title: Transcriptome in alveolar epithelial type II cells isolated from normal and COPD lungs of adult human

summary: Alveolar epithelial type II (ATII) cells play a critical role in homeostasis and repair process of the lungs. In lung diseases such as chronic obstructive pulmonary disease (COPD), ATII cells are damaged and fall into apoptosis or senescence. Until to date, global gene expression of ATII cells in COPD lungs has not been analyzed. We isolated ATII cells from three non-COPD and three COPD patients using a FACS method. Then, we performed microarray analysis to compare gene expression profiles of ATII cells between non-COPD and COPD patients.

overall_design: Primary ATII cells were isolated from lung tissues obtained from thoracic surgery using FACS. We profiled the gene expression of ATII cells from three non-COPD and three COPD patients. This study was approved by the Ethics Committee at Tohoku University School of Medicine and Ishinomaki Red Cross Hospital. All subjects gave informed consent.


title: Role of REST in the pathogenesis of uterine fibroids

status: Public on Oct 06 2012

city: Kansas City

first: Vargheese

middle: M

last: Chennathukuzhi

state: KS

address: 3901 Rainbow Boulevard

country: USA

institute: University of Kansas Medical Center

summary: The loss of REST in uterine fibroids promotes aberrant gene expression and enables mTOR pathway activation

overall_design: We used siRNA to knockdown REST/ NRSF in cultured primary myometrial smooth muscle cells (SMCs) and global gene expression was analyzed using microarrays.


title: Expression data from normal melanocyte, melanoma cells and their exosomes (mRNA)

status: Public on Oct 10 2012

city: Louisville

first: Hongying

last: Hao

state: KY

address: 505 South Hancock Street

department: Surgery

institute: University of Louisville

summary: Exosomes are small membraneous vesicles secreted into body fluids by tumors. Tumor exosomes contain intact and functional mRNAs, small RNAs (including miRNAs), and proteins that can alter the cellular environment to favor tumor growth. Further exploration into the molecular profiling of exosomes may increase our understanding of their roles in melanoma progression in vivo, and may have potential application in biomarker studies. In the present study, we used mRNA array profiling to identify thousands of exosomal mRNAs associated with melanoma progression and metastasis. Similarly, miRNA array profiling identified specific miRNAs, such as hsa-miR-31, -185, and -34b, involved in melanoma invasion. Our results indicate that melanoma-derived exosomes have unique gene expression signatures and miRNA profiles that may have important functions in melanoma metastasis and progression.

overall_design: Total RNA from cells and exosomes were isolated using mirVana total RNA isolation kit according to the manufacturer’s guidelines. RNA was quantified using Nanodrop ND-1000. The integrity of these total RNAs was assessed using Agilent 2100 Bioanalyzer. Total high-quality RNA was converted to cDNA, transcribed and labelled, and then hybridized to human HG-U133 plus 2 arrays (Affymetrix) then scanned according to the standard protocol recommended by Affymetrix. Two different RNA preparations from two cell lines and their exosomes were used.

first: Deyi

last: Xiao

first: Joanna

last: Ohlendorf

first: Yinlu

last: Chen

first: Douglas

middle: D

last: Taylor

first: Shesh

last: Rai

first: Sabine

last: Waigel

first: Wolfgang

last: Zacharias

first: Kelly

last: McMasters


title: Defining the Genomic Signature of the Parous Breast

status: Public on Oct 25 2012

city: Philadelphia

first: Julia

last: Santucci-Pereira

state: PA

address: 333 Cottman Ave, P2051

institute: Fox Chase Cancer Center

summary:
It is widely accepted that a woman’s lifetime risk of developing breast cancer at menopause is reduced by early full term pregnancy and multiparity. This phenomenon is associated with the development and differentiation of the breast, which ultimately imprints a specific genomic profile in the mammary epithelium. In the present work we demonstrate that this profile represents a permanent signature that could be associated with the breast cancer risk reduction conferred by pregnancy.
We have compared the gene expression profile of normal breast biopsies performed in 71 parous (P) and 42 nulliparous (NP) postmenopausal women. All samples were hybridized to Affymetrix HG_U133 Plus 2.0 oligonucleotide arrays.

overall_design: We compared the gene expression profile of normal breast core biopsies from 71 parous (women that had a full term pregnancy) and 42 nulliparous (women that never completed a pregnancy) postmenopausal women from Sweden. All samples were hybridized to Affymetrix HG_U133 Plus 2.0 oligonucleotide arrays.

first: Suraj

last: Peri

first: Ricardo

last: López de Cicco

first: Michael

last: Slifker

first: Eric

last: Ross

first: Irma

middle: H

last: Russo

first: Patricia

middle: A

first: Alan

last: Arslan

first: Ilana

last: Belitskaya-Lévy

first: Anne

last: Zeleniuch-Jacquotte

first: Pal

last: Bordas

first: Per

last: Lenner

first: Janet

last: Åhman

first: Yelena

last: Afanasyeva

first: Robert

last: Johansson

first: Fathima

last: Sheriff

first: Göran

last: Hallmans

first: Paolo

last: Toniolo

first: Jose


title: Expression data from murine fibroblasts overexpressing Fbxl10

status: Public on Oct 05 2012

city: Bonn

first: Andreas

last: Janzer

address: Sigmund Freud St. 25

department: Pathology

country: Germany

institute: University of Bonn

summary:
Posttranslational modifications on histone tails control gene expresssion levels in an either positive or negative way. Therefore enzymes which modifiy the modifications on the histon tails, like histone demethylases, are able to strictly regulate the transcriptom.
To analyse the regulatory role of histone demethylase Fbxl10 we generated a stable cell line permanently overexpressing HA-tagged Fbxl10 and identified the transcriptome changes compared to untransfected control cell line by microarray.

overall_design: Tet-off Mefs were transfected with a plasmid containing HA-Fbxl10 cDNA and a Hygromycin resistence plasmid and cell clones were selected for HA-Fbxl10 expression. Three independent RNA samples were generated from untransfected Tet-off Mef cells (C1-C3) and from Tet-off Mef HA-Fbxl10 (D1-D3) and hybridisated on Affymetrix microarray.

first: Jutta

last: Kirfel


title: Basal gene expression data of 21 cell lines (18 cancer and 3 non-tumorigenic)

city: Berlin

first: Philip

last: Groth

address: Muellerstr. 178

department: Therapeutic Research Group Oncology

institute: Bayer Pharma AG

summary:
We profiled basal gene expressed levels of 21 cell lines (18 cancer and 3 non-tumorigenic) using Affymetrix HG-U133_plus2 GeneChip microarrays.
Goal of the experiment was to benchmark a number of algorithms for biomarker detection all of which utilize gene expression data.

overall_design: Cell lines were cultivated in appropriate media according to supplier recommendations. Goal was to acquire a basal gene expression profile of 21 common cell lines.

first: Oliver

last: Politz


title: Expression data from HepG2 cells before and after RNF43 knockdown

status: Public on Oct 04 2012

city: Hangzhou

first: Chunyang

last: Xing

address: 79# Qingchun Road

country: China

institute: First Affiliated Hospital, School of Medicine, Zhejiang University

summary:
It has been demonstrated that Ring finger protein 43 (RNF43) is overexpressed in colorectal cancer and mediates cancer cell proliferation. We found that RNF43 was frequently overexpressed in HCC, and knockdown of RNF43 could induce apoptosis and inhibit proliferation, invasion, colony formation and xenograft growth of HCC cells. Suggesting that RNF43 is involved in tumorigenesis and progression of HCC.
We used microarrays to profile gene expression patterns before and after RNF43 knockdown, and identified differentially expressed genes during this process.

overall_design: HepG2 cells were transfected with RNF43 siRNA or negative control siRNA in triplicate. Forty-eight hours after transfection, total RNA was extracted,labeled and hybridized to HG-U133 Plus 2.0 arrays.

first: Lin

last: Zhou


title: Compound C prevents the unfolded protein response during glucose deprivation through a mechanism independent of AMPK and BMP signaling.

status: Public on Oct 11 2012

city: Ariake

first: Akihiro

last: Tomida

state: Koto-ku, Tokyo

department: Cancer Chemotherapy Center

country: Japan

institute: Japanese Foundation for Cancer Research (JFCR)

summary: Inhibiting the unfolded protein response (UPR) can be a therapeutic approach, especially for targeting the tumor microenvironment. We found that compound C (also known as dorsomorphin) prevented the UPR and exerted enhanced cytotoxicity during glucose deprivation. The UPR-inhibiting activity of compound C was not associated with either AMPK or BMP signaling inhibition.

overall_design: To induce the UPR, we treated HT1080 cells for 18 hours under ER stress conditions by adding 10 mM 2-Deoxy-D-glucose (2DG) to culture medium. UPR inhibitors (compound C, versipelostatin and phenformin) were added just before 2DG was added in medium. Total 8 samples were prepared for RNA extraction and hybridization on Affymetrix microarrays.

first: Sakae

last: Saito


title: Expression data from normal melanocyte, melanoma cells and their exosomes

first: Hongying

last: Hao

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

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Identification of FOXP3-dependent transcripts in human FOXP3 expressing Jurkat T cells

status: Public on Nov 26 2012

city: Braunschweig

last: Jeron

state: Nierdersachsen

address: Inhoffenstraße 7

department: Viral Immunology

institute: Helmholtz Center for Infection Research

summary: The transcription factor (TF) Forkhead Box P3 (FOXP3) is constitutively expressed in high levels in natural occurring CD4+CD25+ regulatory T cells (nTreg) and is not only the most accepted marker for that cell population, but is considered lineage determinative. Chromatin immunoprecipitation (ChIP) of transcription factors in combination with genomic tiling microarray analysis (ChIP-on-Chip) has been shown to be an appropriate tool to identify FOXP3 transcription factor binding sites (TFBS) on a genome-wide scale. In combination with microarray expression analysis the ChIP-on-Chip technique allows to identify direct FOXP3 target genes. This dataset shows expression data of resting and mitogen stimulated (PMA / ionomycin) retrovirally transduced Jurkat T cells either expressing FOXP3(Δ2) (J-FOXP3) or an empty vector control (J-GFP).

overall_design: Expression profile of resting and PMA/ionomycin stimulated J-GFP and J-FOXP3 cells was analyzed (one microarray per condition).

first: Wiebke

last: Hansen

first: Jan

last: Buer

last: Geffers

first: Dunja

last: Bruder


title: EWS TC-71 cell lines: IGF-1R resistant

status: Public on Oct 03 2012

city: Bologna

first: Andrea

last: Grilli

state: Italy

address: v. di Barbiano 1/10

department: Laboratory of Experimental Oncology

country: Italy

institute: Rizzoli Orthopaedic Institute

summary: Ewing's Sarcoma cell lines were made resistant to different IGF-1R drugs to investigate mechanisms and pathways modulated by the resistance.

overall_design: EWS TC-71 cell line was exposed to increasing concentration to three different anti-IGF-1R drugs (HAb AVE1642, TKI NVP-AEW541,  HAb CP-751,871, cell lines named respectively as TC/AVE, TC/AEW or TC/CP) for at least six months. Expression profile of resistant cell variants was compared either singularly for each resistance or commonly vs. parental cell line. Two technical replicates for resistant variants and three biological replicated for parental cell were present.


title: Changes in EHEC virulence on exposure to epithelial cell secreted factors

city: College Station

first: Tarun

last: Bansal

state: TX

address: 3122 TAMU

department: Chemical Engineering

institute: Texas A & M University

summary:
EHEC is a food-borne pathogen that colonizes human GI tract and leads to infection. To understand the process of colonization and to decipher if any factors secreted by intestinal epithelial cells help EHEC during the infection process, we studied expression of EHEC virulence gene expression when exposed to intestinal epithelial cell conditioned medium. In our study, we observed that exposure to epithelial cell conditioned medium for 1 h and 3 h increases expression of 32 out of 41 EHEC LEE virulence genes. In addition, expression of the shiga toxin 1 (Stx1) gene is up-regulated at 1 h of exposure. Also, 17 genes encoded by prophage 933W, including those for Stx2, are also upregulated at both time-points. The increase in 933W prophage expression is mirrored by a 2.7-fold increase in intracellular Stx2 phage titers. Consistent with the increase in virulence gene expression, we observed a 5-fold increase in EHEC attachment to epithelial cells when exposed to conditioned medium, suggesting that EHEC utilizes host cell molecules to increase virulence and infectivity. The molecule(s) responsible for increased EHEC virulence is heat-sensitive as heating the conditioned medium to 95oC abolishes the increase in attachment to epithelial cells. A similar decrease was observed when the conditioned medium was treated with proteinase-K to degrade the proteins. The secreted molecule(s) was found to be larger than 3 kDa and strongly suggests that the HCT-8 secreted molecule that increases EHEC virulence and colonization is a protein-based molecule.
Affymetrix E. coli Genome 2.0 Arrays were used to determine the changes in EHEC virulence gene expression on exposure to intestinal epithelial cell-secreted factors (through growth in conditioned medium).

overall_design: Overnight cultures of EHEC were diluted in LB medium to a turbidity of 0.1 at 600 nm. The cells were allowed to grow to a turbidity of 1.0 at 600 nm at 37°C and the EHEC cells were then resuspended in either fresh or conditioned medium. The cultures were then allowed to grow for 1 h or 3 h before cell pellets were collected by centrifugation and stored at -80°C. Total RNA was isolated from the cell pellets (173) and RNA quality was assessed using gel electrophoresis. Escherichia coli Genome 2.0 arrays (Affymetrix, Santa Clara, CA, USA) containing 10,208 probe sets for all 20,366 genes present in four strains of E. coli, including EHEC, were used to profile changes in gene expression using RNA samples for each treatment.

first: Thomas

middle: K

last: Wood

first: Arul

last: Jayaraman


title: Gene expression by antigen activated OT-I T cells in vivo in the presence and absence of IL-2

city: Miami

middle: R

last: Malek

state: FL

address: 1600 NW 10th Avenue

department: Microbiology/Immunology

institute: University of Miami

summary:
Much is known concerning the cellular and molecular basis for CD8+ T memory immune responses. Nevertheless, conditions that selectively support memory generation have remained elusive. Here we show that an immunization regimen that delivers TCR signals through a defined antigenic peptide, inflammatory signals through LPS, and growth and differentiation signals through the IL-2R initially favors antigen-specific CD8+ T cells to rapidly and substantially develop into tissue-residing T effector-memory cells by TCR transgenic OVA-specific OT-I CD8+ T cells. Amplified CD8+ T memory development depends upon a critical frequency of antigen-specific T cells and direct responsiveness to IL-2. A homologous prime-boost immunization protocol with transiently enhanced IL-2R signaling in normal mice led to persistent polyclonal antigen-specific CD8+ T cells that supported protective immunity to Listeria monocytogenes. These results identify a general approach for amplified T memory development that may be useful to optimize vaccines aimed at generating robust cell-mediated immunity.
Gene expression analysis was performed for OT-I T cells on day 3 and day 5 after activation with ovalbumin and LPS in vivo with and without treatment with IL-2 using an agonists IL-2/anti-IL-2 complexes (IL2/Jes-6.1)

overall_design: OT-I T cells were purified and adoptively transferred into congenic syngenic mice. 24 hours later mice were immunization with ovalbumin and LPS. 24 hr later some mice received agonist IL2/anti-IL2. 3 and 5 days after immunization, the activated OT-I T cells were purifed by FACS and total RNA was isolated for genome wide expression analysis using Affymetrix Mouse Gene ST1.0 arrays


title: The Rho Exchange Factors Vav2 and Vav3 Control a Lung Metastasis–Specific Transcriptional Program in Breast Cancer Cells

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

summary: The guanosine triphosphatases of the Rho and Rac subfamilies regulate protumorigenic pathways and are activated by guanine nucleotide exchange factors (Rho GEFs), which could be potential targets for anticancer therapies. We report that two Rho GEFs, Vav2 and Vav3, play synergistic roles in breast cancer by sustaining tumor growth, neoangiogenesis, and many of the steps involved in lung-specific metastasis. The involvement of Vav proteins in these processes did not correlate with Rac1 and RhoA activity or cell migration, implying the presence of additional biological programs. Microarray analyses revealed that Vav2 and Vav3 controlled a vast transcriptional program in breast cancer cells through mechanisms that were shared between the two proteins, isoform-specific or synergistic. Furthermore, the abundance of Vav regulated transcripts was modulated by Rac1-dependent and Rac1-independent pathways. This transcriptome encoded therapeutically targetable proteins that played non redundant roles in primary tumorigenesis and lung-specific metastasis, such as integrin-linked kinase (Ilk), the transforming growth factor–b family ligand inhibin bA, cyclooxygenase-2, and the epithelial cell adhesion molecule Tacstd2. It also contained gene signatures that predicted disease outcome in breast cancer patients. These results identify possible targets for treating breast cancer and lung metastases and provide a potential diagnostic tool for clinical use.

overall_design: All microarray experiments were performed by the personnel of the Genomics and Proteomics Unit of our Institution. Transcriptomal changes were determined using the Mouse Gene 1.0 ST arrays (Affymetrix). Two independent experiments were performed to identify the Vav2/Vav3-dependent transcriptome. In the first one, we compared the transcriptomes of Control, KD2/3(A) and KD2/3(B) to identify Vav family-dependent genes. In the second one, we compared the transcriptomes of KD2/3(A) and KD2/3+V2/3 cells. In all cases, total cellular RNA was extracted from three independent exponential cultures of the appropriate cell lines using the RNAeasy kit (Qiagen), quantified using 6000 Nano Chips (Agilent Technologies, Santa Clara, CA), and used (2.3 μg/sample) to generated labeled cRNA probes according to the manufacturer’s instructions (Affymetrix). Upon microarray hybridization, the raw data was normalized, filtered and analyzed with the Bioconductor software (www.bioconductor.com) using the Affy and Siggenes applications. Generation of knockdown cell lines. The shRNA-mediated knockdown of transcripts for Vav2 and Vav3 was carried out using already packaged Mission TRC lentiviral particles (Sigma-Aldrich) according to the manufacturer’s protocol. The catalogue numbers and shRNA sequences yielding the greatest knockdown were clone number TRC0000097094 (5’-CCGGGCCTGCATCTCTGGTTTAGATCTCGAGATCTAA ACCAGAGATGCAGGCTTTTTG-3’) for the mouse Vav2 mRNA; TRC0000097124 (5’-CCGGCCAGCATTTCTCGTCTTAAATCTCGAGATTTAA GACGAGAAATGCTGGTTTTTG-3’) for the mouse Vav3 mRNA. Lentiviral particles containing the empty pLOK.1puro vector (Sigma-Aldrich) were used to generate the “Control” 4T1 cells used in these experiments. Cells were incubated with lentiviral particles in the presence of 8 μg/ml polybrene (Sigma), selected with puromycin (1 μg/ml; Sigma), and used as either pools or isolated clones. Two clones of double Vav2;Vav3 knockdown cells (designated KD2/A(A) and KD2/3 (B)) were used in these experiments. Generation of rescued 4T1 cell lines. To generate the rescued KD2/3(A) cell line expressing both Vav2 and Vav3, cells were first infected with lentiviral particles produced from the pCCM33 vector (encoding wild type, HA-tagged Vav2) and then with lentiviral particles containing the pCQS1 vector (encoding wild type, Myc-tagged Vav3). Cells were then selected with hygromycin (present in the Vav2-encoding pCCM33 vector) and susbsequently sorted by flow cytometry to isolate GFP positive cells (which was expressed bicistronically from the same Vav3-encoding pCQS1 vector). A clone of double reconstituted cells was used in the microarray experiments and designated as KD2/3+V2/V3.

first: Carmen

last: Citterio

first: Mauricio

last: Menacho-Márquez

first: Ramón

last: García-Escudero

first: Romain

last: Larive

first: Olga

last: Barreiro

first: Francisco

last: Sánchez-Madrid

first: Jesús

last: Paramio

first: Xosé

last: Bustelo


title: Complement Factor H deficiency results in decreased neuroretinal expression of Cd59a in aged mice.

status: Public on Oct 02 2012

city: Copenhagen

first: Carsten

last: Faber

address: Blegdamsvej 3

department: Fac. of Health Science, ISIM

country: Denmark

institute: University of Copenhagen

summary:
Purpose: The complement system is closely linked to the pathogenesis of age-related macular degeneration (AMD). Several complement genes are expressed in retinal pigment epithelium (RPE), and complement proteins accumulate in drusen. Further, a common variant of complement factor H (CFH) confers increased risk of developing AMD. Because the mechanisms by which changes in the function of CFH influence development of AMD are unclear, we examined ocular complement expression as a consequence of age in control and CFH null mutant mice.

Methods: Gene expression in neuroretinas and RPE/choroid from young and aged WT and Cfh-/- C57BL/6J mice was analysed by microarrays. Expression of a wide range of complement genes was compared to expression in splenocytes and in liver tissue by qRT-PCR.

Results: An age-associated increased expression of complement, particularly C1q, C3 and Factor B, in the RPE/choroid coincided with increased expression of the negative regulators Cfh and Cd59a in the neuroretina. Young mice deficient in CFH expressed Cd59a similar to WT, but failed to upregulate Cd59a expression with age. Both hepatic and splenic expression of Cd59a increased with age regardless of Cfh genotype.

Conclusions: While the connection between CFH deficiency and failure to up-regulate CD59a remains unknown, these results suggest that expression of CD59 is tissue-specific and that neuroretinal regulation depends on CFH. This could contribute to the visual functional deficits and morphological changes in the Cfh-/- mouse retina that occur with age, and further suggests that deficient neuroretinal regulation of complement could represent an early event in AMD.

overall_design: Gene expression in neuroretinas and RPE/choroid from young and aged WT and Cfh-/- mice, 4 biological replicates in each group.

first: Jennifer

last: Williams

first: Helene

middle: B

last: Juel

first: John

last: Greenwood

first: Mogens

last: Nissen

first: Stephen

middle: E

last: Moss


title: Colorectal adenocarcinomas and matched normal colonic tissues

city: Urbana

first: Chieh-Chun

last: Chen

state: Illinois

address: 1206 West Gregory Drive

department: Bioengineering

institute: University of illinois

summary: Five colorectal adenocarcinomas and matched normal colonic tissues were analyzed with Affymetrix HG-U133-Plus-2.0 microarrays. Two labs independently generated microarray data with the same array platform on the same biological samples.

overall_design: Colorectal adenocarcinomas and matched normal colonic RNA sample were purchased from Oncomatrix, Inc., San Diego, CA. The RNA from each biological sample was distributed to and processed in two laboratories at Stanford University.

first: Guixian

last: Lin

first: Xuming

last: He

first: Hanlee

last: Ji

first: Leming

last: Shi

first: Ronald

last: Davis

first: Sheng

last: Zhong


title: Timecourse gene expression profiling of DLBCL cell line Karpas422 after EZH2 inhibitor treatment

city: Shanghai

first: Shannon

last: Chuai

state: Shanghai

address: Building 8, Lane 898 Halei Road, Pudong New Aera

institute: Novartis

summary:
Ezh2 protein is the enzymatic component of the Polycomb Repressive Complex (PRC)-2, which represses its target genes by methylating lysine 27 of histone H3 (H3K27) and regulates cell proliferation and differentiation during embryonic development. Recently, hot-spot mutations of Ezh2 have been identified in diffused large B cell lymphomas (DLBCLs) and follicular lymphomas (FLs). To investigate if tumor growth is dependent on the enzymatic activity of Ezh2, we have developed a potent and selective small molecule inhibitor, EI1, which inhibits the enzymatic activity of Ezh2 through direct binding and competing with the methyl group donor S-Adenosyl methionine (SAM). EI1-treated cells exhibit genome-wide loss of H3K27 methylation. Furthermore, inhibition of Ezh2 by EI1 in DLBCL cells carrying the Y641 mutations results in decreased proliferation, cell cycle arrest and apoptosis. These results provide strong validation of Ezh2 as a potential therapeutic target for the treatment of cancer with the Ezh2 mutation.
In this microarray experiment we examined the global gene expression changes in DLBCL cell line Karpas422 (Ezh2Y641N) after EI1 treatment for up to 6 days.

overall_design: Total RNA was prepared from KARPAS422 at 1 day, 2 days, 3 days, and 6 days after DMSO or EZH2 inhibitor (5 uM) treatment with biological triplicates and hybridized to Affimetrix U133 Plus 2 microarray chips according to the manufacturers protocol (Affymetrix, CA).

first: Lin

last: Teng

first: Wei

last: Qi

first: HoMan

last: Chan


title: The effect of trypsin-2 on human tongue squamous cell carcinoma cell line gene expression

city: Helsinki

first: Suvi-Tuuli

last: Vilen

address: Haartmaninkatu 8

department: Dentistry

country: Finland

institute: University of Helsinki

summary:
The level of trypsin-2 has been shown to correlate with the malignancy and metastatic potential of many cancer.
We used microarrays to detail how tryspin-2 overexpression changes the gene profile of human tongue squamous cell carcinoma cell line (HSC-3).

overall_design: We compared trypsin-2 overexpressing HSC-3 line to HSC-3 which was transfected with control vector and because of that did not expressed trypsin-2 at all.

first: Suvi


title: DICER1 hotspot mutations cause defective miRNA processing

status: Public on Oct 01 2012

city: Vancouver

first: Michael

middle: S

last: Anglesio

state: BC

department: Obstetrics and Gynecology

country: Canada

institute: University of British Columbia

summary: Recurrent somatic hotspot mutations of DICER1 appear to be clustered around each of four critical metal binding residues in the RNase IIIB domain of DICER1. This domain is responsible for cleavage of the 3’ end of the 5p-miRNA strand of a pre-mRNA hairpin. To investigate the effects of these cancer-associated “hotspot” mutations we engineered mouse Dicer1-deficient ES cells to express wild-type and an allelic series of the mutant human DICER1 variants. Global miRNA and mRNA profiles from cells carrying the metal binding site mutations were compared to each other and wild-type human DICER1. The miRNA and mRNA profiles generated through the expression of the hotspot mutations were virtually identical, and the DICER1 hotspot mutation carrying cells were distinct from both wild-type and Dicer1-deficient cells. Further, miRNA profiles showed mutant DICER1 results in a dramatic loss in processing of mature 5p-miRNA strands but were still able to create 3p-strand miRNAs. Messenger-RNA profile changes were consistent with the loss of 5p-strand miRNAs and showed enriched expression for predicted targets of the lost 5p derived miRNAs. We therefore conclude that cancer-associated somatic hotspot mutations of DICER1, affecting any one of four metal binding residues in the RNase IIIB domain, are functionally equivalent with respect to miRNA-processing and are hypomorphic alleles, yielding a global loss in processing of mature 5p-strand miRNA. We further propose that this resulting 3p-strand bias in mature miRNA expression likely underpins the oncogenic potential of these hotspot mutations.

overall_design: A total of 28 Affymetrix Mouse Gene ST arrays were done for mRNA expression profiling of various DICER1 mutants (n=14), wildtype controls (n=6), vector only (n=3) and parental cell lines (n=5).

first: Yemin

last: Wang

first: Janine

last: Senz

first: Adrian

last: Wan

first: Alireza

last: Heravi-Moussavi

first: Clara

last: Salamanca

first: Sarah

last: Maines-Bandiera

first: David

middle: G

last: Huntsman

first: Gregg

last: Morin


title: Expression profile of human HepG2 cells treated with PADMA28 ethanolic extracts or EtOH solvent control

city: Innsbruck

first: Oliver

middle: Alexander

last: Wrulich

address: Innrain 80-82

department: Medical Biochemistry

country: Austria

institute: Medical University Innsbruck

summary: The aim of this study was to analyze the influence of PADMA28 ethanolic extracts on HepG2 gene expression. PADMA28 (Swissmedic Nr. 58436) is an Indo-Tibetan polyherbal preparation used for the treatment of symptoms associated with circulatory disorders.

overall_design: Triplicate cultures of HepG2 cells were treated with either PADMA28 or EtOH solvent control for 18 hours. After cell harvest, the triplicates were pooled and total RNA was extracted. The RNA was analyzed using Affymetrix Human Genome U133 Plus 2.0 microarrays (one array per treatment).

first: Angela

last: Klein

first: Marcel

last: Jenny

first: Peter

last: Gruber

first: Kathrin

last: Becker

first: Dietmar

last: Fuchs

first: Florian

last: Ueberall

first: Johanna

last: Gostner


title: Dexamethasone induced gene expression changes in the human trabecular meshwork

city: Iowa City

first: Markus

last: Kuehn

state: IA

address: 375 Newton Road

department: Ophthalmology and Visual Sciences

institute: University of Iowa

summary:
One of the undesirable side effects of glucocorticoid use is the potential development of elevated intraocular pressure and glaucoma. The precise mechanisms through which steroid use induces ocular hypertension are unclear.
The purpose of this study was to identify gene expression changes induced by steroids in the human trabecular meshwork and the underlying sclerocorneal tissue.

overall_design: The anterior segment of five pairs of adult human donor eyes were maintained in a profusion organ culture system.

first: Young

last: Kwon


title: Gene Expression Profiling Reveals Biological Insights into the Pathophysiology of Waldenströms macroglobulinemia

city: Little Rock

first: Yiming

last: Zhou

state: AR

address: 4301 West Markham St., Slot 776

institute: Myeloma Institute for Research and Therapy

summary:
Waldenströms macroglobulinemia (WM) is a rare lymphoproliferative disorder with apparent morphologic and immunophenotypic heterogeneity and its origins are still poorly understood. In this study, using Gene-Expression Profiling (GEP), we compared the global mRNA expression patterns of CD19+ WM B cells (WM-BC) and CD138+ WM plasma cells (WM-PC) with those of normal CD19+ peripheral blood B cells (PB-BC), tonsil-BC (T-BC), CD138+ T-PC and bone marrow PC (N-PC).
Keywords: Comparison of different immological cells

overall_design: The sample cohort studied consisted of CD19-selected peripheral blood B cells (PB-BC; n = 7), tonsil B cells (T-BC; n = 7), bone marrow B cells from WM (WM-BC; n = 12), tonsil plasma cells (T-PC; n = 9), bone marrow plasma cells from healthy donors (N-PC; n = 10), WM plasma cells (WM-PC, n = 9), and MM plasma cells (MM-PC; n = 11).

first: Wei

last: Xiong

first: John

last: shaughnessy

first: Fenghuang

last: Zhan


title: Expression data from T-cells isolated from healthy mice or mice with polyposis

status: Public on Sep 30 2012

city: Chicago

first: Nichole

last: Blatner

state: IL

address: 303 East Superior Street, Lurie 3-250

department: Robert H. Lurie Comprehensive Cancer Center

institute: Northwestern University

summary: There is much controversy about the role of T-regulatory cells (Treg) in human colon cancer. High densities of tumor-infiltrating Treg can correlate with better or worse clinical outcomes depending on the sutdy. Treg have potent anti-inflammatory functions that have been shown to control cancer progression. However, Treg isolated from patient with colon cancer or in mouse models of polyposis do not have the ability to suppress inflammation and instead promote cancer. Gene expression was preformed to determine differences between Treg isolated from healthy mice and Treg isolated from polyp-ridden mice.

overall_design: Treg (CD4+Foxp3-GFP+) and CD4+ non-Treg (CD4+Foxp3-GFP-) were isolated from various organs of healthy Foxp3-GFP reporter mice or polyp-ridden Foxp3-GFPxAPCΔ468 reporter mice

first: Jeffery

last: Ericson

first: Khashayarsha

last: Khazaie

first: Christophe

last: Benoist

first: Fotini

last: Gounari

first: Katherine

last: Rothamel


title: Changes in microRNA and mRNA expression with differentiation of human bronchial epithelial cells [mRNA]

city: Bethesda

first: Steven

last: Kern

state: MD

address: 10 Center Drive

department: Critical Care Medicine Department

institute: National Institutes of Health

summary:
Normal human bronchial epithelial (NHBE) cells cultured in an air-liquid interface (ALI) system form a polarized, pseudostratified epithelium composed of basal, ciliated and goblet cells that closely resemble the in vivo airway epithelium structure. ALI cultures of NHBE cells provide a unique in vitro system to investigate airway epithelial biology, including developmental, structural and physiologic aspects. In this study, we wanted to investigate mRNA expression patterns during airway epithelium differentiation.
By using microarrays, we studied the changes in expression of mRNAs in normal human bronchial epithelial cells as they differentiate from an undifferentiated monolayer to a differentiated pseudostratified epithelium after 28 days of air-liquid interface (ALI) culture, when epithelial cells differentially express basal, ciliated and goblet cell markers.

overall_design: Normal human bronchial epithelial cells were cultured in an air-liquid interface (ALI) system and harvested at three different time-points: subconfluent, confluent and day 28 of ALI. Samples were processed for total RNA extraction and hybridization on Affymetrix microarrays.  All the experiments were performed by triplicate.

first: Asuncion

last: Martinez-Anton

first: Milena

last: Sokolowska

first: A

last: Davis

first: Sara

last: Alsaaty

last: Taubenberger

first: Junfeng

last: Sun

first: Robert

middle: L

last: Danner

first: Michael

last: Eberlein

first: Carolea

last: Logun

first: James

last: Shelhamer


title: Expression data from replicating and quiescent liver cells isolated from mice young liver

city: Jerusalem

first: Amir

last: Eden

address: Givat Ram

department: Cell & Developmental Biology

country: Israel

institute: Hebrew University

summary:
We have developed a new transgenic mouse strain, expressing a CyclinB1-GFP fusion reporter, which marks replicating cells in the S/G2/M phases of the cell cycle to isolate live replicating and quiescent cells from the liver.
We used microarrays to compare the transcriptome of relicating and quiescent liver cells and reveal gene expression programs associated with cell proliferation in vivo

overall_design: Livers of three individual 3.5 week old, weaned CyclinB1-GFP mice were dissociated into single cells.Replicating (GFP-positive) and quiescent (GFP-negative) liver cells were FACS-sorted  for RNA extraction and hybridization on Affymetrix microarrays.

first: Yuval

last: Dor

first: Agnes

last: Klochendler


title: Angio-modulation in endothelial cells: an unexpected role of desmoglein-2 in regulating actin dynamics and its relevance to angiogenesis deregulation in systemic sclerosis

city: Florence

first: Betti

last: Giusti

address: viale Morgagni, 85

department: Dpt. of Medical and Surgical Critical Care

institute: University of Florence

summary: Gene expression study of DSG2 silenced human microvascular endothelial cells

overall_design: Affymetrix GeneChip Human Genome U133 Plus 2.0 Array were used to examine differentially expressed genes between normal microvascular endothelial cells and DSG2 silenced microvascular endothelial cells

first: Luciana

last: Rossi

first: Alberto

last: Magi


title: Changes in microRNA and mRNA expression with differentiation of human bronchial epithelial cells

last: Kern

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

overall_design: Refer to individual Series

first: Jeffery


title: Genome-wide identification of binding sites of Evi1 in human myeloid cell lines

city: Pamplona

first: Maria

last: Odero

address: Pio XII, 55

institute: University of Navarra

summary:
The EVI1 gene codes for a transcription factor with important roles in development and leukemogenesis. Overexpression of EVI1 in acute myeloid leukemia (AML) is one of the worst prognostic factors in patients with and without 3q26 rearrangements. Evi1 acts in several pathways through the interaction with proteins with important functions in hematopoiesis; however, the role of Evi1 as a transcription factor is not well known, and only some Evi1 target genes have been identified in mice. Our aim was to investigate the pathways and direct target genes of EVI1. Differential expression profiles after EVI1 knockdown allowed us to identify 125 genes involved in cell growth, differentiation and signal transduction that could be related to EVI1. Moreover, we looked for potential EVI1 binding sites within the region 1000 bp upstream of the transcription start sites of all human genes. We selected a total of 70 genes from the bioinformatics search, genes related to EVI1 by literature, and genes differentially expressed in the expression array. ChIP in the TF1 and HEL cell lines with two EVI1 antibodies demonstrated that EVI1 binds to the proximal promoter regions of 18 of these genes, most of them involved in important differentiation and proliferation pathways, confirming the important role of EVI1. Interestingly, EVI1 binds to the proximal region of its promoter, suggesting that it could be regulating its own transcription. Further functional studies are in progress. These data provide a starting point for further studies aimed at uncovering the mechanism for EVI1-induced transformation leukemias.

Keywords: Gene expression analysis after transient knockdown of EVI1.

overall_design: 12 samples. Three replicates per experimental condition. Two cell lines (HTB-58, TF-1). Transient EVI1 knockdown using anti-EVI1 siRNA molecules vs. control siRNA.

first: Iria

last: Vázquez

first: Miren

last: Maicas

first: Asunción

last: García-Sánchez

first: Elizabeth

last: Guruceaga

first: Nerea

last: Marcotegui

first: Laura

last: Garcia-Ortí

first: Oskar

last: Marin

first: Carmen

last: Vicente

first: Ion

last: Cristóbal

first: Ana

last: Conchillo

first: María

last: Gómez-Benito


title: Regulation of gene expression in the postnatally developing monkey hippocampal formation

city: Fribourg

first: Pierre

last: Lavenex

address: Chemin du Musée 5

department: Medicine

country: Switzerland

institute: University of Fribourg

summary:
The hippocampus is part of a brain network essential for memory function. Paradoxically, the hippocampus is also the brain structure that is most sensitive to hypoxic-ischemic episodes. Here we show that the expression of genes associated with glycolysis and glutamate metabolism in astrocytes and the coverage of excitatory synapses by astrocytic processes undergo significant decreases in the CA1 field of the monkey hippocampus during postnatal development. Given the established role of astrocytes in the regulation of glutamate concentration in the synaptic cleft, our findings indicate that a developmental decrease in astrocytic processes underlies the selective vulnerability of CA1 during hypoxic-ischemic episodes in adulthood, its decreased susceptibility to febrile seizures with age, as well as contribute to the emergence of selective, adult-like memory function.
Regulation of gene expression in the postnatally developing hippocampus might contribute to the emergence of selective memory function. However, the mechanisms that underlie the co-regulation of expression of hundreds of genes in different cell types at specific ages in distinct hippocampal regions have yet to be elucidated. By performing genome-wide microarray analyses of gene expression in distinct regions of the monkey hippocampal formation during early postnatal development, we identified one particular group of genes exhibiting a down-regulation of expression, between birth and six months of age in CA1 and after one year of age in CA3, to reach expression levels observed at 6-12 years of age. Bioinformatics analyses using NCBI, miRBase, TargetScan, microRNA.org and Affymetrix tools identified a number of miRNAs capable of regulating the expression of these genes simultaneously in different cell types, i.e., in neurons, astrocytes and oligodendrocytes. Interestingly, sixty-five percent of these miRNAs are conserved across species, from rodents to humans; whereas thirty-five percent are specific to primates, including humans. In addition, we found that some genes exhibiting greater down-regulation of their expression were the predicted targets of a greater number of these miRNAs. In sum, miRNAs may play a fundamental role in the co-regulation of gene expression in different cell types. This mechanism is partially conserved across species, and may thus contribute to the similarity of basic hippocampal characteristics across mammals. This mechanism also exhibits a phylogenetic diversity that may contribute to more subtle species differences in hippocampal structure and function observed at the cellular level.

overall_design: Sixteen male rhesus monkeys (Macaca mulatta; four 1-day-olds, four 6-month-olds, four 1-year-olds and four 6-12-year-olds) were used for this study. Monkeys were injected with an overdose of sodium pentobarbital (50 mg/kg i.v., Fatal-Plus, Vortech Pharmaceuticals, Dearborn, MI) and the brain rapidly extracted. Five-millimeter thick slices of the brain were cut and stored overnight in RNAlaterä (Ambion, Austin, TX) at 4oC. Brain slices were then frozen in liquid nitrogen and re-sectioned at 100 µm for microdissection. Five hippocampal regions were microdissected, including the entorhinal cortex (all layers at the mid-rostrocaudal level; intermediate division, Ei), and all layers of the dentate gyrus, CA3, CA1 and subiculum at mid-rostrocaudal level of the body of the hippocampus (at the level of the lateral geniculate nucleus). Only the mid-transverse portion of each region was dissected to ensure the specificity of the sample. RNA was isolated with Trizol® and single stranded cDNA synthesized starting with 10 µg of total RNA. The sample from each region from each monkey was run on a separate chip, thus totaling 4 (animals per age) X 4 (ages) X 5 (regions) = 80 independent chips.


title: autologous pairs of cutaneous melanocyte and melanoma cell cultures

status: Public on Sep 28 2012

city: Rome

first: diego

last: arcelli

address: Via delle Messi d'Oro 156

institute: Regina Elena National Cancer Institute

summary: Early-passage (<10 passages) cultures of melanoma cells from metastatic lymph node lesions and normal adult melanocytes explanted in parallel from the adjacent, non-involved skin of 5 patients were compared by cDNA arrays. Differences between normal and neoplastic counterparts were then assessed upon adjustment for individual factors.

overall_design: cDNA expression profiles comparison between normal and neoplastic counterparts in a strictly autologous setting

first: Patrizio

last: Giacomini

first: Diego

last: Arcelli


title: Impact of Ischemia and Procurement Conditions on Gene Expression in Renal Cell Carcinoma

status: Public on Sep 27 2012

city: INDIANAPOLIS

first: Nick

last: Liu

state: Indiana

address: 535 Barnhill Drive Suite 420

department: Department of Urology

institute: Indiana University Hospital

summary:
Previous studies have shown that ischemia alters gene expression in normal and malignant tissues. There are no studies that evaluated effects of ischemia in renal tumors. This study examines the impact of ischemia and tissue procurement conditions on RNA integrity and gene expression in renal cell carcinoma.
We used microarray analysis to evaulate the effect of ischemia and tissue procurement conditions on the gene expression changes in renal cell carcinoma

overall_design: Ten renal tumors were resected without renal hilar clamping from 10 patients with renal clear cell carcinoma.  Immediately after tumor resection, a piece of tumor was snap frozen. Remaining tumor samples were stored at 4C, 22C and 37C and frozen at 5, 30, 60, 120, and 240 minutes. Histopathologic evaluation was performed on all tissue samples, and only those with greater than 80% tumor were selected for further analysis. RNA integrity was confirmed by electropherograms and quantitated using RIN index. Gene expression study was done on Affymetrix HG 133 Plus 2.0 Platform. Altered gene expression was assessed by paired, two-sample t-test between the zero time point and aliquots from various conditions obtained from the same tumor.

first: Gennady

last: Bratslavsky


title: Gene expression profiling of control and Meis1 deleted bone marrow

status: Public on Sep 26 2012

city: Cincinnati

first: Ashish

last: Kumar

state: OH

address: 3333 Burnet Ave

department: Bone Marrow Transplant and Immune Deficiency

institute: Cincinnati Children's Hospital Medical Center

summary: The transcription factor Meis1 is preferentially expressed in hematopoietic stem cells (HSCs) and over-expressed in certain leukemias. However, the functions of Meis1 in hematopoiesis remain largely unknown. Using inducible knock-out mice, we found that Meis1 is required for the maintenance of hematopoiesis under stress and over long term while steady-state hematopoiesis was sustained in the absence of Meis1. Bone marrow cells of Meis1 deficient mice showed reduced colony formation, contained significantly fewer numbers of long- term HSCs and these Meis1-deficient HSCs exhibited loss of quiescence. Further, we found that Meis1 deletion led to the accumulation of reactive oxygen species (ROS) in HSCs and decreased expression of genes implicated in hypoxia response. Finally, ROS scavenging by N-acetyl cysteine or stabilization of hypoxia-signaling by knockdown of the VHL protein led to reversal of the effects of Meis1-deletion. Taken together, these results demonstrate that Meis1 protects and preserves HSCs by restricting oxidative metabolism.

overall_design: Lineage negative cells were harvested from Meis1-flox/CreER or control mice and incubated with 4-OHT for 48 hours. Total RNA was extracted and used for the profiling experiment.


title: Pluripotent Stem Cells Escape From Senescence-Associated DNA Methylation Changes [Illumina]

status: Public on Sep 24 2012

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

type: Methylation profiling by genome tiling array

summary: Pluripotent stem cells evade replicative senescence, whereas other primary cells lose their proliferation and differentiation potential after a limited number of cell divisions – and this is accompanied by specific senescence-associated DNA methylation (SA-DNAm) changes. Here, we investigate SA-DNAm changes in mesenchymal stromal cells (MSC) upon long-term culture, irradiation-induced senescence, immortalization and reprogramming into induced pluripotent stem cells (iPSC) using high density HumanMethylation450 BeadChips. SA-DNAm changes are highly reproducible and occur particularly in intergenic and non-promoter regions of developmental genes. We demonstrate that ionizing irradiation, although associated with a very similar senescence phenotype, does not affect SA-DNAm. Furthermore, overexpression of the catalytic subunit of the human telomerase (TERT) or conditional immortalization with a doxycycline-inducible system (TERT and SV40 TAg) result in telomere extension but do not influence SA-DNAm. In contrast, we demonstrate that reprogramming into iPSC prevented SA-DNAm changes. Our results indicate that replicative senescence is associated with an epigenetically controlled process which stalls cells in a particular differentiated state, whereas irradiation-induced senescence and immortalization are not causally related to this process. Absence of SA-DNAm in pluripotent cells may play a central role for their escape from cellular senescence.

overall_design: Samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

last: Koch

first: Kristina

last: Reck

first: Kaifeng

last: Shao

first: Qiong

last: Lin

first: Patrick

last: Ziegler

first: Sylvia

last: Joussen

first: Gudrun

last: Walenda

first: Wolf

last: Drescher

first: Bertram

last: Opalka

first: Tobias

last: May

first: Tim

last: Brümmendorf

first: Martin

last: Zenke

first: Tomo

last: Saric


title: Genetic module and miRNome trait analyses reflect the distinct biological features of endothelial progenitor cells from different anatomic locations

status: Public on Sep 21 2012

city: Taipei City

first: Tse-Shun

last: Huang

address: No.155, Sec.2, Linong Street

department: Institute of Microbiology and Immunology

country: Taiwan

institute: National Yang-Ming University

summary:
Background: Endothelial progenitor cells (EPCs) play a fundamental role in post-natal vascular repair, yet EPCs from different anatomic locations possess unique biological properties. The underlying mechanisms are unclear.     Method: We performed transcriptome analysis for EPCs isolated from 2 different sources: cord blood (CB) or adult peripheral blood (PB). Both gene expression microarray and small RNA sequencing (smRNA-seq) technologies were applied.
Results: EPCs from CB expressed abundant genes involved in cell cycle, hypoxia signalling and blood vessel development, correlating with the phenotypes that CB-EPCs proliferated more rapidly, migrated faster, and formed tubule structure more efficiently. smRNA-seq further deciphered miRNome patterns in EPCs isolated from CB or PB: 54 miRNAs were enriched in CB-EPCs, while another 50 in PB-EPCs. Specifically, CB-EPCs expressed more angiogenic miRNAs such as miR-31, while PB-EPCs possessed more tumor suppressive miRNAs including miR-10a. Knocking down miR-31 levels in CB-EPCs suppressed cell migration and microtubule formation, while overexpressing miR-31 in PB-EPCs helped to recapitulate some of CB-EPC functions.
Conclusion: Our results show the foundation for a more detailed understanding of EPCs from different anatomic sources. Stimulating the expression of angiogenic microRNAs or genes in EPCs of low activity (such as those from patients with cardiovascular diseases) might allow the development of novel therapeutic strategies.

overall_design:
EPC from cord blood or peripheral blood that outgrown after 2-4 week culture were collected. The RNA are extracted and profiled by Affymetrix GeneChip U133 plus 2.0 expression array.
This submission represents gene expression microarray component of study.

first: Cheng-Chung

last: Cheng

first: Hung-Hao

last: Lo

first: Yi-Chieh

first: Shi-Ting

last: Chang

first: Shing-Jyh

first: Hsei-Wei

last: Wang


title: Expression data from serous ovarian carcinomas, serous ovarian borderline tumors and surface epithelium scrapings from normal ovaries

city: Oslo

first: Bente

middle: Vilming

last: Elgaaen

address: Ullernchausseen 70

department: Department of Gynecological Oncology

country: Norway

institute: Oslo University Hospital

summary:
Objectives and goals: The causes and molecular pathology of ovarian cancer are essentially unknown. However, it is generally understood that serous ovarian borderline tumors (SBOT) and well differentiated (WD) serous ovarian carcinomas (SC) have a similar tumorigenetic pathway, distinct from moderately (MD) and poorly differentiated (PD) SC. The aim of this study was to identify mRNAs differentially expressed  between MD/PD SC, SBOT and superficial scrapings from normal ovaries (SNO),and to correlate these mRNAs with clinical parameters.

Results: From the global gene expression analyses, thirty mRNAs differentially expressed between MD/PD SC, SBOT and SNO were selected and validated by RT-qPCR, verifying 21 mRNAs to be significantly differentially expressed (p<0.01). Of these, 13 mRNAs were differentially expressed in MD/PD SC compared with SNO (p<0.01) and were correlated with clinical parameters. VEGFA was significantly upregulated (FC=6.1, p=6.0x10-6), and correlated with progression-free survival (p=0.037). ZNF385B was significantly downregulated (FC=-130.5, p=1.2x10-7), and correlated with overall survival (p=0.03). An increased TPX2 (p=0.03) and FOXM1 (p=0.044) expression correlated with optimal normalization of serum CA125 after treatment. Furthermore, we present a common molecular pathway for MD/PD SC, including VEGFA, FOXM1, TPX2, BIRC5 and TOP2A, all significantly upregulated and interacting with TP53.

Conclusions: We have identified 21 mRNAs differentially expressed (p<0.01) between MD/PD SC, SBOT and SNO. Thirteen were differentially expressed in MD/PD SC, including VEGFA and ZNF385B, correlating with survival, and FOXM1 and TPX2, correlating with normalization of serum CA125.

overall_design: By the use of oligonucleotid microarrays (Affymetrix U133 Plus 2.0 Arrays) differences in mRNA expression between eleven MD/PD SC, eight SBOT and four SNO samples were analyzed. Differentially expressed mRNAs were selected for validation by RT-qPCR in additional samples totaling 21 MD/PD SC, 13 SBOT and seven samples of SNO.  Each mRNA was run in quadruple. The mRNAs differentially expressed in MD/PD SC compared with SNO were correlated with clinical parameters.

middle: V

first: Ole

last: Olstad

first: Leiv

last: Sandvik

first: Elin

last: Ødegaard

first: Torill

last: Sauer

first: Anne

middle: C

last: Staff

first: Kaare

last: Gautvik


title: Cellular Origin and Pathophysiology of Chronic Lymphocytic Leukemia

city: Essen

first: Marc

middle: JS

last: Seifert

state: NRW

address: Virchowstraße 173

department: IFZ

institute: University Hospital Essen

summary:
The cellular origin of chronic lymphocytic leukemia (CLL) is debated. Transcriptome analysis of CLL and normal peripheral blood and splenic B cell subsets displayed highest similarity of CLL to mature CD5+ B cells. We identified a distinct CD5+CD27+ post-germinal center B cell subset, and revealed that immunoglobulin V gene mutated CLL are more similar to mutated CD5+ B cells, whereas unmutated CLL are more related to unmutated CD5+ B cells. Stereotyped immunoglobulin V gene rearrangements were significantly enriched among CD5+ B cells, providing further genetic evidence for a derivation of CLL from CD5+ B cells. Moreover, we identified deregulated expression patterns providing novel insights into the pathophysiology of CLL, including downregulation of EBF1 and KLF family members.
Transcriptome profiling of CLL and healthy human blood and splenic mature B cell subsets. Identification of deregulated transcription patterns with implications on CLL pathobiology.

overall_design:
Human mature B cell subsets and CLL with mutated (mCLL) and unmutated V gene status (uCLL) were purified from peripheral blood and spleen. Samples of 5 to 7 donors each were collected and processed in three batches in a two rounded in vitro transcription protocol. Retrieved data were batch corrected and subjected to analysis.
Human mature CD5+ B cell subsets and CLL with mutated (mCLL) and unmutated V gene status (uCLL) were purified from peripheral blood.

first: Ralf

last: Kueppers


title: Integrated bioinformatic and wet-lab approach to identify potential oncogenic networks in neuroblastoma: MEIS1

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

summary: The pediatric tumor neuroblastoma is the second cause of cancer-related death in children. Although several recurrent gene aberrations have been found, the main signaling networks in the neuroblastoma cell, that can give important clues for more specific, more efficient treatment, is still unknown. Here we demonstrate an analysis of the MEIS1 pathway in neuroblastic tumors. It suggests important regulatory connections to tumor differentiation, cell cycle, and cell death.

overall_design: Time-course experiment of MEIS1-shRNA induction, with 5 timepoints.

first: Dirk

last: Geerts

first: Jan

last: Koster

first: Rogier

last: Versteeg


title: Pluripotent Stem Cells Escape From Senescence-Associated DNA Methylation Changes

first: Wolfgang

last: Wagner

first: Carmen

last: Koch

first: Kristina

last: Reck

first: Kaifeng

last: Shao

first: Qiong

last: Lin

first: Patrick

last: Ziegler

first: Sylvia

last: Joussen

first: Gudrun

last: Walenda

first: Wolf

last: Drescher

first: Bertram

last: Opalka

first: Tobias

last: May

first: Tim

last: Brümmendorf

first: Martin

last: Zenke

first: Tomo

last: Saric


title: Commonly altered genomic regions in acute myeloid leukemia are enriched for somatic mutations involved in chromatin-remodeling and splicing

city: Berlin

first: Anna

last: Dolnik

address: Augustenburger Platz 1

department: Campus Virchow-Klinikum (CVK)

institute: Charité Universitätsmedizin Berlin

summary: Acute myeloid leukemia (AML) is characterized by molecular heterogeneity. As commonly altered genomic regions point to candidate genes involved in leukemogenesis, we used microarray-based comparative genomic hybridization and single nucleotide polymorphism profiling data of 391 AML cases to further narrow down genomic regions of interest. Targeted-resequencing of 1000 genes located in the critical regions was performed in a representative cohort of 50 AML samples comprising all major cytogenetic subgroups. We identified 120 missense/nonsense mutations as well as 60 insertions/deletions affecting 73 different genes (~3.6 tumor-specific aberrations/AML). While most of the newly identified alterations were non-recurrent, we observed a number of mutations affecting genes involved in epigenetic regulation including known candidates like TET2, TET1, DNMT3A and DNMT1, as well as mutations in the histone methyltransferases NSD1, EZH2 and MLL3. Furthermore, we found mutations in the splicing factor SFPQ and in the non-classical regulators of mRNA-processing CTCF and RAD21. These splicing-related mutations affected 10% of AML patients in a mutually exclusive manner. In conclusion, we could identify a significant enrichment of alterations in genes involved in aberrant splicing and epigenetic regulation in genomic regions commonly altered in AML, highlighting their important role in the molecular pathogenesis of AML.

overall_design: All samples were obtained from untreated patients at the time of diagnosis. Cells used for microarray analysis were collected from the purified fraction of mononuclear cells after Ficoll density centrifugation.

first: L

last: Bullinger

first: K

last: Doehner

first: H


title: The effect of ACSL4 expression on overall gene expression in breast cancer cell lines

status: Public on Sep 19 2012

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

country: France

institute: IARC WHO

summary: ACSL4 expression appears to be inversely associated with steroid hormone and growth factor receptor expression in breast cancer and positively correlated with an aggressive breast cancer phenotype.  Neither MCF-7 nor SKBr3 cells normally express ACSL4, and when manipulated to do so, develop basal-like characteristics, including increased proliferation, migration and anchorage independent growth.  We used an Affymetrix array platform to assess changes in individual gene expression as a function of conditional and stable expression of ACSL4 in MCF-7 and SKBr3 cells.

overall_design: In experiment 1, MCF-7 Tet-ON cells were transfected with ACSL4 cDNA and induced to express ACSL4 by addition of 1ug/ml of doxycycline (A) or vehicle (C) for 72 hours.  Three controls (C) and three doxycycline-induced (A) samples were evaluated for gene expression.  In experiment 2, MCF-7 cells were stably transfected with either an empty vector (C) or Lenti-ORF-ACSL4 (A).  In experiment 3, SKBr3 cells were stably transfected with either an empty vector (C) or Lenti-ORF-ACSL4 (A).

first: Xinyu

last: Wu

first: Yirong

last: Li

first: Jinhua

last: Wang

first: Xin

last: Wen

first: Max

middle: T

last: Marcus

first: Garrett

last: Daniels

first: David

middle: Y

last: Zhang

first: Fei

last: Ye

first: Ling

last: Adams

first: Baljit

last: Singh

last: Zavadil

first: Peng

last: Lee

first: Marie

last: Monaco


title: Analysis of TALE homeobox genes in neuroblastic tumors: ganglioneuroblastoma and ganglioneuroma

first: Richard

last: Volckmann

summary: A large proportion of patients suffering from the malignant pediatric tumor neuroblastoma die of progressive disease despite intensive therapy. Neuroblastomas belong to the group of neuroblastic tumors, together with the more benign, differentiated ganglioneuroblastomas and ganglioneuromas. Little is known of the genes driving the differentiation processes in these tumor types. A search for the transcription factors differentially expressed between ganglioneuromas, ganglioneuroblastomas, and neuroblastomas in a series of 110 neuroblastic tumors (NB110) identified a large number of HOX- and TALE (Three Amino acid Loop Extension)-class homeobox transcription factor genes. The MEIS1-3, PBX1 and -3, and PKNOX1 TALE genes showed highest expression in neuroblastomas and lowest in ganglioneuromas and ganglioneuroblastomas. The PKNOX2 and TGIF1-2 genes showed the opposite expression pattern. This suggests an involvement of TALE genes in neuroblastoma differentiation. Expression of MEIS1, a known oncogene in haematopoietic tumors, was high in all neuroblastomas, and strongly correlated with undifferentiated histology. Consequently, we generated IMR-32 neuroblastoma cells capable of inducible shRNA-mediated MEIS1 knockdown. We observed differentiation, growth arrest and induction of apoptosis upon MEIS1 down-regulation. Affymetrix profiling of time-course experiments using these cells allowed the identification of MEIS1 target genes. Analysis of the target genes in the NB110 series showed that 323 of these were also significantly correlated to MEIS1 expression and to tumor differentiation in neuroblastic tumors. Genes involved in the cell cycle and in developmental pathways were over-represented in this gene set. We conclude that MEIS1 governs several of the signal transduction routes important for neuroblastoma survival and differentiation.

overall_design: 12 ganglioneuroma (gn) and 10 ganglioneuroblastoma (gnb) were analyzed.

first: Rogier

last: Versteeg


title: Analysis of TALE homeobox genes in neuroblastic tumors and Cell lines


title: Expression data from prostate cancer Docetaxel-resistant cells

city: New York

first: Josep

last: Domingo-Domenech

state: New York

address: Annenberg Building, Room 24-16

department: Pathology

institute: Mount Sinai School of Medicine

summary: Docetaxel is the standard first line therapy for hormone-refractory prostate cancer patients. Here we generated models of Docetaxel resistance in prostate cancer cells to study the molecular pathways that drive the acquisition of resistance to this therapy. We used microarrays to detail the global program of gene expression underlying the acquisition of Docetaxel resistance in prostate cancer cells.

overall_design: Parental Docetaxel-sensitive prostate cancer cell lines (DU145 and 22Rv1) and selected Docetaxel-resistant cells (DU145-DR and 22Rv1-DR) were harvested for RNA extraction and hybridization on Affymetrix microarrays. Samples were analyzed in triplicates in order to increase the resolution of expression profiles.

first: Carlos

last: Cordon-Cardo


title: Expression data from BMP9-treated human dermal microvascular endothelial cells (HMVEC-D)

city: Scarborough

first: Calvin

last: Vary

state: Maine

address: 81 Research Drive

department: Maine Medical Center Research Institute

institute: Maine Medical Center

summary: BMP9 signaling has been implicated in hereditary hemorrhagic telangiectasia and vascular remodeling, acting via the HHT target genes, endoglin and ALK1. This study sought to identify endothelial BMP9-regulated proteins that could affect the HHT phenotype. Gene ontology analysis of cDNA microarray data obtained following BMP9 treatment of primary human endothelial cells indicated regulation of chemokine, adhesion, and inflammation  pathways.

overall_design: The sample set is comprised of three biological replicate control human dermal microvascular endothelial cells, and three treated (5 ng/ml human recombinant BMP9) biological replicate human dermal microvascular endothelial cells

middle: P


title: Conversion of human fibroblasts into vascular cells (methylation)

status: Public on Sep 18 2012

city: La Jolla

first: Rathi

middle: D

last: Thiagarajan

state: CA

address: 2880 Torrey Pines Scenic Drive

department: Reproductive Medicine

institute: UCSD

summary: We report a novel technique to reprogram human fibroblasts into endothelial and smooth muscle cells using partial iPSC reprogramming and chemically defined media. Using appropriate media conditions for differentiation of human pluripotent cells to CD34+ vascular progenitor cells, we show that temporary expression of pluripotent transcription factors and treatment with chemically-defined media, will induce differentiation of human fibroblasts to CD34+ vascular progenitor cells. Sorted CD34+ cells can then be directed to differentiate into vascular endothelial cells expressing a variety of smooth muscle markers.

overall_design: We have assessed the global DNA methylation (Illumina Infinium HD 450K DNA methylationBeadChips) and transcriptional (Illumina HT12v4 Gene Expression Bead Array) profiles of transdifferentiated endothelial cells and smooth muscle, human embryonic stem cell (hESC) and human induced pluripotent stem cell (hiPSC) differentiated CD34+ angioblasts, hESCs,  hiPSC, primary smooth muscle and primary human umbilical vein endothelial cells using microarrays.

first: Leo

last: Kurian

first: Ignacio

last: Sancho-Martinez

first: Emmanuel

last: Nivet

first: Krystal

last: Moon

first: Caroline

last: Pendaries

first: Cecile

last: Volle-Challier

first: Francoise

last: Bono

first: Jean-Marc

last: Herbert

first: Yun

last: Xia

first: Mo

last: Li

first: Julian

last: Pulecio

first: Nuria

last: Monserrat

first: Sergio

last: Ruiz

first: Aitor

last: Aguirre

first: Ilir

last: Dubova

first: Francesca

last: Boscolo

first: Jeanne

middle: F

last: Loring

first: Louise

last: Laurent

first: Juan

last: Belmonte


title: Expression data from 5 IFN type I-derived Dendritic Cells

status: Public on Sep 20 2012

city: Montpellier

first: Geneviève

last: Garcin

address: UM2. Place Eugene Bataillon. Bat 24.

institute: CNRS UMR5235

summary: Type I interferon (IFN) is a family of 15 cytokines (in human 13α, 1β,1ω) which exert several cellular functions through the binding to a common receptor. Despite the initial activation of the same Jak/Stat signalling pathway, the cellular response may be different depending on the type I IFN subtype. We investigated the activity of different type I IFN subtypes - IFNα1, α2, α8, α21, ω and β- on the differentiation of DC. Transcriptome analyses identified two distinct groups, the IFNα/ω-DC and the IFNβ-DC. 78 genes, 7 chemokines and expression levels of cell surface markers characteristic of DC distinguished IFNα-DC and IFNβ-DC. These differences are unlikely to impact the efficacy of T cell functional response since IFNα2-DC and IFNβ-DC were equipotent in inducing the proliferation and the polarization of allogenic naïve CD4 T cells into Th1 cells and in stimulating autologous memory CD4 or CD8 T cells. In contrast, IFNα2-DC were found to be more efficient than IFNβ-DC in the phagocytic uptake of dead cells.

overall_design: Human blood monocytes were differentiated in DC by using 5 differents IFN type I (IFNα2, α1, α8, α21 and β). After 3 days of differentiation RNA were extracted and analyzed by affymetrix microarray.

first: Genevi¨ve

first: Yann

last: Bordat

first: Paul

last: Chuchana

first: Dani¨le

last: Monneron

first: Helen

middle: K

last: Law

first: Jacob

last: Piehler

first: Gilles

last: Uze


title: Drug tolerance development of mouse Bcr/Abl pre-B ALL cells on irradiated MEFs

city: Monrovia

first: Nora

last: Heisterkamp

address: 1218 S Fifth Avenue

department: Department of Systems Biology

institute: Beckman Research Institute City of Hope

summary: Although cure rates for acute lymphoblastic leukemia (ALL) have increased, development of resistance to drugs and patient relapse are common. The environment in which the leukemia cells are present during the drug treatment is known to provide significant survival benefit. Here, we have modeled this process by culturing murine Bcr/Abl-positive acute lymphoblastic leukemia cells in the presence of stroma while treating them with a moderate dose of two unrelated drugs, the farnesyltransferase inhibitor lonafarnib and the tyrosine kinase inhibitor nilotinib. This results in an initial large reduction in cell viability of the culture and inhibition of cell proliferation. However, after a number of days, cell death ceases and the culture becomes drug-tolerant, enabling cell division to resume. We used gene expression profiling to analyze changes in the transcriptome of these leukemia cells over a 3-4 week period, taking samples at the start, the point at which most of the leukemia cells had been eradicated while a small percentage survived, and at the end when the cells were proliferating again.

overall_design: We used two different pre-B ALL cell lines 8093 and Bin-2, derived from two BCR/ABL transgenic mice. 8093 is a leukemia on an inbred f11 C57Bl/6J background whereas Bin2 was derived from ALL on a mixed genetic background. Each was treated with the tyrosine kinase inhibitor nilotinib = AMN107 (20 nM for 8093, 50 nM for Bin-2, abbreviated with nil or n) or with the farnesyltransferase inhibitor (FTI) Lonafarnib/SCH66336 (1 mM for 8093, 0.25 mM for Bin-2; abbreviated with lon or l) in the presence of an irradiated mouse embryonic fibroblast feeder layer. Cells loosely attached to the top of the feeder layer or present in the medium were harvested for RNA isolation. Except where noted, all samples were taken in biological triplicates (separate plates). Samples were taken at t=0 (begin/start); on day 3 for Bin-2 (nil and lon) when the viability was 5-10% based on Trypan blue exclusion, on d4 for 8093 (lon, viability 20%) or d3 (nil, 5-10% viability) at the midpoint when cells start to develop resistance, and on d30 (Bin-2 x lon), d21 (Bin-2 x nil), d26 (8093 x lon) and d 20 (8093 x nil) when the viability of the culture was completely restored (around 90% viability), and the cells started proliferating agin in the presence of the drug. Cells were kept in the presence of drug throughout the entire treatment, which was added fresh with medium changes. The same feeder layer was kept during the entire period.

first: Niklas

last: Feldhahn

first: Sonia

last: Stoddart

first: John

last: Groffen


title: Bcl6 expression specifies the T follicular helper cell program in vivo

status: Public on Sep 17 2012

city: Bethesda

first: Lai

last: Wei

address: 10 Center Dr. Room 2B47

institute: NIH/NEI/NCCAM

summary: T follicular helper (Tfh) cells play a pivotal role in germinal center reactions, which requires Bcl6 transcription factor. To analyze their relationships with other effector T cell lineages and their stability in vivo, we developed and analyzed a new Bcl6 reporter mouse alone or together with other lineage reporter systems. Assisted with genome-wide transcriptome analysis, we show substantial plasticity of T cell differentiation in the early phase of immune response. At this stage, CXCR5 appears to be expressed in a Bcl6-independent manner. Once Bcl6 is highly expressed, Tfh cells can persist in vivo and some of them develop into memory cells. Together, our results indicate Bcl6 as a bona fide marker for Tfh polarized program.

overall_design: Three group of samples, with 2 biological replicates within each group and total of 6 samples were analyzed.

first: Liu

last: Xindong

first: Yan

last: Xiaowei

first: Tian

last: Qiang

first: Dong

last: Chen


title: Conversion of human fibroblasts into vascular cells

first: Rathi

last: Thiagarajan

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

overall_design: Refer to individual Series


title: Effects of co-culture of  Endothelial Cells with Mesenchymal Stem Cells on Gene Expression

status: Public on Sep 15 2012

city: Houston

first: LI

last: SHEN

state: TX

address: 1400 Pressler Street

institute: MD Anderson Cancer Center

summary: Study designed to explore the effects of endothelial cell/MSC co-culture on individual gene expression profile of each cell type

overall_design: 4 independent samples from each of 4 groups: MSCs cultured alone; Pulmonary endothelial cells cultured alone; MSCs co-cultured with PECs then FACS separated; PECs co-cultured with MSCs then FACS separated

first: Shibani

last: Pati

first: Aarif

last: Khakoo

first: Jianhu

last: Zhang


title: Data expression in alveolar macrophages induced by lipopolysaccharide in humans

city: Marcy L'Etoile

first: Frederic

last: Reynier

address: Chemin de l'Orme

institute: bioMerieux

summary: Rationale: Lipopolysaccharide (LPS) is ubiquitous in the environment. Inhalation of LPS has been implicated in the pathogenesis and/or severity of several lung diseases, including pneumonia, chronic obstructive pulmonary disease and asthma. Alveolar macrophages are the main resident leukocytes exposed to inhaled antigens.   Objectives: To obtain insight into which innate immune pathways become activated within human alveolar macrophages upon exposure to LPS in vivo.

overall_design: In seven healthy humans sterile saline was instilled into a lung segment by bronchoscope, followed by instillation of LPS into the contralateral lung. Six hours later a bilateral bronchoalveolar lavage was performed and whole-genome transcriptional profiling was done (Affymetrix HG-U133 Plus 2.0) on purified alveolar macrophages, comparing cells exposed to saline or LPS from the same individuals.

first: Alex

last: de Vos

first: Jacobien

middle: J

last: Hoogerwerf

first: Paul

last: Bresser

first: Jaring

last: van der Zee

first: Malick

last: Paye

first: Alexandre

last: Pachot

first: Bruno

last: Mougin

first: Tom

last: van der Poll


title: Ascorbic acid depletion and scorbutic extracellular matrix in mice deficient in endoplasmic reticulum thiol oxidases

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

summary: Endoplasmic reticulum (ER) thiol oxidases initiate a disulfide relay to oxidatively-fold secreted proteins. We found that combined loss-of-function mutations in genes encoding the ER thiol oxidases ERO1alpha, ERO1beta and PRDX4, compromised the extracellular matrix in mice and interfered with the intracellular maturation of procollagen. These severe abnormalities were associated with an unexpectedly-modest delay in disulfide bond formation in secreted proteins but a profound, five-fold lower procollagen 4 hydroxyproline content and enhanced cysteinyl sulfenic acid modification of ER proteins. Tissue ascorbic acid content was lower in mutant mice and ascorbic acid supplementation improved procollagen maturation and lowered sulfenic acid content, in vivo. In vitro, the presence of a sulfenic acid donor accelerated the oxidative inactivation of ascorbate by an H2O2 generating system. Compromised ER disulfide relay thus exposes protein thiols to competing oxidation to sulfenic acid, resulting in depletion of ascorbic acid, impaired procollagen proline 4-hydroxylation and a non-canonical form of scurvy.

overall_design: double and triple mutants and wild type

first: E

last: Zito

first: D

last: Ron


title: Microarray analysis of gene expression changes in human A549 lung cancer cells upon siRNA knockdown of FAM60A and SDS3

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

country: USA

institute: Stowers Institute

summary:
The Sin3 histone deacetylase (HDAC) complex is a 1.2 MDa chromatin modifying complex that can repress transcription by binding to gene promoters and deacetylating histones.  The Sin3/HDAC complex can affect cell cycle progression through multiple mechanisms and is among the targets of anticancer drugs, called HDAC inhibitors.  We describe the identification of a new subunit of the Sin3 complex named family with sequence similarity 60 member A (FAM60A).  We show that FAM60A/Sin3 complexes normally suppress the epithelial-to-mesenchymal transition (EMT) and cell migration.  This occurs through transcriptional repression of genes that encode components of the TGF-beta signaling pathway.  This work reveals that FAM60A and the Sin3 complex are upstream repressors of TGF-beta signaling, EMT and cell migration and extends the known biological roles of the Sin3 complex.  This experiment investigates the role of FAM60A in gene expression by comparing A549 lung cancer cells treated with or without siRNA against FAM60A.
The Sin3 histone deacetylase (HDAC) complex is a 1.2 MDa chromatin modifying complex that can repress transcription by binding to gene promoters and deacetylating histones. SDS3 is a core component of the Sin3 complex. The Sin3/HDAC complex can affect cell cycle progression through multiple mechanisms and is among the targets of anticancer drugs, called HDAC inhibitors.  We describe the identification of a new subunit of the Sin3 complex named family with sequence similarity 60 member A (FAM60A).  We show that FAM60A/Sin3 complexes normally suppress the epithelial-to-mesenchymal transition (EMT) and cell migration.  This occurs through transcriptional repression of genes that encode components of the TGF-beta signaling pathway.  This work reveals that FAM60A and the Sin3 complex are upstream repressors of TGF-beta signaling, EMT and cell migration and extends the known biological roles of the Sin3 complex. As a base line to better understand the relationship between FAM60A and the Sin3 complex, this experiment investigates the gene expression changes which occur in A549 lung cancer cells when the Sin3 complex is perturbed by knockdown of a core component via siRNA against SDS3.

overall_design:
FAM60A siRNA knockdowns were compared to a non-targeting control in triplicate, for a total of 6 samples.
SDS3 siRNA knockdowns were compared to a non-targeting control in triplicate, for a total of 6 samples.

first: Karen

last: Smith

first: Jerry

last: Workman


title: Expression data from HeLa cells transfected with SLC44A5

city: Nishigo

first: Mayumi

last: Sugimoto

state: Fukushima

address: Odakurahara 1 Odakura

institute: National Livestock Breeding Center

summary:
We identified SLC44A5 as a gene associated with birth weight in cattle based on genome wide association studies.
To identify the mechanisms involved in growth and choline transporter, we performed genome-wide mRNA expression analysis in HeLa cells transfected with SLC44A5.

overall_design: HeLa cells were transfected with negative control, siRNA against SLC44A5, bovine SLC44A5 expression plasmid, and an empty vector control for RNA extraction and hybridization on Affymetrix microarrays.

first: Yoshikazu


title: Identification of differentially regulated genes upon shRNA-mediated knock-down of HLX in the URE leukemia cell line

status: Public on Sep 14 2012

city: Bronx

first: Boris

last: Bartholdy

state: NY

address: 1300 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

summary: To study the role of Hlx in hematopoietic differentiation and tumorigenesis, URE cells were infected with short-hairpin-containing pSIH1-H1-copGFP lentiviral vector (System Biosciences, Mountain View, CA) containing either nucleotide sequences targeting luciferase (shControl) or HLX (shHLX). After 24hrs incubation in Iscove’s modified Dulbecco’s medium (IMDM) containing FBS, mIL-3, mIL-6 and mSCF with lentiviral supernatants in the presence of 8ug/ml polybrene, cells were cultured in fresh medium for several days. Subsequently, GFP+ cells were sorted by FACS and RNA was prepared.

overall_design: URE cells were infected with short-hairpin-containing pSIH1-H1-copGFP lentiviral vector (System Biosciences, Mountain View, CA) containing either nucleotide sequences targeting luciferase (shControl) or HLX (shHLX). After 24hrs incubation in Iscove’s modified Dulbecco’s medium (IMDM) containing FBS, mIL-3, mIL-6 and mSCF with lentiviral supernatants in the presence of 8ug/ml polybrene, cells were cultured in fresh medium for several days. Subsequently, GFP+ cells were sorted by FACS and RNA was prepared. Three replicates of each, shControl and shHLX-transduced cells were used. The goal was to study the role of Hlx in hematopoietic differentiation and tumorigenesis.

first: Masahiro

last: Kawahara

first: Britta

last: Will

first: Laura

last: Barreyro

first: Constantine

middle: S

last: Mitsiades

first: Ulrich

last: Steidl


title: Identification of differentially regulated genes in hematopoietic stem cells and URE leukemia cell line


title: Temporal transcriptional profiling of polyamine-depleted NIH3T3 cells

status: Public on Sep 11 2012

city: Rehovot

first: Guy

last: Landau

address: Herzl 234

department: Molecular Genetics

institute: Weizmann Institute of Science

summary:
Polyamines are absolutely required for cell growth and proliferation. While polyamine depletion results in reversible cell cycle arrest, the actual mechanism of growth inhibition is still obscure.
This work aimed at determining the cellular processes affected by reduction in the intracellular polyamine levels

overall_design: In order to reveal the general transcriptional responses to polyamine depletion in mammalian cells, NIH3T3 mouse fibroblasts were treated with 1mM L-Difluoromethylornithine (DFMO), G1 cellular fractions were collected by sorting at 0,12, 24, 48 and 96 hours upon addition of the reagent, total RNA was extracted, reverse-transcribed, fragmented, labeled and hybridized to Affymetrix MoGene 1.0 ST  DNA array.

first: Avichai

last: Ran

first: Zippi

last: Bercovich

first: Ester

last: Feldmesser

first: Shirley

last: Horn-Saban

first: Eduard

last: Korkotian

first: Jasmine

last: Jacob-Hirsh

first: Gideon

last: Rechavi

first: David

first: Chaim

last: Kahana


title: Neuroblastoma cell lines treated with DAC (2'-deoxy-5-azacytidine), a DNA-methylation inhibitor

status: Public on Sep 13 2012

city: Ghent

first: Maté

last: Ongenaert

address: De Pintelaan 185 - MRB

department: Center for Medical Genetics

country: Belgium

institute: Ghent University

summary: 8 neuroblastoma (NB) cell lines (CLB-GA, IMR-32, SH-SY5Y, N206, CHP-902R, LAN-2, SK-N-AS, SJNB-1) were profiled on the Affymetrix HGU-133plus2,0 platform before and after treatment with DAC (2'-deoxy-5-azacytidine) to investigate the influence on expression after inhibiting DNA-methylation

overall_design: 8 NB cell lines were included (CLB-GA, IMR-32, SH-SY5Y, N206, CHP-902R, LAN-2, SK-N-AS, SJNB-1), before and after treatment with 3 micromolars of DAC for 3 days

first: Anneleen

last: Decock

first: Jasmien

last: Hoebeeck

first: Jo

last: Vandesompele

first: Frank

last: Speleman


title: Identification of differentially regulated genes upon overexpression of HLX in wild-type hematopoietic stem cells

first: Boris

last: Bartholdy

summary: The goal was to study the role of Hlx in hematopoiesis.

overall_design: Sorted Lin-Kit+Sca-1+ cells from wild-type FVB/nJ bone marrow were infected with control (pCAD-IRES-GFP) or Hlx lentivirus (pCAD-IRES-GFP-Hlx) and cultured for 2 days in Iscove’s modified Dulbecco’s medium (IMDM) containing FBS, mIL-3, mIL-6 and mSCF with lentiviral supernatants in the presence of 8ug/ml polybrene. Subsequently, GFP+ cells were sorted by FACS and RNA was prepared. Three replicates of each, control vector transduced and HLX-transduced cells were used.

first: Masahiro

last: Kawahara

first: Britta

last: Will

first: Laura

last: Barreyro

first: Constantine

middle: G


title: Microarray analysis of femoral artery injury in mice

status: Public on Sep 10 2012

city: Philadelphia

first: Richard

last: Assoian

state: PA

address: 421 Curie Blvd

department: Pharmacology

institute: University of Pennsylvania

summary: To determine the differential expression of genes at sites of vascular injury in mice

platform_organism:
Mus musculus
synthetic construct

overall_design: Four male, 5-6 mo old SMA-GFP mice (numbered 57, 60, 61, and 63) were subjected to fine wire femoral artery injury.  The left femoral artery of each mouse was injured, and the contralateral artery was used as an uninjured control.  The mice recovered from the injury procedure for 14 days, at which time they were sacrificed. The femoral arteries were removed and the adventitial side was extensively cleaned. The arteries were carefully opened longitudinally and immediately imaged for GFP.  GFP-negative regions of the arteries, representing sites of vascular injury were microdissected, quick-frozen on dry ice, and stored in liquid nitrogen. Uninjured arteries were isolated and analyzed similarly; the entire uninjured artery was frozen.  Total RNA was prepared.  A 100-ng portion of each sample was subjected to linear amplification and hybridized to Affymetrix mouse gene 1.0ST.


title: Expression of BRAF inhibitor resistant colon cancer lines

first: Scott

last: Kopetz

address: 1515 Holcombe Blvd, Unit 426

summary: Colon cancer cell lines with partial sensitivity to the BRAF inhibitor PLX4720 were grown in increasing concentration of the drug to develop acquired resistance.  Gene expression was performed for comparison of the resistant clones to the parental lines.


title: Expression of constitutively active FOXO3 in murine forebrain leads to a loss of neural progenitors

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

country: Germany

institute: Ulm University

summary: We have generated transgenic mice with tetracycline-regulated conditional expression of a constitutively active allele of FoxO3 under the control of the forebrain-specific CaMKIIa promoter. In adult animals, there was a reduction of brain weight by 30% and an almost complete loss of the dorsal dentate gyrus with normal cortical layering. Interestingly, the adult mice showed motor hyperactivity and a selective loss of long-term memory with normal spatial learning. We observed enhanced apoptosis starting from day E10.5. Performing microarray expression analyses and Q-PCR validation with E12.5 forebrain RNA, we observed an over-representation of thalamic markers and an under-representation of cortical markers in transgenic as compared to control animals. Immunohistochemical data show a loss of progenitors in the lateral ventricles. Up-regulation of Pik3ip1 as a target gene of FoxO3 could be responsible for the observed increase in apoptosis. The obtained forebrain expression signature is reminiscent of a Pax6 knockdown phenotype showing that expression of this FoxO3 allele during development affected neural progenitor survival and overall brain development. Conclusion: Neural progenitors are vulnerable to constitutively active FoxO3-induced apoptosis.

overall_design: We sought to determine the transcriptional differences in forebrains from E12.5 mice expressing a constitutively active alleleof FoxO3 under the control of the forebrain-specific CaMKIIa promoter. To this end two time-pregnant dams were sacrificed 12 days after the vaginal plug was detected, and the embryos were prepared. Visual staging of the embryos confirmed their age. Genotyping and luciferase measurements were performed in order to assess presence and acitivity of the transgenes.

first: Uta

last: Schmidt-Strassburger

first: Thomas

last: Wirth

first: Nina

last: Ushmorova


title: Temporal transcriptional profiling of growth resumption following polyamine-depletion

first: Guy

last: Landau

summary:
Polyamines are absolutely required for cell growth and proliferation. While polyamine depletion results in reversible cell cycle arrest, the actual mechanism of growth inhibition is still obscure.
This experiment aimed at determining the cellular processes elicited by re-addition of polyamines to polyamine-depleted (growth arrested) cells.

overall_design: In order to reveal the general transcriptional responses to polyamine re-addition, NIH3T3 mouse fibroblasts were first treated with 1mM L-Difluoromethylornithine (DFMO) for 96 hours and then growth stimulated by spermidine. Cells were collected at 0, 30, 60, 120, 240, 360, 480 and 600 min upon addition of spermidine to polyamine-depleted (growth arrested) cells. Total RNA was isolated, reverse-transcribed, fragmented, labeled and hybridized to Affymetrix MoGene 1.0 ST  DNA array.

first: Avichai

last: Ran

first: Zippi

last: Bercovich

first: Ester

last: Feldmesser

first: Shirley

last: Horn-Saban

first: Eduard

last: Korkotian

first: Jasmine

last: Jacob-Hirsh

first: Gideon

last: Rechavi

first: David

last: Ron

first: Chaim


title: Mitochondrial 12S hypermethylation in HeLa cells and A1555G cybrids

city: Hershey

first: Nuno

last: Raimundo

address: 500 University Dr, College Of Medicine, Room C4769

department: Cellular and Molecular Physiology

institute: Penn State College of Medicine

summary: This dataset investigates the transcriptional effect of mitochondrial 12S rRNA hypermethylation, both by overexpressing the mitochondrial methyltransferase mtTFB1 in HeLa cells and by using A1555G cybrids, where the 12S rRNA is hypermethylated. HeLa cells overexpressing a methyltransferase-deficient mtTFB1 (mtTFB1[G65A]) and wild-type A1555A cybrids were used as controls.

overall_design: four samples with 12S rRNA hypermethylation (two cell lines, with two biological replicates each) versus four samples with basal 12S rRNA methylation (two cell lines, with two biological replicates each)

first: Gerald

last: Shadel


title: Grhl2 regulated genes in the mouse lung epithelial MLE15 cell line

city: Boston

first: Maria

middle: Isabel

last: Ramirez

state: MA

address: 72 E. Concord St. E603

department: Medicine

institute: Boston University School of Medicine

summary: The Grainyhead family of transcription factors controls morphogenesis and differentiation of epithelial cell layers in multicellular organisms by regulating cell junction- and proliferation-related genes. Grainyhead-like 2 (Grhl2) is expressed in developing mouse lung epithelium and is required for normal lung organogenesis. The specific epithelial cells expressing Grhl2 and the genes regulated by Grhl2 in normal lungs are mostly unknown. In these studies, we identified the NK2 homeobox 1 transcription factor (Nkx2-1) as a direct transcriptional target of Grhl2. By binding and transcriptional assays, and by confocal microscopy we showed that these two transcription factors form a positive feed-back loop in vivo and in cell lines, and are co-expressed in lung bronchiolar and alveolar type II cells. The morphological changes observed in flattening lung alveolar type II cells in culture are associated with down-regulation of Grhl2 and Nkx2-1. Reduction of Grhl2 in lung epithelial cell lines results in lower expression levels of Nkx2-1 and of known Grhl2 target genes. By microarray analysis we identified that in addition to Cadherin1 and Claudin4, Grhl2 regulates other cell interaction genes such as semaphorins and their receptors, which also play a functional role in developing lung epithelium. Impaired collective cell migration observed in Grhl2 knockdown cell monolayers is associated with reduced expression of these genes and may contribute to the altered epithelial phenotype reported in Grhl2 mutant mice. Thus, Grhl2 functions at the nexus of a novel regulatory network, connecting lung epithelial cell identity, migration and cell-cell interactions.

overall_design:
To identify genes regulated by GRHL2 in lung epithelial cells, we performed cDNA microarray analyses in MLE15 cells transduced with Grhl2-shRNA and compared to a non-silencing control.
Independent transductions of MLE15 cells using Grhl2-shRNA (n=3) and a non-silencing control (n=2) were analyzed.

first: S

last: Varma

first: Y

last: Cao

first: J-B

last: Tagne

first: M

last: Lakshminarayanan

first: J

last: Li

first: T

middle: B

last: Friedman

first: R

last: Morell

first: D

last: Warburton

middle: N

last: Kotton

middle: I

last: Lenburg

last: Milton


title: Gene expression of differentiating hESCs into otic progenitors

status: Public on Sep 12 2012

city: Sheffield

first: Marcelo

middle: Nicolas

last: Rivolta

state: Yorkshire

address: Western Bank

department: Biomedical Science

institute: University of Sheffield

summary: Stem cells, with their potential to generate different lineages, could offer a solution by replacing damaged or lost cells within the inner ear. We have shown that human embryonic stem cells can be induced to differentiate into otic progenitors, and then into hair cell-like cells and neurons that display expected electrophysiological properties. More importantly, once these otic progenitors are transplanted into animals with induced hearing loss, they differentiate and elicit a significant recovery of auditory function.   The generation of otic progenitors is triggered by FGF signalling. In this dataset we have analysed the global gene expression profile of undifferentiated hESCs and compared with cultures that have been treated with FGF3 and 10, the two ligands involved in otic induction, or cultures that have been allowed to differentiate under basal conditions without FGF (DFNB).

overall_design: Global gene expression profiles were obtained from hESC lines H14, Shef3 and Shef1 by hybridizing samples from undifferentiated cells (Day 0) and cells exposed to either FGF3+10- or DFNB medium for 14 days. Three experimental conditions are therefore produced: hESC, FGF3+10 and DFNB.


title: Expression data comparing adult human islets to human embryonic stem cell-derived insulin-positive and insulin-negative cells

status: Public on Sep 09 2012

city: Toronto

first: Michael

last: Wheeler

state: Ontario

address: 1 King's College Circle

department: Physiology

institute: University of Toronto

summary: The study was completed to compare expression profiles of primary human beta cells (in the form of adult human islets), to the expression profile of hESC-derived beta-like cells. A HES3 line modified by homologous recombination to express GFP under the insulin promoter allowed us to FACS sort the hESC-derived cells into purified insulin-positive (presumably beta-like cells), and insulin-negative populations.

overall_design: Expression profile of adult human islets from cadaveric donors is compared to insulin-positive and insulin-negative populations of hESC-derived beta-like cells

first: Kacey

last: Prentice


title: Transcriptional response of Escherichia coli O157:H7 to cinnamaldehyde

status: Public on Sep 08 2012

city: Winnipeg

first: Richard

middle: A

last: Holley

state: Manitoba

address: 250 Ellis Building

department: Department of Food Science

institute: University of Manitoba

summary: Cinnamaldehyde is a natural antimicrobial and has been found to be effective against many foodborne pathogens including Escherichia coli O157:H7. Although its antimicrobial effects have been well investigated, limited information is available on its effects at the molecular level. Sublethal treatment at 200 mg/l cinnamaldehyde inhibited growth of E. coli O157:H7 at 37oC and for ≤ 2 h caused cell elongation, but from 2 to 4 h growth resumed and cells reverted to normal length. To understand this transient behaviour, genome-wide transcriptional analysis of E. coli O157:H7 was performed at 2 and 4 h exposure to cinnamaldehyde. Drastically different gene expression profiles were obtained at 2 and 4 h. At 2 h exposure, cinnamaldehyde induced overexpression of many oxidative stress-related genes, reduced DNA replication, and synthesis of protein, O-antigen and fimbriae. At 4 h, many cinnamaldehyde-induced repressive effects on E. coli O157:H7 gene expressions were reversed and oxidatve stress genes were nolonger differentially expressed.

overall_design: Duplicate E. coli O157:H7 cultures with or without 200 mg/l cinnamaldehyde were incubated at 37°C for ≤ 4 h. Cinnamaldehyde-induced changes in gene expression profiles were compared at 2 and 4 h using Affymetrix Ginechip 2.0 microarrays.

first: Jeyachchandran

last: Visvalingam

first: Juan

last: Hernandez-Doria