and the gene expression profile of these cells was compared. We used a lentiviral vector (pLKO.1) expressing short hairpin RNAs targeting either luciferase (control shLUC) or HSPA9 (shHSPA9-433) to knock down expression of HSPA9.

overall_design: We isolated CD34+ cells from human cord blood (Day 0), transduced cells with a lentiviral vector (Day 1), selected for transduced cells with puromycin and differentiated them in erythroid culture media before FACS isolation of the CD34+/CD71- population (Day 5). Four independent CD34+ populations were isolated, differentiated and sorted for biologic replicates.

first: Matthew

first: Kilannin

last: Krysiak

first: Cara

last: Shirai

first: Jin

last: Shao

first: Tuoen

last: Liu

last: Ndonwi


title: Transcriptome profile in human hepatoma HepG2 cells treated with antioxidant-rich Barringtonia racemosa leaf extract

status: Public on Mar 23 2016

city: Onna-son, Kunigami-gun

first: Nurhanani

last: Razali

state: Okinawa

address: 1919-1 Tancha

department: Membranology

institute: Okinawa Institute of Science and Technology Graduate University (OIST)

summary: The water extract of the leaf of B. racemosa had been reported to posses high phenolic content and showed high antioxidant activities. However, scientific data on the molecular mechanisms underlying the beneficial properties of the leaf extract are still lacking. In this study, the effects of the leaf extract on the expression of genes in cultured HepG2 cells were investigated using microarray technology. The leaf extract significantly regulated the expression of genes involved with consequential impact on the glycolysis, gluconeogenesis and metabolism of xenobiotics.

overall_design: HepG2 cells were seeded and treated with an 50 µg/ml of the water leaf extract of B. racemosa for 24 h. Following this, cells were trypsinized and then preciptated by centrifugation. Cells were washed with phosphate buffer saline (PBS) before total cellular RNA (tcRNA) were extracted from the cells. tcRNA from both untreated and B. racemosa leaf-treated HepG2 cells were selected for RNA extraction and hybridization on Affymetrix microarrays. All experiments were done in triplicate. The microarray analysis was performed on Affymetrix Human Gene 1.0 S.T Array according to the manufacturer's protocol. The gene sets were then subjected to analysis of variance (ANOVA) in the Partek Genomics Suite software to determine significantly expressed genes which was set according to P value less than 0.05 and fold change difference of equal to or greater than 1.5.

first: Kin Weng

last: Kong

first: Sarni

last: Mat-Junit

first: Azlina

last: Abdul-Aziz


title: Expression data of human neuroblastoma cell lines

status: Public on Feb 19 2016

city: Philadelphia

first: Pichai

last: Raman

state: PA

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

summary: Human neuroblatoma cell lines (N=25) and retinal pigmented epithelium cell lines (N=4) were analyzed for gene expression under untreated/baseline growth conditions.

overall_design: Expression profiling and characterization of a set of Neuroblastoma and retinal pigmented epithelium cell lines

first: Kristina

middle: A

last: Cole

first: Michael

last: Russell


title: Gene expression profiles of canonical and non-canonical NF-κB signaling pathways in Hodgkin’s lymphoma

status: Public on Feb 18 2016

city: Berlin

first: Claus

last: Scheidereit

address: Robert Roessle Str. 10

department: Signal Transduction in Tumor Cells

institute: Max Delbrueck Center for Molecular Medicine

summary: Malignant Hodgkin's lymphoma (HL) cells are characterized by constitutive activation of the canonical as well as the non-canonical NF-κB signaling cascades. We depleted subunit combinations corresponding to either canonical (p50/RelA) or non-canonical (p52/RelB) dimers in the HL cell line L-1236 and performed Affymetrix microarray analysis. Knockdown of p52/RelB affected the expression of a significantly higher number of genes than the knockdown of p50/RelA. The two sets of target genes presented a partial overlap, however they also revealed specific genes that are involved in distinct aspects of tumor biology.

overall_design: The knockdown of subunit combinations corresponding to either canonical (p50/RelA, experimental group 1) or non-canonical (p52/RelB, experimental group 2) NF-κB heterodimers were carried out in L-1236 cells. Two distinct siRNA sequences for every NF-κB subunit and two non-targeting siRNA sequences (control) were used for each experimental group. Experiments were performed in biological triplicates.

first: Kivia

last: de Oliveira

first: Matthias

last: Heinig

first: Norbert

last: Huebner


title: Human alveolar epithelial cells (A549) exposed to cigarette smoke extract

status: Public on Feb 16 2016

city: Mexico City

first: Marco

last: Checa

address: Calada de Tlalpan 4502, Colonia XVI Delegación Tlalpan

department: Pulmonary Fibrosis

country: Mexico

institute: Instituto Nacional de Enfermedades Respiratorias

summary:
Human alveolar epithelial cells were exposed to cigarette smoke extract (CSE) for 1, 3  and 5 weeks at 1%, 5% and 10%, and gene expression was evaluated by complete transcriptome microarrays.
In this study we explored the effect of cigarette smoke on the gene expression profile.

overall_design: Human alveolar epithelial cells stimulated with three different concentractions of CSE (1%, 5% and 10%) and for 1, 3 and 5 weeks were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Moisés

last: Selman

first: Annie

last: Pardo


title: Studies on progenitor endothelial cells; exploring mechanisms for improvement of cardiovascular diseases

status: Public on Feb 24 2016

city: Jeddah

first: Sherin

last: Bakhashab

address: Abdullah Sulyman

department: Biochemistry

country: Saudi Arabia

institute: King Abdulaziz University

summary: Transcriptomic analysis of primary CD34+ cells. CD34+ cell were induced in vitro with hypoxia (3 hours), high glucose and high glucose plus hypoxia. Subsequently, the effect of metformin (anti-diabetic drug) on all conditions was studied to take advantage of transcriptomics to prospectively explore the mechanism of this drug to reduce the risk of cardiovascular diseases in type II diabetic patients.

overall_design: Total RNA isolated from 20 samples; 10 different conditions each has 2 repeats; labeled, and hybridized to Affymetrix Human Gene 1.0 ST Array.

first: Jolanta

last: Weaver

first: Iokim

last: Spyridopoulos

first: Hans-Juergen

last: Schulten

first: Jayapal

last: Manikandan

first: Sahira

last: Lary

first: Farid

last: Ahmed

first: Mohammed

middle: H

last: Alqahtani


title: miRNA expression data from CD73-positive Rods, Müler glia and E 17.5 Retinal Progenitors

status: Public on Feb 09 2016

city: Mexico city

first: Monica

last: Lamas

state: Distrito Federal

address: Calzada de los Tenorios 235

department: Pharmacobiology

institute: CINVESTAV

summary: During retinal development, progenitor cells give rise to six different types of neurons, and one glial cell. This process requires the expression of genes that confer specific functions and identity to each cell. Previous works have reported the miRNAs expression profile in retina, but is still necessary to further define individual retinal cell populations profiles. We isolated postmitotic mice CD73-positive Rods,  Müller glial cells and Retinal Progenitors Cells (E17.5); we then analyzed their miRNA profile expression by microarrays.

overall_design: Using wild type mice we FACS-isolated postmitotic CD73-positive Rods (posnatal day 5). We isolated primary Müller glia cultures from postnatal day 8 mice and retinal progenitors cells from E17.5 mouse embryos; we then sent the samples to the gene expression unit at Instituto de Medicina Genomica (INMEGEN), to analyze their miRNA profile expression by microarrays.

first: Heberto

last: Quintero


title: Urinary miRNA biomarkers for early detection of pancreatic adenocarcinoma (PDAC)

status: Public on Jan 28 2016

city: London

first: Silvana

last: Debernardi

address: Charterhouse Square

department: Molecular Oncology

institute: Barts Cancer Institute

summary:
Currently, the majority of patients diagnosed with pancreatic ductal adenocarcinoma (PDAC) present with locally invasive and/or metastatic disease, resulting in five-year survival of less than 5%. The development of an early diagnostic test is, therefore, expected to significantly impact the patient’s prognosis.
In this feasibility study, we demonstrate for the first time the utility of miRNA biomarkers for non-invasive, early detection of PDAC in urine specimens.

overall_design: Using Affymetrix microarrays, we established a global miRNA profile of urine specimens of 13 PDAC, six chronic pancreatitis (CP), and seven healthy (H) individuals. In order to test the reproducibility of the Affymetrix platform, three biological replicates (sample VG extraction 1, 2, 3) and two technical replicates of the same healthy samplewere also prepared (samples 1_VG_rep1 and 1_VG_rep2; 2_VG_rep1 and 2_VG_rep2).

first: Nathalie

middle: J

last: Massat

first: Tomasz

middle: P

last: Radon

first: Ajanthah

last: Sangaralingam

first: Ana

last: Banissi

first: Darren

last: Ennis

first: Thomas

last: Dowe

first: Claude

last: Chelala

first: Stephen

last: Pereira

first: Hemant

last: Kocher

first: Bryan

last: Young

first: Giles

last: Bond-Smith

first: Robert

last: Hutchins

first: Tatjana

last: Crnogorac-Jurcevic


title: Expression data from U87 xenograft tissues

status: Public on Feb 01 2016

city: Beer-Sheva

first: Varda

last: Shoshan-Barmatz

address: Ben Gurion

department: Life Sciences

country: Israel

institute: Ben Gurion University

summary:
U87 xenograft tumors treated with scrambled siRNA (Tas_73, Tas_78) or siRNA against VDAC1 (Tas_57, Tas_61)
We used microarrays to detail the global effect of siRNA against VDAC1 on subcotenous xenograft U87 cells tumors

overall_design: U87 GBM xenograft treated with scrambled siRNA or VDAC1 siRNA were excised for RNA extraction and hybridization on Affymetrix microarrays.


title: Expression data analysis from RPMI 8226 cells irraidated to C-ions.

status: Public on Jan 05 2016

city: Caen Cedex

first: Brigitte

last: Sola

address: CHU Côte de Nacre

department: UFR de médecine

institute: Université de Caen

summary:
Multiple Myeloma (MM) is an hematological malignancy. MM cells are resistant to X-ray irradiations. We irradiated RPMI 8226 cancer cells with C-ions, which are more energetic than X-ray irradiations. We found that MM cells, RPMI 8226, are also resistant to C-ion irradiations.
We used microarrays to investigate the mechanisms of MM cell resistance to C-ion irradiations.

overall_design: MM cells, RPMI 8226, were subjected to 0 or 6 Gy doses of C-ion irradiations. RNA were extratred from each batch of cells one day after irradiations and subjected to microarray analysis.

first: Julie

last: Cahu


title: Phenotypic and genomic analysis of multiple myeloma minimal residual disease clonal plasma cells: a new model to understand chemoresistance  [HuGene-1_0 Expression]

city: Pamplona

first: Bruno

last: Paiva

address: Av. Pio XII, 55

country: Spain

institute: Clinica Universidad de Navarra

summary: Persistence of chemoresistant minimal residual disease (MRD) plasma cells (PCs) relates to inferior survival in multiple myeloma (MM). MRD PCs are therefore a minor clone able to recapitulate the initial tumor burden at relapse and accordingly, its characterization may represent a unique model to understand chemoresistance; unfortunately, the MRD clone has never been biologically investigated. Here, we compared the antigenic profile of MRD vs. diagnostic clonal PCs in 40 elderly MM patients enrolled in the GEM2010MAS65 study, and showed that the MRD clone is enriched by cells over-expressing integrins (CD11a/CD11c/CD29/CD49d/CD49e), chemokine receptors (CXCR4) and adhesion molecules (CD44/CD54). Genetic profiling of MRD vs. diagnostic PCs showed identical copy number alterations (CNAs) in 3/8 cases, 2 patients with linear acquisition of additional CNAs in MRD clonal PCs, and 3 cases with variable acquisition and loss of CNAs over time. The MRD clone showed significant downregulation of genes particularly related to protein processing in endoplasmic reticulum, as well as novel deregulated genes such as ALCAM that is prognostically relevant in MM and identifies chemoresistant PCs in vitro. Together, we show that therapy-induced clonal selection is already present at the MRD stage, in which chemoresistant PCs show a specific phenotypic signature that may result from the persistence of clones with different genetic and gene expression profiles.

overall_design: Gene expression profiling (GEP) was performed in matched diagnostic and MRD clonal PCs from 7 cases with adequate RNA extracted from CD138+ and patient-specific phenotypically aberrant FACS-purified tumor cells, respectively.

first: Luis

last: Corchete

first: Norma

last: Gutierrez

first: Maria-Belen

last: Vidriales

first: Patricia

last: Maiso

first: Idoia

last: Rodriguez

first: Diego

last: Alignani

first: Maria

last: Sanchez

first: Paloma

last: Barcena

first: Maria-Asuncion

last: Echeveste

first: Miguel

last: Hernandez

first: Ramón

last: García-Sanz

first: Enrique

last: Ocio

first: Albert

last: Oriol

first: Mercedes

last: Gironella

last: Palomera

first: Felipe

last: De Arriba

first: Yolanda

last: Gonzalez

first: Juan-Jose

last: Lahuerta

first: Joan

last: Blade

first: Alberto

last: Orfao

first: Joshua

last: Epstein

first: Bart

last: Barlogie

first: María-Victoria

last: Mateos

first: Jesús

middle: F

last: San Miguel


title: SNP arrays of tumors derived from human prostate epithelial cells transformed with the oncogenes N-Myc and myrAKT1

status: Public on Jan 29 2016

city: Seattle

first: John

middle: K

last: Lee

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology Division

institute: Fred Hutchinson Cancer Research Center

type: Genome variation profiling by genome tiling array

summary:
MYCN amplification and overexpression are common in neuroendocrine prostate cancer (NEPC). However, the impact of aberrant N-Myc expression in prostate tumorigenesis and the cellular origin of NEPC have not been established. We define N-Myc and activated AKT1 as oncogenic components sufficient to transform human prostate epithelial cells to prostate adenocarcinoma and NEPC including the small cell prostate carcinoma (SCPC) variant with phenotypic and molecular features of aggressive, late-stage human disease. We directly show that prostate adenocarcinoma and NEPC can both arise from a common epithelial clone. Further, N-Myc is required for tumor maintenance and destabilization of N-Myc through Aurora A kinase inhibition reduces tumor burden. Our findings establish N-Myc as a driver of NEPC and a target for therapeutic intervention.
SNP array data of experimentally generated human NEPC tumors and a cell line.

overall_design: Copy number analysis of Affymetrix CytoScan HD arrays was performed according to manufacturer's instructions on DNA extracted from three fresh-frozen N-myc/myrAKT1 prostate tumors and the N-Myc/myrAKT1 prostate cell line LASCPC-01.


title: Phenotypic and genomic analysis of multiple myeloma minimal residual disease clonal plasma cells: a new model to understand chemoresistance

first: Bruno

last: Paiva

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

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

overall_design: Refer to individual Series


title: Glucose Metabolic Remodeling through Phosphoenolpyruvate Carboxykinase Isoform 2 Regulates Prostate Cancer Cell Tumorigenicity

status: Public on Jan 04 2016

city: Frederick

first: Steven

middle: X.

last: Hou

state: Maryland

address: 1050 Boyles St. Bldg. 560

institute: NCI

summary: Patients with aggressive prostate cancer generally present with poor outcomes. Identifying the factors regulating prostate cancer aggressiveness may open new avenues in therapy. Specifically, information from prostate cancer patient databases revealed that higher phosphoenolpyruvate carboxykinase isoform 2 (PCK2) levels correlate with more aggressive tumors and lower survival rates. Herein, we show that high tumorigenic prostate cancer cell clones express high levels of PCK2. We found that elevated levels of PCK2 are critical for the glucose metabolic remodeling and the maintenance of tumor-initiating cells (TICs) in aggressive prostate cancer. Our data suggest that PCK2 promotes tumorigenicity by lowering acetyl-CoA levels through reducing the mitochondrial tricarboxylic acid (TCA) cycle. Thus, PCK2 is a potential therapeutic target for aggressive prostate cancer.

overall_design: 2 subclones have been isolated from DU145 cells. The epithelial like (EL) clone has a high tumorigenicity ability and enriched tumor initiating cells than mesenchymal like (ML) clone. Genes with differential expression pattern between these two clones were detected by gene micorarray.

first: Jiangsha

last: Zhao

first: Jieran

last: Li

first: Xiankun

last: Zeng

first: Teresa

last: Fan

middle: X


title: microRNA expression in Tim-3 knockdown RAW264.7 cell

status: Public on Jan 14 2016

city: Beijing

first: Gencheng

last: HAN

address: 27 Taiping Road, Haidian District

department: Department of Immunology

institute: Beijing Institute of Basic Medical Sciences

summary:
RAW264.7 cell was stably transfected with Tim-3 siRNA(SI)  or negative control(NC) and were analyzed for microRNA expression
Differerently expressed microRNA in Tim-3 knockdown RAW264.7 cells were summarized and were used for further analysis

overall_design: RAW264.7 cells stably transfected with Tim-3 siRNA(SI)  or negative control(NC) and were used to collect microRNA without any other treatment

first: Xingwei

last: Jiang

first: Tingting

last: Zhou


title: Expression data at each site in colon cancer

status: Public on Jan 06 2016

city: Mitaka

first: Takaaki

last: Kobayashi

state: Tokyo

address: 6-20-2 Shinkawa

department: Surgery

institute: Kyorin university

summary:
Colon cancer invade to depper layer and the expression of major molecules at cancer front change. But the screening of expression changing at cancer front has not be adequtely clarified.
We compared gene expression at cancer front with it at cancer center.

overall_design: We got cancer cells from cancer front(F) and cancer center(C) by lasermicrodissection.

first: Eriko

last: Nozaki


title: Expression profile of Ewing sarcoma and osteosarcoma

status: Public on Jan 03 2016

first: Guenther

middle: HS

last: Richter

address: Augustenburger Platz 1

department: Department of Pediatrics, Division of Oncology and Hematology

institute: Charité - Universitätsmedizin Berlin

summary: The expression profile of primary pediatric Ewing sarcoma (ES) and osteosarcoma (OS) were analyzed.

overall_design: 8 Ewing sarcoma patient samples (TUM-ES0XXX) and 10 osteosarcoma patient samples (TUM-OS0XXX) were analyzed.

first: Günther

first: Oxana

last: Schmidt

first: Olivia

last: Prazeres da Costa

first: Thorsten

last: Buch

first: Stefan

last: Burdach


title: To identify genes responsive to treatment with the HIF2a inhibitor PT2399

status: Public on Jan 01 2016

city: Boston

first: William

middle: G

last: Kaelin

address: M457, 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary:
HIF2a function is both necessary and sufficient for the growth of VHL-null clear cell Renal Cell Carcinoma (ccRCC). Targeting HIF2a function can therefore be a promising therapeutic strategy.
We used microarray analysis to characterize a novel pharmacological inhibitor of HIF2a named PT2399. By comparing genes that are responsive to PT2399 in parental cells vs cells lacking HIF2a, by virtue of CRISPR-mediated genetic editing, we characterized gene signatures that are regulated by PT2399 in a HIF2a dependent manner.

overall_design:
Cells were treated with either DMSO (control) or 2uM PT2399 for indicated time periods, total RNA was extracted and analyzed.
Please note that the experiments with 786O Parental and HIF2a null cells were conducted independently.

first: Hyejin

last: Cho

first: Abhishek

last: Chakraborty

last: Kaelin Jr


title: Gene expression characterization of high and low grade clear cell renal cell carcinoma

city: Royal Oak

first: Bryan

last: Thibodeau

state: MI

address: 3811 West 13 Mile Road

department: BioBank

institute: Beaumont Research Institute

summary:
Patients undergoing either partial or radical nephrectomy at William Beaumont Hospital (Royal Oak, MI) were consented prior to surgery with local IRB oversight. Samples were collected at time of surgery and stored at -80°C according to CAP (College of American Pathologist)-accredited standard operating procedures. Disease pathology of frozen samples was validated with hematoxylin and eosin stained tissue sections from adjacently collected formalin fixed paraffin embedded tissue.
The objective of this study was to examine the gene expression patterns of clear cell carcinoma in relation to adjacent normal kidney as well as other benign kidney conditions. In particular, the goal was to identify gene expression that could differentiate high grade ccRCC from low grade ccRCC.

overall_design: Samples from patients with high grade ccRCC (Fuhrman grades 3 & 4, n=16) were compared to normal kidney samples (n=14) and also to samples from patients with benign kidney conditions (n=6). Samples from patients with low grade ccRCC (Fuhrman grades 1 & 2, n=13) were then also compared to normal kidney samples (n=14) and also to samples from patients with benign kidney conditions (n=6).

first: Matthew

last: Fulton

first: Laura

middle: E

last: Fortier

first: Timothy

last: Geddes

first: Barbara

last: Pruetz

first: Jason

last: Hafron

first: George

middle: D

last: Wilson


title: Immediate Transcriptional Changes in Response to High Dose Radiation Exposure

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: One of the most likely risks astronauts on long duration space missions face is exposure to ionizing radiation associated with highly energetic and charged heavy (HZE) particles.  Since access to medical expertise on such a mission is limited at best, early diagnosis and mitigation of such exposure is critical.  In order to accurately determine the dosage within 1 hour post-exposure, dose-dependent “biomarkers” are needed.  Therefore, we performed a dose-course transcriptional analysis for radiation exposure at 0, 0.3, 1.5, and 3.0 Gy with corresponding time point at 1 hour (hr) post-exposure using Affymetrix® GeneChip® Human Gene 1.0 ST v1 Array chips.  The analysis of our data suggests a set of sensitive genetic biomarkers specific to each radiation level as well as generic radiation response biomarkers. Upregulated biomarkers can then be used within lab-on-a-chip (LOC) systems to detect exposure to ionizing radiation.

overall_design: A total of sixteen human samples representing radiation exposure at levels 0 Gy, 0.3 Gy, 1.5 Gy and 3.0 Gy at time point 1 hour (hr) post-exposure were constructed.  Blood samples were extracted from four human volunteers, and were irradiated.  Leukocytes were extracted, and gene expression was measured.  Samples for all four volunteers were measured at 1 hr for all four dose levels, resulting in four replicates at each dose level.  Thus, a total of 4 samples at each of the four radiation levels were sampled, yielding the total of 16 samples.

middle: C

first: Robert

middle: M

last: Flight

first: Brigitte

last: Fasciotto

first: Rosendo

last: Estrada

first: John

last: Eaton

first: Phani

last: Patibandla

first: Sabine

last: Waigel

first: Dazhuo

last: Li

first: Xiaohong

last: Kirtley

first: Palaniappan

last: Sethu

middle: S

last: Keynton


title: Differentiation of human parthenogenetic pluripotent stem cells reveals multiple tissue and isoform specific imprinted transcripts

city: Jerusalem

first: Shiran

last: Bar

address: Edmond J. Safra Campus, Givat Ram

department: Genetics

institute: The Hebrew University, Jerusalem

summary: Parental imprinting results in a monoallelic parent-of-origin dependent gene expression. However, many imprinted genes identified by differential methylation do not exhibit complete monoallelic expression.  Previous studies demonstrated a complex tissue-dependent expression patterns for some imprinted genes. Still, the complete magnitude of this phenomenon remains largely unknown. Differentiating human parthenogenetic induced pluripotent stem cells into different cell types and combining DNA methylation with novel 5' RNA sequencing methodology, enabled us to identify tissue- and isoform-dependent imprinted genes in a genome wide manner. We show that nearly half of all imprinted genes expresses both biallelic and monoallelic isoforms, that are controlled by tissue specific alternative promoters. This study provides the first global analysis of tissue-specific imprinting in humans, and implies that alternative promoters are central in the regulation of imprinted genes.

overall_design: Gene expression analysis was performed on a total of 6 human cell lines, including 4 iPSCs differentiated to neural progenitors and sorted using NCAM1 (2 control and 2 Parthenogenetic), and 2 iPSCs differentiated to endodermal progenitors (1 Control and 1 Parthenogenetic)

first: Yonatan

last: Stelzer

first: Nissim

last: Benvenisty


title: Effects of Combined Persistant Organic Pollutants on Global Gene Expression in Human HepaRG Cells

city: Paris

first: Lawrence

last: Aggerbeck

address: 45 rue des Saints Peres

institute: INSERM UMR S-747

summary:
The exposure to and contamination by Persistent Organic Pollutants (POPs), which include pesticides used worldwide and polyaromatic hydrocarbons, is detrimental to human health and diverse ecosystems. Although most mechanistic studies have focused on single compounds, living organisms are exposed to multiple environmental xenobiotics, simultaneously, throughout their lives. The experimental evidence useful for assessing the effects of exposure to pollutant mixtures is scarce. We investigated the effects of exposure to a combination of two POPs, which employ different xenosensors, on global gene expression in a human hepatocyte cell model, HepaRG.
Whole genome microarrays were used to investigate the effects on the HepaRG transcriptome following exposure to the combination of POPs as compared to each compound individually.

overall_design: Differentiated HepaRG cells were treated with either 2,3,7,8 tetrachlorodibenzo-p-dioxin, alpha-endosulfan (an organochlorine pesticide), the mixture or the DMSO vehicle for 30 hours after which RNA was extracted for hybridization on Affymetrix whole human genome microarrays.

first: Martine


title: Drosha knock-down gene expression in HSPCs

city: Duarte

first: Krist

last: Azizian

state: CA

address: 1500 E. Duarte Rd.

department: Molecular and Cellular Biology

institute: Beckman Research Institute of City of Hope

summary: Genome-wide expression differences are compared for a normal and mutant cell line.

overall_design:
The data compares the effect of a gene mutation on genome-wide expression.
empty vector (EV), shDrosha (shDr); shDr denotes hematopoietic stem-progenitor cells (HSPCs) transduced with a short-hairpin RNA targeting the miRNA-processing enzyme Drosha

middle: T

last: Rossi


title: Contact inhibition controls miR-223 stabilization via p27kip1 expression

status: Public on Dec 31 2015

city: Columbus

first: Francesca

last: Lovat

address: 460 W 12th ave

institute: The Ohio State University

summary: The control of cell cycle progression mostly relays on the concerted activity of cyclins, CDKs and CDKs inhibitor. Recent data demonstrated that microRNAs, by regulating the expression of these proteins, contribute to the control of cell cycle progression. Here we provide evidences that the CDK inhibitor p27Kip1 directly regulates microRNAs stability thereby influencing cell cycle exit following contact inhibition. By the use of wild type and p27 knock-out cells we uncovered several microRNAs whose expression is linked to the cell cycle exit in a p27-dependent manner. By studying one of this microRNA, miR-223, we provide evidence that p27 is an RNA binding protein able to bind miR-223 to stabilize its expression. High miR-223 levels participate in the control of cell proliferation.

platform_organism:
Homo sapiens
Mus musculus

overall_design: Overall, we identify a previously completely unknown and conserved function of p27Kip1 that contributes to the proper regulation of cell cycle progression impinging on microRNA expression.

first: Joshua

last: Armenia

first: Linda

last: Fabris

first: Stefania

last: Berton

first: Sara

last: D’Andrea

first: Ilenia

last: Segatto

first: Cristian

last: Taccioli

first: Luciano

last: Cascione

first: Carlo

last: Croce

first: Alfonso

last: Colombatti

first: Andrea

last: Vecchione

first: Barbara

last: Belletti

first: Gustavo

last: Baldassarre


title: Human induced pluripotent stem cells derived from a sporadic Alzheimer's disease patient

city: Sydney

first: Henry

last: Chung

state: NSW

address: High St

department: Clinical Sciences Bld

institute: Prince of Wales Hospital

summary: Induced pluripotent stem cell (iPSC) disease models have been generated for a number of diseases, and some have shown their potential utilization for pathological and drug toxicological evaluations. We have generated two hiPSC clones from a non-familial Alzheimer’s patient (AD-iPSCs), which expressed typical undifferentiated markers and fulfilled standard pluripotency assays. Genome-wide microarray analysis revealed that AD-iPSCs are highly similar to control hiPSCs and hESCs, albeit with some noticeable differences in several genes: DNAJC15, GRPR, NAIP and SNORD116-18. Several other biomarkers were differentially expressed in AD-iPSC clones, which were implicated in memory impairment and AD. Furthermore, well characterized familial AD-associated genes (APP, PSEN1, PSEN2) and non-familial (A2M, APOE, GAP43, MAOA, MPO, PLAT, PLAU, SORL1, SNCA) exhibited different expression patterns but were largely reset upon reprogramming into a pluripotent state. Overall, hiPSCs can be good candidates for AD modeling and may represent an in vitro alternative to studying disease mechanisms and drug discovery/toxicology studies.

overall_design: Fibroblasts and two hiPSC clones from a non-familial Alzheimer’s patient (AD-iPSCs) were analyzed. For each cell sample, 2-3 biological replicates were obtained.

first: Ruby

last: Lin

first: Kuldip

last: Sidhu


title: Patterns of gene expression in human fetal and adult liver

status: Public on Dec 29 2015

city: Providence

first: Jennifer

middle: Ann

last: Sanders

state: RI

address: 593 Eddy Street

department: Pediatric Endocrinology

institute: Rhode Island Hospital

summary: DNA methylation is an important epigenetic control mechanism that has been shown to be associated with gene silencing through the course of development, maturation and aging. However, only limited data are available regarding the relationship between methylation and gene expression in human development. We analyzed the methylomes and transcriptomes of three human fetal liver samples (gestational age 20-22 weeks) and three adult human liver samples. Genes whose expression differed between fetal and adult numbered 7,673. Adult overexpression was associated with metabolic pathways and, in particular, cytochrome P450 enzymes, while fetal overexpression reflected enrichment for DNA replication and repair. Analysis for DNA methylation using the Illumina Infinium 450K HumanMethylation BeadChip showed that 42% of the quality filtered 426,154 methylation sites differed significantly between adult and fetal tissue (q≤0.05). Differences were small; 69% of the significant sites differed in their mean methylation beta value by ≤0.2. There was a trend among all sites toward higher methylation in the adult samples with the most frequent difference in beta being 0.1. Characterization of the relationship between methylation and expression revealed a clear difference between fetus and adult. Methylation of genes overexpressed in fetal liver showed the same pattern as seen for genes that were similarly expressed in fetal and adult liver. In contrast, adult overexpressed genes showed fetal hypermethylation that differed from the similarly expressed genes. An examination of gene region-specific methylation showed that sites proximal to the transcription start site or within the first exon with a significant fetal-adult difference in beta (>0.2) showed an inverse relationship with gene expression. Nearly half of the CpGs in human liver show a significant difference in methylation comparing fetal and adult samples. Sites proximal to the transcription start site or within the first exon that show a transition from hypermethylation in the fetus to hypomethylation or intermediate methylation in the adult are associated with inverse changes in gene expression. In contrast, increases in methylation going from fetal to adult are not associated with fetal-to-adult decreased expression. These findings indicate fundamentally different roles for and/or regulation of DNA methylation in human fetal and adult liver.

overall_design: Triplicate normal human adult and fetal liver were used for nucleic acid isolation and gene expression profiling using Affymetrix Human Gene 1.0 ST arrays.

first: Philip

middle: A

last: Gruppuso


title: Transcriptomic Dynamics of Human Macrophage Response to Leishmania major infection

city: Tunis-Belvedere

first: Dhafer

last: Laouini

address: 13, place Pasteur. BP74

country: Tunisia

institute: Institut Pasteur de Tunis

summary:
Leishmania (L.) are obligated intracellular protozoan parasites that develop electively in macrophages. These cells that are acting as a safe shelter for the pathogens but also as their ultimate killer, making them the alpha and the omega during leishmaniasis diseases. Macrophages are able to secrete a remarkably diverse set of regulators known to influence the physiological functions and differentiation of neighboring cells to trigger an adaptive immune response of protective Th1-type cells, whereas parasites have developed a wide range of mechanisms to circumvent the host’s immune responses. Most of our understanding of this host-parasite conflict, in the context of macrophage invasion by L. major metacyclic promastigotes, has been gleaned from studies investigating the macrophage responses at late and unique time points after infection.
To investigate the dynamics of this duel, we have analyzed the transciptomic profile of monocyte-derived human macrophages at different time points during the first 24h upon in vitro infection using high throughput microarray platform.
The gene expression profile of 17,838 genes showed high expression variability between the three human donors at different time points post infection. Cross comparison between the three donors allowed the identification of a common set of expressed genes coding for inflammatory and chemotactic molecules, transcription factors, apoptosis inhibition, glucose synthesis and heme metabolism.
The findings presented in this work suggest that transcriptome dynamics of macrophages early during the first 24h post infection enable to identify novel key pathways deregulated upon L. major invasion. Our reported set of expressed genes will be useful in future rounds of data mining and functional analyses.

overall_design: In total 27 samples from three different donors were analyzed. For each donor, samples at 0h, 3h, 6h, 12h and 24h of culture were used as controls. For each donor, samples of cells infected with metacyclic Leishmania major parasites at 3h, 6h, 12h and 24h post-infection were analyzed.

first: Ghada

last: Mkannez

first: Fatma

middle: Z

last: Guerfali

first: Rabiaa

last: Sghaier

first: Hanène

last: Attia

first: Imen

last: Rabhi

first: Axel

last: Rasche

first: Béatrice

last: Regnault

first: Adriani

last: Daskalaki

first: Koussay

last: Dellagi


title: Gene expression profiling in NK cells of patients infected with Leishmania mexicana

city: Cambridge

first: Madeline

last: Lancaster

state: Cambridgeshire

address: Cambridge Biomedical Campus, Francis Crick Avenue

department: Cell Biology Division

institute: MRC Laboratory of Molecular Biology

summary:
The aim of this study was to identify differences in the NK-cell response towards Leishmania mexicana lipophosphoglycan (LPG) between patients with localized (LCL) and diffuse (DCL) cutaneous leishmaniasis through gene expression profiling, in an attempt to pinpoint alterations in the signaling pathways responsible for the NK-cell dysfunction in patients with DCL.
To determine the gene expression profiling in non stimulated and LPG-stimulated NK cells we include samples of controls, LCL and DCL patients. We performed microarrays (Human Gene 1.0 ST, Affymetrix) to identify differentially expressed transcripts between non stimulated and LPG-stimulated NK cells between controls, LCL and DCL samples.

overall_design: Human NK cells from controls, LCL and DCL patients were divided in two conditions: non stimulated and LPG-stimulated (6h) cells, different number of biological replicates were analyzed: four replicates for controls, two replicates for LCL and 3 replicates for DCL patients samples with a total of 18 microarrays.

first: Edith

last: Fernández-Figueroa

first: Ivan

last: Imaz-Rosshandler

first: Juan

last: Castillo-Fernández

first: Haydee

last: Miranda-Ortíz

last: Fernández-López

first: Ingeborg

last: Becker-Fauser

first: Claudia

last: Rangel-Escareño


title: Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip

status: Public on Dec 16 2015

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

summary: A human gut-on-a-chip microdevice was used to coculture multiple commensal microbes in contact with living human intestinal epithelial cells for more than a week in vitro and to analyze how gut microbiome, inflammatory cells, and peristalsis-associated mechanical deformations independently contribute to intestinal bacterial overgrowth and inflammation. This in vitro model replicated results from past animal and human studies, including demonstration that probiotic and antibiotic therapies can suppress villus injury induced by pathogenic bacteria. By ceasing peristalsis-like motions while maintaining luminal flow, lack of epithelial deformation was shown to trigger bacterial overgrowth similar to that observed in patients with ileus and inflammatory bowel disease. Analysis of intestinal inflammation on-chip revealed that immune cells and lipopolysaccharide endotoxin together stimulate epithelial cells to produce four proinflammatory cytokines (IL-8, IL-6, IL-1β, and TNF-α) that are necessary and sufficient to induce villus injury and compromise intestinal barrier function. Thus, this human gut-on-a-chip can be used to analyze contributions of microbiome to intestinal pathophysiology and dissect disease mechanisms in a controlled manner that is not possible using existing in vitro systems or animal models.

overall_design: 6 samples, 2 biological replicates for each 3 conditions.

first: Hyun

middle: J

last: Kim

first: Donald

last: Ingber


title: The effects of CEP-37440, an inhibitor of focal adhesion kinase, in vitro and in vivo on inflammatory breast cancer cells.

status: Public on Dec 14 2015

city: Philadelphia

first: Sandra

middle: Viviana

last: Fernandez

address: 233 South 10th Street

institute: Thomas Jefferson University

summary: CEP-37440 at low concentration (1,000 nM) decreased the proliferation of the human inflammatory breast cancer (IBC) cell line FC-IBC02, while not affecting the proliferation of normal breast epithelial cells. CEP-37440 decreased the cell proliferation of FC-IBC02 by blocking the auto-phosphorylation kinase activity of FAK (Tyr 397). This cell line did not expressed ALK. In vivo, CEP-37440 significantly decreased FC-IBC02 breast tumor xenografts growth with maximum of 40% tumor growth inhibition. None of the FC-IBC02 breast xenografts mice treated with CEP-37440 developed brain metastasis in contrast to the control group in which 20% of the mice developed brain metastasis. Expression array analyses in FC-IBC02 cells showed that CEP-37440 affects the expression of genes related to apoptosis specifically related to the interferon signaling pathway.

overall_design: Cell proliferation assays were performed in the presence of several concentrations of CEP-37440 using IBC and triple negative breast cancer (TNBC) non-IBC cell lines. We studied the expression of total FAK1, phospho-FAK1 (Tyr 397), total ALK and phospho-ALK (Tyr 1604) in these cells by ELISA. FC-IBC02 cells were treated with 1,000 nM CEP-37440 during 48 h, and expression arrays were performed in order to define pathways dysregulated by CEP-37440.

first: Israa

last: Salem

first: Manal

last: Alsalahi

first: Lucy

last: Aburto

first: Inna

last: Chervoneva

first: Sankar

last: Addya

first: Laura

last: Austin

first: Bruce

last: Ruggeri

first: Massimo

last: Cristofanilli

middle: V


title: Microarray on mouse soleus muscles from DMP1 Cre Mbtps1 knockout mice compared with littermate controls

city: Rensselaer

first: Sridar

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary: Interestingly, the DMP1 cre Mbtps1 knockout mice do not demonstrate a noticeable bone phenotype despite gene expression changes.  Only change was in bone stiffness.  However, muscles from DMP1 cre Mbtps1 knockout mice did show a phenotype:  changes in contractile force (increased); changes in myosin heavy chain expression, and an increase in myocyte regeneration evidenced by centralized nuclei in type I myosin heavy chain expressing cells.  As a result, we wanted to know if these physiological changes were accompanied by changes in gene expression.  We found that a number of genes were increased---including those associated with improved muscle performance and with activation of satellite cells, e.g., muscle stem cells.  These changes in gene expression support our hypothesis which is that the bone (osteocytes) signal a change in muscle function via a cross-talk mechanism.

overall_design: Soleus muscles from three controls and three knockout mice were dissected and flash frozen in liquid nitrogen.  Muscles were then extracted for total RNA and subjected to array analysis

first: Jeffrey

middle: P

last: Gorski


title: Derivation and differentiation of haploid human embryonic stem cells [expression array]

status: Public on Mar 16 2016

first: Ido

last: Sagi

address: Givat Ram

institute: The Hebrew University of Jerusalem

summary: Diploidy is a fundamental genetic feature in mammals, in which haploid cells normally arise only as post-meiotic germ cells that serve to insure a diploid genome upon fertilization. Gamete manipulation has yielded haploid embryonic stem (ES) cells from several mammalian species, but as of yet not from humans. Here we analyzed a large collection of human parthenogenetic ES cell lines originating from haploid oocytes, leading to the successful isolation and maintenance of human ES cell lines with a normal haploid karyotype. Haploid human ES cells exhibited typical pluripotent stem cell characteristics such as self-renewal capacity and a pluripotency-specific molecular signature. Although haploid human ES cells resembled their diploid counterparts, they also displayed distinct properties including differential regulation of X chromosome inactivation and genes involved in oxidative phosphorylation, alongside reduction in absolute gene expression levels and cell size. Intriguingly, we found that a haploid genome is compatible not only with the undifferentiated pluripotent state, but also with differentiated somatic fates representing all three embryonic germ layers, despite a persistent dosage imbalance between the autosomes and X chromosome. We expect that haploid human ES cells will provide novel means for studying human functional genomics, development and evolution.

overall_design: Gene expression analysis was performed on a total of 2 samples of haploid and diploid human parthenogenetic embryonic stem cells in G1.

first: Dieter

last: Egli

first: Nissim

last: Benvenisty


title: Expression data from human fetal cardiac MSCs

status: Public on Feb 19 2016

city: Stockholm

first: Karl-Henrik

last: Grinnemo

address: KFC Novum, 6th floor

department: Molecular Medicine and Surgery

institute: Karolinska Institutet

summary:
The instrinsic regenerative capacity of human fetal cardiac mesenchymal stromal cells (MSCs) has not been fully characterised. Here we demonstrate that we can expand cells with characteristics of cardiovascular progenitor cells from the MSC population of human fetal hearts with only minor fluctuations over time in culture (from day 15 to day 48).
We used microarray to compare the gene-expression profile of cultured human fetal cardiac MSCs over time (from day 15 to day 48).

overall_design: MSCs from human fetal hearts were cultured on GelTrex in a defined medium stimulating the canonical Wnt/beta-catenin pathway. Samples from three different time points (day 15, 27 and 48) were compared on microarray.

first: Agneta

last: Mansson-Broberg


title: Transcriptome of HEK293 cells (HEK293-CT) and HEK293 cells stably over-expressing the BAHD1 gene (HEK-BAHD1)

status: Public on Dec 11 2015

city: Jouy-en-Josas

first: Helene

last: Bierne

address: Domaine de Vilvert, bat 442, INRA Micalis

department: Micalis Institute

institute: INRAE - University PARIS SACLAY

summary: Comparison of gene expression profile of HEK293-CT cells and HEK293 cells stably over-expressing the BAHD1 gene (HEK-BAHD1)

overall_design: We used micrarrays to identify the repertoire of genes differentially expressed upon overexpression of the chromatin repressor BAHD1 in HEK293 cells.

first: Guillaume

last: Soubigou

first: Emanuele

last: Libertini

first: Jean-Yves

last: Coppee


title: Expression data of cDNA from the ACHN control and Kindlin-2-depleting cells

city: Beijing

first: Huiying

last: He

address: 38# Xueyuan Road, Haidian District

institute: Peking University Health Science Center

summary:
Kindlin-2, an integrin-interacting FERM-domain-containing protein, has been known to play critical roles for tumor progression. However, the role of Kindlin-2 in renal cell carcinoma (RCC) progression has not been reported. We aim to investigate the role of Kindlin-2 in the progression of RCC and the underlying mechanisms.
To uncover the related pathway in which Kindlin-2 is involved to promote clear cell renal cell carcinoma progression, ACHN control and Kindlin-2-depleting cells were analyzed by Affymetrix GeneChip human Gene 1.0 ST Arrays.

overall_design: ACHN cells were transfected with control short hairpin RNA (shRNA) or Kindlin-2 shRNA. ACHN control and Kindlin-2-depleting cells cDNAs were hybridized to Affymetrix GeneChip Human Gene 1.0 ST arrays. Data were analyzed by Expression Console 1.4.1.

first: Muhan

last: Li


title: Transcriptome of HEK293 cells stably knockdown for the BAHD1 gene with a shRNA

summary: Comparison of gene expression profile of HEK293 cells stably expressing a shRNA control (SilX-CT) or a shRNA against BAHD1 (SilX-BAHD1)

overall_design: We used microarrays to identify the repertoire of genes differentially expressed upon knockdown of the chromatin repressor BAHD1 in human HEK293 cells.

first: Alice

last: Lebreton

last: Coppée


title: Age, sexual dimorphism and disease associations in the developing human fetal lung transcriptome

status: Public on Dec 22 2015

city: Boston

first: Alvin

middle: T.

last: Kho

state: MA

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

summary: Whole human fetal lung transcriptome profiles from estimated gestational ages 54 to 137 days post conception. Maternal cigarette smoking status is indicated by cotinine levels measured in the corresponding placenta.

overall_design:
Time series with biological replicates.
Whole lung transcriptome profiles, lung development, human fetus, in utero cigarette smoke exposure

first: Sunita

last: Sharma

first: Roger

last: Gaedigk

first: Carrie

last: Vyhlidal

first: J

last: Leeder

first: Kelan

last: Tantisira

first: Scott

last: Weiss


title: Targeting the EWS/ETS transcriptional program by BET bromodomain inhibition in Ewing sarcoma

status: Public on Dec 08 2015

city: Berlin

first: Guenther

middle: HS

last: Richter

address: Augustenburger Platz 1

institute: Charité - Universitätsmedizin Berlin

summary: Ewing sarcomas (ES) are highly malignant, osteolytic bone or soft tissue tumors, which are characterized by early metastasis into lung and bone. Genetically, ES are defined by balanced chromosomal EWS/ETS translocations, which give rise to chimeric proteins (EWS-ETS) that generate an oncogenic transcriptional program associated with altered epigenetic marks throughout the genome. By use of an inhibitor (JQ1) blocking BET bromodomain binding proteins (BRDs) we strikingly observed a strong down-regulation of the predominant EWS-ETS protein EWS/FLI1 in a dose dependent manner. Microarray analysis further revealed JQ1 treatment to block a typical ES associated expression program. The effect on this expression program could be mimicked by RNA interference with BRD3 or BRD4 expression, indicating that the EWS/FLI1 mediated expression profile is at least in part mediated via such epigenetic readers. Consequently, contact dependent and independent proliferation of different ES lines was strongly inhibited. Mechanistically, treatment of ES resulted in a partial arrest of the cell cycle as well as induction of apoptosis. Tumor development was suppressed dose dependently in a xeno-transplant model in immune deficient mice, overall indicating that ES may be susceptible to treatment with epigenetic inhibitors blocking BET bromodomain activity and the associated pathognomonic EWS-ETS transcriptional program in ES.

overall_design: Ewing sarcoma cell lines A673 and TC-71 were treated for 48 hours with 2 microM JQ1 or DMSO control.

first: Tim

last: Hensel

first: Chiara

last: Giorgi

first: Oxana

last: Schmidt

first: Thorsten

last: Buch

first: Stefan

last: Burdach

first: Beat

last: Schäfer

first: Günther

middle: H


title: GBM miR338-p5

status: Public on Dec 10 2015

city: Brno

first: Andrej

last: Besse

address: Kamenice 5

country: Czech Republic

institute: Masaryk University

summary: Glioblastoma multiforme (GBM) is the most aggressive form of brain tumors. Despite radical surgery and radiotherapy supported by chemotherapy, the disease still remains incurable with extremely low median survival rate of 12-15 months from the time of initial diagnosis.  The main cause of treatment failure is considered to be the presence of cells that are resistant to such treatment. MicroRNAs (miRNAs) as regulators of gene expression are involved in the tumor pathogenesis, including GBM. MiR-338 is a brain specific miRNA which has been described to target pathways involved in proliferation and differentiation. In our study, miR-338-3p and -5p were differentially expressed in GBM tissue in comparison to non-tumor brain tissue. Overexpression of miR-338-3p with miRNA mimic did not show any changes in proliferation rates in GBM cell lines (A172, T98G, U87MG). On the other hand, pre-miR-338-5p notably decreased proliferation and caused cell cycle arrest. Since radiation is currently the main treatment modality in GBM, we combined overexpression of pre-miR-338-5p with radiation, which led to significantly decreased of cell proliferation, and increased cell cycle arrest and apoptosis in comparison to only irradiated cells. To better elucidate the mechanism of action, we performed gene expression profiling analysis that revealed targets of miR-338-5p being Ndfip1, Rheb, ppp2R5a. These genes have been described to be involved in DNA damage response, proliferation and cell cycle regulation. To our knowledge, this is the first study to describe role of miR-338-5p in GBM and its potential to improve sensitivity of GBM to radiation.

overall_design: Study was performed on three glioblastoma multiforme cell lines A172, T98G and U87MG. This experiment was performed on Affymetrix GeneChip Human Gene ST 1.0 to elucidate the targets of miRNA-338-5p. Cell lines were seeded 24 hours prior transfection. After transfection with pre-miR338-5p or negative control cell were cultured for 24 hours and harvested. RNA was isolated using MirVana miRNA Isolation Kit (Ambion, USA) and checked for RNA integrity by Bioanalyzer 2100 and purity by ratios 260/280>1.8 and 260/230>1.8 by Nanodrop2000.


title: Global gene expression profiling of FOP- or resFOP-iMSCs after chondrogenic differentiation

status: Public on Dec 09 2015

city: Kyoto

first: Makoto

last: Ikeya

address: 53 kawahara-cho, shogoin

department: Center for iPS Cell Research and Application(CiRA)

institute: Kyoto University

summary: Comparison of gene expressions among  FOP- or resFOP-iMSCs after chondrogenic differentiation with or without Activin-A.

last: Toguchida

first: M


title: De novo homozygous deletion of segmental KAL1 and entire STS cause Kallmann syndrome and X-linked ichthyosis in a Chinese family

status: Public on Dec 05 2015

city: Wuhan, People’s Rep

first: Hao

last: Xu

address: Jiefang Ave.

department: Urology

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Kallmann syndrome is a genetically heterogeneous condition and a treatable form of male infertility. Defects in KAL1 gene have been implicated in Kallmann syndrome, which can be associated with X-linked ichthyosis in contiguous gene syndromes. In order to uncover the genetic cause of two brothers with Kallmann syndrome and X-linked ichthyosis, a custom semiconductor targeted resequencing panel to detect seventeen Kallmann syndrome causal genes and STS gene was designed. Next-generation sequencing was performed using this panel in the two affected brothers and their normal parents. To validate the result, we applied CytoScan™ HD array, quantitative real-time PCR and direct PCR electrophoresis analysis with the participants. The patients received clinical assessment, human chorionic gonadotropin treatment and follow-up for 39 months. The results showed that the two affected siblings have the same de novo deletion at Xp22.3 including exons 9-14 of KAL1 gene and entire STS gene but showed different phenotypes in some respects. The secondary sex characteristics of the patients were greatly improved after treatment. We firstly reported that a de novo homozygous deletion contribute to KS with bilateral cryptorchidism and unilateral renal agenesis or normal kidney development and developed a cost-effective and reliable semiconductor targeted resequencing panel for genetic diagnosis of Kallmann syndrome in routinely obtained samples.

overall_design: One of the two brothers with Kallmann syndrome and X-linked ichthyosis was analyzed for validation the results of the deletion detected by next-generation sequencing.

first: Zongzhe

last: Li

first: Tao

last: Wang

first: Shaogang

first: Jihong

last: Liu

first: Dao Wen


title: Antitumor activity of the novel multi-kinase inhibitor EC-70124 in triple negative breast cancer

status: Public on Dec 01 2015

city: Oviedo

first: Francisco

last: Moris

address: Edificio Cientifico Tencológico, Campus El Cristo

institute: EntreChem SL

summary: Disseminated triple negative breast cancer (TNBC) is an incurable disease with limited therapeutic options beyond chemotherapy. Therefore, identification of druggable vulnerabilities is a mind aim. Protein kinases play a central role in cancer and particularly in TNBC. They are involved in many oncogenic functions including migration, proliferation, genetic stability or maintenance of stem-cell like properties.  In this article we describe a novel multi-kinase inhibitor with antitumor activity in this cancer subtype. EC-70124 is a hybrid indolocarbazole analog obtained by combinatorial biosynthesis of Rebeccamycin and Staurosporine genes that showed antiproliferative effect and in vivo antitumoral activity. Biochemical experiments demonstrated the inhibition of the PI3K/mTOR and JAK/STAT pathways. EC-70124 mediated DNA damage leading to cell cycle arrest at the G2/M phase. Gene set enrichment analyses identified several deregulated functions including cell proliferation, migration, DNA damage, regulation of stem cell differentiation and reversion of the epithelial-mesenchymal transition (EMT) phenotype, among others. Combination studies showed a synergistic interaction of EC-70124 with docetaxel, and an enhanced activity in vivo. Furthermore, EC-70124 had a good pharmacokinetic profile. In conclusion these experiments demonstrate the antitumor activity of EC-70124 in TNBC paving the way for the future clinical development of this drug alone or in combination with chemotherapy.

overall_design: Total RNA was extracted from MDA-MB-231 cells treated or not with EC-70124

first: Alberto

last: Ocana

first: Maria

last: Cuenca-Lopez

first: Veronica

last: Corrales-Sánchez

last: Morís

first: Atanasio

last: Pandiella

first: Gary

last: Bader

first: Veronique

last: Voisin


title: Gene expression profiles of human CD45RA+CCR7-CD8+ T cells

first: Ruka

last: Setoguchi

address: Yoshidakonoe-cho

summary:
Human CD8+ T cells are functionally heterogeneous and can be divided into distinct subsets according to CCR7 and CD45RA expression levels. Among the subsets, CCR7-CD45RA+ CD8+ T cells are considered to be terminally differentiated cells and designated as Temra. Temra show attenuated ability to proliferate and produce IFN-gamma in response to TCR stimulation, while Temra show improved function after IL-15 treatment.
To clarify the transcriptional signatures induced by the stimulations, Temra were purified using flow cytometry, stimulated with IL-15 or with anti-CD3/CD28 (TCR stimulation), or cultured without stimulation for 2 days, and subjected to microarray analysis.

overall_design: 16 total samples were analyzed in this study.


title: Gene expression in Vemurafenib-treated A375 and A2058 melanoma cell lines

status: Public on Dec 02 2015

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

institute: FMI

summary:
Human melanoma cell line A375 and A2058 were incubated with DMSO (control group) or Vemurafenib (1 μM in DMSO) for 72 hours.
Total RNA was isolated with Qiagen RNA isolation kit; 1.5 μg of total RNA was used as template for cDNA synthesis.

overall_design: A375 and A2058 human melanoma cell lines were treated with DMSO (control) and Vemurafenib (examination). Triplicates per group were processed and analysed in parallel.

first: Gongda

last: Xue

first: Stephane

last: Thiry

last: Rollof