title: Integrative genomic characterization of oral squamous cell carcinoma identifies frequent somatic drivers (methylation)

first: Jiexin

last: Zhang

address: 1515 Holcombe Blvd

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

summary:
Oral cavity squamous cell carcinoma (OSCC) is a disease with extensive morbidity and mortality and few useful molecular targets.
Multiplatform integrated genomic analysis was performed in order to identify genomic drivers and molecularly discernible tumor subtypes.
mRNA, miRNA and methylation data are all submitted to GEO

overall_design: We measured methylation of 42 OSCC tumors, 2 normal oral epithelial tissues, and 2 normal blood samples with Illumina HumanMethylation450 arrays

first: Curtis

last: Pickering

middle: J

last: Frederick

first: Jeffrey

last: Myers


title: Transcript levels in mouse liver

status: Public on Jan 01 2013

city: Philadelphia

first: Utham Kashyap

last: Valekunja

state: PA

address: 3400 Civic Center Boulevard,

department: Department of Systems Pharmacology & Therapeutics, Perelman School of Medicine,

country: USA

institute: University of Pennsylvania

summary: Total RNA was isolated from liver samples of C57/BL6 mice over a circadian time course, 3 biological replicate samples per time point were collected and processed individually. RNA from each individual biological replicate sample was extracted using RNeasy mini kit (Qiagen Cat# 74106) and hybridized on an Affymetrix mouse Gene ST1.0 microarray.

overall_design: Examination of mouse liver tissue at 4 time-points around the clock in free-running, continuous conditions (constant darkness, temperature and food available ad libitum).

first: Utham

middle: K

first: Akhilesh

middle: B

last: Reddy


title: Integrative genomic characterization of oral squamous cell carcinoma identifies frequent somatic drivers

city: Houston

state: TX

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Expression data from U87MG cells expressing EGFRvIII

city: New York

first: Shao-shan

middle: Carol

last: Huang

state: NY

address: 12 Waverly Pl

department: Biology

institute: New York University

summary:
EGFRvIII is the most common deletion mutant of EGFR in human cancer and its levels are highly correlated with poor prognosis in GBM.  The deletion of exons 2-7 removes most of the extracellular ligand binding domain, so it is unable to bind EGF or other EGFR-binding ligands.  Nevertheless, the mutant receptor is constitutively phosphorylated, and is capable of activating downstream signaling pathways at a low level.
To comprehensively identify the downstream signaling consequences of the EGFRvIII, we incorporated phosphoproteomic, transcription profiling and DNase-Seq data from U87MG glioblastoma cells expressing titrated levels of this mutant receptor.

overall_design: Total RNA were extracted from U87MG cells engineered to expressed different levels of EGFRvIII: medium (U87M; 1.5 million copies of EGFRvIII receptor per cell), high (U87H; 2 million copies per cell), super-high (U87SH; 2.5 million copies per cell), and kinase-dead EGFRvIII (U87DK; 2 million copies of kinase dead EGFRvIII per cell).  RNA was hybridized to Affymetrix microarrays.

middle: C

first: Paul

middle: H

first: William

last: Gordon

first: Ernest

last: Fraenkel


title: Expression data from fosb gene modified mouse

city: Fukuoka

first: Yusaku

last: Nakabeppu

state: Fukuoka

address: 3-1-1 Maidashi Higashi-ku

department: Department of Immunobiology and Neuroscience

country: Japan

institute: Medical Institute of Bioregulation, Kyushu University

summary:
To examine fosB regulation of neurogenesis, depression and epilepsy, we compared the gene expression profiles of wild type, fosBd/d and fosB-null mice by microarray analysis.
Microarray analysis revealed that genes related to neurogenesis, depression and epilepsy are altered in the hippocampus of fosB-null mice.

overall_design: Total RNA from the hippocampus of wild-type, fosBd/d and fosB-null mice was prepared using ISOGEN and RNeasy Mini kits.  For DNA microarray experiments, total RNA (100ng) was added to poly-A control and treated with WT Expression Kit. cDNA was labeled using WT terminal labeling kit and hybridized with Affymetrix GeneChip Mouse Gene 1.0 ST platform (GPL6246).

first: Hiroko

last: Nomaru

first: Noriko

last: Yutsudo


title: Expression data from mesodermal Tbx1-knockout ears at E12.5

city: Bronx

first: Tingwei

last: Guo

address: 1301 Morris Park Avenue, Room 408

department: Genetics

institute: Albert Einstein College of Medicine

summary:
The T-box transcription factor Tbx1 is expressed in the otic vesicle and surrounding periotic mesenchyme during inner ear development. Mesenchymal Tbx1 is essential for inner ear development, with conditional mutants displaying defects in both auditory and vestibular systems. We have previously identified reduced expression of retinoic acid metabolic genes in the periotic mesenchyme of mesoderm conditional Tbx1 mutants, using the T-Cre mouse line, implicating retinoic acid in mesenchymal-epithelial signaling downstream of Tbx1 in the periotic mesenchyme.

In order to identify downstream effectors of mesenchymal-epithelial signaling downstream of mesenchymal Tbx1, we have utilized a gene profiling approach comparing embryonic day 12.5 periotic tissue from T-Cre-mediated conditional Tbx1 mutants (Mest-KO) and conditional heterozygous control litter mates (control).

overall_design: E12.5 T-Cre-mediated conditional Tbx1 mutants (Mest-KO) and control (T-Cre conditional Tbx1 heterozygotes) embryos were microdissected to isolate the otic vesicle and surrounding periotic mesenchyme. Left and right tissue from each individual embryo was pooled, and 5 control and 5 mutant embryos were analyzed on individual microarrays using Affymetrix Mouse Gene ST 1.0 chips.

first: Dennis

last: Monks

first: Bernice

middle: E

last: Morrow


title: Role of adhesion receptors in mast cell disease-evolution

city: Vienna

first: Martin

last: Bilban

country: Austria

institute: Medical University of Vienna

summary: Systemic mastocytosis (SM) is an incurable neoplasm characterized by abnormal accumulation of neoplastic mast cells (MC) in vascularized organs. In indolent SM, MC express several different adhesion-molecules including CD2 and CD58, and form focal tissue-aggregates, whereas in advanced SM, MC often lack CD2 and produce a more diffuse infiltration-pattern. To explore the functional role of CD2 in the pathology of SM, stable CD2+ and CD2− subclones of the human MC-leukemia cell line HMC-1 were generated and injected intraperitoneally into pfp/rag2 mice. CD2+ HMC-1 cells formed solid mastocytomas in the peritoneum and lungs, whereas CD2− cells produced diffuse infiltration. CD2+ and CD2− HMC-1 subclones all displayed the driver-mutant KIT D816V, exhibited the same growth-kinetics, and displayed identical adhesion-receptors including CD44 and selectin-ligands. To explore the mechanism of organ invasion, E- and P-selectin-deficient scid mice (scid-select) were employed. While massive HMC-1 infiltrates were detected in the lungs of control mice, infiltration was markedly reduced or absent in scid-select mice. The invasion-receptor CD44 was detectable in all MC infiltrates, with most abundant expression in the invasion-front. Together, our data show that selectins mediate organ-invasion of MC and CD2-CD58 interactions contribute to a more focal infiltration-pattern which is lost during progression to MC leukemia.

overall_design: HMC1 cells were sorted by FACS for expression of CD2 surface expression. 2 subclones were obtained (CD2+ or CD2-) and compared by gene expression profiling using U133 plus 2.0 GeneChips

first: Peter

last: Valent


title: dcEF-regulated gene expression of human lung cancer cells

city: Taipei

first: Ji-Yen

last: Cheng

address: 128 Academia Road, Section 2, Nankang

department: Research Center for Applied Sciences

country: Taiwan

institute: Academia Sinica

summary:
Highly metastatic cancer cells have been observed to move directionally in response to direct current (dc) electric fields (EFs) of physiological strength. The phenomenon, which is called electrotaxis or galvanotaxis, suggests the involvement of physiological EF in cancer metastasis.
To explore this conjecture, we compared the influence of dcEF on gene expressions of a highly invasive (CL1-5) and a low invasive (CL1-0) lung cancer cell lines.

overall_design: Gene expression of human lung cancer cells with (experimental samples) or without (control samples) dcEF stimulation in physiological strength was analyzed. Two cell lines, CL1-0 and CL1-5, were treated with the same condition and compared in this study. Each condition has three biological replicates for each cell line.

first: Ching-Wen


title: Transcriptome analysis of patients with recurrent aphthous stomatitis suggests novel therapeutic targets

city: Gainesville

first: M Cecilia

last: Lopez

state: FL

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

summary: Gene expression patterns in tissue from control individuals is similar to non-ulcerated tissue from afflicted individuals, whereas marked differences were observed in ulcerated materials. Gene expression differences in ulcerated tissues provide clues to potential treatment options.

overall_design: Comparison of gene expression between normal tissue from control individuals and ulcer and non-ulcer tissue from afflicted individuals.

first: L

last: Baccaglini

first: M

first: D

middle: W

last: Theriaque

first: I

last: Bhattacharrya

first: F

middle: L

last: Needell

first: H

middle: V

last: Baker


title: FaDu treated with citric buffer vs. rCTGF

first: Muh-Hwa

last: Yang

address: No.155, Sec.2, Li-Nong Street

department: Institute of Clinical Medicine

institute: National Yang-Ming University

overall_design:
FaDu treated with citric buffer for 24 hours
FaDu treated with rCTGF 100 ng/mL for 24 hours


title: Nitric oxide effect in Escherichia coli O157:H7

city: Saint-Genès-Champanelle

first: Christine

last: MARTIN

address: Centre de Theix

department: MICA

country: France

institute: INRA

summary: Untreated or NOR-4 treated wild type cells or nsrR knockout cells

overall_design: NOR-4 treament or nsrR knockout

first: Alain

middle: P

last: Gobert

first: Josée

last: Harel


title: Expression data of statin treated HUVEC cells transfected siRNA KLF2 or KLF4.

city: 4-6-1, Komaba, Meguroku

first: Takahide

last: Kohro

state: Tokyo

institute: LSBM, RCAST

summary:
KLF2 and KLF4 are important transcriptional factors in endothelial cells, however their roles in statin treatment has not been elucidated. Here we report the comprehensive change of transcripts of statin treated HUVECs transfected with  siRNA KLF2 or KLF4.
We used repeated microarray analysis of HUVECs treated with pitavastatin for 4hours. Before statin treatment, cells were transfected with siRNA KLF2 or KLF4.

overall_design: HUVECs were used within the first 6 passages.  For studies, HUVECs were cultivated in medium EGM2MV containing pitavastatin at a concentration of 1 micromolar.

first: Takashi

last: Maejima

first: Tatsuhiko

last: Kodama

first: Youichiro

last: Wada


title: shRNA knockdown of the transcription factor NF-YA (NFYA)

status: Public on Dec 31 2012

city: Boston

first: Joseph

middle: Daniel

last: Fleming

state: MA

address: 240 Longwood Ave

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

summary:
NF-Y, a trimeric transcription factor (TF) composed of two histone-like subunits (NF-YB (NFYB) and NF-YC (NFYC)) and a sequence-specific subunit (NF-YA), binds to the CCAAT motif, a common promoter element. Genome-wide mapping reveals 5,000-15,000 NF-Y binding sites depending on the cell type, with the NF-YA and NF-YB subunits binding asymmetrically with respect to the CCAAT motif. Despite being characterized as a proximal promoter TF, only 25% of NF-Y sites map to promoters. A comparable number of NF-Y sites are located at enhancers, many of which are tissue specific, and nearly half of NF-Y sites are in select subclasses of HERV LTR repeats. Unlike most TFs, NF-Y can access its target DNA motif in inactive (non-modified) or polycomb-repressed chromatin domains. Unexpectedly, NF-Y extensively co-localizes with FOS in all genomic contexts, and at promoters and enhancers this often occurs in the absence of JUN and the AP-1 motif. NF-Y also co-associates with a select cluster of growth-controlling and oncogenic TFs, consistent with the abundance of CCAAT motifs in the promoters of genes overexpressed in cancer. Interestingly, NF-Y and several growth-controlling TFs bind in a stereo-specific manner, suggesting a mechanism for cooperative action at promoters and enhancers. Our results indicate that NF-Y is not merely a commonly-used, proximal promoter TF, but rather performs a more diverse set of biological functions, many of which are likely to involve co-association with FOS.
Scrambled control (shSCM) and NF-YA pLKO.1-shRNAs were designed by Sigma-Aldrich. The puromycin resistance cassette was replaced with an EGFP cassette. Viral production and transduction were carried out as previously described (Benatti et al. 2011). HeLaS3 cells were transduced with shSCM or shNF-YA viral supernatants, in triplicate, and cells collected after 48 hr of incubation. Total RNA was prepared by Trizol extraction and Qiagen RNeasy kit purification, converted to biotinylated aRNA and hybridized to U133 Plus 2.0 GeneChip expression arrays using the 3’ IVT Express Kit (Affymetrix, USA) following the manufacturer’s protocol. Arrays were RMA normalized (Irizarry et al. 2003), gene expression levels calculated, differential expression determined using the following R packages from the Bioconductor project: affy (Gautier et al. 2004), limma (Smyth 2004).

overall_design: HelaS3 cells were transduced with shSCM or shNF-YA in triplicate for 48hrs.

middle: D

first: Kevin

last: Struhl

first: Paolo

last: Benatti

first: Carol

last: Imbriano


title: Gene expression profiling of seborrheic keratosis

city: Seoul

first: Eun Young

last: Seo

address: Yongon-dong 28, Chongno-gu

department: Department of Dermatology

country: South Korea

institute: Seoul National University College of Medicine

summary: Seborrheic keratosis is benign cutaneous neoplasm, the etiology of which is not well-known. To characterize differential gene expression profiles in seborrheic keratosis, we investigated the genome-wide patterns of gene expression from skin with seborrhic keratosis and uninvolved normal skin using cDNA microarrays.

overall_design: Comparative RNA expression profiles from non-lesional and lesional skin of 4 patients with seborrheic keratosis

first: Eun-Young

first: Jin-Ho

last: Chung


title: mmu-miR-15a-3p activity in mouse cells

city: Bethesda

first: Aliaksandr

last: druz

state: MD

address: 14A Service Rd. Room 176

department: NIDDK

institute: NIH

summary: We intended to investigate effects of mmu-miR-15a-3p on gene expression in mice

overall_design: We used microarrays to compare gene expression in mouse B/CMBA.Ov cell lines transfected with mmu-miR-15a-3p and negative control mimic

last: Druz

last: Shiloach

first: Chithra

last: Keembiyehetty


title: Expression data of HUVEC cells after statin treatment

summary:
3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitors, statins, are known to exert endothelial athero-protective effects through the induction of specific transcriptional factors and their downstream target genes besides lowering LDL-cholesterol.  However its critical mechanism has not still been elucidated.  Here we report the comprehensive change of transcripts induced by pitavastatin.
We used repeated microarray analysis of HUVECs treated with pitavastatin for 4-hours, we identified a group of consistently up - or down - regulated genes.

overall_design: HUVECs were used within the first 6 passages.  For studies, HUVECs were cultivated in medium EGM2MV containing pitavastatin at a concentration of 1 μM, and same concentration of DMSO was used as a control sample.


title: Intratumoral diversity in Follicular lymphoma

first: Michael

middle: R

last: Green

address: 1515 Holcombe Blvd, Unit 903

department: Lymphoma/Myeloma

institute: MD Anderson Cancer Center

summary: Follicular lymphoma (FL) shows heterogenous expression of the cell surface B-cell marker, CD20. In order to investigate whether this heterogeneity also marks underlying transcriptional heterogeneity, we sorted tumor B-cells from 8 FL specimens based upon their intermediate or high expression of CD20 and transcriptionally profiled them.

overall_design: CD20 intermediate and CD20 high tumor B-cells were sorted by FACS, RNA extracted, and profiled using Affymetrix U133 plus 2.0 microarrays.

first: Ash

last: Alizadeh

first: Ron

last: Levy


title: NOD2 and desease associated variant NOD2-L1007fsinsC dependent genomewide transcriptional regulation in stable Flp-In HEK cells

city: Kiel

first: Susanne

last: Billmann

address: Schittenhelmstraße 12

country: Germany

institute: Institute of Clinical Molecular Biology Christian-Albrechts-Universität Kiel

summary: NOD2 is an intracellular receptor for the bacterial cell wall component muramyl dipeptide (MDP) and variants of NOD2 are associated with chronic inflammatory diseases of barrier organs e.g. Crohn disease, asthma and atopic eczema. It is known that activation of NOD2 induces a variety of inflammatory and antibacterial factors. The exact transcriptomal signatures that define the cellular programs downstream of NOD2 activation and the influence of the Crohn-associated variant L1007fsinsC are yet to be defined.  To describe the MDP-induced activation program, we analyzed the transcriptomal reactions of isogenic HEK293 cells expressing NOD2wt or NOD2L1007fsinsC to stimulation with MDP. Importantly, a clear loss-of-function could be observed in the cells carrying the Crohn-associated variant L1007fsinsC, while the NOD2wt cells showed differential regulation of growth factors, chemokines and several antagonists of NF-κB, e.g. TNFAIP3 (A20) and IER3.

overall_design: To elucidate the MDP-induced activation program we generated isogenic HEK293 cells stably expressing wildtype NOD2 or NOD2L1007fsinsC using a FRT-recombinase based approach. Cells carrying the inserted vector cassette were used as controls (mock-transfectant). To comprehensively analyze NOD2-mediated innate immune responses we analyzed transcriptomal signature patterns using genome-wide cDNA microarrays. Samples were harvested from cell cultures under normal growth conditions 0 h, 2 h and 6 h after MDP‑ stimulation of the cells.

first: Andreas

last: Till

first: Robert

last: Haesler

first: Martin

last: Kerick

first: Adedayo

last: Hanidu

first: Jun

last: Li

first: Philip

last: Rosenstiel

first: Stefan

last: Schreiber


title: Genome-wide expression profiling of laser micro-dissected macrophages from ruptured and stable atherosclerotic human plaques

city: Newcastle upon Tyne

first: Kelvin

last: Lee

state: Tyne and Wear

address: International Centre for Life, Central Parkway

department: Cardiovascular Research

country: United Kingdom

institute: Institute of Genetic Medicine, University of Newcastle upon Tyne

summary:
Objective: Resident macrophages play an important role in atheromatous plaque rupture.  The macrophage gene expression signature associated with plaque rupture is incompletely defined due to the complex cellular heterogeneity in the plaque. We aimed to characterise differential gene expression in resident plaque macrophages from ruptured and stable human atheromatous lesions. A cell-specific approach has the potential to address the question of gene expression differences between particular cell types in stable and unstable plaques with greater precision than approaches based on the study of whole plaques. Using laser micro-dissection, we isolated total RNA from macrophage-rich regions of stable and ruptured human atheromatous plaques derived from carotid endarterectomy samples which were comprehensively characterized using clinical, radiological and histological criteria, and carried out genome-wide gene expression profiling using microarrays.
Results: The profiles were characteristic of activated macrophages.  At a false discovery rate of 10%, 914 genes were differentially expressed between stable and ruptured plaques. The findings were confirmed in fourteen further stable and ruptured samples for a subset of eleven genes with the highest expression differences (p<0.05).  Pathway analysis revealed that components of the PPAR/Adipocytokine signaling pathway were the most significantly upregulated in ruptured compared to stable plaques (p=5.4x10-7).  Two key components of the pathway, fatty-acid binding-protein 4 (FABP4) and leptin, showed nine-fold (p=0.0086) and five-fold (p=0.0012) greater expression respectively in macrophages from ruptured plaques.
Conclusions: We found differences in gene expression signatures between macrophages isolated from stable and ruptured human atheromatous plaques. Our findings indicate the involvement of FABP4 and leptin in the progression of atherosclerosis and plaque rupture, and suggest that down-regulation of PPAR/adipocytokine signaling within plaques may have therapeutic potential.

overall_design: Methods: We performed genome-wide expression analyses of isolated macrophage-rich regions of stable and ruptured human atherosclerotic plaques.  Plaques present in carotid endarterectomy specimens were designated as stable or ruptured using clinical, radiological and histopathological criteria.  Macrophage-rich regions were excised from 5 ruptured and 6 stable plaques by laser micro-dissection.  Total RNA were subjected to two cycles of linear amplification. Transcriptional profiling was performed using Affymetrix HG-U133 plus 2.0 GeneChip arrays.

first: Mauro

last: Santibanez-Koref

first: Tuomo

last: Polvikoski

first: Daniel

last: Birchall

first: Alexander

last: Mendelow

first: Bernard

last: Keavney


title: Gene expression profiling of enforced HOXA1 expression in melanoma cell line (SkMel30)

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: We recently reported an oncogenomics-guided screening approach designed to identify genetic drivers of early stage melanoma metastasis, and in this study we functionally validate the top-scoring candidate, homeobox transcription factor A1 (HOXA1), by demonstrating HOXA1‘s robust effects on melanoma cell invasion, metastasis and tumorigenicity.  Transcriptome and pathway profiling analyses of cells expressing HOXA1 reveal up-regulation of factors involved in diverse cytokine pathways that include the TGFβ signaling axis, which we further demonstrate to be required for HOXA1-mediated cell invasion.  Transcriptome profiling also informed HOXA1’s ability to potently down-regulate expression of microphthalmia-associated transcription factor (MITF) and other genes required for melanocyte differentiation, suggesting a mechanism by which HOXA1 expression de-differentiates cells into a pro-invasive precursor cell state concomitant with TGFβ activation.  Our analysis of publicly available datasets indicate that the HOXA1-induced gene signature successfully categorizes melanoma specimens based on their metastatic potential and, importantly, is capable of stratifying melanoma patient risk for metastasis based on expression in primary tumors.

overall_design: The HOXA1-induced transcription analysis was conducted using RNAs extracted from SkMel30 cells transduced with either control or HOXA1, followed by hybridization of labeled cDNA onto Affymetrix GeneChips (Human Genome U133Plus2.0).

first: Kenneth

last: Scott

first: Joanna

last: Wardwell-Ozgo


title: Expression data from mesodermal Tbx1-knockout ears, otic vesicles, and periotic mesenchyme

first: Tingwei

last: Guo

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

overall_design: Refer to individual Series


title: Identification of genes regulated by knockdown of HSF1 or RPA1

city: Ube

first: Eiichi

last: Takaki

state: Yamaguchi

address: minami-kogushi, 1-1-1

institute: Yamaguchi university

summary: Transcription factor access to regulatory elements is prevented by the nucleosome. Heat shock factor 1 (HSF1) is a winged helix transcription factor that plays roles in control and stressed conditions by gaining access to target elements, but mechanisms of HSF1 access have not been well known in mammalian cells. We show a physical interaction between the wing motif of human HSF1 and replication protein A (RPA), which is involved in DNA metabolism. Depletion of RPA1 abolishes HSF1 access to the promoter of HSP70 in unstressed conditions, and delays its rapid activation in response to heat shock. The HSF1-RPA complex leads preloading of RNA polymerase II and opens chromatin structure by recruiting a histone chaperone FACT. Furthermore, this interaction is required for melanoma cell proliferation. These results provide a mechanistic basis for constitutive HSF1 access to nucleosomal DNA, which is important for both basal and inducible gene expression.

overall_design: To examine whether the HSF1-RPA complex regulates the expression of genes, mRNA levels in MEFs with/without HSF1- or RPA1-shRNA were analyzed by DNA microarray analysis using GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix).

first: Mitsuaki

last: Fujimoto

first: Akira

last: Nakaki


title: Gene expression analysis of CCL28 signaling in ishematopoietic stem and progenitor cells (HSPC) in culture

city: Los Angeles

first: Mattias

last: Magnusson

state: CA

address: 621 Charles E Young Drive South, 2204

department: MCDB

institute: UCLA

summary: We identified chemokine (C-C motif) ligand 28 (CCL28) as a novel growth factor for HSPCs with the ability to enhance the proliferation potential of fetal, neonatal and adult CD34+ HSPCs after one week of culture in serum-free medium containing limiting stem cell factor (SCF) concentrations. Importantly, CCL28 could increase the progenitor potential of CB- and bone marrow (BM) derived CD34+ cells as measured by colony assays. Furthermore, treatment of CB CD34hiCD38loCD90+CD45RA- cells with CCL28 significantly enhanced the ability of the cells to long-term repopulate immunodeficient mice compared to SCF-treated cultures. Our findings show that CCL28 is a potent growth factor for human HSCs and suggest that it should be further exploited in clinical strategies for ex vivo expansion.

overall_design: Human CD34+CD38-CD45RAlowCD90+ cord blood cells were cultured in vitro for 18 hrs with CCL28 and SCF or SCF alone.

first: Christine

last: Karlsson

first: Aurélie

last: Baudet

first: Natsumi

last: Miharada

first: Ann-Margreth

last: Carlsson

first: Jonas

last: Larsson


title: Expression data from U87-2M1 glioma cells transduced with baculoviral control decoy vector or baculoviral miR-10b decoy vector

city: Singapore

first: Jia Kai

last: Lim

address: 31 Biopolis Way #04-01, Nanos

country: Singapore

institute: Institute of Bioengineering and Nanotechnology

summary:
MicroRNA-10b may target numerous genes in gliomagenesis. The target genes of miR-10b may differ according to the cellular context.
We used microarray analyses to determine the phenotypic effects and gene targets of miR-10b by silencing miR-10b in invasive U87-2M1 glioma cells.

overall_design: Early passage U87-2M1 cells treated with the baculoviral control decoy vector or miR-10b decoy vector were selected for RNA extraction and hybridization on microarray

first: Jiakai

last: Lin


title: Expression data from FDFT1 overexpression lung cancer cell lines.

first: Michael

last: Hsiao

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

department: Genomics Research Center

summary:
FDFT1 catalyzes the first reaction in the mevalonate/isoprenoid pathway, we demonstrated that FDFT1 down-regulation by two shRNAs significantly reduced cell migration and invasion in highly invasive lung cancer cell lines in vitro, as well as in lung metastases in vivo.
We used microarrays to detail the FDFT1 regulated gene expression underlying invasion-metastasis cascade and identified distinct classes of up-regulated genes during this process.

overall_design: Lung adenocarcinoma cells with FDFT1 overexpression were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Yi-Fang

last: Yang


title: Expression data from U87 glioma cells and U87-2M1 glioma cells

summary:
An experimental lung metastasis assay was used to derive an invasive subline of U87 that is metastatic in mice.
We used microarray analyses to find out over-represented gene ontologies that can explain the observed enhanced invasiveness of U87-2M1 cells.

overall_design: Early passage U87-2M1 cells and parental U87 glioma cells from ATCC were selected for RNA extraction and hybridization on microarray


title: Effects of silencing miR-10b in an U87-2M1 glioma line - an invasive in vivo derived subline of U87 glioma cells


title: Profiling of p53-responsive genes in human breast cancer cells harboring endogenous ts-p53 E285K

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary: The ts-p53 E285K protein is a rare p53 mutant with temperature-sensitive (ts) loss of function characteristics. In cancer cells, which express ts-p53 E285K intriniscally, endogenous wild type p53 activity is reconstituted by appropriate cultivation temperature (permissive condition). At non-appropriate cultivation temperature (restrictive condition) this p53 mutant is inactive. The present study took advantage of this mechanism and employed IPH-926 lobular breast cancer cells and BT-474 ductal breast cancer cells, which both harbor endogenous ts-p53 E285K, for the transcriptional profiling of p53-responsive genes. This new approach eliminated the need for genetic modification or cytotoxic stimulation to achive a p53 response in the cells being investigated .

overall_design:
Three subseqent passages of IPH-926 lobular breast cancer cells (harboring ts-p53 E285K) were seeded into two parallel culture dishes each and were allowed to adopt to restrictive and permissive condition for 24 h before analysis on Affymetrix U133 Plus 2.0 microarrays. Subsequently, this experiment was repeated with BT-474 ductal breast cancer cells (also harboring ts-p53 E285K). To gate out non-specific temperature effects, the same experiment was also performed with MCF-7 breast cancer cells (harboring wt p53). Probe sets differentially expressed at restrictive versus permissive condition in MCF-7 were considered as non-specifically regulated. These probe sets were excluded from the final statistical analysis of  IPH-926 and BT-474 expression data.
response to restored p53 activity

first: R

first: M

last: Christgen

first: U

last: Lehmann


title: PBEF Knockdown in HMVEC-LBI

city: Kansas City

first: Shui

last: Ye

state: MO

address: 2401 Gillham Road

department: Medical Genetics Research

institute: Children's Mercy Hospital

summary: This study employed Affymetrix GeneChips to profile transcriptome of human pulmonary microvascular endothelial cells (HMVEC-L) treated with PBEFsiRNA to gain insight into transcriptional regulations of PBEF on the endothelial function. We isolated and labeled mRNAs from PBEF siRNA transfected HMVEC-L and hybridized them to Affymetrix GeneChip HG-U133 plus 2. Differentially expressed genes and canonical pathways were analyzed. Expressions of selected genes were validated by RT-PCR or western blotting. Several important themes are emerged from this study. First, PBEF induces the upregulation and downregulation of multiple genes in the endothelium. Expression of 373 genes were increased and 64 genes decreased by at least 1.3 fold in the PBEFsiRNA treated group compared to the control group of PBEFscRNA treated HMVEC-L. Second, the microarray results confirmed some previous reports of PBEF mediated gene expressions in some pathways but provided a more complete repertoire of molecules in those pathways. Third,  most of affected canonical pathways or differentially expressed genes in PBEF siRNA treated HMVEC-L over their controls  have not previously been reported to be PBEF-responsive. Our first transcriptome analysis of human pulmonary microvascular endothelial cells treated with PBEFsiRNA has provided important insights into the transcriptional regulation of gene expression in HMVEC-L cells by PBEF. Further in-depth follow-up analysis of the transcriptional regulation reported in this study may shed light on molecular mechanisms underlying PBEF mediated endothelial functions and dysfunctions in the physiology and the pathogenesis of inflammatory conditions, cancer, diabetes, coronary heart disease and provide new leads of therapeutic targets to those diseases.

overall_design: 6 sample microarray study - 3 replicates of the PBEF knockdown and 3 replicates of the SC RNA.

first: S


title: Expression data from serum-stimulated NIH 3T3 cells stably expressing control (pLKO.1) vector or shRNAs targeting Net or Sap-1

city: Philadelphia

first: Michele

last: Wozniak

address: 210 S. 33rd St., 510 Skirkanich

department: Bioengineering

institute: University of Pennsylvania

summary: Although much is known about focal adhesion signaling induced by cell adhesion, how adhesion directs changes in transcription to control cell behavior is far less understood.  Here we describe a novel mechanism by which changes in adhesion switch the activities of the mitogen-activated protein kinases (MAPKs) c-Jun N-terminal kinase (JNK) and p38, resulting in the differential activation and promoter occupancy of the SRF cofactors, the ternary complex factors (TCFs) Sap-1 and Net.  Adhesion-induced MAPK/TCF switching controls immediate early gene expression and proliferation.  This mechanism is of physiological relevance, as proliferative regulation by the TCFs is conserved in an ex ovo model of angiogenesis.  Furthermore, microarray analysis identified novel genes and adhesive functions regulated by Sap-1 and Net.  Thus our data identify the TCFs as key regulators of adhesion-induced transcription and cell behavior.

overall_design: [mRNA profiling]: NIH 3T3 cells were plated on fibronectin-coated plastic for two hours, then rinsed with PBS and serum-starved overnight.  20% bovine serum was then added to the cells for one hour.  Cells from three biological replicates were lysed and RNA extracted with a Qiagen RNeasy mini kit and prepared for hybridization on Affymetrix GeneChip Mouse Gene 1.0 ST microarrays.

middle: A

first: Christopher

middle: S

last: Chen


title: Characteristic expression of major histocompatibility complex and immune privilege genes in human pluripotent stem cells and the derivatives

first: Chun

middle: Ying

last: Yu

address: 128 Academia Road, Section 2

department: Genomic Research center

institute: Academia sinica

summary: Pluripotent stem cells, including human embryonic stem (hES) and induced pluripotent stem (hiPS) cells, have been regarded as useful sources for cell?based transplantation therapy. However immunogenicity of the cells remains the major determinant for successful clinical application. We report the examination of several hES cell lines (NTU1 and H9), hiPS cell lines, and their derivatives (including stem cell?derived hepatocytes) for the expression of major histocompatibility complex (MHC), natural killer (NK) cell receptor (NKp30, NKp44, NKp46) ligand, immune?related genes, human leukocyte antigen (HLA) haplotyping, and the effects in functional mixed lymphocyte reaction (MLR). Flow cytometry showed lower levels (percentages and fluorescence intensities) of MHC class I (MHC?I) molecules, β2?microglobulin and HLA?E in undifferentiated stem cells, but the levels were increased after co?treatment with interferon gamma and/or in vitro differentiation. Antigen presenting cell markers (CD11c, CD80 and CD86) and MHC?II (HLA?DP, DQ and DR) remained low throughout the treatments. Recognitions of stem cells/derivatives by NK lysis receptors were lower or absent. Activation of responder lymphocytes was significantly lower by undifferentiated stem cells than by allogeneic lymphocytes in MLR, but differentiated NTU1 hES cells induced a cell number?dependent lymphocyte proliferation comparable with that by allogeneic lymphocytes. Interestingly activation of lymphocytes by differentiated hiPS cells or H9 cells became blunted at higher cell numbers. Real?time RT?PCR showed significant differential expression of immune privilege genes (TGF?β2, Arginase 2, Indole 1, GATA3, POMC, VIP, CALCA, CALCB, IL?1RN, CD95L, CR1L, Serpine 1, HMOX1, IL6, LGALS3, HEBP1, THBS1, CD59 and LGALS1) in pluripotent stem cells/derivatives when compared to somatic cells. It is concluded that pluripotent stem cells/derivatives are predicted to be immunogenic, though evidences suggest some levels of potential immune privilege. In addition, differential immunogenicity may exist between different pluripotent stem cell lines and their derivatives

overall_design: Confirmed hiPSC cells and their parental cells were selected for RNA extraction and Affymetrix array analysis. To minimize the clone variation, we selected two clones from each type of iPSC.

first: H

middle: F

last: Kuo

middle: N

last: Ho

first: C

middle: Y


title: Alterations of methylome and transcriptome in human melanoma: the inverse relationship between epigenome integrity and BRAF mutation

city: Duarte

first: Arthur

last: Li

address: 1500 E Duarte Rd

institute: City of Hope

summary: Melanoma is the deadliest form of skin cancer with rising incidence and mortality rates. Oncogenic mutation in BRAF gene is the single most frequent genetic alteration in human melanoma; however, this event per se is not sufficient to produce melanoma in vivo. We have investigated whether epigenetic changes, specifically aberrant DNA methylation and dysregulation of gene expression, alone or in combination with this genetic event, are involved in the genesis of human melanoma. We have constructed the whole ‘‘of primary human melanomas in relation to their BRAF mutational status. Our methylation profiling identified a large number of hyper- or hypomethylated genes in melanoma tumors, many of which being novel and having the potential to serve as biomarkers. Gene ontology analysis revealed that gene categories involved in neuronal cell morphology and development, and skin and neurological disorders were highly enriched. Frequently methylated targets included developmental regulatory transcription factors and homeobox genes, which are mostly subjected to bivalent histone marking and Polycomb occupancy in embryonic stem cells. Notably, several genes involved in the MEK-ERK and the PI3K pathways, two of the most frequently perturbed pathways in human melanoma, showed extensive methylation changes. Gene expression profiling identified a long list of dysregulated genes, many of which being involved in melanocytes development and differentiation, and showing concomitant aberrant DNA methylation. Sub-typing of the melanoma tumors based on BRAF mutational status revealed that tumors with a mutated BRAF had distinctive and more pronounced changes in both DNA methylation and gene expression profiles than tumors carrying the wildtype BRAF. The differentially compromised methylome and transcriptome of melanomas (dependent on BRAF mutation) deserves special attention because many epigenetic alterations, including DNA methylation-mediated regulation of gene expression, are potentially reversible. The dichotomous integrity of epigenome in human melanoma holds great promise for the field of personalized medicine.

overall_design: Methylome: Eleven primary human melanoma speciemens versus five normal human melanocyte samples. Transcriptome: Ten primary human melanoma speciemens versus four normal human melanocyte samples

first: Stella

last: Tommasi

first: Albert

last: Zheng

middle: X

first: Xiwei

last: Wu

first: Ahmad

last: Besaratinia


title: NF-kB2 mutation targets survival, proliferation and differentiation pathways in the pathogenesis of B-lineage lymphomas

city: Augusta

first: Brian

last: McCarthy

state: GA

address: 1410 Laney Walker Blvd.

department: Cancer Center

institute: Georgia Health Sciences University

summary: Abnormal NF-kB2 activation has been reported in several types of human leukemia and lymphomas although the exact mechanisms and affected pathways are not clear. We have investigated these questions through the use of a unique transgenic mouse model with lymphocyte-targeted expression of p80HT, a lymphoma associated NF-kB2 mutant. Microarray analysis, verified at the RNA and protein level identified new downstream targets and confirmed established regulatory networks. 201 genes were significantly changed, with 126 being upregulated and 75 downregulated. Pathway analysis uncovered both known and unknown interactions between factors important in the development of human B cell lymphomas and multiple myeloma, including cyclins D1 and D2, TRAF1, CD27, BIRC5/survivin, IL-15 and IL-10. Critical roles for STAT3 and TNF receptors are highlighted. Six target genes of STAT3 were identified: cyclins D1and D2, IL-10, survivin, IL-21 and Blimp1. Interfering with STAT3 signaling induced apoptosis in multiple myeloma cell lines. Novel pathways for NF-kB2 are proposed that involve IL-10 and other genes in the differentiation of plasma cells, evasion of apoptosis and proliferation. These pathways were verified with publically available human microarrays. Several treatment strategies based on these findings are discussed.

overall_design: RNA was isolated from the B cells of p80HT transgenic mice on the C57BL/6J x SJL/J background , which produced serum monoclonal immunoglobulin (M-protein) (n=3), and the B cells from wild type (WT) littermates (n=3) using Trizol reagent according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA). RNA was further prepared with the Ambion WT Expression kit (Life Techologies Corp., Carlsbad, CA) then run on the Mouse Gene 1.0ST microarray chip (Affymetrix, Santa Clara, CA).

first: Han

last: Ding


title: DNA methylation data from human lymphoblasts [Illumina]

status: Public on Dec 28 2012

city: Iowa City

first: Jeffrey

last: Plume

state: IA

address: 500 Newton Rd.

department: Psychiatry

institute: University of Iowa

summary: DNA methylation profiling of IAS subjects

overall_design: Lymphoblasts RNA isolated from Iowa Adoption Study participants to compare the relationship between DNA methylation and gene expression on a genome-wide scale

middle: M

first: Robert

last: Philibert


title: Expression data from human mesenchymal stem cell and osteosarcoma cells

status: Public on Dec 30 2012

first: Lingtao

address: 4650 Sunset Blvd.

department: Children hispotial of Los angeles, Dept. of Pathology, MS# 103

institute: University of Southern California

summary:
To determine whether enhanced self-renewal and tumorigenicity in UT2 cells (derived from the second human–mouse xenotransplantation of U2OS cell-formed osteosarcoma tissues) correlate with increased expression of stem/progenitor cell-associated genes, we measured global gene expression in MSC, U2OS and UT2 cells by microarray analysis.
Compared to U2OS and MSC, molecules involved in regulation of self-renewal signaling pathways of cancer stem cells were also up-regulated in UT2 cells, including those in the Notch, Wnt, and TGF-beta pathways. These data suggest a genetic basis for the enhanced self-renewal and tumorigenicity of osteosarcoma-initiating cell in UT2 cells.

overall_design: MSC, U2OS and UT2 cells were selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to analysis stem/progenitor cell-associated genes and molecules involved in regulation of self-renewal signaling pathways of cancer stem cells between UT2 cells and its parent cells: U2OS (MSC works as positive control here).


title: Expression data from human lymphoblasts [Affymetrix]

summary: Transcriptional profiling of IAS subjects


title: A cross platform genome wide comparison of the relationship of promoter DNA methylation to gene expression


title: A systems approach identifies progeroid Ercc1[-/Δ] mice as a model system for kidney aging.

status: Public on Dec 21 2012

city: Koeln

first: Bernhard

last: Schermer

address: Kerpener Str. 62

department: Dept. II for Internal Medicine

institute: Universitaet zu Koeln

summary: Using these samples, it has been shown that the transcriptional landscape in glomeruli of Ercc1[-/Δ] mice at a rather young age of 14 weeks mimics that of mice which have undergone real-life renal aging. Thus, young Ercc1[-/Δ] mice can be used as a model system for glomerular aging in future studies.

overall_design: The RNAs origin from glomerular tissues of mice of 2 distinct genotypes at 3 distinct stages of age. Between 3 and 6 replicates have been prepared per group.

first: Valerie

last: Bartels

first: Peter

last: Frommolt

first: Bianca

last: Habermann

first: Joachim

last: Schultze

first: Marianne

last: Roodbergen

first: Jan

middle: H

last: Hoeijmakers

first: Björn

last: Schumacher

last: Nürnberg

first: Martijn

last: Dollé

first: Thomas

last: Benzing

first: Roman-Ulrich

last: Müller

first: Christine

last: Kurschat


title: Expression data from active human umbilical cord mesenchymal stem cell (active HUMSC) and inactive human umbilical cord mesenchymal stem cell (inactive HUMSC)

city: Taipei

first: Kuo-Ching

last: Chao

address: 252, Wu Hsing Street

department: Department of Internal Medicine

institute: Taipei Medical University Hospital

summary:
Active HUMSC with distinct binding rate to MDA MB-231 breast cancer cells, distinct ability in suppressing tumorigenesis,distinct cell in cell features and distinct features under TEM then inactive HUMSC
We used microarrays to detail the difference gene expression between active HUMSC and inactive HUMSC

overall_design: HUMSC with high MDA MB-231 breast cancer cells suppression rate was selective as active HUMSC and HUMSC with low MDA MB-231 breast cancer cells suppression rate was selective as inactive HUMSC


title: Gene expression changes following knockdown of Kdm2b on mESCs

status: Public on Dec 26 2012

city: Sheffield

first: Ian

last: Sudbery

address: Firth Court, Western Bank

department: Molecular Biology and Biotechnology

institute: University of Sheffield

summary:
In order to study the effects of Kdm2b binding at CpG islands, Kdm2b was knocked down in mouse embryonic stem cells using shRNA and gene expression profiled using Affymetrix arrays
Depletion of KDM2B affects the gene expression of a subset of polycomb targets

overall_design: RNA from 4 samples stably expressing shKdm2b and 4 samples stably expressing a control shRNA was hybridized to Affymetrix Mouse Gene 1.0 ST Arrays

middle: J

last: Klose

first: Anca

last: Farcas

first: Sheena

last: Lee


title: Gene expression profile of Hodgkin’s lymphoma cells after knock-down of PRAME

city: Halle (Saale)

first: Martin

middle: Sebastian

last: Staege

state: Sachsen-Anhalt

address: Ernst-Grube-Str. 40

department: Universitätsklinik u. Poliklinik für Kinder- u. Jugendmedizin

summary:
By using high-density DNA microarrays, we analyzed the gene-expression profile of Hodgkin's lymphoma cell line L-428 after knock-down of the tumor antigen PRAME (preferentially expressed antigen in melanoma)
Kewitz and Staege, submitted

overall_design: RNA was extracted from established Hodgkin's lymphoma cell line L-540 and hybridized with Affymetrix HG_U133A microarrays.

first: Stefanie

last: Kewitz


title: Stau2 RIP-Chip in Mouse E13-14 Cortex

city: Rensselaer

first: Sridar

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary:
The double-stranded RNA binding protein Staufen2 (Stau2) is asymmetrically localized and segregated during asymmetric cell divisions in the developing mouse cortex and promotes intermediate progenitor cell fate.
We carry out RNA immunoprecipitation with a Stau2 specific antibody, followed by microarray analysis to identify Stau2 assoicated RNAs that may be shuttled asymmetrically into one daughter cell thus affecting cell fate.

overall_design: Cortex was dissected from E13-14 timed-pregnant Swiss Webster Mice (Taconic) and RNA immunoprecipitation followed by microarray analysis was carried out to identy Stau2 associated RNA cargos.

first: Gretchen

last: Kusek

first: Sally

last: Temple

first: Scott

last: Tenenbaum


title: Role of TAZ as mediator of Wnt signaling (SW480)

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

summary:
To investigate the role of TAZ downstream of the abberrant Wnt signaling in CRC cells, we compared the expression profiles of parental SW480 cells (empty vector) transfected with siControl, siTAZ, sibeta-catenin or reconstituted with wild type APC and transfected with siControl

Keywords: expression profiling by array

overall_design: We collected RNA from parental SW480 cells (empty vector) transfected with siControl, siTAZ, sibeta-catenin or from SW480 cells reconstituted with wild type APC and transfected with siControl. Cells were left untreated in normal culturing conditions before harvesting. Samples were then processed for total RNA extraction and hybridization on Affymetrix microarrays. Four biological replicas (A, B, C, D) were used for each of the 4 conditions (1: siControl, control cells; 2: siTAZ cells; 3: sibeta-catenin (sibcat) cells; 4.APC reconstituted cells) for a total of 16 samples.

first: Luca

last: Azzolin

first: Francesca

last: Zanconato

first: Silvia

last: Bresolin

first: Mattia

last: Forcato

first: Giuseppe

last: Basso

first: Michelangelo

last: Cordenonsi

first: Stefano

last: Piccolo


title: Expression data from AML1-ETO (AE)-expressing murine bone marrow (BM) cells treated with retinoids

status: Public on Dec 25 2012

city: East Melbourne

first: Lynette

last: Chee

address: A'Beckett Street

department: Research

country: Australia

institute: Peter MacCallum Cancer Centre

summary: AE-expressing murine BM cells treated with all-trans retinoic acid (ATRA) in semi-solid methycellulose-based cultures show an increase in self-renewal capacity whilst treatment with a specific RARa agonist NRX195183 reduces their clonogenicity. Gene expression analysis was performed to further investigate the molecular mechanisms underlying these observations. Upregulated gene sets were identified in the ATRA-treated AE BM cells.

overall_design: 3 C57Bl/6 AML1-ETO-stop/+/Mx-Cre+ mice (#D203, 218 and 220) were treated with polyI:C to excise the stop codon allowing AML1-ETO expression. 2-4 weeks following completion of polyI:C administration, mice were euthanised and BM cells harvested. BM cells were cultured in semi-solid methylcellulose assays with cytokines for 2 weeks; then cells were harvested, pooled and replated in suspension cultures containing cytokines and the respective treatments - DMSO (control), ATRA and the specific RARa agonist NRX195183. At the 8 hour (8H) and 24 hour (24H) timepoints, cells were harvested for RNA extraction and processing.

first: Jason

last: Ellul


title: Expression data from murine liver tissue upon depletion of regulatory T cells

city: Zurich

first: Stefan

last: Zoller

address: Universitatstrasse 16

department: Genetic Diversity Centre

country: Switzerland

institute: ETH Zurich

summary:
Regulatory T cells (Treg) play a pivotal role in modulating immune responses and were shown to decrease atherosclerosis in murine models. How this effect is brought about remains elusive.
We used microarrays to detail the global programme of gene expression in liver tissue from chimeric DEREG x Ldlr-/- mice +/- diphteria toxin enabling selective depletion of Treg.

overall_design: Chimeric DEREG x Ldlr-/- mice were kept on a high fat diet for 8 weeks and treated with DT (vehicle) or PBS (placebo) i.p. for 8 weeks. Upon harvest, liver tissue was ascertained from animals from both groups and a gene array was performed.

first: Roland

last: Klingenberg


title: Expression data of treated LNCaP-abl cells

city: New York

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary:
We introduce a family of multivalent peptidomimetic conjugates that modulate the activity of the androgen receptor (AR). Bioactive ethisterone ligands were conjugated to a set of sequence-specific peptoid oligomers. Certain multivalent peptoid conjugates enhance AR-mediated transcriptional activation. We identify a linear and a cyclic conjugate that exhibit potent anti-proliferative activity in LNCaP-abl cells, a model of therapy-resistant prostate cancer. The linear conjugate blocks AR action by competing for ligand binding. In contrast, the cyclic conjugate is active despite its inability to compete against endogenous ligand for binding to AR in vitro, suggesting a non-competitive mode of action. These results establish a versatile platform to design competitive and non-competitive AR modulators with potential therapeutic significance.
We use microarray analysis to further elucidate the mechanism of AR antagonism and show that the compounds (cyc and n=8) are distinct.

overall_design:
We used microarray analysis to see genone-wide effects on LNCaP-abl cells with moduators of AR activity
LNCaP-abl cells were treated with compound and RNA was extracted and hybridized on Affymetrix microarrays

Treatments:
Vehicle is just Ethanol treated LNCaP-abl cells that were used as a control.
n=8 and cyc are peptoid conjugates that modulate AR activity. n=8 is linear and cyc is a cyclic compounds.  We wanted to look at gene expression when LNCaP-abl cells were treated with these compounds to show that they are distinct.
C3 is a small molecule that inhibits the interaction between AR and beta-catenin (co-regulator protein). Initial results with this compound show potent anti-proliferative activity in LNCaP-abl cells and we wanted to further investigate the mechanism of action of this compound.

first: Kent

last: Kirshenbaum

first: Paul

last: Levine


title: Noggin vs BMP4 overexpression Epidermis

first: Sridar

last: Chittur

summary:
The study was performed to determine if there were alterations in the total RNA pool among the epidermal keratinocytes of K14 promotor-driven noggin overexpression compared with K14 promotor-driven BMP4 overexpression transgenic animals, which will directly relate to cellular chemistry and immune and sensory function. The total study is also aimed at determining alterations of transcrption factors and/or regulation of gene function, including methylation states and micro RNA control in keratinocytes following sensory challenge, particularly neuropathic and chronic pain conditions.

Keywords: Comparison of RNA expression between BMP4-oex and Nog-oex transgenic epidermal keratinocytes

overall_design: Eight-ten epidermis strips were laser captured per animal, and six (6) animals were used per transgenic condition. Recovered RNA samples were pooled from 2 groups of 3 noggin transgenics and 2 groups of 3 BMP4 transgnics to create four pools for hybridization.

first: Frank

middle: L

last: Rice

first: Phillip

last: Albrecht


title: Kidney transplantation (Affymetrix set)

city: Stanford

first: Minnie

last: Sarwal

address: 703 Welch Road

department: Pediatric Nephrology

institute: Stanford University

summary: In this study, we examined transcriptional profiles from 3 different microarray platforms, across 103 peripheral blood samples with and without acute rejection, to find a critical gene-set for the diagnosis of acute renal rejection that matched biopsy diagnosis, irrespective of patient demographics, clinical confounders, concomitant infection, immunosuppression usage or sample processing methods. We hypothesized that changes in peripheral blood expression profiles correlate with biopsy-proven rejection, and that these changes could be used as biomarkers for the diagnosis and prediction of acute rejection.

overall_design:
We performed cross-sectional microarray analysis of 103 matched peripheral blood samples collected at a single time point, timed with a biopsy where acute rejection was either confirmed as present (60 AR samples) or absent (62 STA samples). The samples were hybridized to one of 3 microarray platforms: Affymetrix (n=75 the 54K HG-U133_Plus2 Array), Agilent (n=26, 44K oligo Array) and cDNA array (n=21, ~30K cDNA). Of 103 samples, 14 were used on both Affy and Agilent arrays; 1 was used in cDNA and Agilent array and 2 were used across 3 array platforms. Microarray data generated from 3 array platforms were cross-compared, by mapping common and overlapping transcripts to Human Gene Organization (HUGO) gene names. Significant gene lists on each platform were identified using Significant Analysis of Microarray (SAM, ref) with a common significance threshold of a false discovery rate (FDR) of <10%.This set contains the data for samples hybridized to Affymetrix arrays.
Disease State: Acute Rejection (AR#sampleid) or Stable (S#sampleid) samples


title: Expression data from breast cancer tumor-initiating cells

city: Penzberg

first: Helmut

last: Burtscher

address: Nonnenwald 2

institute: Roche Pharma

summary: We have generated tumorigenic (S2N) and non-tumorigenic (S2), normal-like to basal-like breast cancer cell lines from primary tumors. At high in vivo inoculation cell numbers of 10^6 cells/mouse both S2N and S2 monolayer as well as sphere culture cells grew at similar rates. However, at low inoculation cell numbers down to 10^3 cells only S2N sphere cells generated xenograft tumors. mRNA profiling revealed a unique cluster pattern of the tumorigenic S2N sphere cells, but a detailed analysis of TIC relevant transcription factors like Oct3, Sox and Nanog family members, Myc, Slug or Twist1 revealed no consistently  increased  expression in the highly tumorigenic cell lines. Our data indicate that the intrinsic genetic and functional markers investigated are not solely indicative of the in vivo tumorigenicity of putative breast tumor-initiating cells.

overall_design: 4 samples with 3 replicates each


title: Kidney transplantation

summary:
In this study, we examined transcriptional profiles from 3 different microarray platforms, across 103 peripheral blood samples with and without acute rejection, to find a critical gene-set for the diagnosis of acute renal rejection that matched biopsy diagnosis, irrespective of patient demographics, clinical confounders, concomitant infection, immunosuppression usage or sample processing methods. We hypothesized that changes in peripheral blood expression profiles correlate with biopsy-proven rejection, and that these changes could be used as biomarkers for the diagnosis and prediction of acute rejection.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
We performed cross-sectional microarray analysis of 103 matched peripheral blood samples collected at a single time point, timed with a biopsy where acute rejection was either confirmed as present (60 AR samples) or absent (62 STA samples). The samples were hybridized to one of 3 microarray platforms: Affymetrix (n=75 the 54K HG-U133_Plus2 Array), Agilent (n=26, 44K oligo Array) and cDNA array (n=21, ~30K cDNA). Of 103 samples, 14 were used on both Affy and Agilent arrays; 1 was used in cDNA and Agilent array and 2 were used across 3 array platforms. Microarray data generated from 3 array platforms were cross-compared, by mapping common and overlapping transcripts to Human Gene Organization (HUGO) gene names. Significant gene lists on each platform were identified using Significant Analysis of Microarray (SAM, ref) with a common significance threshold of a false discovery rate (FDR) of <10%.This set contains the data for samples hybridized to Affymetrix arrays.
Refer to individual Series


title: CXCR4 activation maintains a stem cell population in tamoxifen-resistant breast cancer cells through AHR signaling

city: San Diego

first: John

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

summary: Targeting the estrogen signaling pathway has proved to be of great value in the treatment of human breast cancer. Tamoxifen, a selective estrogen receptor modulator (SERM), is the most widely used antiestrogen. However, only 40-50% of patients with estrogen receptor (ER) positive breast cancer benefit from tamoxifen treatment and 30-50% acquire resistance and the disease progresses. Continuous treatment with conventional therapy may contribute to cancer progression in recurring cancers through the accumulation of drug resistant cancer progenitors. We found that MCF7 tamoxifen-resistant (TAM-R) cells possess a significantly higher proportion of cancer progenitor cells than tamoxifen-sensitive MCF7 cells. Our results indicate that the chemokine receptor CXCR4 plays an important role in the maintenance of cancer progenitors in a tamoxifen-resistant cell line and downregulation of CXCR4 signaling by small molecule antagonists specifically inhibits growth of a stem-like cell population in tamoxifen-resistant tumors both in vitro and in vivo. Whole genome gene expression analysis revealed aryl hydrocarbon receptor (AhR) signaling as one of the top networks that is differentially regulated in MCF7(TAM-R) xenograft tumors treated with the CXCR4 antagonist AMD3100 as compared to MCF7 tumors. Further, small molecule antagonists of AhR signaling specifically inhibit the progenitor population in MCF7(TAM-R) cells suggesting that the aryl hydrocarbon receptor could be a putative target for the treatment of tamoxifen-resistant breast cancers. Introduction transplants remains limited by the ability to expand these cells ex vivo. An unbiased screen with primary human HSCs identified a purine derivative, StemRegenin 1 (SR1), that promotes the ex vivo expansion of CD34+ cells. Culture of HSCs with SR1 led to a 50-fold increase in cells expressing CD34 and a 17-fold increase in cells that retain the ability to engraft immunodeficient mice. Mechanistic studies show that SR1 acts by antagonizing the aryl hydrocarbon receptor (AHR). The identification of SR1 and AHR modulation as a means to induce ex vivo HSC expansion should facilitate the clinical use of HSC therapy.

overall_design: Tamoxifen resistant or sensitive xenografts; mice treated with estrogen and/or CXCR4 modulators

first: A

last: Dubrovska

last: Hartung

first: L

middle: C

last: Bouchez

first: J

first: C

last: Cho

first: P

middle: G

last: Schultz


title: Role of TAZ as mediator of Wnt signaling

first: Silvio

last: Bicciato

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

overall_design: Refer to individual Series


title: Expression profiles of leukemia cells of acute-type adult T-cell leukemia (ATL) patients

status: Public on Dec 20 2012

city: miyazaki city

first: kentarou

last: nagai

state: miyazaki

department: Miyazaki university

institute: biochemistry

summary: We recently mapped 605 chromosomal breakpoints in 61 ATL cases by spectral karyotyping and identified chromosome 14q11 as one of the most common chromosomal breakpoint regions. To map the precise location of chromosomal breakpoints at 14q11, we performed single-nucleotide polymorphism (SNP)-based comparative genomic hybridization on leukemia cells from acute-type ATL patients. The breakpoints accumulated frequently adjacent to the T cell receptor alpha/delta chain locus (TCRα/δ) with chromosomal deletions at 14q11 and a recurrent 0.9 Mb interstitial deletion was identified at a region including part of the TCRα/δ locus. Because leukemia-associated genes are frequently located near the breakpoint cluster regions, we then analyzed the gene expression profiles of ATL cells and identified N-myc downstream regulated gene 2 (NDRG2) as one of the genes that are down-regulated in ATLL cells among the 25 genes mapped to the region adjacent to the recurrently deleted regions at 14q11.

overall_design: We compared the gene expression profiles of ATL cells from seven acute-type ATL patients and CD4+ T lymphocytes from the peripheral blood of five healthy volunteers as references using oligonucleotide microarrays.

first: Kazuhiro

last: Morishita


title: Evolution of human-specific microRNA miR-941 [Ago2_IP]

city: shanghai

first: Song

last: Guo

address: 320 Yue Yang Road

country: China

institute: PICB

summary: miRNA-mediated gene expression silencing has previously been shown to be important for a variety of physiological and pathological processes. Here, we have explored the role of one bona fide human-specific miRNA (miR-941) in evolution of the human-specific expression and function. Using combination of high-throughput sequencing (GSE26545), miRNA transfection and large-scale PCR of various human populations, we have shown that emergence and rapid expansion of miR-941 might take place on the human evolutionary linage between six and one million years ago. Functionally, miR-941 could be associated with hedgehog and insulin signaling pathways, and thus might potentially play a role in evolution of human longevity. Human-specific effects of miR-941 regulation are detectable in human brain and affect genes involved in neurotransmitter signaling. Furthermore, emergence of miR-941 on the human evolutionary linage was accompanied by the accelerated loss of its binding sites. Taken together, these results strongly implicate the contribution of miR-941 in evolution of the human-specific phenotype.

overall_design: Ago2 Immunoprecipitation (Ago2-IP) experiments after miR-941 overexpression were conducted in 293T cell line. Briefly, All transfections were performed using human 293T cells cultured in 6-well tissue culture plates. Lipofectamine 2000 (Invitrogen) was used for a Synthetic miR-941 or a scrambled oligo transfection, at 30 nmol/l each (final concentration) per 1x106 cells/well of a 6-well plate using DharmaFECT (GE Healthcare). Total 5x106 cells were collected and subjected to Ago2 immunoprecipitation (Ago2-IP) using the RNA isolation kit Mouse Ago2 (Wako Chemicals) according to the manufacturer's instructions. For a negative control, immunoprecipitation was performed using nonimmune IgG beads prepared with the antibody immobilization bead kit (Wako Chemicals). The IP pull down RNA was used as template for an “in vitro” transcription reaction generating biotin-labeled antisense cRNA. The cRNA was analyzed on affymetrix Human Genome U133 Plus 2.0 arrays following the manufacturer’s instructions. R RMA package was used to quantify gene expression levels.

first: Haiyang

last: Hu

first: Philipp

last: Khaitovich


title: Molecular-genetic correlates of fatigue in cancer patients receiving localized external beam radiation therapy

city: Bethesda

first: Jennifer

last: Barb

address: 12 South Drive Bldg 12A Room 2001

department: DCB

institute: NIH

summary: The etiology behind cancer-related fatigue (CRF) is currently unknown. The physiological mechanisms of CRF are based on limited evidence that genetic factors, energy expenditure, metabolism, aerobic capacity, and the individual's immune response to inflammation are responsible for the experience of CRF. Gene expression profiling using microarray analysis from white blood cells of men with non-metastatic prostate cancer shows significant, differential expression of 463 probesets during localized external beam radiation therapy (EBRT). Pathway analysis shows a central role of SNCA (alpha-synuclein gene) among these differentially expressed probesets. Significant expression of SNCA was confirmed by qPCR (p<.001) and ELISA (p<.001) over time during EBRT. A significant correlation was noted between averaged fatigue scores and delta CT values of SNCA expression using confirmatory qPCR over time during EBRT (R=-.90, p=.006). Development of fatigue experienced by these men during EBRT may be mediated by SNCA expression. Pathways related to alpha-synuclein may serve as useful biomarkers to understand the mechanisms behind the development of fatigue.

overall_design: A longitudinal design exploring the association between changes in gene expression and fatigue symptoms of men with non-metastatic prostate cancer receiving external beam radiation therapy. Blood samples were collected from ten subjects at 7 timepoints for microarray analysis: baseline (before EBRT); days 1, 7, 14, 21, 42 of EBRT; and 30 days post-EBRT. Baseline data obtained from subjects were compared to data obtained from age-, race-, and gender-matched healthy controls.

first: Leorey

last: Saligan

first: Peter

last: Munson

first: Chao-Pin

last: Hsiao

first: Xiao-Min

last: Wang

first: Dan

first: Aradhana

last: Kaushal

first: Deborah

last: Citrin

first: Raymond

last: Dionne


title: Evolution of human-specific microRNA miR-941

sample_organism:
Macaca mulatta
Pan troglodytes
Homo sapiens


title: Evolution of human-specific microRNA miR-941 [miRNA transfection]

sample_organism:
Macaca mulatta
Homo sapiens

overall_design: miRNA transfection experiments were conducted in 6 cell lines: two human derived kidney cell lines (HEK and 293T), one human skin fibroblast cell line (HSF2), two macaque derived kidney cell lines (LLCMK2 and FrhK-4), and one macaque skin fibroblast cell line (MSF). Briefly, cells were plated in 0.5 ml of growth medium 24h prior to transfection without antibiotics. miR-941 mimics-Lipofectamine 2000 (Invitrogen) complexes were prepared freshly before transfection based on the manufacturer’s protocol. Cells were transfected in six-well plates using miRNA mimics-Lipofectamine 2000 with a final oligonucleotide concentration of 10nmol/L. In parallel, negative control transfections with mock oligonucleotides were conducted according to the manufacturer’s protocol. After 24h, cells were harvested and total RNA were extracted using Trizol reagent (Invitrogen) and further processed and hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays following the manufacturer’s instructions. The R RMA package was used to quantify gene expression levels.


title: A tRNA-derived microRNA modulates the DNA damage response and is downregulated in B cell lymphoma

status: Public on Dec 19 2012

first: Roy

middle: Louis

last: Maute

address: 1130 St. Nicholas Ave., ICRC 507

department: Institute for Cancer Genetics

institute: Columbia University

summary: Sequencing studies from several model systems have suggested that diverse and abundant small RNAs may derive from tRNA, but the function of these molecules remains undefined.  Here we demonstrate that one such tRNA fragment, cloned from human B cells and designated CU1276, in fact possesses the functional characteristics of a microRNA, including a DICER1-dependent biogenesis, physical association with Argonaute proteins, and the ability to repress mRNA transcripts in a sequence-specific manner.  The gene expression profiling undertaken for this study was done in order to assay mRNA-level changes in 293T cells upon modulation of CU1276 levels, and thereby to identify direct targets of this sequence.  Ultimately, we fully validated the endogenous gene RPA1 as a CU1276 target.

overall_design: This study includes four biological replicates each of the following groups:  293T transiently transfected with empty vector, 293T transiently transfected with chr1.tRNA68-Gly(GCC) expressing vector, and 293T transiently transfected with CU1276 hairpin expressing vector.

first: Christof

last: Schneider

first: Pavel

last: Sumazin

first: Antony

last: Holmes

first: Andrea

last: Califano

first: Katia

last: Basso

first: Riccardo

last: Dalla-Favera


title: CD4+ and CD8+ T cells responding to LCMV-Armstrong or LCMV-Clone 13

city: Philadelphia

first: E

middle: John

last: Wherry

address: 421 Curie Blvd.

institute: University of Pennsylvania


title: Expression data from 4T1 cells cultured with 3mM glucose and 20mM lactic acid

city: Hangzhou

first: Zonghui

last: Ding

state: Zhejiang

address: 88 Jiefang Road

institute: Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine

summary:
Via aerobic glycolysis-Warnburg effect, cancer cells can convert 85-90% of glucose they acquire to lactic acid, which is thus ubiquitously abundant in solid tumor environment. We also observed that lactic acid effectively rescues cancer cells from glucose staration.
In order to understand the biological function of lacitc acid, we did the microarrays.

overall_design: murine breast cancer 4T1 cells were incubated in RPMI-1640 containing 3mM glucose and 20mM lactic acid for 1 day, 3 days, 4 days, 5 days, 7 days, 9 days and 11 days. 4T1 cells were incubated in RPMI-1640 containing 3mM glucose as control. We extracted the RNA and hybridized on the microarrays. We sought to obtain temporal genes that prolonged the cell life with lactic acid during the glucose starvation.

first: Hao

last: Wu

first: Xun

last: Hu


title: Whole genome expression in human tissues

city: Tokyo

first: Fuyuki

last: Miya

address: 35 Shinanomachi, Shinjuku-ku

department: School of Medicine

institute: Keio University

type: Expression profiling by genome tiling array

type: Non-coding RNA profiling by genome tiling array


title: Role of TAZ as mediator of Wnt signaling (MII)

first: Silvio

last: Bicciato

summary:
To investigate the role of TAZ downstream of APC and beta-catenin in mammary epithelial cells cells, we compared the expression profiles of MCF10-T1k (MII) cells transfected with siControl, siAPC, siAPC+siTAZ, sibeta-catenin, or sibeta-catenin+siTAZ.

Keywords: expression profiling by array

overall_design: We collected RNA from MII cells transfected with siControl, siAPC, siAPC+siTAZ, sibeta-catenin, or sibeta-catenin+siTAZ. Cells were left untreated in normal culturing conditions before harvesting. Samples were then processed for total RNA extraction and hybridization on Affymetrix microarrays. Four biological replicas (A, B, C, D) were used for each of the 5 conditions (1: siControl, control cells; 2: siAPC cells; 3: siAPC+siTAZ cells; 4: sibeta-catenin (sibcat) cells; 5: sibeta-catenin+siTAZ) for a total of 20 samples.

first: Luca

last: Azzolin

first: Francesca

last: Zanconato

first: Silvia

last: Bresolin

first: Mattia

last: Forcato

first: Giuseppe

first: Michelangelo

last: Cordenonsi

first: Stefano

last: Piccolo


title: Expression data from fibroblast-like synoviocytes (FLS) transfected with mimic-miR-23b or mimic-NC

city: Shanghai

last: Shen

address: 145 Shan Dong Middle Road

department: Department of Rheumatology

institute: Renji Hospital, JiaoTong University School of Medicine

summary:
We found microRNA miR-23b was down-regulated in local inflammatory tissues of autoimmune disease such as RA, SLE and related mouse models such as CIA, lpr, EAE. Re-expression of miR-23b significantly inhibits autoimmune pathogenesis of CIA, Lpr and EAE.
To identify potential targets of miR-23b, we use microarray gene-expression analysis to identify transcripts which could be repressed by miR-23b.
RA: rheumatoid arthritis,  CIA: Collagen-induced arthritis, SLE: systemic lupus erythematosus, EAE: experimental autoimmune encephalomyelitis

overall_design: We tansfected fibroblast-like synoviocytes (FLS) with mimic-miR-23b or mimic-NC.Cells were collected and total RNA was extracted for the Affymetrix GeneChip® Human Genome U133 Plus 2.0 Array

first: Wen

last: Pan

first: Shu

last: Zhu

first: Youcun

last: Qian


title: The effect of Crem absence on gene expression in mouse

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana


title: Lentiviral vector-based insertional mutagenesis identifies new clinically relevant cancer genes involved in the pathogenesis of hepatocellular carcinoma

city: Milan

first: Marco

last: Ranzani

address: via olgettina 58

department: TIGET

institute: HSR-TIGET

summary: We devised a novel insertional mutagenesis approach based on lentiviral vectors to induce hepatocellular carcinoma in three mouse models and identified four novel cancer initiating genes. Two genes are the well characterized Braf and Sos1, while the other two are Fign, encoding an AAA ATPase whose functions are poorly understood, and the complex Dlk1-Dio3 imprinted region which has been recently implicated in cancer and stemness. Activation of Fign or Braf and upregulation of the Dlk1-Dio3 imprinted region are functionally interconnected and may altogether control cell transformation, stemness and energy metabolism. Moreover, all the genes identified play a relevant role in human hepatocarcinogenesis as their expression levels and/or transcriptional signatures induced by their deregulation predict a different clinical outcome in hepatocellular carcinoma patients. These series consists of  mRNA expression microarray data (The GeneChip® Mouse Gene 1.0 ST Array, Affymetrix) from 8 non-tumoral liver and 21 hepatocellular carcinoma induced by insertional mutagenesis.

overall_design: LV.ET.LTR was administered to newborn mice with 3 different genetic backgrounds. Hepatocellular carcinomas were induced in all the mouse models. Vector integrations were retrieved form each single liver mass. From 21 liver masses, RNA was collected to perform whole transcriptome analysis.

first: Daniela

last: Cesana

first: Cynthia

last: Bartholomä

last: Sanvito

first: Mauro

last: Pala

first: Fabrizio

last: Benedicenti

first: Pierangela

last: Gallina

first: Lucia

last: Sergi

first: Stefania

last: Merella

first: Alessandro

last: Bulfone

first: Claudio

last: Doglioni

first: Christof

last: VonKalle

first: Yoon

last: Kim

first: Manfred

last: Schmidt

first: Giovanni

last: Tonon

first: Luigi

last: Naldini

first: Eugenio

last: Montini


title: Gene expression and methylation profiling in primary AML cells treated with decitabine and cytarabine

status: Public on Dec 18 2012

city: StLouis

first: Nobish

last: Varghese

address: 4444 Forest Park Ave.

institute: Washington University in St.Louis


title: Nuclear protein (Nupr)-1 is required for pancreatic adenocarcinoma development in Pdx1-cre;LSL-KrasG12D;Ink4a/Arffl/fl mice

status: Public on Dec 16 2012

city: Quebec

first: Ezequiel

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

summary: Nuclear Protein 1 (Nupr1) is a major actor of the cell stress response required for KrasG12D-driven formation of pancreatic intraepithelial neoplastic (PanINs) lesions in mice. We investigated the impact of Nupr1-depletion on the development and biology of murin pancreatic adenocarcinomas (PDAC) in the Pdx1-cre;LSL-KrasG12D;Ink4a/Arffl/fl (KIC) mice. We found that only one half of Nupr1-deficient mice developed PDAC. This is related to increased caspase 3 activity and low IER3 expression in Nupr1-deficient;KIC in the pancreas. Moreover, when Nupr1-deficient;KIC mice do develop PDAC, tumors present with impaired epithelial-to-mesenchymal transition (EMT). Transcriptoma analysis revealed that Nupr1-deficient and Nupr1wt;KIC PDACs presented enrichment of gene signatures of the human classical- and quasi-mesenchymal (QM)-PDAC respectively. Moreover, Nupr1-deficient;KIC PDACs shared with human classical-PDACs overexpression of Kras-activation genes. In addition, cells derived from Nupr1-deficient;KIC PDACs formed fewer microspheres in vitro compared to Nupr1wt;KIC cells, indicative of stemness impairment in the absence of Nupr1. Finally, we found that Nupr1-deficient;KIC cells were more sensitive to some anticancer drugs than their Nupr1wt counterpart. Hence, this study establishes the pivotal role of Nupr1 in PDAC progression after PanIN and in PDAC EMT in vivo, with an impact in PDAC cell stemness. As a consequence, according to absence or presence of Nupr1, KIC mice develop tumors that phenocopy human classical- or QM-PDAC, respectively, thus becoming attractive models for preclinical drug trials.

overall_design: We investigated the impact of the homozygous deletion of the Nupr1 gene on pancreatic adenocarcinoma development and biology in the Pdx1-cre;LSL-KrasG12D;Ink4a/Arffl/fl (KIC) mouse model.

first: Carla

middle: E

last: Cano

first: Tewfik

last: Hamidi

first: Maria

last: Garcia

first: Daniel

last: Grasso

first: Céline

last: Loncle

first: Stéphane

first: Gwen

last: Lomberk

first: Nelson

last: Dusetti

first: Laurent

last: Bartholin

first: Raul

last: Urrutia

first: Juan

last: Iovanna


title: Expression data from vehicle or PD-0332991 treated human T-ALL lines

status: Public on Dec 13 2012

city: Paris

first: Camille

last: Lobry

address: 16 rue de la Grange aux Belles

department: IRSL Inserm U944 / CNRS UMR7212

institute: Inserm

summary:
Cyclin D3 is critical hematopoiesis and loss of cyclin D3 leads to resistance to transformation of bone marrow progenitors by Notch1-IC.
We used a small molecule targeting cyclin D3:CDK4/6 activity to study whether its inhibition is an effective therapeutic strategy. We analyzed T-ALL lines in vitro with PD-0332991 or vehicle control to determine genes affected by the drug.

overall_design: CEM, Jurkat, DND41, and CUTL-1 cell lines were treated with 1 uM PD-0332991 or DMSO for 15 hours prior to RNA extraction and hybridization to Human Genome U133 Plus 2.0 Affymetrix arrays.

first: Catherine

last: Sawai

first: Philmo

last: Oh

first: Delphine

last: Ndiaye-Lobry

first: Jamieson

last: Bretz

first: Jacquelyn

last: Freund

first: Alexandros

last: Strikoudis

first: Lali

last: Genesca

first: Thomas

last: Trimarchi

first: Michelle

middle: A

last: Kelliher

first: Marcus

last: Clark

first: Jean

last: Soulier

first: Selina

last: Chen-Kiang

first: Iannis

last: Aifantis


title: Distinct gene expression profiles associated with the susceptibility of pathogen-specific CD4 T cells to HIV-1 infection

city: Silver Spring

first: Haitao

last: Hu

address: 503 Robert Grant Ave

department: US Military HIV Research Program

institute: Walter Reed Army Institute of Research

summary: Analysis of global gene expression profiles of flow cytometry-sorted, different pathogen-specific CD4+ T cell populations from the same peripheral blood mononuclear cells (PBMC), to identify molecular parameters that regulate differential susceptibilities of these CD4+ T cells to HIV infection. The results reveal distinct gene expression profiles between CMV-specific and tetanus toxoid/Candida-specific CD4+ T cells that involved selective upregulation of comprehensive innate antiviral

overall_design: Total RNA extracted from CFSE-low, flow-sorted pathogen-specific CD4+ T cells were analyzed for global gene expression. Changes in gene expression were compared between CMV to combined TT/Candida, or TT/CMV and Candida/CMV.

first: Silvia

last: Ratto-Kim


title: Pancreatic cancer circulating tumor cells express a cell motility gene signature that predicts survival after surgery

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary:
Most cancer deaths are caused by metastases, which are the end-results of circulating tumor cells (CTC) that detach from the cancer primary and succeed to survive in distant organs. The aim of the present study was to develop a gene signature of CTC and to assess its prognostic relevance after surgery for pancreatic ductaladenocarcinoma (PDAC).
A negative depletion fluorescence activated cell sorting (FACS) procedure was developed and validated with spiking experiments using cancer cell lines in whole human blood samples. This FACS-based method was used to enrich for CTC from the blood of 10 patients who underwent surgery for PDAC. Total RNA was isolated from 4 subgroup samples, i.e. CTC, haematological cells (G), original tumor (T), and non-tumoral pancreatic control tissue (P). After RNA quality control, samples of 6 patients were eligible for further analysis. Whole genome microarray analysis was performed after double linear amplification of RNA. The ‘Ingenuity Pathway Analysis’ software and AmiGO were used for functional data analyses. A CTC gene signature was developed and validated with the nCounter system on expression data of 78 primary PDAC using Cox regression analysis for disease-free (DFS) and overall survival (OS).
Using stringent statistical analysis, we finally retained 8,152 genes to compare expression profiles of CTC vs. other subgroups, and found 1,059 genes to be differentially expressed. The pathway with the highest expression ratio in CTC was p38 mitogen-activated protein kinase (p38 MAPK) signaling, known to be involved in cancer cell migration. In the p38 MAPK pathway TGF-β1, cPLA2, and MAX were significantly upregulated. In addition, 9 other genes associated with both p38 MAPK signaling and cell motility were over-expressed in CTC. High co-expression of TGF-1 and our cell motility panel (≥ 4 out of 9 genes for DFS and ≥ 4 out of 9 genes for OS) in primary PDAC was identified as an independent predictor of DFS (p=0.041, HR (95% CI) = 1.885 (1.025 – 3.559)) and OS (p=0.047, HR (95% CI) = 1.366 (1.004 – 1.861)).
Pancreatic CTC isolated from blood samples using a FACS-based negative depletion method,express a cell motility gene signature. The expression of this newly defined cell motility gene signature in the primary tumor is able to predict survival of patients who undergo surgical resection for pancreatic cancer.

overall_design: Total RNA was isolated from circulation tumor samples (CTC), haematological cells (G), original tumor (T), and non-tumor pancreatic control tissue (P) of patients with pancreatic ductal adenocarcinoma (PDAC). Gene expression profiles of CTC were compared to G, T, and  P. The aim of the current study was to develop a ‘negative depletion strategy’ to isolate CTC without the exclusion of any particular subset of CTC, and to study their gene-expression profiles in order to find novel therapeutic targets and prognostic markers in patients with pancreatic cancer.

first: G

last: Sergeant

first: R

last: van Eijsden

first: T

last: Roskams

first: V

last: Van Duppen

first: B

last: Topal


title: Bacillus anthracis' lethal toxin induces broad transcriptional responses in human peripheral monocyte.

status: Public on Dec 12 2012

city: Gainesville

first: M Cecilia

last: Lopez

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

summary: Anthrax lethal toxin directly targets human peripheral monocytes and causes multiple aberrant gene responses that would be expected to result in defects in human monocyte’s normal signaling transduction pathways and nction. This study provides further insights into the mechanisms associated with the host immune system collapse during an anthrax infection, and suggests that anthrax LT may have additional targets outside the well-known MAPK pathway.

overall_design:
There were 4 replicates, 1 control and 1 toxin treated from 4 donors, with 8 samples total.
key word : Toxin response

first: Kassidy

last: Chauncey

first: M

first: Gurjit

last: Sidhu

first: Sarah

last: Szarowicz

first: Henry

middle: V

last: Baker

first: Frederick

middle: S

last: Southwick


title: Smoking is Associated with Shortened Airway Cilia

city: New York

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary:
Background: Whereas cilia damage and reduced cilia beat frequency have been implicated as causative of reduced mucociliary clearance in smokers, theoretically mucociliary clearance could also be affected by cilia length. Based on models of mucociliary clearance predicting cilia length must exceed the 6 -7 μm airway surface fluid depth to generate force in the mucus layer, we hypothesized cilia height may be decreased in airway epithelium of normal smokers compared to nonsmokers.
Methodology/Principal Findings: Cilia length in normal nonsmokers and smokers was evaluated in aldehyde-fixed, paraffin-embedded endobronchial biopsies, and air-dried and hydrated samples brushed from human airway epithelium via fiberoptic bronchoscopy. In 28 endobronchial biopsies, healthy smoker cilia length was reduced 15% compared to nonsmokers (p<0.05). In 47 air-dried samples of airway epithelial cells, smoker cilia length was reduced 13% compared to nonsmokers (p<0.0001). Analysis of the length of individual, detached cilia in 17 samples, smoker cilia length was reduced 9% compared to nonsmokers (p<0.05). Finally, in 16 fully hydrated, unfixed samples, smoker cilia length was reduced 7% compared to nonsmokers (p<0.05).

overall_design: Conclusions/significance: Models predict that a reduction in cilia length would reduce mucociliary clearance, suggesting that smoking-associated shorter airway epithelial cilia plays a significant role in the pathogenesis of smoking-induced lung disease.

first: Philip

last: Leopold

first: Michael

last: O'Mahony

first: Julie

last: Lian

first: Harvey

last: Ben-Gary

first: Ronald

last: Crystal


title: FMR1 targets distinct mRNA sequence elements to regulate protein expression [Affymetrix]

first: Manuel

last: Ascano

address: 1230 York Avenue Box 186

department: HHMI/Laboratory of RNA Molecular Biology

institute: The Rockefeller University

summary: Fragile-X Syndrome (FXS) is a multi-organ disease leading to mental retardation, macro-orchidism in males, and premature ovarian insufficiency in female carriers. FXS is also a prominent monogenic disease associated with autism spectrum disorders (ASD). FXS is typically caused by the loss of FRAGILE X-MENTAL RETARDATION 1 (FMR1) expression, which encodes for the RNA-binding protein (RBP), FMR1 (or FMRP). We report the discovery of the RNA recognition elements (RREs), binding sites, and mRNA targets for wild-type and I304N mutant FMRP isoforms as well as its paralogs, FXR1 and FXR2. RRE frequency, ratio, and distribution determine target mRNA association with FMRP. Among highly-enriched targets, we identified many genes involved in ASD and demonstrate that FMRP can affect their protein levels in cell culture, mice, and human brain. Unexpectedly, we discovered that these targets are also dysregulated in Fmr1-/- mouse ovaries, showing signs of premature follicular overdevelopment. These results indicate that FMRP targets shared signaling pathways across different cellular contexts. As it is become increasingly appreciated that signaling pathways are important to FXS and ASD, our results here provide an invaluable molecular guide towards the pursuit of novel therapeutic targets for these devastating neurological disorders.

overall_design: The mRNA profile of RNA recovered from FLAG-antibody immunoprecipitated FMRP was compared to the mRNA profile of the starting lysate material.

first: Neelanjan

last: Mukherjee

first: Pradeep

last: Bandaru

first: Jason

middle: B

last: Miller

first: Jeff

last: Nusbam

first: David

last: Corcoran

first: Christine

last: Langlois

first: Mathias

last: Munschauer

first: Markus

last: Hafner

first: Zev

last: Williams

first: Uwe

last: Ohler

first: Thomas

last: Tuschl


title: shRNA knockdown of ZMIZ1 in human T-cell Acute Lymphoblastic Leukemia cell line CEM

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

institute: University of Michigan

summary:
Human T-cell Acute lymphoblastic Leukemia cell line CEM was transfected with either shRNA against ZMIZ1 or scrambled shRNA.  Four (non-paired) biological replicates of each condition had mRNA assays performed using Affymetrix HG_U133_plus_2 arrays, with 54675 probe-sets.  A supplementary Excel workbook holding the same processed data as the series matrix file is provided, with some probe set annotation, and a simple statistical comparison. The raw (.CEL) files are also provided.

Keywords: Expression profiling by array

first: Lesley

last: Rakowski

first: Derek

middle: D

last: Garagiola

first: Sarah

last: Caruso

first: Morgan

last: Jones

first: Ivan

last: Maillard

first: Mignon

last: Loh

first: Mark

last: Chiang


title: Small molecule activation of PKM in cancer cells induces serine auxotrophy

city: Cambridge

first: Charles

last: Kung

address: 38 Sidney St., Suite 2

institute: Agios Pharmaceuticals

summary: Proliferating tumor cells use aerobic glycolysis to support their high metabolic demands.  Paradoxically, increased glycolysis is often accompanied by expression of the lower activity PKM isoform, effectively constraining lower glycolysis.  Here, we report the discovery of novel PKM activators with a unique allosteric binding mode.  Characterization of how these compounds impact cancer cells revealed an unanticipated link between glucose and amino acid metabolism.  PKM activation resulted in a metabolic rewiring of cancer cells manifested by a profound dependency on the non-essential amino acid serine for continued cell proliferation.  Induction of serine auxotrophy by PKM activation was accompanied by reduced carbon flow into the serine biosynthetic pathway and increased expression of high affinity serine transporters.  These data support the hypothesis that PKM expression confers metabolic flexibility to cancer cells that allows adaptation to nutrient stress.

overall_design: A549 cancer cells were treated with compound-16 for up to 24 hours in the presence and absence of serine in the media.

last: Hixon

first: Sung

last: Choe

first: Kevin

last: Marks

first: Stefan

last: Gross

first: Erin

last: Murphy

first: Byron

last: DeLaBarre

first: Giovanni

last: Cianchetta

first: Shalini

last: Sethumadhavan

first: Shunqi

last: Yan

first: Yi

last: Gao

first: Fang

last: Cheng

first: Xiling

last: Wang

first: Shaohui

last: Qian

last: Saunders

first: Ed

last: Driggers

first: Hin

middle: K

last: Woo

first: Kaiko

last: Kunii

first: Stuart

last: Murray

first: Hua

last: Yang

first: Katharine

last: Yen

first: Wei

last: Liu

first: Lewis

last: Cantley

first: Matthew

last: Vander Heiden

first: Shinsan

last: Su

first: Shengfang

last: Jin

first: Francesco

last: Salituro

first: Lenny

last: Dang


title: Transient low-dose decitabine treatment of primary AML samples

first: Nobish

last: Varghese

summary: Genome-wide DNA methylation profiling of primary AML samples treated with 100nM decitabine (DAC), cytarabine (AraC), or DMSO. Eight distinct AML samples were grown using an in vitro stromal co-culture system for 4 days and then treated with either DAC, Ara-C or DMSO for 3 days. DNA was prepared for genome-wide methylation analysis with the Illumina Infinium 450k Human DNA methylation BeadChip. DNA from each sample/treatment was analyzed on duplicate arrays.

overall_design: Bisulfite-converted DNA from 24 samples was hybridised to the Illumina Infinium 450k Human Methylation Beadchip in duplicate (replicates are indicated by array plate number).

first: Jeffery

last: Klco

first: David

last: Spencer


title: Microarray Analysis of a Familial Hypertrophic Cardiomyopathy Mouse Model Rescued by a Phospholamban Knockout

city: Cincinnati

first: sudarsan

last: rajan

address: 3333 Burnet Ave

institute: CCHMC

summary:
Familial hypertrophic cardiomyopathy (FHC) is a disease characterized by ventricular hypertrophy, fibrosis, and aberrant systolic and/or diastolic function. Our laboratories have previously developed 2 mouse models that affect cardiac performance. One transgenic mouse model encodes an FHC-associated mutation in α-tropomyosin (Tm180) that displays severe cardiac hypertrophy with fibrosis and impaired physiological performance. The other model was a gene knockout of phospholamban (PLB), a regulator of calcium uptake in the sarcoplasmic reticulum of cardiomyocytes; the hearts of these mice exhibit hypercontractility with no pathological abnormalities. Previous work in our laboratories show that the hearts of mice that were genetically crossed between the Tm180 and PLB KO mice rescues the hypertrophic phenotype and improves their cardiac morphology and function.
We used microarrays to detail the global program of gene expression underlying cardiac remodeling and rescue of the hypertrophic cardiomyopathic phenotype and identified distinct classes of regulated genes during this process.

overall_design: To understand the changes in gene expression that occur over time in these animal models (Tm180, PLB KO, Tm180/PLB KO and nontransgenic control mice), we conducted microarray analyses of left ventricular tissue at 4 and 12 months of age.

first: Sudarsan

last: Rajan

first: Marco

last: Alves

first: Jose

last: Pena

first: Anil

last: Jegga

first: Bruce

last: Aronow

first: Evangelia

last: Kranias

first: Beata

last: Wolska

middle: F

last: Wieczorek


title: Expression data from CL1-0 and CL1-5 lung cancer cell line.

status: Public on Dec 11 2012

city: Taipei

first: Michael

last: Hsiao

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

department: Genomics Research Center

institute: Academia Sinica

summary:
A lung cancer cell model of invasive transformation was developed to select progressively invasive cell populations from a parental cell line of human lung adenocarcinoma, CL1. Five progressive sub-clones namely, CL1-1, CL1-2, CL1-3 CL1-4, and CL1-5 were selected using transwell and displayed increasing invasion potential (Chu et al, 1997).
Here, we used microarrays to analyze and compare gene expression profiles between CL1-0 and CL1-5 for the identification of invasion/metastasis associated gene signatures.

overall_design: CL1-0 and CL1-5 lung cancer cell lines were used for RNA extraction and hybridization on Affymetrix microarrays. A total of 6 chips were used for microarray analysis including three biological repeats from CL1-0 and three biological repeats from CL1-5.

first: Yi-Hua

last: Jan