title: Gene expression profiling of HPV-negative oropharyngeal cancers and Normal benign uvula, tonsil from European American patients

summary: Head and neck cancer (HNC) is the fifth most common malignancy worldwide with an annual mortality rate of 200,000. About 90% of HNC can be classified as head and neck squamous cell carcinomas (HNSCC), of which approximately 75% are attributed to alcohol and tobacco consumption and 25 are associated with human papillomavirus (HPV), predominantly HPV16. HPV-associated OPC have better prognosis and a more favorable response to therapy as compared to HPV-negative tumors. Differences in risk factors, age of presentation, clinical behavior and gene expression profiles indicate that HPV-positive and HPV-negative tumors develop via different molecular mechanisms and are biologically distinct. HPV has been characterized as a risk factor for OPC based on race, life style and sexual behavior, impacting survival outcomes for both African American (AA) and European American (EA) patients. According to some reports, the rate of HPV-associated tumors is much lower in AA patients as compared to EA patients in United States. In general, however, AA males have a higher incidence of HNC than any other racial/gender group, and a mortality rate almost three-fold that observed in EA males. Overall, AA patients tend to present with more HPV-negative OPC and have worse prognosis as compared to both HPV-positive and HPV-negative EA patients. This study aimed to compare the gene expression profiles of HPV-negative oropharyngeal squamous cell carcinoma (OPC) and normal benign uvula/tonsil tissues from European American patients and determine what biological processes and pathways are affected in HPV-negative OPCs in EA patients. Additional datasets in this study explore gene expression differences in HNC from EA and AA patients.

overall_design: ANALYSIS 8: Two-condition, one-color experiment:  European American (EA) HPV-negative oropharyngeal tumor samples and  normal benign uvula/tonsil tissues. Biological replicates:  8 EA HPV active samples and 4 EA Normal samples.


title: IL7R: WT vs  mutant in vitro and in vivo.

status: Public on Jan 08 2014

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: The screening of putative candidate genes downstream of IL7R-INS in vitro KSL/CLP and in vivo (depicted as B-neoplasm, Notch-T-ALL, or myeloid disorder) in comparison to WT.

overall_design: Five-condition experiment: WT-KSL vs. INS-KSL cells; WT-CLP vs.INS-CLP; WT/ICN vs. INS/ICN; WT-CMP vs. INS-CMP. Biological replicate: each 1, One replicate per array.

first: Kazuaki

last: Yokoyama


title: Gene expression data from precision cut human liver slices treated to diclofenac

status: Public on Jan 22 2014

city: Leiden

first: Steven

last: Wink

state: Zuid Holland

address: Einsteinweg 55

department: Division of Toxicology

country: Netherlands

institute: LACDR

summary: Drug-induced liver injury (DILI) is an important clinical problem. Here we used a genomics approach to establish the critical drug-induced toxicity pathways that act in synergy with the pro-inflammatory cytokine tumor necrosis factor  (TNF) to cause cell death of liver HepG2 cells. Transcriptomics of the cell injury stress response pathways initiated by two hepatoxicants, diclofenac and carbamazepine, revealed the endoplasmic reticulum (ER) stress/translational initiation signaling and Nrf2 antioxidant signaling as two major affected pathways, which was similar to that observed for the majority of ~80 DILI compounds in primary human hepatocytes. The ER stress was primarily related to PERK and ATF4 activation and subsequent expression of CHOP, which was all independent of TNFα signaling. Identical ATF4 dependent transcriptional programs were observed in primary human hepatocytes as well as primary precision cut human liver slices. Targeted RNA interference studies revealed that while ER stress signaling through IRE1α and ATF6 acted cytoprotective, activation of the ER stress protein kinase PERK and subsequent expression of CHOP was pivotal for the onset of drug/TNF-induced apoptosis. While inhibition of the Nrf2-dependent adaptive oxidative stress response enhanced the drug/TNF cytotoxicity, Nrf2 signaling did not affect CHOP expression. Both hepatotoxic drugs enhanced expression of the translational initiation factor EIF4A1, which was essential for CHOP expression and drug/TNF-mediated cell killing. Our data support a model in which enhanced drug-induced translation initiates PERK-mediated CHOP signaling in an EIF4A1 dependent manner, thereby sensitizing towards caspase-8-dependent TNF induced apoptosis.

overall_design: Liver slices (diameter 4 mm, thickness 250 µm) were pre-incubated at 37°C for 1h individually in a well containing 1.3 ml Williams’ medium E with glutamax-1 (Gibco, Paisley, UK), supplemented with 25 mM D-glucose and 50 µg/ml gentamicin (Gibco, Paisley, UK) (WEGG medium) in a 12-well plate with shaking (90 times/min) under saturated carbogen atmosphere.

first: Lisa

last: Fredriksson

first: Bram

last: Herpers

first: Giulia

last: Benedetti

first: Mackenzie

last: Hadi

first: Hans

last: de Bont

first: Geny

last: Groothuis

first: Mirjam

last: Luijten

first: Erik

last: Danen

first: Marjo

last: de Graauw

first: John

last: Meerman

first: Bob

last: van de Water


title: Gene expression profiling of HPV-inactive oropharyngeal cancers and normal benign tissue (uvula, tonsil) from  European American patients

status: Public on Mar 05 2014

city: Columbia

first: Diego

last: Altomare

state: SC

address: 715 Sumter Street, Room 617

department: Department of Drug Discovery and Biomedical Sciences

country: USA

institute: University of South Carolina

summary: Head and neck cancer (HNC) is the fifth most common malignancy worldwide with an annual mortality rate of 200,000. About 90% of HNC can be classified as head and neck squamous cell carcinomas (HNSCC), of which approximately 75% are attributed to alcohol and tobacco consumption and 25 are associated with human papillomavirus (HPV), predominantly HPV16. HPV-associated OPC have better prognosis and a more favorable response to therapy as compared to HPV-negative tumors. Viral oncoproteins are capable of transforming primary human keratinocytes from either genital or oral epithelia in vitro and most likely play the same role in vivo, by disrupting cell-cycle regulatory pathways leading to a genetic progression to ano-genital cancer and OPC. However, the precise mechanisms by which HPV mediates malignant transformation of keratinocytes in the upper digestive tract epithelia are not entirely clear.  HPV E7-mediated inactivation of pRb results in overexpression of p16INK4A, which is commonly used as a clinical surrogate marker for HPV positivity/activity. However, high p16INK4A alone has insufficient sensitivity and specificity as a biomarker of HPV positivity in different mucosal sub-sites of HNC. Therefore, increasing emphasis is being placed on the assessment of viral load and E7 oncogene expression, resulting in further classification of HPV positive OPC as HPV-active and HPV-inactive. This study aimed to compare the gene expression profiles of HPV-inactive oropharyngeal squamous cell carcinoma (OPC) and normal benign uvula/tonsil tissues from European American patients and determine what biological processes and pathways are affected in HPV-inactive OPCs in this ethnic group.

overall_design: ANALYSIS 7: Two-condition, one-color experiment:  European American (EA) HPV-inactive oropharyngeal tumor samples and  normal benign uvula/tonsil tissues. Biological replicates:  4 EA HPV inactive samples and 4 EA Normal samples.

first: Swati

last: Tomar

first: Sangeeta

last: Kowli

first: Susannah

last: Kassler

first: Natalie

last: Sutkowski

first: M

middle: B

last: Gillespie

first: Kim

middle: E

last: Creek

first: Lucia

last: Pirisi


title: Drug-induced liver injury

first: Steven

last: Wink

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Expression data from human hepatocellular carcinoma cell line HepG2

summary:
Drug-induced liver injury (DILI) is an important clinical problem. Here we used a genomics approach to establish the critical drug-induced toxicity pathways that act in synergy with the pro-inflammatory cytokine tumor necrosis factor (TNF) to cause cell death of liver HepG2 cells. Transcriptomics of the cell injury stress response pathways initiated by two hepatoxicants, diclofenac and carbamazepine, revealed the endoplasmic reticulum (ER) stress/translational initiation signaling and Nrf2 antioxidant signaling as two major affected pathways, which was similar to that observed for the majority of ~80 DILI compounds in primary human hepatocytes. The ER stress was primarily related to PERK and ATF4 activation and subsequent expression of CHOP, which was all independent of TNFα signaling. Identical ATF4 dependent transcriptional programs were observed in primary human hepatocytes as well as primary precision cut human liver slices. Targeted RNA interference studies revealed that while ER stress signaling through IRE1α and ATF6 acted cytoprotective, activation of the ER stress protein kinase PERK and subsequent expression of CHOP was pivotal for the onset of drug/TNF-induced apoptosis. While inhibition of the Nrf2-dependent adaptive oxidative stress response enhanced the drug/TNF cytotoxicity, Nrf2 signaling did not affect CHOP expression. Both hepatotoxic drugs enhanced expression of the translational initiation factor EIF4A1, which was essential for CHOP expression and drug/TNF-mediated cell killing. Our data support a model in which enhanced drug-induced translation initiates PERK-mediated CHOP signaling in an EIF4A1 dependent manner, thereby sensitizing towards caspase-8-dependent TNF induced apoptosis.
We sought to determine the effect of co-exposure of certain drugs associated with idiosyncratic DILI with the cytokine TNFalpha to mimic drug exposure with inflammation signaling in HepG2 cells

overall_design: Human hepatoma HepG2 cells were obtained from American Type Culture Collection (ATCC, Wesel, Germany), cultured in DMEM supplemented with 10% (v/v) FBS, 25 U/mL penicillin and 25 µg/mL streptomycin and used for experiments between passage 5 and 20.

first: Lisa

last: Fredriksson

first: Bram

last: Herpers

first: Giulia

last: Benedetti

first: Mackenzie

last: Hadi


title: Murine pulmonary arterial smooth muscle cells: Wild-type vs. NOX1 deficiency (mRNA profiling)

first: Satoshi

last: Kondo

summary: NOX1 is a catalytic subunit of nonphagocytic NADPH oxidase, mainly localized to smooth muscle cells in the vasculature. We investigated the pathology underlying the pulmonary arterial hypertension-like phenotype demonstrated in mice deficient in the Nox1 gene (Nox1-KO). Spontaneous enlargement and hypertrophy of the right ventricle, accompanied by hypertrophy of pulmonary vessels, were demonstrated in Nox1-KO at 9-18 weeks of age. Since an increased number of α-smooth muscle actin-positive vessels was observed in Nox1-KO, pulmonary arterial smooth muscle cells (PASMCs) were isolated and characterized by flow cytometry and TUNEL staining. In Nox1-/Y PASMC, the number of apoptotic cells was significantly reduced without any change in the expression of endothelin-1, and hypoxia-inducible factors HIF-1a and HIF-2a, factors implicated in the pathogenesis of PAH. Transcriptional profiling of mouse pulmonary arterial smooth muscle cells in wild-type and NOX1-KO was analyzed.

overall_design: Pulmonary arterial smooth muscle cells were harvested from 3 mice.

first: Kazumi

last: Iwata

first: Yabe

middle: N

last: Chihiro


title: Murine pulmonary arterial smooth muscle cells: Wild-type vs. NOX1 deficiency

status: Public on Jan 21 2014

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


title: Murine Osteoclasts: Stat5 flox vs. Stat5 cKO

status: Public on Dec 09 2013

summary: Transcriptional profiling of mouse osteoclasts comparing control osteoclasts from Stat5 flox mice with osteoclasts from Stat5 cKO mice.

overall_design: Two-condition experiment, Stat5 flox cells vs. Stat5 cKO cells

first: Jun

last: Hirose

first: Sakae

last: Tanaka


title: The landscape of somatic alterations in epigenetic genes across 21 pediatric cancers

status: Public on Dec 31 2013

city: Memphis

first: Shann-Ching

last: Chen

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St. Jude Children's Research Hospital

summary: As a part of the St Jude Children’s Research Hospital-Washington University Pediatric Cancer Genome Project (PCGP), we adapted deep sequencing technologies and have sequenced 1025 tumor samples from 21 diseases covering brain, solid tumors and leukemias.  We analyzed the genomic DNA sequences, copy number variations and structural rearrangements of 633 genes whose proteins are involved in epigenetic machineries, including those that covalently modify DNA and histones, and structurally reorder chromatin.  To examine gene expression level of mutated histone genes, we analyzed gene expression in a group of 40 non-ETP T-lineage ALL samples using Affymetrix GeneChip HT HG-U133+ PM arrays (including 37 samples deposited in GSE28703 and 3 additional arrays not studied previously).  The results provide us the knowledge of potential therapeutic targets for pediatric cancer treatment and improvement of personalized therapy.

overall_design: Gene expression profiling was performed on 40 non ETP T-lineage acute lymphoblastic leukemia samples. No control or reference samples were included.

first: Robert

last: Huether

first: Li

last: Dong

first: Linda

last: Holmfeldt

first: Jinghui

last: Zhang

first: Charles

middle: G

last: Mullighan

first: James

middle: R

last: Downing


title: Common primitive-definitive hematopoietic precursors  vs.  Definitve hematopoietic progenitor cells

status: Public on Nov 27 2013

summary: Transcriptional profiling of mouse ES cell-derived hemaopoitic cells comparing common primitive-definitive hematopoietic precursors (CD41SP) with definitve hematopoietic progenitor cells (KA45)

overall_design: RNA isolated from two separate experiments was pooled and used for comparison

first: Toshiyuki

last: Yamane


title: Human lung cancer cell lines DMS-273 (SCLC) and NCI-H1437 (NSCLC): scrambled vs. shRNA clones

status: Public on Nov 15 2013

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

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

department: PEBC

country: Spain

institute: IDIBELL

summary: Transcriptional profiling of two human lung cancer cell lines, DMS-273 (small cell lung cancer) and NCI-H1437 (non-small cell lung cancer), stably transfected either with innocuous scrambled shRNAs or SETDB1-specific.The objective was to identify global gene expression changes due to the depletion of the H3K9me3 methyltransferase SETDB1.

overall_design: 3 replicates for DMS-273 and 1 Control; 2 replicates for NCI-H1437 and 1 Control

first: Manuel

last: Rodriguez-Paredes


title: Time Course of Young Adults Vaccinated with Meningococcal MCV4 and MPSV4 Vaccines

status: Public on Dec 15 2013

city: Atlanta

first: Shuzhao

last: Li

state: GA

address: 954 Gatewood Rd NE

department: Emory Vaccine Center

institute: Emory University

summary:
We performed systems analyses of immune responses to the meningococcal polysaccharide (MPSV4) and conjugate (MCV4) vaccines in healthy adults.
The goal was to identify innate gene signatures that correlate to antibody responses induced by these vaccines.

overall_design: Healthy adult volunteers (18-45 years of age) were randomized to be vaccinated subcutaneously with MPSV4 (Menomune®, n=13) or intramuscularly with MCV4 (MenactraTM, n=17) (Sanofi Pasteur, Swiftwater, PA). Whole blood samples were collected using CPT tubes at days 0, 3 and 7 post-vaccination. Peripheral blood mononuclear cells (PBMC) were isolated from fresh blood and used for DNA microarray experiments.

first: Helder

middle: I

last: Nakaya

first: Bali

last: Pulendran


title: Murine Ba/F3 Cells: Ba/F3 cells expressing wild type JAK2 (WT cells) vs. Ba/F3 cells expressing JAK2 V617F mutant (VF cells)

status: Public on Oct 31 2013

first: Satoshi

last: Kondo

summary: Transcriptional profiling of transformed Ba/F3 cells by myeloproliferative neoplasm-associated JAK2 V617F mutant comparing control Ba/F3 cells expressing wild type JAK2.

overall_design: Two-condition experiment, WT cells vs. VF cells.  One replicate per array.

first: Megumi

last: Funakoshi-Tago

first: Kenji

last: Tago


title: Modulation of NKG2D ligand expression and metastasis in tumors by spironolactone via RXR-gamma activation

status: Public on Oct 22 2013

first: David

last: Finkelstein

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Tumor metastasis and lack of NKG2D ligand (NKG2DL) expression are associated with poor prognosis in patients with colon cancer. Here we found that spironolactone (SPIR), an FDA-approved diuretic drug with a long-term safety profile, can upregulate NKG2DL expression in multiple colon cancer cell lines by activating the ATM-Chk2-mediated checkpoint pathway, which in turn enhances tumor elimination by natural killer cells. SPIR can also upregulate the expression of metastasis-suppressor genes TIMP2 and TIMP3, thereby reducing tumor cell invasiveness. Although SPIR is an aldosterone antagonist, its anti-tumor effects are independent of the mineralocorticoid receptor pathway. Instead, by screening the human nuclear hormone receptor siRNA library, we identify retinoid X receptor gamma (RXR gamma) as being indispensable for the anti-tumor functions of SPIR. Collectively, our results strongly support the use of SPIR or other RXR gamma-agonists with minimal side effects for colon cancer prevention and therapy.

overall_design: Two replicates of two cell types with and without drug

first: Wai-Hang

last: Leung

first: Queenie

middle: P

last: Vong

first: Wenwei

last: Lin

first: Laura

last: Janke

first: Taosheng

first: Wing


title: Identification of TEAD4 target genes in colorectal cancer cells

status: Public on Jan 01 2014

city: Shanghai

first: Chen-Ying

last: Liu

address: 1665 Kong Jiang Road

country: China

institute: Xinhua Hospital, Shanghai Jiao Tong University

summary: We have identified TEAD4 as a key prognosis factor in colorectal cancer. To elucidate the potentail mechanism and function of TEAD4 in colorectal caner, we generated two stable cell lines expressing different shRNA targeting TEAD4 in the mesenchymal-like LoVo cells and the differential genes were detected by microarray.

overall_design: LoVo colorectal cancer cells stably expressing pLKO.1 control shRNA or sh1_shTEAD4 or sh2_shTEAD4

first: Long

last: Cui


title: The mechanism of elevated S100A6 (Calcyclin) Enhances Tumorigenesis in clear cell renal cell carcinoma

status: Public on Nov 25 2013

city: Beijing

first: xu

last: zhang

address: Fuxing road

institute: PLA general hospital

summary:
Among all types of urological cancers, the clear cell renal cell carcinoma is the second leading cause of death in adults. This is mainly due to lack of promising prognosis or predictors, and effective target therapy. S100A6 (calcyclin), a member of S100 family of proteins, is reported to be elevated in many types of cancers. In the present study, we analyzed the expression of S100A6 in mRNA, in proteins and tissues. The mechanism of enhancing tumorigenesis was studied to understand the role of S100A6 in clear cell renal cell carcinoma tumorigenesis. Microarray and bioinformatic analyses were performed in the stable transfection of overexpression and knockdown of S100A6, comparing with each empty vector control in order to find the different expression genes and explore the mechanism.
The microarray analysis of clear cell renal cell carcinoma 786-O cell line treated with overexpression and knockdown S100A6.

overall_design: Four samples: overexpression S100A6 sample and vector control sample, knockdown S100A6 and vector control sample, each sample had three replicates.

first: Xiang-Jun

last: Lyu


title: mRNA and microRNA in spleens of miR-17~92 transgenic mice

status: Public on Nov 05 2013

city: Columbus

first: Sukhinder

last: Sandhu

state: OH

address: 460 W 12th Ave

institute: The Ohio State University Wexner Medical Center

summary: spleen B-cells isolated from 9 mice of 6-9 months of age were profilied for mRNA expression  using 3D-gene.

overall_design: 3 transgenic mice from two founder lines and 3 wild types as control

first: Carlo

last: Croce


title: A map of the PPARα transcription regulatory network for primary human hepatocytes

status: Public on Dec 18 2013

city: Research Triangle Park

first: Patrick

middle: D

last: McMullen

state: North Carolina

address: 6 Davis Drive, P.O. Box 12137

institute: The Hamner Institutes for Health Sciences

summary: Nuclear receptor activation in liver leads to coordinated alteration of the expression of multiple gene products with attendant phenotypic changes of hepatocytes. Peroxisome proliferators including endogenous fatty acids, environmental chemicals, and drugs induce a multi-enzyme metabolic response that affects lipid and fatty acid processing. We studied the signaling network for the peroxisome proliferator-associated receptor alpha (PPARα) in primary human hepatocytes using the selective PPARα ligand, GW7647. We measured gene expression over multiple concentrations and times and conducted ChIP-seq studies at 2 and 24 hours to assess genomic binding of PPARα. Over all treatments there were 192 genes differentially expressed. Of these only 51% showed evidence of PPARα binding – either directly at PPARα response elements or via alternative mechanisms. Almost half of regulated genes had no PPARα binding.  We then developed two novel bioinformatics methods to visualize the dose-dependent activation of both the transcription factor circuitry for PPARα and the downstream metabolic network in relation to functional annotation categories. Available databases identified several key transcription factors involved with the non-genomic targets after GW7647 treatment, including SP1, STAT1, ETS1, ERα, and HNF4α. The linkage from PPARα binding through gene expression likely requires intermediate protein kinases to activate these transcription factors. We found enrichment of functional annotation categories for organic acid metabolism and cell lipid metabolism among the differentially expressed genes. Lipid transport processes showed enrichment at the highest concentration of GW7647 (10μM). While our strategy for mapping transcriptional networks is evolving, these approaches are necessary in moving from toxicogenomic methods that derive signatures of activity to methods that establish pathway structure, showing the coordination of the activated nuclear receptor with other signaling pathways.

overall_design: Primary hepatocytes from four donors were exposed to 0, 0.001, 0.01, 0.1, 1.0, or 10.0μM GW7647 for 2, 6, 12, 24, or 72 hours.


title: Gene expression in human breast cancer cell lines regulated by HIC1 gene

status: Public on Aug 22 2013

first: Gang

last: Xiao

address: 227 South Chongqing Road

institute: Shanghai Jiao-Tong University School of Medicine

summary: This study aimed to further our understanding of the role that hypermethylatioted in cancer 1 (HIC1) plays in breast cancer progression. Microarrays were searched for some genes that had correlated expression with HIC1 mRNA. According to fold-change screening between restoring expression of HIC1 and its respective control cells in MDA-MB-231 cells, or HIC1 knockdown and its respective control cells in HBL100, both up-regulated and down-regulated genes were shown.

overall_design: The restoring expression HIC1 in MDA-MB-231 cells were respectively noted as MDAMB-231-HIC1 and the respective controls were noted as MDA-MB-231-GFP cells. HIC1 knockdown in HBL100 cells were noted as HBL100-shHIC1 and the respective control HBL100-shCtrl cell.

first: Guangcun

last: Cheng

first: Xueqing

last: Sun

first: Jinglong

last: Wang

first: Jianhua


title: Human liver infected by HBV: tumoral part vs non tumoral part of the liver

status: Public on May 23 2013

city: Nantes

first: Boris

last: HALGAND

address: 1, rue Gaston Veil

country: France

institute: INSERM

summary: transcriptionnal profiling comparing tumoral and non tumoral part of human liver infected by hepatitis B virus

overall_design:
Expression profiling of induced hepatitis B virus tumor from human liver and expression profiling of hepatitis B virus infected non tumoral part of the liver from french patients

Please note that there are 62 raw files (i.e.'AFE_raw_files.tar' linked to the Series records) for 124 samples since two samples were on the same array, one in Cy3 and  one in Cy5. The corresponding raw data file for each sample is indicated in the Sample description field.

first: Catherine

last: Chevalier

first: Marine

last: Cornec

first: Cyrille

last: Feray


title: Lhx2-regulated genes in hematopoietic stem cell (HSC)-like cells differentiated from mouse embryonic stem (ES) cells

status: Public on Aug 26 2013

first: Satoshi

last: Kondo

summary:
We previously demonstrated that hematopoietic stem cell (HSC)-like cells are robustly expanded from mouse embryonic stem (ES) cells by enforced expression of Lhx2, a LIM-homeobox domain (LIM-HD) transcription factor.
Here we established an ES cell line which conditionally expressed Lhx2 by Tet-On system. The ES cells were differentiated into HSC-like cells by Lhx2 expression. Lhx2-regulated genes were identified by comparing the HSC-like cells with those cultured in the absence of Lhx2 expression.

overall_design: Mouse ES with inducible Lhx2 were differentiated on OP9 stromal cells into hematopoietic lineage. On day 5 of the differentiation induction,Lhx2 expression was started by the addition of doxycycline (dox) and the cells were cultured on OP9 stromal cells in the presence of IL-6 and SCF. On day 20, HSC-like cells were harvested and re-seeded onto OP9 stromal cells in the absence of Lhx2 expression by dox-removal for 3 days. these cells were compared with the original HSC-like cells.

first: Kenji

last: Kitajima


title: Murine lung exposed to cigarette smoke and poly(I:C): Thioredoxin-1 vs. Saline Treated

status: Public on Sep 01 2013

city: Kyoto

first: Naoya

last: Tanabe

address: 54 Shogoin-kawahara-cho, Sakyo-ku

institute: Kyoto University

summary: Transcriptional profiling  of lung in mice exposed to cigarette smoke and poly(I:C) and treated or not with Thioredoxin-1

overall_design: Total RNA samples were pooled from 3 murine lungs for each experimental group.

first: Yuma

last: Hoshino


title: Expression profiling of circulating miRNAs in Luminal A breast cancer

status: Public on Apr 24 2013

city: Nottingham

first: Graham

middle: Roy

last: Ball

state: Notts

address: Clifton Lane

department: Science and Technology

country: United Kingdom

institute: Nottingham Trent University

summary:
Breast cancer is a common disease with distinct tumor subtypes which can be phenotypically characterized by estrogen receptor, progesterone receptor and HER2/neu receptor status. MiRNAs play regulatory roles in tumor initiation and progression. Altered miRNA expression has been demonstrated in a variety of cancer states to date presenting the potential for exploitation as cancer specific biomarkers. Blood presents an attractive medium biomarker discovery.
This study investigated systemic miRNAs differentially expressed in Luminal A (ER+PR+HER2/neu-) breast cancer and their effectiveness as oncologic biomarkers in the clinical setting. Blood samples were prospectively collected from consenting patients with Luminal A breast cancer (n=10) and controls (n=10). RNA was extracted, reverse transcribed and subjected to microarray analysis (n=10 Luminal A; n=10 Control).  Differentially expressed miRNAs were identified by artificial neural network (ANN) data-mining algorithms.

overall_design: Ethical approval was granted by the Clinical Research Ethics Committee, Galway Roscommon University Hospital Group. Written informed consent was obtained from all study participants.   Blood samples were prospectively collected from 20 women; this included 10 consecutive women with a new diagnosis of Luminal A breast cancer and 10 healthy control participants. Luminal A status was confirmed with immunohistochemistry and fluorescence in situ hybridization (FISH). The blood samples for the healthy control group were collected from women residing in the same catchment area as the cancer cases. These women had no personal history of malignancy and no current inflammatory or infectious condition.  Venous non-fasting whole blood samples were collected in BD vacutainers ® containing 18mg dipotassium EDTA anticoagulant (BD-Plymouth, PL6 7BP, UK). Total RNA was extracted from blood (1ml) using TRI Reagent BD (Molecular Research Centre, Inc). RNA concentration and integrity were evaluated by NanoDrop spectrophotometry (NanoDrop ND-1000 Technologies Inc., DE, USA) and Agilent Bioanalyzer RNA 6000 NanoChip Kit Series II (Agilent Technologies, Germany) analysis, respectively. MiRNA microarray profiling  Expression profiling of circulating miRNAs was performed using TaqMan miRNA arrays and assays in accordance with the manufacturer’s instructions (Taqman Low Density Array Human microRNA Card A and Card B, Applied Biosystems, Foster City, CA, USA). In short, total RNA was reverse transcribed using Megaplex primer pool A (Applied Biosystems) which contained sequence-specific primers for 381 specific miRNAs plus 3 controls (pool A).  An additional panel of 384 miRNAs (381 miRNAs and 3 controls, pool B) was performed on a subset of 4 cancers and 4 controls. Real-time quantitative PCR was performed for 667 miRNAs, using A and B microfluidic cards, each containing primers and probes for 381 specific miRNAs plus 3 controls and thermal-cycled on an Applied Biosystems 7900HT instrument.  The TLDA cards contain three endogenous controls (RNU44, RNU48 and MammU6 which is repeated four times on each card). Each card also contains a negative control, an assay unrelated to any human species, ath-miR-159a.

first: Ailbhe

middle: M

last: McDermott

first: Nicola

last: Miller

first: Deirdre

last: Wall

first: Karl

middle: J

last: Sweeney

first: Michael

last: Kerin


title: Knockdown of Hnrnpa0, a del(5q) Gene, Alters Myeloid Cell Fate in Murine Cells through Regulation of AU-rich Transcripts

status: Public on Aug 08 2013

first: Shann-Ching

last: Chen

summary: The post-transcriptional control of mRNA stability plays a critical role in numerous biological functions, including the immune response, cell cycle regulation and DNA damage response.  HNRNPA0, which encodes an RNA-binding protein shown to regulate transcript stability via binding to the AU-rich elements (AREs) of mRNAs, is located within the commonly deleted segment of 5q31.2 in therapy-related myeloid neoplasms (t-MNs) with a del(5q).  We hypothesized that loss of HNRNPA0 leads to alterations in hematopoietic differentiation due to changes in the expression of its target AU-rich transcripts.  Using RNAi interference to model Hnrnpa0 loss in primary murine cells and an experimental cell system, we found that reduced Hnrnpa0 expression leads to a shift from monocytic towards granulocytic differentiation.  Microarray-based global expression profiling revealed that Hnrnpa0 knockdown disproportionally impacts ARE-containing transcripts and alters expression of myeloid specification genes.  The biological importance of ARE-containing genes in myeloid neoplasms is further supported by changes in gene expression of ARE-mRNAs in t-MN del(5q) patients, predicted by pathway analysis to activate tumor growth. Together, our findings suggest that alterations in ARE-containing genes can positively regulate the cellular proliferation of del(5q) cells and implicate haploinsufficiency of HNRNPA0 as one of the key initiation mutations in the pathogenesis of t-MN.

overall_design: Gene expression profiling was performed on 38 single t-MN tumor samples. No control or reference samples were included.

first: David

last: Young

first: Angela

last: Stoddart

first: Joy

last: Nakitandwe

first: Zhijian

last: Qian

first: James

last: Downing

first: Michelle

last: Le Beau


title: Expression profiling of mouse embryonic stem cells (ESCs) (cell line V6.5, 129SvJae/C57B6 F1 background), and mouse ESC-derived Neural Precursor Cells (NPCs)

status: Public on Feb 20 2013

city: Cambridge

last: Lodato

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

summary: ESCs and NPCs are two setm cell types which rely on expression of the transcription factor Sox2.  We profilled gene expression in ESCs and NPCs to correlate genome-wide Sox2 ChIP-Seq data in these cells with expression of putative targets

overall_design: Three biological replicates each of ESCs and NPCs were prepared and assays using Affymetrix Gene Expression Arrays

middle: A

first: Rudolf

last: Jaenisch

first: Laurie

last: Boyer


title: Wnt5a-deficient vs. wild-type E18 liver

status: Public on Feb 07 2013

first: Satoshi

last: Kondo

summary: Transcriptional profiling of E18.5 livers derived from Wnt5a-deficient (KO) mice compared to those from littermate wild-type (WT) mice. RNA samples were extracted from whole livers derived from E18.5 fetuses.

overall_design: Two-condition experiment: Wnt5a KO vs. WT whole livers. Total RNA samples were extracted from E18.5 whole livers. KO and WT samples were a mixture of RNA solutions derived from two Wnt5a KO livers and two WT livers, respectively.

first: Sei

last: Kakinuma


title: Gene Regulation by Estrogen Signaling and DNA Methylation in MCF7 Breast Cancer Cells

status: Public on Dec 31 2012

city: Huddinge

first: Milica

last: Putnik

address: Hälsovägen 7

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

summary:
Estrogen signaling and epigenetic modifications, in particular DNA methylation, are involved in regulation of gene expression in breast cancers. Here we investigated a potential regulatory cross-talk between these two pathways by identifying their common target genes and exploring potential underlying molecular mechanisms in human MCF7 breast cancer cells. Principal Findings: Gene expression profiling revealed that the expression of approximately 150 genes was influenced by both 17β-estradiol (E2) and a hypomethylating agent 5-aza-2’-deoxycytidine (DAC). Based on gene ontology (GO), CpG island prediction analysis and previously reported estrogen receptor (ER) binding regions, we selected six genes for further analysis (BTG3, FHL2, PMAIP1, BTG2, CDKN1A and TGFB2). GO analysis suggests that these genes are involved in intracellular signaling cascades, regulation of cell proliferation and apoptosis, while CpG island prediction of promoter regions reveals that the promoters of these genes contain at least one CpG island. Using chromatin immunoprecipitation, we show that ERα is recruited to CpG islands in promoters, but neither in an E2- nor in a DAC-dependent fashion. DAC treatment reactivates the expression of all selected genes although only the promoters of BTG3 and FHL2 genes are methylated, with E2 treatment showing no effect on the methylation status of these promoters. Conclusions: We identified a set of genes regulated by both estrogen signaling and DNA methylation. However, our data does not support a direct molecular interplay of mediators of estrogen and epigenetic signaling at promoters of regulated genes.
The aim of the study was to identify genes regulated by estrogen signaling and DNA methylation, using microarray approach.

overall_design: We compared the effects of E2 and DAC on global gene expression profiles in MCF7 cells. By comparing C_E2 (MP5-MP8 average) with C_EtOh samples (MP1-MP4 average), 802 genes were identified as up-regulated by E2, while 851 genes were identified as down-regulated by E2. 1017 genes were identified as up-regulated by DAC, by comparing A_EtOh (MP9-MP12 average) samples with C_EtOh, suggesting that DNA methylation is involved in their regulation. To identify possible common targets, we have compared the DAC up-regulated genes with E2-regulated genes. 88 annotated genes are found to be up-regulated by both E2 and DAC, suggesting that E2 has a hypomethylation-like effect on the regulation of these genes. 58 annotated genes are found to be down-regulated by E2 and up-regulated by DAC, suggesting that E2 has a hypermethylation-like effect on the regulation of these genes.

first: Chunyan

last: Zhao

first: Jan-Åke

last: Gustafsson

first: Karin

last: Dahlman-Wright


title: Expression data from airway epithelial cells from patients with asthma, rhinitis, and helathy controls

status: Public on Feb 05 2013

city: Amsterdam

first: Ariane

last: Wagener

address: Meibergdreef 9

institute: Academic Medical Center

summary:
The link between upper and lower airways in patients with both asthma and allergic rhinitis is still poorly understood. As the biological complexity of these disorders can be captured by gene expression profiling we hypothesized that the clinical expression of rhinitis and/or asthma is related to differential gene expression between upper and lower airways epithelium.
We used micro array to profile gene expression of primary nasal and bronchial epithelial cells from the same individuals and examining the impact of allergic rhinitis with and without concomitant allergic asthma on expression profiles.

overall_design: 17 subjects were included in a cross-sectional study (6 allergic asthma and allergic rhinitis; 5 allergic rhinitis; 6 healthy controls). RNA was extracted from isolated and cultured epithelial cells from bronchial brushes and nasal biopsies, and analyzed by microarray (Affymetrix U133+ PM Genechip Array).

middle: H

first: Silvia

last: Luiten

first: Aeilko

last: Zwinderman

first: Cornelis

last: van Drunen

first: Peter

last: Sterk


title: Mouse adult testes: Total RNA vs. IP RNA

status: Public on Apr 01 2013

address: Tebiro 6-10-1

institute: Toray Industries,Inc.

summary: RNAs that are enriched in AGO2 Immunoprecipitated (IP) products or PIWIL1 IP products were identified from mouse(BALB/C) adult testes by examine the ratio of total RNA signal intensity to AGO2 IP RNA or PIWIL1 IP RNA signal intensity.

overall_design: Two-condition experiment,Total RNA extracted from mouse adult testes vs. AGO2 IP RNA extracted from mouse adult testes and total RNA extracted from mouse adult testes vs. PIWIL1 IP RNA extracted from mouse adult testes.

first: Takahiro

last: Nishibu


title: The DSIF subunits Spt4 and Spt5 have several unexpected, distinct roles in regulating immunoglobulin class switch recombination

summary: Class-switch recombination (CSR), induced by activation-induced cytidine deaminase, can be divided into two phases: DNA cleavage of the switch (S) regions, and the joining of the cleaved ends of the different S regions. Here, we show that the DSIF complex (Spt4 and Spt5), a transcription elongation factor, is required for CSR in CH12F3-2A cells, and Spt4 and Spt5, carry out independent functions in CSR. Depleting Spt5 reduced the H3K4me3 levels and DNA cleavage at the Sα region, whereas Spt4 knockdown did not perturb the H3K4me3 status or S region cleavage. Thus, we conclude that Spt5 plays a role similar to the histone chaperone FACT by regulating histone modification and DNA cleavage in CSR. Assay systems using synthetic repair substrates revealed that both Spt4 and Spt5 are required for non-homologous end joining and homologous recombination. Taken together, Spt4 and Spt5 are involved in multiple CSR steps, and can function independently.

overall_design: Spt4 or Spt5 were knocked down in CH12F3-2A cells in the presence of CD40L, IL4, TGFb (CIT) stimulation. RNA from each samples were extracted and relative difference in transcript level were compared with control RNAi-treated, CIT-stimulated samples.

first: Andre

last: Stanlie

first: Nasim

last: Begum

first: Hideo

last: Akiyama

first: Tasuku

last: Honjo


title: LPS/GalN-induced liver injury model: wild-type vs. TMX-deficient mice

status: Public on May 01 2012

summary: Liver transcriptional profiles of untreated or LPS/GalN-treated wild-type and TMX-/- mice.

overall_design: 2 genotype, 2 agent sets.

first: Yoshiyuki

last: Matsuo

first: Junji

last: Yodoi


title: The Genetic Basis of Hypodiploid Acute Lymphoblastic Leukemia

status: Public on Jan 15 2013

first: Linda

last: Holmfeldt

state: Tennessee

summary: The genetic basis of hypodiploid acute lymphoblastic leukemia (ALL), characterized by aneuploidy and poor outcome, is unknown. Here, using complementary genome-wide profiling approaches, we show that hypodiploid ALL comprises two major subtypes that differ in the severity of aneuploidy, transcriptional profile and submicroscopic genetic alterations. Near haploid cases with 24-31 chromosomes frequently harbor alterations targeting receptor tyrosine kinase- and Ras signaling (71%) and IKZF3 (AIOLOS; 13%). In contrast, low hypodiploid ALL cases with 32-39 chromosomes are characterized by TP53 alterations (88%), almost half of which are present in non-tumor cells, and have alterations of IKZF2 (HELIOS; 53%) and RB1 (41%). Both near haploid and low hypodiploid tumors exhibit activation of Ras and PI3K signaling pathways, and are sensitive to PI3K inhibition, indicating that these drugs should be explored as a new therapeutic strategy for this frequently lethal form of leukemia.

overall_design: Gene expression profiling was performed on 117 single diagnosis tumor samples and one relapse sample [SJHYPO117]. No control or reference samples were included.

first: Ernesto

last: Diaz-Flores

first: Lei

last: Wei

first: Jinghui

last: Zhang

first: Li

last: Ding

first: Debbie

last: Payne-Turner

first: Michelle

last: Churchman

first: Anna

last: Andersson

first: Shann-Ching

last: Chen

first: Kelly

last: McCastlain

first: Jared

last: Becksfort

first: Jing

last: Ma

first: Gang

last: Wu

first: Samir

last: Patel

first: Susan

middle: L

last: Heatley

first: Guangchun

last: Song

first: John

last: Easton

first: Matthew

last: Parker

first: Xiang

first: Michael

last: Rusch

first: Kristy

last: Boggs

first: Erin

last: Hedlund

first: Christina

last: Drenberg

first: Sharyn

last: Baker

first: Deqing

last: Pei

first: Cheng

last: Cheng

first: Robert

middle: S

last: Fulton

first: Lucinda

first: David

last: Dooling

first: Kerri

last: Ochoa

first: Mark

last: Minden

first: Ian

last: Lewis

first: L

last: To

first: Paula

last: Marlton

first: Gordana

last: Raca

first: Wendy

last: Stock

first: Geoffrey

last: Neale

first: Hans

last: Drexler

first: Ross

last: Dickins

first: Sheila

last: Shurtleff

first: Ching-Hon


title: Circadian patterns of gene expression in the human brain and disruption in major depressive disorder [control set]

status: Public on Apr 20 2013

city: Ann Arbor

first: Andy

middle: W

last: Lin

state: MI

address: 205 Zina Pitcher Place

department: MBNI

institute: University of Michigan

summary: A cardinal symptom of Major Depressive Disorder (MDD) is the disruption of circadian patterns. Yet, to date, there is no direct evidence of circadian clock dysregulation in the brains of MDD patients. Circadian rhythmicity of gene expression has been observed in animals and peripheral human tissues, but its presence and variability in the human brain was difficult to characterize. Here we applied time-of-death analysis to gene expression data from high-quality postmortem brains, examining 24-hour cyclic patterns in six cortical and limbic regions of 55 subjects with no history of psychiatric or neurological illnesses ('Controls') and 34 MDD patients. Our dataset covered ~12,000 transcripts in the dorsolateral prefrontal cortex (DLPFC), anterior cingulate cortex (AnCg), hippocampus (HC), amygdala (AMY), nucleus accumbens (NAcc) and cerebellum (CB). Several hundred transcripts in each region showed 24-hour cyclic patterns in Controls, and >100 transcripts exhibited consistent rhythmicity and phase-synchrony across regions. Among the top ranked rhythmic genes were the canonical clock genes BMAL1(ARNTL), PER1-2-3, NR1D1(REV-ERB), DBP, BHLHE40(DEC1), and BHLHE41(DEC2). The phasing of known circadian genes was consistent with data derived from other diurnal mammals. Cyclic patterns were much weaker in MDD brains, due to shifted peak timing and potentially disrupted phase relationships between individual circadian genes. This is the first transcriptome-wide analysis of cyclic patterns in the human brain and demonstrates a rhythmic rise and fall of gene expression in regions outside of the suprachiasmatic nucleus in control subjects. The description of its breakdown in MDD suggest novel molecular targets for treatment of mood disorders.

overall_design: Sample collection, including human subject recruitment and characterization, tissue dissection, and RNA extraction, was described previously (see Evans 2003 Neurobiol Dis 14:240-250, Li 2004 Biol Psychiatry 55:346-352). RNA samples for different regions came from the same set of brains from 86 control subjects. Sample size varied by region: AnCg (n=70 controls), DLPFC (n=83), CB (n=51), AMY (n=32), HC (n=63) and NAcc (n=66). Many of the samples were run on two or more chips, resulting in the following chip counts for each region: AnCg = 124, DLPFC = 161, CB = 79, AMY = 62, HC = 108 and NaCC = 136. We ran each sample on at least two microarrays using the Affymetrix U133-A or U133Plus-v2 GeneChips, however, we only used the U133A part of the U133Plus-v2 GeneChip in our analysis. We applied RMA (Robust Multi-array Analysis) (see Irizarry 2003 Biostatistics 4:249-264, Irizarry 2003 Nucleic Acids Res 31:e15) to summarize probe set expression levels, using a custom Chip Definition File, resulting in expression data for 11,911 ENTREZ transcripts. Microarray data for each region were analyzed separately. All downstream analyses were performed in R. Details of the data processing, including data cleaning and normalization, are located in the Supplementary Materials (section 1). After data filtering, 1,424 microarrays remained, corresponding to 776 unique RNA samples in six regions.

first: Jun

middle: Z

last: Li

first: Blynn

last: Bunney

first: Fan

last: Meng

first: Megan

last: Hagenauer

last: Walsh

first: Marquis

last: Vawter

first: Simon

last: Evans

first: Prabhakara

middle: V

last: Choudary

first: Preston

last: Cartagena

first: Jack

last: Barchas

first: Alan

middle: F

last: Schatzberg

first: Edward

last: Jones

first: Richard

last: Myers

first: Stanley

last: Watson

first: Huda

last: Akil

first: William


title: The histone chaperone Spt6 is required for AID target determination through H3K4me3 regulation

status: Public on Feb 01 2013

city: Kamakura

first: Satoshi

last: Kondo

summary: H3K4me3 plays a critical role in the activation-induced cytidine deaminase (AID)-induced DNA cleavage of switch (S) regions in the immunoglobulin heavy chain (IgH) locus during class-switch recombination (CSR). The histone chaperone complex facilitates chromatin transcription (FACT) is responsible for forming H3K4me3 at AID target loci. Histone chaperone suppressor of Ty6 (Spt6) also participates in regulating H3K4me3 for CSR and for somatic hypermutation (SHM) in AID target loci. H3K4me3 loss was correlated with defects in AID-induced DNA breakage and reduced mutation frequencies in IgH loci, in both S and variable regions, and in non-IgH loci, such as metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and small nucleolar RNA host gene 3 (SNHG3). Global gene expression analysis revealed that Spt6 can act as both a positive and negative transcriptional regulator in B cells, affecting approximately 5% of the genes that includes suppressor of Ty4 (Spt4) and AID. Interestingly, Spt6 regulates CSR and AID expression through two distinct histone modification pathways, H3K4me3 and H3K36me3, respectively. Spt6 is a unique histone chaperone, capable of regulating the histone epigenetic state of both AID targets and the AID locus.

overall_design: CH12F3-2A cells were transfected with control and Spt6 siRNAs; 24h later, cells were stimulated with CIT to induce CSR. Total RNA was extracted from control and Spt6 siRNA treated cells for mRNA expression profiling.

first: N

last: Begum

first: A

last: Stanlie

first: H

last: Akiyama

first: T

last: Honjo


title: Discordant cellular response to pre-surgical letrozole in bilateral synchronous ER+ breast cancers with a KRAS mutation or FGFR1 gene amplification

status: Public on Jul 17 2012

city: Nashville

first: Justin

last: Balko

address: 777 Preston Research Building

department: Medicine

institute: Vanderbilt University

summary: This clinical case resulted from an ongoing trial at Vanderbilt University and abroad where ER+ breast cancer patients are administered 2-3 weeks of aromatase inhibitor therapy leading up to definitive surgical resection of the tumor. In this case, we describe a study patient presenting with bilateral primary ER+ breast tumors. Short term hormonal therapy substantially reduced proliferation in one tumor, while the second was essentially unchanged.  Extensive molecular and genetic workup of the two tumors yielded divergent lesions in the two tumors; an activating KRAS mutation in the responsive tumor, and an amplification of the FGFR1 locus in the treatment-refractory tumor.

overall_design: Surgical tumor specimens from ER+ breast cancer patient 7603 who was administered letrozole for 16 days leading up to definitive surgery were utilized for RNA extraction and hybridization to Affymetrix Gene expression microarrays.

first: Carlos

last: Arteaga


title: Downregulation of the Wnt antagonist Dkk2 links loss of Sept4 and myofibroblastic transformation of hepatic stellate cells

status: Public on Jun 03 2012

first: Akira

last: Myomoto

address: Yoshida-Shimoadachi

institute: Kyoto Univ.

summary:
Background/Aims: Sept4, a subunit of the septin cytoskeleton specifically expressed in quiescent hepatic stellate cells (HSCs), is downregulated through transdifferentiation to fibrogenic and contractile myofibroblastic cells. Since Sept4−/− mice are prone to liver fibrosis, we examined the unknown molecular network underlying liver fibrosis by probing the association between loss of Sept4 and accelerated transdifferentiation of HSCs.

Methods: We compared the transcriptomes of Sept4+/+ and Sept4−/− HSCs by differential DNA microarray analysis and quantitative RT-PCR. Based on reduced dickkopf2 (Dkk2) gene expression in Sept4−/− HSCs, we tested whether supplementing Dkk2 could suppress myofibroblastic transformation of Sept4−/− HSCs. We used a lymphoid enhancer-binding factor/transcription factor-luciferase reporter assay to test whether Dkk2 can exert anti-fibrotic effects by interfering with the canonical Wnt pathway.

Results: We observed consistent upregulation of Dkk2 in primary cultured HSCs and in a carbon tetrachloride hepatitis model in mice, which decreased with loss of Sept4. Supplementing Dkk2 suppressed the induction of pro-fibrotic genes (α-smooth muscle actin and 2 collagen genes) and induced an anti-fibrotic gene (Smad7) in Sept4−/− HSCs. In human liver specimens with inflammation and fibrosis, Dkk2 immunoreactivity appeared to be positively correlated with the degree of fibrotic changes.

Conclusions: Pro-fibrotic transformation of HSCs through the loss of Sept4 is partly due to reduced expression of Dkk2 and its homologues, and the resulting disinhibition of the canonical Wnt pathway.

overall_design: We induced Liver Cirrhosis to SEPT4-KO or wild type mouse by CCl4, and examined mRNA expression profiling in hepatic stellate cell of these mouse.

first: Atsuko

last: Yanagida

first: Keiko

last: Iwaisako

first: Etsuro

last: Hatano

first: Kojiro

last: Taura

first: Fumiaki

last: Sato

first: Masato

last: Narita

first: Hiromitsu

last: Nagata

first: Hiroyuki

last: Asechi

first: Shinji

last: Uemoto

first: Makoto

last: Kinoshita


title: Tracing the conversion process for primordial germ cells to pluripotent stem cells

status: Public on Apr 24 2012

first: Satoshi

last: Kondo

summary: The overall gene expression profiles revealed by this system provide novel insight into how pluripotency is acquired in germ-committed cells.

overall_design: In the study presented here, we employed FACS sorting to purify pluripotent candidate cells during the culture period

first: Go

last: Nagamatsu

first: Takeo

last: Kosaka

first: Shigeru

last: Saito

first: Keiyo

last: Takubo

first: Hideo

first: Tetsuo

last: Sudo

first: Katsuhisa

last: Horimoto

first: Mototsugu

last: Oya

first: Toshio

last: Suda


title: CD34 marks angiogenic tip cells in human vascular endothelial cell cultures.

status: Public on Jan 05 2012

first: Ingeborg

last: Klaassen

address: Meibergdreef 15

department: Ophthalmology

institute: AMC

summary: The functional shift of quiescent endothelial cells into tip cells that migrate and stalk cells that proliferate is a key event during sprouting angiogenesis. We previously showed that the sialomucin CD34 is expressed in a small subset of cultured endothelial cells and that these cells extend filopodia: a hallmark of tip cells in vivo. In the present study, we characterized endothelial cells expressing CD34 in endothelial monolayers in vitro. We found that CD34-positive human umbilical vein endothelial cells show low proliferation activity and increased mRNA expression of all known tip cell markers, as compared to CD34- negative cells. Genome-wide mRNA profiling analysis of CD34-positive endothelial cells demonstrated enrichment for biological functions related to angiogenesis and migration, whereas CD34-negative cells were enriched for functions related to proliferation. In addition, we found an increase or decrease of CD34-positive cells in vitro upon exposure to stimuli that enhance or limit the number of tip cells in vivo, respectively. Our findings suggest cells with virtually all known properties of tip cells are present in vascular endothelial cell cultures and that they can be isolated based on expression of CD34. This novel strategy may open alternative avenues for future studies of molecular processes and functions in tip cells in angiogenesis.

overall_design: Four HUVEC donors were FACS-sorted by CD34 and divided in CD34-positive and CD34-negative fractions.

first: Martin

last: Siemerink

first: Ilse

last: Vogels

first: Arjan

last: Griffioen

first: Cornelis

last: Van Noorden

first: Reinier

middle: O

last: Schlingemann


title: Discovery of novel recurrent mutations and rearrangements in early T-cell precursor acute lymphoblastic leukemia by whole genome sequencing

status: Public on Nov 23 2011

first: Charles

middle: G

last: Mullighan

address: 262 Danny Thomas Place

institute: St Jude Children's Research Hospital

summary: Early T-cell precursor acute lymphoblastic leukaemia (ETP ALL) is an aggressive malignancy of unknown genetic basis. We performed whole genome sequencing of tumour and normal DNA from 12 children with ETP ALL and assessed the frequency of somatic alterations in 52 ETP and 42 non-ETP T-ALL samples by sequencing and DNA copy number analysis. ETP ALL was characterised by a high frequency of activating mutations in genes regulating cytokine receptor and Ras signalling (67% of cases; NRAS, KRAS, FLT3, IL7R, JAK3, JAK1, SH2B3 and BRAF); alterations disrupting haemopoietic development (58%; GATA3, ETV6, RUNX1, IKZF1, EP300); and inactivating mutations in histone modifying genes (48%; EZH2, EED, SUZ12, SETD2 and EP300). We also identified new targets of mutation including DNM2, ECT2L and RELN. Ten of 12 ETP ALL cases harboured chromosomal rearrangements, several of which complex and resulted in the expression of novel chimeric in-frame fusion genes disrupting haemopoietic regulators. Thus, similar to myeloid malignancies, mutations that drive proliferation, impair differentiation and disrupt histone modification are hallmarks of ETP ALL. Moreover, the global transcriptional profile of ETP ALL was similar to that of normal and myeloid leukaemia haemopoietic stem cells. These findings suggest that addition of myeloid-directed therapies might improve the poor outcome of ETP ALL.

overall_design: Gene expression profiling was performed on 52 single diagnosis tumor samples. No control or reference samples were included.

first: Jinghui

last: Zhang

first: Li

last: Ding

first: Linda

last: Holmfeldt

first: Gang

last: Wu

first: Susan

last: Heatley

first: Debbie

last: Payne-Turner

first: John

last: Easton

first: Xiang

last: Chen

first: Jianming

last: Wang

first: Michael

last: Rusch

last: Lu

first: Shann-Ching

first: Racquel

last: Collins-Underwood

first: Jing

last: Ma

first: Kathryn

last: Roberts

first: Stanley

middle: B

last: Pounds

first: Lei

last: Wei

first: Anatoly

last: Ulyanov

first: Jared

last: Becksfort

first: Pankaj

last: Gupta

first: Robert

last: Huether

first: Richard

last: Kriwacki

first: Matthew

last: Parker

first: Daniel

last: McGoldrick

first: David

last: Zhao

last: Alford

first: Stephen

last: Espy

first: Kiran

middle: C

last: Bobba

first: Guangchun

last: Song

first: Deqing

last: Pei

first: Cheng

last: Cheng

first: Stefan

last: Barbato

first: Dario

last: Campana

first: Elaine

last: Coustan-Smith

first: Sheila

first: Susana

last: Raimondi

first: Maria

last: Kleppe

first: Jan

last: Cools

first: Kristin

last: Shimano

first: Michelle


title: miRNA expression profiles of PRC SiRNA vs scramble transfected XTC.UC1 cells

status: Public on Nov 22 2011

city: angers

first: frederique

last: savagner

address: 4 rue larrey

institute: Inserm

summary:
PGC-1 related coactivator (PRC) shares structural and functional features with PGC-1{alpha}. It regulates several metabolic pathways and mitochondrial biogenesis. Its specific role in the early programming of cell proliferation suggests a finely regulated crosstalk between the mitochondrial functions and the cell cycle status.  To explore the PRC-regulated pathways, we used a cell-line model of mitochondrial-rich tumors, presenting an oxidative metabolism and a specific increase in PRC expression.
We looked for the feedback loop exerted by miRNAs on the regulation of PRC-related mitochondiral functions

overall_design: Expression profiles of miRNA at 48h PRC SIRNA treatment compared to scramble in XTC.UC1 cells. In duplicate.

first: D

last: Guillotin

first: S

last: Carat

first: F

last: Savagner


title: Metastable primordial germ cell-like state induced from mouse embryonic stem cells by Akt activation

status: Public on Apr 30 2010

first: Satoshi

last: Kondo

summary: Specification to primordial germ cells (PGCs) occurs under the mesoderm induction signals during gastrulation.  Here, we found that Akt activation in embryonic stem (ES) cells generated self-renewing spheres during mesodermal differentiation induction and that the differentiation status of the sphere cells was in between ES cells and PGCs.  Essential regulators for PGC specification and their downstream germ cell-specific genes were expressed in the spheres, showing that the cells of the sphere commenced the differentiation to germ lineage.  However, the spheres could not proceed to spermatogenesis after transplantation to testes.  Meanwhile, the transfer of the spheres to the original feeder-free ES cell culture conditions induced chaotic differentiation.  In contrast, when the spheres were cultured on mouse embryonic fibroblasts or in the presence of ERK-cascade and GSK3 inhibitors, the reversion to the ES cell-like cell states was induced.  These results indicate that the Akt signaling brings about a novel metastable and pluripotent state between ES cells and PGCs.

overall_design: Five samples were analyzed, which included the Akt-Mer-expressing ES cell (ESC) line #21 treated with or without 4OHT (4-hydroxytamoxifen), the #21 ESC-derived primordial germ cell (PGC)-like sphere cells and the ESC-like cells reverted from #21 PGC-like sphere cells.  The PGC-like sphere cells derived from another Akt-Mer ESC line #42 was also examined.

first: Noriko

last: Yamano

first: Tohru

last: Kimura

first: Toru

last: Nakano


title: RNA interference screening identifies the Insulin/IGF-1 receptor pathway as a mechanism of escape from hormone dependence in breast cancer

status: Public on Apr 11 2012

first: Todd

last: Miller

address: 2220 Pierce Ave, 777 PRB

institute: Vanderbilt Univ

summary:
A significant fraction of breast cancers exhibit de novo or acquired resistance to estrogen deprivation.
A kinome-wide siRNA screen identified a role for Insulin Receptor (InsR) in the hormone-independent growth of ER+ breast cancer cells
We used gene expression microarrays to identify genes and pathways that are altered by insulin stimulation of ER+ MCF-7 human breast cancer cells.

overall_design: MCF-7 cells were treated with serum-free medium +/- insulin for 4 or 24 hrs prior to RNA harvest for analysis.

first: Emily

last: Fox

first: Carlos

last: Arteaga


title: Cells isolated from diaphragm of mdx mouse: satellite cells vs. PDGFRa+ cells

status: Public on Dec 08 2011

summary:
Transcriptional profiling of mouse skeletal muscle-derived cells comparing satellite cells with PDGFRa+ cells.
Satellite cells and PDGFRa+ cells were directly isolated from diaphragm of dystrophic mdx mouse by FACS.

overall_design: Two-condition experiment, satellite cells vs. PDGFRa+ cells. Freshly isolated. One replicate per array.

first: Akiyoshi

last: Uezumi

first: Kunihiro

last: Tsuchida


title: Differentiational potency of induced pluripotent stem cells into cardiomyocytes

status: Public on Sep 19 2009

first: Shinji

last: Kaichi

address: Kawahara-machi54, Shogoin, Sakyo-ku

department: Pediatrics

institute: Kyoto university

summary: Transcriptional profiling of mouse induced pluripotent stem (iPS) cells with the low potency (strain 20D17) compared to control iPS cells with the normal potency (strain 38C2).

overall_design:
Two-condition experiment: iPS cells strain 20D17 vs. control iPS cells strain 38C2.

Biological replicates: 2 strain 20D17, 2 strain 38C2, independently grown and harvested. One replicate per array.

first: Koji

last: Hasegawa


title: Identification of MVH target mRNA

status: Public on Aug 31 2011

city: Irvine

first: Ippei

last: Nagamori

state: CA

address: 2226B GNRF

institute: University of California, Irvine

summary: During mammalian spermatogenesis the mouse VASA homolog (MVH), a germ cell-specific DEAD-box type RNA binding protein, localizes in a germline-specific RNA granule termed the chromatoid body (CB). Genetic analyses have revealed that MVH is essential to progress through spermatogenesis, although the molecular mechanisms of its function remain elusive. We found that the acetyltransferase HAT1 and its cofactor, p46, are specifically co-localized with MVH in the CB and acetylate MVH at Lys-405, leading to inactivation of its RNA binding activity. Notably, the acetylation is developmentally regulated, paralleling the temporally regulated co-localization of HAT1 and p46 in the CB. We have identified 858 mRNAs as MVH targets, a large proportion of which correspond to previously identified translationally arrested genes. Importantly, eIF4B mRNA, a target of MVH, is selectively released from MVH-RNP when MVH is acetylated, paralleling an increase in eIF4B protein. These findings reveal a novel signaling pathway that links acetylation to RNA processing in the control of spermatogenesis.

overall_design:
IMVH target mRNA was purified from MVH immuno precipitated complex, followed by RNA purification and identified by DNA chip.
In this study, we identified more than 800 MVH target mRNA in testis.

first: Paolo

last: Sassone-Corsi


title: High-throughput sequencing of small RNAs in Zostera marina

status: Public on Sep 30 2011

city: Udine

first: Emanuele

last: De Paoli

state: UDINE

address: via delle Scienze 206

department: Agricultural, Food, Environmental and Animal Sciences

country: Italy

institute: University of Udine

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Zostera marina tissues (including leaves, flowers, roots and rhizoids). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the genome under study.

overall_design: Small RNA libraries were derived from leaves, flowers, roots and rhizoids of Zostera marina. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen), and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Kayti Tigani for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.

first: Monica

last: Accerbi

first: Pamela

last: Green

first: Blake

last: Meyers


title: Temporal Dynamics and Genetic Control of Transcription in the Human Prefrontal Cortex

status: Public on Oct 27 2011

city: Baltimore

first: Carlo

last: Colantuoni

state: MD

address: 733 N Broadway

department: Neurology

institute: Johns Hopkins Univ. School of Medicine

summary:
In order to gain a global molecular perspective on how the human genome gives rise to the brain, we explore the temporal dynamics and genetic control of transcription in human dorsolateral prefrontal cortex in an extensive series of brain tissue from fetal development through aging. We discover a wave of gene expression changes occurring during fetal development which are reversed in early postnatal life. One half century later in life, this phenomenon is mirrored in aging as well as neurodegeneration. While we identify thousands of robust associations of individual genetic polymorphisms with gene expression, we also demonstrate that there is no association between the total extent of genetic differences between subjects and the global similarity of their transcriptional profiles. Hence, the human genome produces a consistent molecular architecture in the prefrontal cortex, despite millions of genetic differences across individuals and races. To enable further discovery, this entire dataset is freely available (GEO).

The gene expression from this study can be interrogated gene-by-gene with a biologist-friendly web application available at http://braincloud.jhmi.edu/plots/.

overall_design:
RNA from 269 human prefrontal cortex samples ranging from fetal development (negative ages) through aging (80 years) were analyzed on custom 2-color microarrays from the National Human Genome Research Institute (NHGRI) microarray core facility using a reference RNA comprised of a pool of all samples. Subjects had no severe neuropathology nor neurological or neuropsychiatric diagnoses.

Preprocessed/normalized data for exploration is contained in the Series Matrix file (see "Download Family" section below). These data are very flexible in that they are well suited to diverse downstream analyses, provided that a well-designed "cleaning" method is first applied. Care should be taken in using a "cleaning" method that is particularly suited to the exact downstream analysis that will be performed. As there is significant biological and technical/experimental heterogeneity in the data (albeit less here with this 2-color technology than is usually associated with large 1-color studies), we recommend using surrogate variable analysis (SVA; PMID:22257669) or other data "cleaning" methodology such as ComBat (PMID:16632515) to focus the data on a particular question.

Another version of the data tuned particularly to identifying canonical patterns of gene expression across the lifespan (at the expense of individual variation) can be downloaded from the "Supplementary file" section below ("GSE30272_ExprsMtxCleanedN269_31SVN.txt"). Here we expand on the previous modeling (Colantuoni 2011, PMID: 22031444) of age patterns across the lifespan in several key ways (manuscript in preparation): 1) We applied splines to capture non-linear gene expression effects while ensuring patterns of gene expression are continuous across the lifespan. The previous analysis used age by decade interaction terms, which are not necessarily continuous. 2) We estimated and adjusted for a much higher number of SVs. The previous analysis used only 2 SVs, here we allowed SVA to automatically determine this number: 31 SVs were used. This much increased "cleaning" further tuned this dataset to age effects. Hence, this newly processed data should only be used for the estimation of canonical, mean patterns of expression across the lifetime. 3) We regressed out SVs while allowing the effects of age and mean gene expression (the intercept) to remain in the data. Previously, SVs were regressed out while ignoring possible correlation between SVs and age, potentially obscuring some age effects. Specifically, using SVA, we employ a 2nd degree basis spline with knots at birth, 1, 10, 20, and 50 years [8 degrees of freedom], i.e. a curve fit to expression across age within each age range between these knots. Each model also allowed an offset at birth, because there were no samples in the third trimester of fetal life. The exact model matrix used to implement this spline analysis in SVA has been included as a supplementary file for download ("GSE30272_ModelMatrix.txt.gz" in the "Supplementary file" section below) and may be useful for incorporating this model into further statistical analysis when beginning from the "uncleaned" data. The individual values for all 31 SVs used in our analysis are also included as a supplementary file ("GSE30272_SVN31Matrix.txt.gz" in the "Supplementary file" section below).

For easy, platform-independent access to images of individual gene expression profiles across human DLPFC development derived from this data processing/cleaning (i.e. data from the Supplementary file "GSE30272_ExprsMtxCleanedN269_31SVN.txt"), visit: http://braincloud.jhmi.edu/plots/.

Raw red-green intensity data are contained in the supplementary file "GSE30272_RAW.tar" (see "Supplementary file" section below). These would need to be converted to log ratios, normalized, and "cleaned" prior to any biological analysis.

While we do not recommend using them for data exploration, the data that are processed as originally described in Colantuoni 2011 (PMID: 22031444) can be re-created by downloading the preprocessed, but not "cleaned" data in the Series Matrix file (see "Download Family" section below) and adjusting for (in regression models) or regressing out (for visualization) the 2 surrogate variables contained in the array/sample annotation in this same Series Matrix file.

SNP genotype data for these subjects can be found in dbGaP under Study ID *phs000417.v1.p1* http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000417.v1.p1.

first: Barbara

middle: K

last: Lipska

first: Tianzhang

last: Ye

first: Thomas

last: Hyde

first: Ran

last: Tao

first: Jeffrey

middle: T

last: Leek

first: Elizabeth

first: Abdel

last: Elkahloun

first: Mary

last: Herman

first: Daniel

middle: R

last: Weinberger

first: Andrew

last: Jaffe

first: Joel

middle: E

last: Kleinman


title: A Notch ligand, Delta-like 1 functions as an adhesion molecule for mast cells

status: Public on Oct 01 2010

first: Satoshi

last: Kondo

summary: To assess the effect of over-expression of Delta-like 1 on OP9 cells on gene expression in terms of Notch signaling and adhesion molecules, gene expressions of OP9, OP9-GFP (carrying GFP gene) and OP9-DL1 (carrying GFP and DL1 gene) cells (Immunity 2002;17:749-756) were analyzed.

overall_design: Gene expression of OP9, OP9-GFP and OP9-DL1 were compared.

first: Akihiko

last: Murata

first: Shin-Ichi

last: Hayashi


title: PRC SiRNA vs scramble transfection in XTC.UC1 cells

status: Public on Jan 07 2009

first: frederique

last: savagner

summary:
PGC-1 related coactivator (PRC) shares structural and functional features with PGC-1{alpha}. It regulates several metabolic pathways and mitochondrial biogenesis. Its specific role in the early programming of cell proliferation suggests a finely regulated crosstalk between the mitochondrial functions and the cell cycle status.
To explore the PRC-regulated pathways, we used a cell-line model of mitochondrial-rich tumors, presenting an oxidative metabolism and a specific increase in PRC expression. Microarray studies of temporal PRC invalidation in these XTC.UC1 cells were compared to the functional status of the mitochondria as well as to the expression level of genes and proteins involved in the oxidative phosphorylation process. Compared with what was observed for PGC-1{alpha}, we explored the role of nitric oxide in the PRC-regulated mitochondrial biogenesis.
We proved that nitric oxide rapidly influences the expression of PRC at the transcriptional level. Focusing on mitochondrial energy metabolism, we demonstrated that PRC differentially controls the respiratory chain complexes and the coupling efficiency, in order to conserve a sufficient level of ATP and to protect the cell from oxidative stress. Our results highlight the key role of the PRC coactivator in the fine modulation of metabolic functions in response to the cell cycle status.

Keywords: Transcriptionnal coactivator invalidation by SiRNA

overall_design: Expression profiles at 0h, 12h, 24h and 48h of PRC SIRNA treatment compared to scramble and referred to time of 20% serum induction. Expression profiles of PRC SIRNA and scramble during serum starvation were referred as -1.

first: Julie

last: Poirier

first: Mahatsangy

last: Raharijaona

first: Jean-Fred

last: Fontaine

first: Rémi

last: Houlgatte

first: Frédérique

last: Savagner


title: Murine Colon26 cells: Primary vs. liver metastasis

status: Public on Jul 23 2008

city: kamakura

first: yoji

last: ueda

address: 6-10-1 Tebiro

institute: Toray Industries, Inc.

summary:
Transcriptional profiling of mouse Colon26 cancer cells comparing control primary tumours in the colon with their liver metastases.

Keywords: Metastatic variant

overall_design: Two-condition experiment, Colon26 primary tumours vs. their liver metastases. Biological replicates: 2 primary tumours, 2 liver metastases, independently grown and harvested. One replicate per array.

first: Masahiro

last: Sonoshita

first: Makoto

middle: M

last: Taketo


title: Molecular Diagnostics in Sepsis: from Bedside to Bench

status: Public on Aug 29 2006

city: St. Louis

first: J

middle: Perren

last: Cobb

state: MO

address: Campus Box 8109, 660 South Euclid Avenue

institute: Washington University in St. Louis

summary:
Accuracy of sepsis prediction was obtained using cross-validation of gene expression data from 12 human spleen samples and from 16 mouse spleen samples. For blood studies, classifiers were constructed using data from a training data set of 26 microarrays. The error rate of the classifiers was estimated on seven de-identified microarrays, and then on a subsequent cross-validation for all 33 blood microarrays. Estimates of classification accuracy of sepsis in human spleen were 67.1%; in mouse spleen, 96%; and in mouse blood, 94.4% (all estimates were based on nested cross-validation). Lists of genes with substantial changes in expression between study and control groups were used to identify nine mouse common inflammatory response genes, six of which were mapped into a single pathway using contemporary pathway analysis tools.
Keywords: genomics, diagnosis, microarray, calprotectin

overall_design: Exploratory studies were conducted using spleens from septic patients and from mice with abdominal sepsis. Seven patients with sepsis after injury were identified retrospectively and compared with six injured patients. C57BL/6 male mice were subjected to cecal ligation and puncture, or to IP lipopolysaccharide. Control mice had sham laparotomy or injection of IP saline, respectively. A sepsis classification model was created and tested on blood samples from septic mice.

first: Philip

last: Chung

first: Jason

last: Laramie

first: Donald

middle: J

last: Meyer

first: Thomas

last: Downey

first: Laurence

last: Tam

first: Huashi

last: Ding

first: Timothy

last: Buchman

first: Irene

last: Karl

first: Gary

middle: D

last: Stormo

first: Richard

last: Hotchkiss

first: Perren