title: Expression data from Control and Six1 expressing MCF7 derived xenograft tumors

status: Public on Apr 01 2012

city: Aurora

first: Heide

last: Ford

state: CO

address: 12800 E 19th Ave RC1 North, Room 5102

department: OB/Gyn

institute: University of Colorado at Denver

summary: Although an important association between lymph node metastasis and poor prognosis in breast cancer was observed decades ago, an active role for the lymphatic system in metastatic dissemination has only recently been examined. We demonstrate that the Six1 homeoprotein promotes peri- and intra-tumoral lymphangiogenesis, lymphatic invasion, and distant metastasis of breast cancer cells. We identify the pro-lymphangiogenic factor, VEGF-C, as required for this process, and demonstrate transcriptional induction as the mechanism of regulation of VEGF-C expression by Six1. Using a different, but complementary animal model, we show that while required, VEGF-C is not sufficient for the pro-metastatic effects of Six1. Verifying the clinical significance of this pro-metastatic Six1-VEGF-C axis, we demonstrate co-expression of Six1 and VEGF-C in human breast cancer.

overall_design: Two Control and two Six1 expressing MCF7 clones were orthotopically injected into NOD/Scid mice forming a total of 3 Control and 3 Six1 tumors that were allowed to grow to 2 cm^3 .  The tumors were dissected and total RNA was isolated from each tumor and hybridized to Affymetrix arrays

first: Douglas

last: Micalizzi


title: Time-series of gene expression in female murine ES cells during EpiSC differentiation

status: Public on Apr 11 2012

city: Berlin

first: Nils

last: Blüthgen

address: Chariteplatz 1

department: Institute of Pathology

country: Germany

institute: Charite Universitätsmedizin Berlin

summary: Embryonic stem cells (ESC) are derived from the inner cell mass of the blastocyst in the presence of leukemia inhibitory factor (LIF). In vivo these cells then differentiate into epi stem cells (EpiSC) that can be derived from the Epiblast in presence of Fgf2 and ActivinA. In this study, female ESCs cultured in 2i medium have been differentiated into EpiSC for 3.5 days in vitro by addition of Fgf2 and Activin A. The gene expression profile was analyzed every 4-12 h using mouse exon arrays.

overall_design: Mouse Pgk12.1 ES cells were differentiated into EpiSC, samples were taken  every 4-12 hours for 84 hours in total

first: E

middle: G

last: Schulz

first: J

last: Meisig

first: N

last: Heard


title: Valproic Acid Confers Functional Pluripotency to Human Amniotic Fluid Stem Cells in a Transgene-free Approach

status: Public on Jul 24 2012

first: Katharina

last: Drews

address: Ihnestr. 63-73

department: Vertebrate Genomics

institute: Max Planck Institute for Molecular Genetics

summary: Induced pluripotent stem cells (iPSCs) with potential for therapeutic applications can be derived from somatic cells via ectopic expression of a set of limited and defined transcription factors. However, due to risks of random integration of the reprogramming transgenes into the host genome, the low efficiency of the process, and the potential risk of virally induced tumorigenicity, alternative methods have been developed to generate pluripotent cells using nonintegrating systems, albeit with limited success. Here, we show that c-KIT+ human first-trimester amniotic fluid stem cells (AFSCs) can be fully reprogrammed to pluripotency without ectopic factors, by culture on Matrigel in human embryonic stem cell (hESC) medium supplemented with the histone deacetylase inhibitor (HDACi) valproic acid (VPA). The cells share 82% transcriptome identity with hESCs and are capable of forming embryoid bodies (EBs) in vitro and teratomas in vivo. After long-term expansion, they maintain genetic stability, protein level expression of key pluripotency factors, high cell-division kinetics, telomerase activity, repression of X-inactivation, and capacity to differentiate into lineages of the three germ layers, such as definitive endoderm, hepatocytes, bone, fat, cartilage, neurons, and oligodendrocytes. We conclude that AFSC can be utilized for cell banking of patient-specific pluripotent cells for potential applications in allogeneic cellular replacement therapies, pharmaceutical screening, and disease modeling.

overall_design: Total RNA obtained from mid gestation human amniotic fluid cells (AFSCs/2nd trimester AFSCs), early gestation human amniotic fluid cells (eAFSCs/1st trimester AFSCs) and human embryonic stem cells (hESCs)  as described in the corresponding Materials and Methods sections.

first: James

last: Adjaye


title: Genome-wide transcriptome profiling reveals the functional impact of rare de novo and recurrent CNVs in autism spectrum disorders.

status: Public on May 05 2012

city: Los Angeles

first: Rui

last: Luo

state: CA

address: 2309 Gonda Bldg, 695 Charles E. Young Dr. South

department: Human Genetics

country: USA

institute: UCLA

summary: Expression profiling of lymphoblast cell lines of autisms from Simons Simplex Families. This experiment aims to utilize blood expression data to study the functional impact and to prioritize rare variants potentially associated with autism.

overall_design: Total RNA obtained from lmyphoblast cell lines derived from 439 Simons Simplex Families.

first: Daniel

middle: H

last: Geschwind


title: The General Transcription Factor TAF7 is Essential for Embryonic Development but Not Essential for the Survival or Differentiation of Mature T Cells (MEF data)

city: Bethesda

first: Dinah

last: Singer

state: Maryland

address: 9000 Rockville Pike

department: Experimental Immunology Branch

institute: National Cancer Institute

summary: TAF7, a component of the TFIID complex that nucleates the assembly of transcription preinitiation complexes, also independently interacts with and regulates the enzymatic activities of other transcription factors, including P-TEFb, TFIIH and CIITA, ensuring an orderly progression in transcription initiation.  Since not all TAFs are required in terminally differentiated cells, we examined the essentiality of TAF7 in cells at different developmental stages in vivo. Germ-line disruption of the TAF7 gene is embryonic lethal between 3.5 and 5.5 days post coitus. TAF7-deleted mouse embryonic fibroblasts (MEFs) globally cease transcription and stop proliferating. In contrast, whereas TAF7 is essential for the differentiation and proliferation of immature thymocytes, it is not required for subsequent, proliferation-independent differentiation of lineage committed thymocytes or their egress into the periphery.  TAF7 deletion in peripheral CD4+ T cells affects only a small number of transcripts. However, TAF7-deleted T cells are not able to undergo activation and expansion in response to antigenic stimuli. These findings suggest that TAF7 is essential for proliferation but not for proliferation-independent differentiation.

overall_design: We previously provided evidence that TAF7 is a regulator of the early steps of transcription initiation, that it affects the expression of about 65% of transcripts in 293 kidney cells, and of those, some are TAF1-dependent while others are TAF1-independent. Therefore, we next asked whether TAF7 is dispensable for a subset of embryonic fibroblast genes or whether it is required globally. Both TAF7f/f and TAF7+/+ MEF lines were infected by MSCV Cre-GFP retroviruses, and the infected cells (GFP+) were isolated by FACS at 24, 48 and 72 hours post infection. Uninfected cells from each line were harvested at the same time, collected by FACS  and processed simultaneously to be used as controls. The experiments were performed in triplicate. All RNAs were extracted using shredders and the Qiagen RNeasy mini kit and their quality assayed before using for hybridization. Total RNA from each of the triplicates was hybridized on the Affymetrix exon array. All exon array data were analyzed with Affymetrix Expression Console SoftwareTM (version 1.1). The Robust Multi-array Analysis (RMA) algorithm was used for gene intensity analysis. Only genes in the “core” set, which represents RefSeq and full-length GenBank mRNAs, were included in the analysis.

first: Anne

last: Gegonne


title: TMPRSS2-ERG, HDACs and EZH2 are involved in an AR-centric transcriptional circuitry that calibrates androgenic response for prostate cancer progression (gene expression data)

status: Public on Apr 27 2012

city: Singapore

first: Kern Rei

last: Chng

address: 60 Biopolis Street #02-01 Genome

department: Cancer Biology and Pharmacology 3

country: Singapore

institute: GIS

summary: Deregulation of the Androgen Receptor (AR) transcriptional network is a common hallmark in prostate cancers. To achieve its precise transcriptional role, AR needs to co-operate specifically with a plethora of cofactors. In prostate cancers, AR transcription collaborators are frequently aberrantly over-expressed, altering the AR signaling pathway to one that promotes oncogenesis. Recently, the prostate cancer recurrent fusion gene, ERG, was shown to promote tumor progression by acting as a repressor of AR signaling. However, the exact mechanics and the functional consequences associated with this crosstalk between ERG and AR still remains relatively unknown. Interestingly, through chromatin immunoprecipitation coupled with massively parallel sequencing, we discover that ERG and other commonly over-expressed transcriptional co-repressors (HDAC1, HDAC2, HDAC3 and EZH2) are wired into an AR-centric transcriptional network via a spectrum of distal enhancers and/or proximal promoters. We show that ERG represses several AR target genes involved in epithelial differentiation. Furthermore, we demonstrated that suppression of the androgen-induced gene, Vinculin, by ERG and histone deacetylases increases cancer cell invasiveness. From our results, we propose that ERG, histone deactelyases and the histone methyltransferase, EZH2, could impede epithelial differentiation and contribute to prostate cancer progression, in part through modulating the transcriptional output of AR.

overall_design: Gene expression profiling of human prostate cancer VCaP cells with time-course dihydrotestosterone (DHT) stimulation using microarrays. Triplicates were generated for each treatment/time point.

first: Kern

middle: R

first: Si

middle: K

last: Tan

first: Cheng

middle: W

last: Chang

first: Chong

last: Yang

first: Shu

middle: Z

last: Hong

first: Edwin

last: Cheung


title: Molecular Insights into Non-teratoma-forming Induced Pluripotent Stem Cells

status: Public on Apr 30 2012

first: Ying

last: Wang

address: Ihnestrasse 63

summary: Human induced pluripotent stem (iPS) cells are capable of differentiating into derivatives of the three embryonic germ layers both in vitro and in vivo. To date the the molecular differences between teratoma-forming cells and non-teratoma-forming cells has not been analysed. A cell line, B1, bears typical ES cell-like morphology, expression of pluripotency-associated genes, and in vitro pluripotency capacity, but fails to form teratomas after subcutaneously injected into immune-deficient mice based on histological analysis. Besides histological analysis, we characterized the tumors derived from line B1, and teratomas derived from bona fida iPS and ES (line H1) cells respectively, using microarray-based gene expression analysis. The expression levels of pluripotency-associated markers in B1 cells were comparable to that in iPS and ES cells, while the complexity of tissue expression commitment was decreased upon spontaneous differentiation of B1 cells as compared to iPS and ES cells.

overall_design: Total RNA obtained from HFF1 (human foreskin fibroblast) cells, line B1, iPS-A4, iPS-B4 and ES (line H1) cells, and their derived tumors in immune-deficient mice.

first: Wang

last: Ying


title: The histone demethylase KDM1A sustains the oncogenic potential of MLL-AF9 leukemia stem cells (expression data)

status: Public on Mar 29 2012

city: Manchester

first: Tim

middle: C

last: Somervaille

state: Lancashire

address: Wilmslow Road

country: United Kingdom

institute: Cancer Research UK Manchester Institute

summary:
Using a mouse model of human MLL-AF9 leukemia, we identified the lysine-specific demethylase KDM1A (LSD1 or AOF2) as an essential regulator of leukemia stem cell (LSC) potential. KDM1A acts at genomic loci bound by MLL-AF9 to sustain expression of the associated oncogenic program, thus preventing differentiation and apoptosis. In vitro and in vivo pharmacologic targeting of KDM1A using tranylcypromine analogues active in the nanomolar range phenocopied Kdm1a knockdown in both murine and primary human AML cells exhibiting MLL translocations. By contrast, the clonogenic and repopulating potential of normal hematopoietic stem and progenitor cells was spared. Our data establish KDM1A as a key effector of the differentiation block in MLL leukemia which may be selectively targeted to therapeutic effect.

To investigate the genetic program regulated by KDM1A in murine MLL-AF9 AML cells enriched for LSCs, we compared the transcriptome of KIT+Gr1+ control and Kdm1a KD cells using exon arrays soon after initiation of KD. At this time, there was no immunophenotypic evidence of differentiation in Kdm1a KD cells. Exonic expression values were condensed into gene-level expression summaries, which represent the mean expression value of the probe sets targeting the length of a given protein coding gene.

overall_design: Three separate samples from two different animals were used. Kdm1a KD samples were compared with control samples. Total six arrays.


title: Genome-wide expression profiling of T6PNE cells in the presence and absence of HNF4α antagonist BIM5078

status: Public on Mar 07 2012

city: La Jolla

first: Roy

middle: M

last: Williams

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

summary: Analysis of the effects of the HNF4α antagonist, BIM5078, at the gene expression level. Results provide important information on the global effects of HNF4α antagonism on human gene expression in a cell line derived from human fetal islets.

overall_design: RNA was isolated from T6PNE cells subjected to 48 hours of treatment with either DMSO or BIM5078.

first: Alice

last: Kiselyuk

first: Fred

last: Levine


title: Clonal Analysis for Identification of Molecular Pathways with Potential Therapeutic Implications in of Rare Gastrointestinal and Endocrine Cancers

city: Scottsdale

first: Michael

middle: Thomas

last: Barrett

state: AZ

address: 13400 East Shea Boulevard

department: Molecular Pharmacology and Experimental Therapeutics

institute: Mayo Clinic Arizona

type: Genome variation profiling by genome tiling array

summary: Genomic analysis of many cancers has led to the identification of novel targets and the development of personalized, targeted therapies. Unfortunately, in the majority of rare tumors, this type of analysis can be particularly challenging. Large series of specimens for analysis are simply not available, allowing recurring patterns to remain hidden. Clinical specimens typically contain variable degrees of non-tumor cells that can mask a potentially critical genomic signature, leaving important clinically relevant events undetected. When analysis is limited to a smaller number of specimens, the effects of heterogeneity within each sample is magnified. In light of these challenges, we used DNA content based flow cytometry to isolate clonal tumor populations from a series of rare cancers for genomic analysis: intrahepatic cholangiocarcinoma, anal carcinoma, adrenal leiomyosarcoma, and pancreatic neuroendocrine tumors. These purified clonal populations are then subject to high definition measurement of copy number aberrations by objectively measuring the height and boundaries of amplicons and by discriminating homozygous from partial deletions. Ranking of these events by copy number facilitates the identification of highly selected aberrations. This approach can garner useful information from a single biopsy. In the cases we describe, several potential therapeutic targets were identified and genomic aberrations correlated with the phenotypic behavior. We propose that clonal genomic analysis can generate unique hypotheses and guide the development of clinical advances for these and other rare tumors.

overall_design: We applied DNA content based flow sorting to isolate the nuclei of clonal populations from tumor biopsies. We coupled this strategy with oligonucleotide array CGH (aCGH) thereby obtaining high definition genomic profiles of clonal populations from different rare tumors including pancreatic neuroendocrine cancers, adrenal leiomyosarcoma, anal carcinoma, and cholangiocarcinoma.

first: Stephen

middle: V

last: Liu

first: Elizabeth

last: Lenkiewicz

first: Lisa

last: Evers

first: Tara

last: Holley

first: Jeffrey

last: Kiefer

first: Christian

last: Ruiz

first: Katharina

last: Glatz

first: Lukas

last: Bubbendorf

middle: J

last: Demeure

first: Cathy

last: Eng

first: Ramesh

last: Ramanathan

middle: D

last: Von Hoff

middle: T


title: Cyclin-dependent kinases are regulators and effectors of oscillations driven by a transcription factor network

status: Public on Feb 03 2012

city: Durham

first: Laura

middle: Anne

last: Simmons Kovacs

state: NC

department: Biology

institute: Duke University

summary:
Yeast cell cycle transcription dynamics in two S. cerevisae strains grown at 37°C: BF264-15DU (MATa ade1 his2 leu2-3, 112 trp1-1 ura3Dns, bar1) (wild type) and a mutant of the wild type strain lacking all Cdk1 activity, cdc28-4.
We compared transcript levels of genes previously shown to be periodically expressed in wild-type cells (Orlando et al, 2008, Nature) to transcript levels in the absence of Cdk1 activity.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Two replicate time courses from cells lacking all Cdk1 activity and one control time course from cells with wild-type Cdk1 activity are included.

middle: A

last: Kovacs

first: Steven

middle: B

last: Haase


title: Genome-wide analysis of cellular SMD or NMD substrates that regulated by Upf1 or PNRC2 in HeLa cell

status: Public on Feb 28 2012

city: Seoul

first: Hana

last: Cho

address: Anam 5ga, Sungbukku

department: School of Life Sciences and Biotechnology

country: South Korea

institute: Korea University

summary: Analysis of cellular SMD or NMD substrates that regulated by Upf1 and/or PNRC2 in HeLa cell. The hypothesis tested in the present study was that endogenous SMD or NMD substrates may co-regulated by Upf1 and PNRC2. Results provide important information that vast range of cellular SMD or NMD substrates are reqired PNRC2 for decay.

overall_design: Total RNA obtained from HeLa cells with downregulation of Upf1 or PNRC2 by siRNA. The up- or down-regulated transcripts were compare to control siRNA treated HeLa cell RNA extract. Significant transcripts were confirmed by replication

first: KyoungMi

last: Kim

first: Junho

last: Choe


status: Public on Jan 31 2012

city: Charlestown

first: Johan

last: Skog

state: MA

address: 149 13th street

department: Molecular Neurogenetics

institute: Massachusetts General Hospital

summary: Primary glioblastoma cells and primary malignant melanoma cells were grown in vitro (less than 15 passages). Exosomes/microvesicles were isolated from the media supernatant at the same time as RNA was extracted from the cells. The goal of the study was to compare the gene expression profiles in exosomes/microvesicles compared to the cells that release them.

overall_design: Analysis of tumor cell RNA (glioma and melanoma) and their corresponding microvesicles.

first: Jian-Bing

last: Fan


title: Opposing effects of estrogen and Runx2 on breast cancer cell proliferation: identification of a reciprocally-regulated gene signature with clinical prognostic value.

status: Public on Mar 06 2012

first: Nyam-Osor

last: Chimge

address: 2250 Alcazar street

department: IGM

institute: USC

summary: Analysis of reciprocal modulation of Runx2 and E2 signaling in BCA. Our objective was to investigate whether the interaction between estrogen and Runx2 signaling in breast cancer (BCa) could help refine an estrogen-responsive gene signature with improved prognostic value.

overall_design: MCF7/Rx2dox BCa cells conditionally expressing Runx2 upon doxycycline treatment were treated with estradiol and/or doxycycline to induce Runx2, and global gene expression was profiled to define genes regulated by estradiol, Runx2, or both.

first: Baruch

last: Frenkel


title: Analysis of gene co-expression networks in skin cells exposed to different doses of ionising radiation at different time points

status: Public on Feb 01 2012

city: davis

first: David

last: Rocke

state: ca

address: 1 shields ave

department: Biostatistics/Public health

institute: UC davis

summary: Most studies have analysed the effects of high dose radiation such as atomic bomb survivors in Japan, people exposed during the Chernobyl nuclear accident, patients undergoing radiation therapy, uranium miners, etc. However, it has been difficult to measure and assess the risk of cancer in people exposed to lower doses of ionising radiation, such as the people living at high altitudes, who are exposed to more natural background radiation from cosmic rays than people at sea level.  We measured the genomic response to X-ray ionising radiation (10 cGy and 100 cGy) in a skin tissue model to compare the effects of low and high dose ionising radiation at different time points.  The microarray data was then analysed using state-of-the art “upside-down pyramid” computational systems biology methods to identify genes contributing to the difference in the response to the different radiation doses.

overall_design: The model is reconstructed skin tissue, which is composed of keratinocytes that make up the epidermal layer, and fibroblasts that make up the dermal layer of the skin. Tissues were irradiated with 0, 10, and 100 cGy X-ray radiation.  Skin plugs were harvested at 0, 3, 8, and 24 hours post irradiation.

first: Reem

last: Yunis


title: Methylome-wide comparison of human genomic DNA extracted from whole blood and from EBV-transformed lymphocyte cell lines

status: Public on Mar 08 2012

city: Richmond

first: Karolina

last: Aberg

state: VA

address: 1112 East Clay Street

department: Center for Biomarker Resarch & Personalized Medicine

institute: Virginia Commonwealth University

type: Methylation profiling by genome tiling array

summary: DNA from Epstein-Barr virus (EBV)-transformed lymphocyte cell lines (LCLs) has proven very useful for studies of genetic sequence polymorphisms. Whether EBV-LCL DNA is suitable for methylation studies is less clear. We conduct a genome-wide methylation investigation using an array set with 45 million probes to investigate the methylome of EBV-LCL DNA and technical duplicates of whole blood (WB) DNA from the same 10 individuals. Methylation sites that show variation between individuals are potentially useful as biomarkers in disease studies. Our comparison is, therefore, focused specifically on these methylation variable sites. The sample correlations (i.e., a measure of whether the rank of the signals remains consistent between two samples from the same individual) for the methylation variable probes ranged from 0.69-0.78 for the WB duplicates and from 0.27-0.72 for WB versus EBV-LCL. To compare the pattern of the methylation signals, we grouped adjacent probes based on their inter-correlations. These analyses showed ~29,000 blocks in WB and ~14,000 blocks in EBV-LCL. Furthermore, merely 31% of the methylated regions detected in WB were detectable in EBV-LCLs. Our study shows that there are substantial differences in the DNA methylation patterns between EBV-LCL and WB. Thus, EBV-LCL DNA cannot be used as a proxy for WB DNA in methylation studies.

overall_design:
The methylation of technical duplicates of DNA extracted from whole blood from 10 individuals, as well as DNA extracted from EBV-transformed lymphocyte cell lines (EBV-LCL) from the same samples of whole blood, are investigated using the Affymetrix GeneChip Human Tiling 2.0R array set. In total, 30 samples from 10 individuals were investigated on 7 arrays.

The supplementary "GSE35204_ChrXX_bgc_qt.txt" files contain the background-corrected and quantile-normalized data for all 30 samples per chromosome. The files include 32 columns: 'Seq' refers to the chromosome, 'Pos' indicates the position in the genome on that chromosome, and columns 3-32 indicate the sample numbers.

first: Amit

middle: N

last: Khachane

first: Gábor

last: Rudolf

first: Srilaxmi

last: Nerella

first: Douglas

last: Fugman

first: Jay

last: Tischfield

first: Edwin

last: van den Oord


title: Exon array analysis in the mouse myoblast cell line, C2C12 cells treated with control-, Cugbp1- or Mbnl1-siRNA

status: Public on Jan 03 2012

city: Nagoya

first: Akio

last: Masuda

state: Aichi

address: 65 tsurumai-cho, Showa-ku

country: Japan

institute: Nagoya University Graduate School of Medicine

summary: CUGBP1 and MBNL1 are developmentally regulated RNA-binding proteins that are causally associated with myotonic dystrophy type 1. Using HITS-CLIP anlysis, we found CUGBP1 and MBNL1 preferentially bind to alternatively spliced introns and exons, as well as to the 3' UTRs.  To analyze more directly the role of CUGBP1/MBNL1 binding in alternative splicing, we performed exon array analysis in C2C12 cells using expression arrays.

overall_design: We analyzed total RNA of C2C12 cells treated with control-, Cugbp1- or Mbnl1-siRNA. RNA was harvested 48 hrs after transfection.

first: A

first: K

last: Ohno


title: MYBL2/CREB1-Dependent Distinct FoxA1 Cistrome Directs G1/S Cell Cycle Progression in Androgen-Independent Prostate Cancer

status: Public on Dec 08 2011

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

type: Genome binding/occupancy profiling by genome tiling array

summary: FoxA1, in conjunction with MYBL2 and CREB1, governs G1/S cell-cycle transition in androgen-independent prostate cancer .

overall_design: FoxA1 whole genome ChIP-on-chip was performed in an androgen-dependent prostate cancer cell line LNCaP and an androgen-independent prostate cancer cell line abl. Whole genome binding sites were compared between these two cell lines.

first: Liguo

last: Wang

first: Chunpeng

last: Zhang

first: Wei

last: Li

first: Qianben


title: Genome-wide analysis of lupus immune complex stimulation of peripheral blood mononuclear cells and how this is regulated by C1q

status: Public on Dec 07 2011

city: Seattle

first: Deanna

last: Santer

address: 1959 NE Pacific St Health Science Bldg BB561 Campus Box 356428

institute: University of Washington

summary: The goal of this study was to determine what genes are up- and down-regulated in response to lupus immune complexes in total peripheral blood mononuclear cells (PBMCs). Our results have shown that novel genes are induced by immune complexes that are likely important for lupus pathogenesis plus that C1q regulates these pathways and induces multiple new pathways not previously identified.

overall_design: Total RNA was isolated from PBMCs from 2 donors after 5 hours with the following condiitons: 1) Unstimulated, 2) Lupus immune complex alone, 3) Lupus immune complex + C1q, 4) C1q alone

first: Ryan

last: Basom

first: Keith

last: Elkon


title: Molecular targeting of CSN5 in human hepatocellular carcinoma: a mechanism of therapeutic response

status: Public on Dec 27 2011

first: Daekwan

last: Seo

state: MD

address: 37 Convent Dr. Rm 4140

department: NCI

institute: NIH

summary: Development of targeted therapy for hepatocellular carcinoma (HCC) remains a major challenge. We have recently identified an elevated expression of the fifth subunit of COP9 signalosome (CSN5) in early HCC as compared to dysplastic stage. In the present study, we explored the possibility of CSN5 being a potential therapeutic target for HCC. We demonstrate that CSN5 knockdown by small interfering (si) RNA caused a block in cell proliferation and cell cycle progression, and induced apoptosis of HCC cells in vitro. The transcriptomic analysis of CSN5 knockdown signature by microarray showed that the anti-proliferative effect was driven by a common subset of molecular alterations including downregulation of CDK6 or ITGB1, which are involved in cell cycle regulation or tumor invasion and functionally interconnected with key oncogenic regulators such as TGFβ1 and MYC. Western blot assay showed that CSN5 depletion significantly increases the phosphorylation of Smad2/3 and decreases the expression of ITGB1, CDK6 and cyclin D1 proteins, restoring the tumor suppressive function of RB and thereby contributing to inhibition of cell cycle progression. In addition, CSN5 knockdown increased the expression of Bak but decreased the level of Bcl-2, subsequently leading to apoptosis through the activation of caspase-3. A chemically modified variant of CSN5 siRNA was then selected for in vivo application based on the growth inhibitory effect and minimal induction of unwanted immune response. Systemic delivery of the CSN5 3/8 variant by stable-nucleic-acid-lipid-particles (SNALP) significantly suppressed the tumor growth in Huh7-luc+ orthotopic xenograft model. Taken together, these results indicate that CSN5 plays a pivotal role in HCC pathogenesis and maybe an attractive molecular target for systemic HCC therapy.

overall_design: Huh7 and HepG2 cells were treated with CSN5 siRNA and negative control siRNA for 48 hours and subjected to Illumina microarray analysis. 4 replicates each.

first: Yun-Han

last: Lee

first: Deakwan

first: Jens

middle: U

last: Marquardt

first: Jesper

last: Andersen

first: Snorri

middle: S

last: Thorgeirsson


title: Genome-wide analysis of lupus immune complex stimulation and how this response is regulated by C1q

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

overall_design: Refer to individual Series


title: Temporal transcriptional changes in human monocytes following acute myocardial infarction: The GerMIFs monocyte expression study

city: Luebeck

first: Heribert

last: Schunkert

address: Ratzeburger Allee 160

department: Medizinische Klinik II

summary:
Monocytes play a central role in the inflammatory response that follows acute myocardial infarction (MI). In order to study phenotypic adaptation of this cell type, we investigated patterns of monocyte gene expression in circulating monocytes at various stages of MI. Circulating monocytes were isolated from venous blood of MI patients at three time points: t1: within 6 hours after onset of chest pain (acute phase), t2: 3 days after MI (subacute phase), t3: 90 days after MI (chronic phase). For comparison, we studied a control group (n=21, data to be submitted later) with stable coronary artery disease.
Using this transcriptomic analysis, we aimed to provide a more comprehensive reference of monocyte biology following acute MI and to aid in the identification of novel pathways and genes influencing the course of MI.

overall_design: Monocytes play a central role in the inflammatory response that follows acute myocardial infarction (MI). In order to study phenotypic adaptation of this cell type, we investigated patterns of monocyte gene expression in circulating monocytes at various stages of MI. Circulating monocytes were isolated from venous blood of MI patients at three time points: t1: within 6 hours after onset of chest pain (acute phase), t2: 3 days after MI (subacute phase), t3: 90 days after MI (chronic phase). For comparison, we studied a control group (n=21, data to be submitted later) with stable coronary artery disease. Illumina Ref-8 v3.0 microarray arrays were used for whole-genome transcriptional profiling.

first: Seraya

last: Maouche

first: Hendrik

last: Sager

first: Zouhair

last: Aherrahrou

first: Stefanie

last: Belz

first: Jessy

last: Brocheton

first: Carole

last: Proust

first: Stephanie

last: Tennstedt

first: Holger

last: Ammerlahn

first: Claas

last: Riedel

first: Jan

last: Stritzke

first: Volkhard

last: Kurowski

first: Kate

last: Rice

first: Alison

middle: H

last: Goodall

first: Christian

last: Hengstenberg

first: Willem

last: Ouwehand

first: Nilesh

last: Samani

first: François

last: Cambien

first: Jeanette

last: Erdmann

first: Patrick

last: Diemert


title: Expression data from the dorsal root ganglia during streptozotocin-induced painful diabetic neuropathy in rats

status: Public on Nov 30 2011

city: Tsukuba-shi, Ibaraki

first: Shunji

last: Yamazaki

address: 21, Miyukigaoka

institute: Astellas Phama Inc.

summary:
FK1706 potentiated nerve growth factor-induced neurite outgrowth, putatively mediated via FKBP-52 and the Ras/Raf/MAPK signaling pathway. It also improved mechanical allodynia accompanied by the recovery of intraepidermal nerve fiber density in a painful diabetic neuropathy in rats.
We analyzed gene expression of the dorsal root ganglia together with measurement of mechanical allodynia in diabetic rats to try to capture the global fingerprint of changes in gene expression associated with FK1706 administration and also to elucidate the putative mechanisms of its neurotrophic activity in vivo.

overall_design: Normal, STZ-treated controls, and STZ + FK1706 groups were used to evaluate gene expression analysis. Dorsal root ganglia from L4 to L6 were collected at the day after 1, 2, and 3 weeks of FK1706 administration, were immediately immersed in RNAlater reagent, and stored as instructed before RNA extraction. Equal amounts of total RNA from five rats were collected for each group.

first: Takashi

last: Matsuda


title: BC ChIP-on-chip in SW480, array A

status: Public on Nov 24 2011

city: Meguro-ku

first: aya

last: nonaka

state: Tokyo

address: 4-6-1, Komaba

institute: The University of Tokyo

summary: Dysregulation of Wnt signaling is involved in carcinogenesis, mainly through activation of beta-catenin/TCF target genes. Although aberrant activation of several Wnt target genes, including CCND1 and MYC, has been reported as promoting proliferation of cancer cells, it is hardly enough to understand malignant phenotypes of cancer cells with aberrant Wnt signaling. To elucidate the transcriptional regulation of beta-catenin/TCF target genes, we examined binding of beta-catenin (BC) to DNA by chromatin immunoprecipitation linked to genome tiling array (ChIP-on-chip).

overall_design: Beta-catenin ChIP vs. Input in SW480 cells.

first: Aya

last: Nonaka

first: Hiroyuki

last: Aburatani


title: Genome-wide analysis of lupus immune complex stimulation of purified CD14+ monocytes and how this response is regulated by C1q

first: Deanna

last: Santer

summary: The goal of this study was to determine what genes are up- and down-regulated in response to lupus immune complexes in purified CD14+ monocyte stimulations. Our results have shown that novel genes are induced by immune complexes but the response is less robust when using purified monocytes versus total PBMCs

overall_design: Total RNA was isolated from CD14+ monocytes from 2 donors after 5 hours with the following conditions: 1) Unstimulated, 2) Lupus immune complex alone, 3) Lupus immune complex + C1q, 4) C1q alone

first: Ryan

last: Basom

first: Keith

last: Elkon


title: Analysis of p53 target genes in melanoma

status: Public on Dec 01 2011

city: New Lambton Heights

first: Kelly

last: Kiejda

state: NSW

address: HMRI

country: Australia

institute: University of Newcastle


title: Synergism between Activin A and BMP4 in directing the formation of definitive endoderm in human embryonic stem cells

status: Public on Nov 10 2011

first: Kee Yew

last: Wong

address: 60, Biopolis Street, #02-01

department: Stem cell Biology

institute: Genome Institute of Singapore

summary: Human embryonic stem cells (HESCs) herald tremendous promise for the production of clinically useful cell types for the treatment of injury and disease. Numerous reports demonstrate their differentiation into definitive endoderm (DE) cells, the germ layer from which pancreatic β cells and hepatocytes arise, solely from exposure to a high dose of recombinant Activin/Nodal. Here, we show that combining a second related ligand, BMP4, in combination with Activin A yields 15 to 20% more DE as compared to Activin A alone. The addition of recombinant BMP4 accelerates the downregulation of pluripotency factors, particularly SOX2, and results in upregulation of endogenous BMP2 and BMP4, which in turn leads to elevated levels of phospho-SMAD1/5/8 over the next three days of differentiation. Combined Activin A and BMP4 treatment also leads to an increase in the expression of DE genes CXCR4, SOX17 and FOXA2 when compared to Activin A addition alone. Comparative microarray studies between DE cells harvested on day 3 of differentiation further reveal a novel set of genes upregulated in response to initial BMP4 exposure.  Several of these, including APLNR, LRIG3, MCC and LZTS1, are expressed either in the mouse primitive streak, the site of DE formation, or in nascent DE itself. Thus, this synergism between Activin A and BMP4 during the in vitro differentiation of HESC into DE suggests a complex interplay between BMP and Activin/Nodal signaling during the in vivo allocation and expansion of the endoderm lineage.

overall_design: 3 biological replicates of 3-day ActivinA treated HES3 human stem cell culture were compared to 3-day ActivinA+Bmp4 treated HES3 human stem cell culture and observed for differential genes expression

first: Kee

middle: Y

first: Adrian

middle: K

last: Teo

first: Yusuf

last: Ali

first: Lawrence

last: Stanton

first: N

middle: R

last: Dunn


title: Using iPSC-derived neurons to uncover cellular phenotypes associated with Timothy syndrome

status: Public on Nov 07 2011

city: Los Angeles

first: Irina

last: Voineagu

address: 695 Chrles E Young Dr

institute: UCLA

summary: Monogenic neurodevelopmental disorders provide key insights into the pathogenesis of disease and help us understand how specific genes control the development of the human brain. Timothy syndrome is caused by a missense mutation in the L-type calcium channel Cav1.2 that is associated with developmental delay and autism. We generated cortical neuronal precursor cells and neurons from induced pluripotent stem cells derived from individuals with Timothy syndrome. Cells from these individuals have defects in calcium (Ca2+) signaling and activity-dependent gene expression and show abnormalities in differentiation. Neurons from individuals with Timothy syndrome show increased expression of markers of the upper cortical layer and decreased expression of callosal projection markers. In addition, the mutation that causes Timothy syndrome leads to an increase in the production of neurons that synthesize norepinephrine and dopamine. This phenotype can be reversed by treatment with roscovitine, a cyclin-dependent kinase and atypical L-type–channel blocker. These findings provide strong evidence that Cav1.2 regulates the differentiation of cortical neurons in humans and offer new insights into the causes of autism in individuals with Timothy syndrome.

overall_design: Total RNA was isolated from control and TS cells: fibroblasts, iPSCs, neurospheres (at day 7 in suspension), neurons at rest (day 45 of differentiation) and neurons kept in 67mM KCl for 9h. For sample titles, D1,D2 and D3 represent independent differentiation experiments. The number after - represents the iPSC cell line number.  GSE25542_non-normalized.txt.gz contains data for 5 outliers.


title: Exon level expression data from the liver of adult control and Dhx32 homozygous mutant mice

status: Public on Nov 17 2011

city: Toronto

first: Mohamed

last: Abdelhaleem

state: Ontario

address: 555 University Avenue

department: Pediatric Laboratory Medicine

country: Canada

institute: Hospital for Sick Children

summary:
We compared the whole mRNA transcript expression from control and homozygous mutant Dhx32 mice by Affymetrix Mouse Exon ST 1.0 Array ST to identify alternatively spliced mRNA transcripts
We include exon level expression data from the liver of three control and three Dhx32 homozygous mutant mice

overall_design: 6 total samples (three control and three Dhx32 homozygous mutant) were analyzed. The p values for alternatively spliced transcripts were calculated by using the algorithms of Partek Genomics Suite version 6.4, on core probes excluding probe sets with signals less than 3.

first: M


title: Analysis of p53 target genes in melanoma part 2

summary: Although mutations in p53 are infrequent in human melanoma, its function is abnormal. In this study, whole genome bead arrays were used to examine the expression of p53 target genes in extracts from 6 melanoma cell lines, compared to extracts derived from diploid human melanocytes and fibroblasts, to provide a global assessment of aberrant p53 function. The expression of these genes was also examined in extracts derived from melanocytes and melanoma cell lines in which p53 expression had been inhibited using shRNA and compared to cells that had been transduced with a control shRNA.

overall_design: Total RNA extracted from 18 samples was analysed representing duplicates of 6 melanoma cell lines, 1 melanocyte cell line and 2 fibroblast cell lines. Melanoma cell lines were compared to normal cell lines. In addition, IgR3, Mel-RM and melanocyte cell lines were transduced with either control shRNA or p53 shRNA to evaluate the effect of p53 on its target genes. Cell lines transduced with control shRNA were compared to cell lines transduced with p53shRNA. Duplicates were analysed.

last: Avery-Kiejda

first: Nikola

last: Bowden

first: Carla

last: Kairupan

first: Amanda

last: Croft

first: Katie

last: Ashton

first: Lyndee

middle: L

last: Scurr

first: Bente

last: Talseth-Palmer

first: Helen

last: Rizos

first: Xu

last: Zhang

first: Rodney

last: Scott

first: Peter

last: Hersey


title: Amygdalar gene expression from Mecp2-null and MECP2-transgenic mice

status: Public on Jan 08 2012

city: Houston

first: Chad

middle: A.

last: Shaw

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: BCM

summary:
A group of postnatal neurodevelopmental disorders collectively referred to as MeCP2 disorders are caused by aberrations in the gene encoding methyl-CpG-binding protein 2 (MECP2). Loss of MeCP2 function causes Rett syndrome (RTT), whereas increased MeCP2 dosage causes MECP2 duplication or triplication syndromes. MeCP2 acts as a transcriptional repressor, however, the gene expression changes observed in the hypothalamus and cerebellum of MeCP2 disorder mouse models suggest that MeCP2 can also upregulate gene expression.
In this study, we compared gene expression changes in the amygdalae of mice lacking MeCP2 (Mecp2-null) and mice overexpressing MeCP2 (MECP2-TG).  We chose the amygdala because it is a neuroanatomical region implicated in the control of anxiety and social behavior, two prominent phenotypes in MECP2-TG mice, and hypothesized that transcriptional profiling of this particular brain region may reveal expression changes relevant to heightened anxiety-like behavior and abnormal social behavior.  A total of 1,060 genes were altered in opposite directions in both MeCP2 mouse models compared with wild-type littermates, with ~60% up-regulated and ~40% down-regulated.  Interestingly, we found a significant enrichment of anxiety- and/or social behavior-related genes among the differentially expressed genes.  To determine whether these genes contribute to the anxiety and social behavior phenotypes in MECP2-TG mice, we performed genetic and pharmacologic studies and found that a reduction in Crh suppresses anxiety-like behavior, and a reduction in Oprm1 improves social approach behavior.  These studies suggest that MeCP2 impacts molecular pathways involved in anxiety and social behavior, and provide insight into potential therapies for MeCP2 disorders. This study is published in Nature Genetics http://dx.doi.org/10.1038/ng.1066.

overall_design: Total amygdala RNA samples were collected from Mecp2-null male mice (n=4), MECP2-transgenic male mice (n=5), and their wild type male littermates at 6 weeks of age (n=4, n=5 for each group respectively).

middle: C

last: Samaco

first: Caleigh

last: Mandel-Brehm

first: Chrisopher

middle: M

last: McGraw

first: Bryan

middle: E

last: McGill

first: Huda

last: Zoghbi


title: Glycine decarboxylase is a metabolic oncogene critical for tumor initiating cells and tumorigenesis in lung cancer

status: Public on Oct 26 2011

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

institute: Cancer Science Institute of Singapore

summary: New approaches to cancer therapies could benefit from a better understanding of the  molecular determinants critical to tumor initiating cells (TICs). Here we show that the metabolic  enzyme glycine decarboxylase (GLDC) is critical for TICs in non-small cell lung cancer (NSCLC). From a  broad range of primary NSCLC tumors, we isolated CD166+ lung TICs that consistently initiated  tumorigenesis in NOD/SCID Il2rγ-/- mice. Lung TICs express high levels of the oncogenic stem cell  factor LIN28B and the metabolic enzyme GLDC. Over-expression of GLDC and other glycine/serine  metabolism enzymes, but not catalytically inactive GLDC, promotes cellular transformation and  tumorigenesis. Metabolomic analysis found that GLDC induces dramatic changes in glycolysis and  glycine/serine metabolism, leading to changes in pyrimidine metabolism to regulate cancer cell  proliferation. Clinically, GLDC over-expression, observed in multiple cancer types, predicts poorer  survival in lung cancer patients. Our findings establish a novel link between glycine metabolism and  tumorigenesis, and provide novel targets for advancing anti-cancer therapy.

overall_design: Total RNA obtained from tumor sphere compared to CD166+ and CD166- selected cells of xenograft, primary tumor and normal donors

first: Wen

first: Ng

last: Shyh-Chang

first: Amit

last: Rai

first: Shivshankar

last: Umashankar

first: Siming

last: Ma

first: Boon

last: Soh

first: Ross

last: Soo

first: Li

last: Sun

first: Bee

last: Tai

first: Min

last: Nga

first: Kishore

last: Bhakoo

first: Senthil

last: Jayapal

first: Massimo

last: Nichane

first: Qiang

last: Yu

first: Dokeu

last: Ahmed

first: Christie

last: Tan

first: Wong

middle: P

last: Sing

first: John

last: Tam

first: Agasthian

last: Thirugananam

first: Paul

last: Robson

first: Monireh

last: Noghabi

first: Yin

last: Pang

first: Haw

last: Ang

first: Kaldis

last: Philipp

first: Sanjay

last: Swarup

first: Elaine

last: Lim

first: Bing


title: Molecular insights into induced pluripotency mediated by the OCT4, SOX2, KLF and c-MYC gene regulatory network

status: Public on Oct 25 2011

city: Berlin

first: Ying

last: Wang

address: Ihnestrasse 63

department: Vertebrate Genomics

institute: Max Planck Institute for Molecular Genetics

summary: Human somatic fibroblasts can be reprogrammed to induced pluripotent stem (iPS) cells by exogenic expression of the Yamanaka factors (OCT4, SOX2, KLF4 and MYC) after about 1 month. To gain some insight into the early processes operative in fibroblast reprogramming, we profiled genome-wide transcription levels using Illumina microarrays in the starting donor cells-human foreskin fibroblast (HFF1) cells and at three time points after OSKM transduction (24 h, 48 h, 72 h), as well as two iPS cell lines (iPS2, iPS4) and hES cell lines (H1, H9). We show that within the context of the viral transduction reprogramming protocol, the donor cell response to viral transfection perturbs redox homeostasis, which induces oxidative damage on the donor cells' protein and DNA. This leads to activation of p53, senescence, and apoptosis, greatly reducing the efficiency of reprogramming.

overall_design: Total RNA obtained from HFF1 (human foreskin fibroblast) cells, OSKM-transduced HFF1 cells after 24h, 48h, 72h, undifferentiated hESCs, iPSCs.

first: Wang

last: Ying


title: Preservation of cone photoreceptors after a rapid yet transient degeneration and remodeling in cone-only Nrl-/- mouse retina

status: Public on Nov 15 2011

city: Rockville

first: Radu

last: Cojocaru

address: 5635 Fishers Lane, Suite 510

institute: Elsevier

summary: Cone photoreceptors are the primary initiator of visual transduction in the human retina. Dysfunction or death of rod photoreceptors precedes cone loss in many retinal and macular degenerative diseases, suggesting a rod-dependent trophic support for cone survival. Rod differentiation and homeostasis are dependent on the basic motif leucine zipper transcription factor NRL. The loss of Nrl in mice (Nrl-/-) results in a retina with predominantly S-opsin containing cones that exhibit molecular and functional characteristics of WT cones. Here we report that Nrl-/- retina undergoes a rapid but transient period of degeneration in early adulthood, with cone apoptosis, retinal detachment, alterations in retinal vessel structure, and activation and translocation of retinal microglia. However, cone degeneration stabilizes by four months of age, resulting in a thinned but intact outer nuclear layer with residual cones expressing S- and M-opsins and a preserved photopic ERG. At this stage, microglia translocate back to the inner retina and reacquire a quiescent morphology. Gene profiling analysis during the period of transient degeneration reveals misregulation of stress response and inflammation genes, implying their involvement in cone death. The Nrl-/- retina illustrates the long-term viability of cones in the absence of rods and may serve as a model for elucidating mechanisms of cone homeostasis and degeneration that would be relevant to understanding diseases of the cone-dominant human macula.

overall_design: Targets were generated from a pair of retinas (one Nrl-/- mouse) per biological replicate.  Four biological replicates were generated for each of the five aging timepoints (1, 2, 4, 6, and 10 months post natal).

first: Jerome

last: Roger

first: Keerthi

last: Ranganath

first: Lian

last: Zhao

middle: I

first: Matthew

last: Brooks

first: Norimoto

last: Gotoh

first: Shobi

last: Veleri

first: Avinash

last: Hiriyanna

first: Rivka

last: Rachel

first: Maria

last: Campos

first: Robert

last: Fariss

first: Wai

middle: T

last: Wong

first: Anand

last: Swaroop


title: Transcriptional failures arrest development after human nuclear transfer

status: Public on Oct 04 2011

city: New York

first: Dieter

last: Egli

state: NY

address: 1150 St. Nicholas Avenue, room 607B, New York NY 10032

institute: Columbia University

summary: Reprogramming occurs after nuclear transfer into zygotes whose genomes have been removed in mitosis, but not after nuclear transfer into zygotes enucleated in interphase. Our results suggest that there is a previously unappreciated barrier to successful human nuclear transfer, and that future studies should focus on the requirements for somatic genome activation.

overall_design: 1-3 embryos were used for analysis. RNA amplification was done using two or three rounds of T7-mediated RNA amplification using the Illumina Total Prep RNA Amplification kit. Somatic cells 1-000 and 1-011 required only one round of RNA amplification because starting amounts of RNA were 100-500ng, while embryonic samples were amplified from single cells or embryos.

first: Kevin

last: Eggan


title: Gene expression in pluripotent stem cells derived after somatic cell genome transfer into human oocytes

status: Public on Oct 06 2011

summary: The exchange of the oocyte’s genome with the genome of a somatic cell, followed by the derivation of pluripotent stem cells, could enable the generation of specific cell types affected in degenerative human diseases.  Such cells, carrying the patient’s genome, might be useful for cell replacement. Here we report that the development of human oocytes activated after genome exchange invariably arrests at the late cleavage stages in association with transcriptional abnormalities. In contrast, if the oocyte genome is not removed and the somatic cell genome is merely added, they efficiently develop to the blastocyst stage.  Human stem cell lines derived from these blastocysts differentiate into cell types of all three germ layers, and a pluripotent gene expression program is established on the genome derived from the somatic cell. This result demonstrates the feasibility of reprogramming human cells using oocytes and identifies the removal of the oocyte genome as the primary cause of developmental failure after genome exchange. Future work should focus on the critical elements that are associated with the human oocyte genome.

overall_design: Stem cells were derived by reprogramming of skin cells using oocytes ('nuclear transfer') or defined factors (iPS cells), or from IVF blastocysts


title: Synthetic double stranded RNA reliably induces innate immunity similar to a live viral vaccine in humans

status: Public on Oct 12 2011

city: port st-lucie

first: Ali

last: Filali

state: Florida

address: 11350 SW Village Parkway, 3rd Floor

institute: Vaccine & Gene Therapy Institute of Florida

summary: Adjuvants are critical for the success of vaccines, and agonists for microbial pattern recognition receptors are promising new candidates. A mechanism for the immune enhancing role of adjuvants is to stimulate innate immunity. We studied the innate immune response in humans to synthetic double stranded RNA (poly ICLC), a ligand for TLR3 and MDA-5 cytosolic RNA helicase. Transcriptional analysis of blood samples from eight volunteers, after subcutaneous administration of poly ICLC showed upregulation of genes involved in multiple innate immune pathways in all subjects, including interferon and inflammasome signaling. Blocking of type I interferon receptor ex vivo significantly dampened the response to poly IC. Comparative transcriptional analysis showed that several innate pathways were similarly induced in volunteers immunized with the highly efficacious Yellow Fever Vaccine. Therefore a chemically defined microbial agonist like poly ICLC can be a reliable and authentic microbial mimic for inducing innate immunity, here for a live attenuated viral vaccine in humans.

overall_design:
GSM813292-GSM813386: RNA expression obtained at different time points from Human blood after poly ICLC administration compared to RNA expression obtained from Human blood after placebo administration
GSM813387-GSM813410: Blocking of type I interferon receptor ex vivo followed by poly IC stimulation

first: Marina

last: Caskey

first: François

last: Lefebvre

first: Abdelali

last: Filali-Mouhim

first: Mark

middle: J

last: Cameron

first: Jean-Philippe

last: Goulet

first: Elias

last: Haddad

first: Gaëlle

last: Breton

first: Christine

last: Trumpfheller

first: Sarah

last: Pollak

first: Irina

last: Shimeliovich

first: Angela

last: Duque-Alarcon

first: Li

last: Pan

first: Annette

last: Nelkenbaum

first: Andres

last: Salazar

last: Schlesinger

first: Ralph

last: Steinman

first: Rafick

last: Sékaly


title: Molecular characterization of two unrelated patients ABCB4 deletions

status: Public on Oct 05 2011

city: Paris

first: Eric

last: Pasmant

address: Faculté de Pharmacie de Paris, 4 avenue de l’Observatoire

country: France

institute: Paris Descartes University

summary: To allow acute characterization of ABCB4 locus constitutional deletion in two patients with cholelithiasis/cholestasis, an Agilent 2X400 array CGH was used. Goal was to obtain genomic rearrangements fine characterization in order to describe ABCB4 constitutional deletions.

overall_design: ABCB4 locus microdeletions characterization vs reference sample (pool of six normal control DNAs)

first: Béatrice

last: Parfait

first: Ingrid

last: Laurendeau

first: Dominique

last: Vidaud

first: Michel


title: Changes in gene expression profiles in patients with 5q- syndrome in CD14+ monocytes caused by lenalidomide treatment

status: Public on Sep 12 2011

city: Prague 2

first: Monika

last: Belickova

address: U nemocnice 1

country: Czech Republic

institute: Institute of Hematology and Blood Transfusion

summary: We detected changes in genes expression in patients with 5q- syndrome in CD14+ monocytes due to treatment with lenalidomide.

overall_design: Total RNA was obtained from CD14+ monocytes from peripheral blood of 6 controls, 6 patients before treatment, and 5 patients during treatment.

first: Jaroslav

last: Cermak

first: Michaela

last: Dostalova

first: Jitka

last: Vesela

first: Zdenek

last: Krejcik

first: Eliska

last: Cechova

first: Zuzana

last: Zemanova

first: Kyra

last: Michalova

first: Hana

last: Votavova

first: Miroslav

last: Caniga

first: Radana

last: Neuwirtova

first: Anna

last: Jonasova


title: Gene expression in blastomeres after transfer of somatic cells into human oocytes

first: Dieter

last: Egli

summary: The exchange of the oocyte's genome with the genome of a somatic cell, followed by the derivation of pluripotent stem cells, could enable the generation of specific cell types affected in degenerative human diseases.  Such cells, carrying the patient's genome, might be useful for cell replacement. Here we report that the development of human oocytes activated after genome exchange invariably arrests at the late cleavage stages in association with transcriptional abnormalities. In contrast, if the oocyte genome is not removed and the somatic cell genome is merely added, they efficiently develop to the blastocyst stage.  Human stem cell lines derived from these blastocysts differentiate into cell types of all three germ layers, and a pluripotent gene expression program is established on the genome derived from the somatic cell. This result demonstrates the feasibility of reprogramming human cells using oocytes and identifies the removal of the oocyte genome as the primary cause of developmental failure after genome exchange. Future work should focus on the critical elements that are associated with the human oocyte genome.

overall_design: Somatic cells were transferred into human unfertilized oocytes to determine if human oocytes can reprogram a somatic cell.

first: Mark

last: Sauer

first: Rudolph

last: Leibel

first: Scott

last: Noggle

first: Robin

last: Goland


title: Genome-wide analysis of transformed MSCs

status: Public on Oct 10 2011

first: TianSheng

last: CHEN

address: 8A Biomedical Grove, Immunos, 05-16

institute: Institute of Medical Biology

summary: Analysis of transformed MSCs at gene expression level. The aim in the present study was that overexpression of MYC in the MSCs alter gene expression of MSCs. Results provide important information of the response of overexpresion of MYCs, such as up- or down-regulated specific anabolic/catabolic cellular functions.

overall_design: Total RNA obtained from transformed MSCs or MSC culture cells at different passages.

first: SaiKiang

last: Lim


title: Epigenetic Based Enrichment of Cancer Stem Cells: Mechanistic and Clinical Implications for Liver Cancer

city: Bethesda

first: Daekwan

last: Seo

address: 37 Convent Dr. Rm 4140

summary: Global transcriptiome changes between SP and NSP cells of liver cancer cell lines w and w/o Zebularine treatment

overall_design: Huh7,WRL68, KMCH FACS sorted in SP and NSP w and w/o Zebularine and subjected to illumina microarray analysis.

first: Jens

last: Marquardt

first: Deakwan

first: Snorri

last: Thorgeirsson


title: ECS-induced gene expression changes in mouse dentate gyrus

status: Public on Sep 01 2011

city: Cambridge

first: Junjie

last: Guo

address: 9 Cambridge Center

institute: Whitehead Institute

summary:
Neuronal activity-dependent gene expression plays important roles in neural plasticity. We use electroconvulsive stimulation (ECS) as an in vivo model for neuronal activation to identify genes that are regulated by neuronal activity.
Dentate gyri (DG) were microdissected 4 hours after sham or ECS treatment for gene expression profiling.

overall_design: 4 total samples were analysed (2 for each condition). Averaged expression values between sham and ECS samples were pair-wise compared.


title: Functional Genomic Analyses Identify Pathways Dysregulated by Progranulin Deficiency Implicating Wnt Signaling

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

summary: Progranulin (GRN) mutations cause frontotemporal dementia (FTD), but GRN's function in the CNS remains largely unknown. To identify the pathways downstream of GRN, we used weighted genome co-expression network analysis (WGCNA) to develop a systems-level view of transcriptional alterations in a human neural progenitor model of GRN-deficiency. This highlighted key pathways such as apoptosis and ubiquitination in GRN deficient human neurons, while revealing an unexpected major role for the Wnt signaling pathway, which was confirmed by analysis of gene expression data from postmortem FTD brain. Furthermore, we observed that the Wnt receptor Fzd2 was one of only a few genes up-regulated at 6 weeks in a GRN knockout mouse, and that FZD2 reduction caused increased apoptosis, while its upregulation promoted neuronal survival in vitro. Together, these in vitro and in vivo data point to an adaptive role for altered Wnt signaling in GRN deficiency-mediated FTD, representing a potential therapeutic target.

overall_design: We therefore developed an in vitro model of GRN deficiency using primary human neural stem cells in which shRNA was used to diminish GRN levels to 50% or below.  We developed a tetracycline inducible system in which transactivator protein rtTA3 and PuroR genes were constituitively expressed under the UBC promoter, while RFP and shRNA were regulated by an inducible tet-On CMV promoter (Gossen and Bujard, 1992).   To control for off-target effects, two hairpins against GRN were used, and a scrambled hairpin was used as a control.

first: Ezra

last: Rosen

first: Eric

last: Wexler

first: Revital

last: Versano

first: Fuying

last: Gao

first: Kellen

middle: D

last: Winden

first: Michael

last: Oldham

first: Lauren

last: Herl

first: Ping

last: Zhou

first: Robert

middle: V

last: Farese

first: Daniel

last: Geschwind


title: Cellular reprogramming by the conjoint action of ERalpha, FOXA1, and GATA3 to a ligand inducible growth state

status: Public on Sep 05 2011

first: Guoliang

last: Li

address: 60 Biopolis Street, #02-01, Genome

department: Computational and Systems Biology

summary: Despite the role of the estrogen receptor alpha (ERalpha) pathway as a key growth driver for breast cells, the phenotypic consequence of exogenous introduction of ERalpha into ERalpha-negative cells paradoxically has been growth inhibition. We map the binding profiles of ERalpha and its interacting transcription factors (TFs), FOXA1 and GATA3 in MCF-7 breast carcinoma cells. We observe that these three TFs form a functional enhanceosome and cooperatively modulate the transcriptional networks previously ascribed to ERalpha alone. We demonstrate that these enhanceosome occupied sites are associated with optimal enhancer characteristics with highest p300 coactivator recruitment, RNA Pol II occupancy, and chromatin opening. The enhancesome binding sites appear to regulate the genes driving core ERalpha function. Most importantly, we show that the transfection of all three TFs was necessary to reprogramme the ERalpha-negative MDA-MB-231 and BT-459 cells to restore the estrogen responsive growth and to transcriptionally resemble the estrogen treated ERalpha-positive MCF-7 cells. Cumulatively, these results suggest that all the enhanceosome components comprising ERalpha, FOXA1 and GATA3 are necessary for the full repertoire of cancer associated effects of the ERalpha.

overall_design: Illumina HumanRef-8 v3 Expression BeadChip was used to measure the gene expression levels from ERalpha negative breast cancer cell MDA-MB-231 with different transfections: with vector control, with ERalpha only, or with ERalpha+FOXA1+GATA3 combined.

first: Say

last: Kong

first: Edison

last: Liu


title: Testosterone-dependent and independent transcriptional networks in the hypothalamus of Gpr54 and Kiss1 knockout male mice

status: Public on Aug 22 2011

city: Vancouver

first: Steven

last: McKinney

state: BC

address: 675 West 10th Ave

department: Molecular Oncology

institute: British Columbia Cancer Agency

summary:
Humans and mice with loss of function mutations in GPR54 (KISS1R) or kisspeptin (KISS1) do not progress through puberty, caused by a failure to release GnRH. The transcriptional networks regulated by these proteins in the hypothalamus have yet to be explored by genome-wide methods.
Using micro-dissected hypothalamic tissues to isolate RNA from our mice, we first set out to define the transcriptional differences among the wild type and knockout mice. Since the GPR54-kisspeptin axis is subject to hormonal feedback and the knockout mice are pre-pubertal, we also tested the hormonal dependence/independence of each differentially expressed transcript. To avoid variation in gene expression due to fluctuations in the levels of circulating hormones during the female estrous cycle, only male mice were used in this study.

overall_design: 17 samples were successfully hybridized; 4 GKO, 5 KKO, 3 WT 3 weeks old, 5 WT 6 weeks old.  We compared GKO to KKO, GKO to WT, KKO to WT and all KO to all WT.

first: Leah

last: Prentice

first: Xavier

last: d’Anglemont de Tassigny

first: Teresa

last: Ruiz de Algara

first: Damian

last: Yap

first: Gulisa

last: Turashvili

last: Poon

first: Margaret

last: Sutcliffe

first: Pat

last: Allard

first: Angela

last: Burleigh

first: John

last: Fee

first: David

middle: G

last: Huntsman

first: William

last: Colledge

first: Samuel

middle: A

last: Aparicio


title: Human Induced Pluripotent Stem Cells Harbor Homoplasmic and Heteroplasmic Mitochondrial DNA Mutations While Maintaining human embryonic stem cells-like Metabolic Reprogramming

status: Public on Jul 08 2011

first: Alessandro

last: Prigione

state: Berlin

address: Robert-Roessle-Str. 10

institute: Max Delbrueck Center for Molecular Medicine

summary: Gene expression analyis of two hESCs, two human neonatal fibroblasts, and four human iPSCs generated with retroviral transduction using the OSKM cocktail.

overall_design: Total mRNA obtained from two fibroblasts (BJ and HFF1), two hESCs (H1 and H9), two BJ-derived iPSCs (iB4 and iB5), and two HFF1-derived iPSCs (iPS2 and iPS4).

first: James

last: Adjaye


title: Expression data from seven rat tissues at multiple ages

city: Shanghai

first: Qi

last: Wang

address: No. 12 Wulumuqi Middle Road

country: China

institute: Huashan hospital, Fudan university,China

summary:
Aging progress is distinctly characterized by systematic and progressive decline of physiological functions with increasing age in virtually all tissues or organs. Addressing the patterns of molecular changes in different tissues and how different tissues interact with each other during aging are an important question in aging.
This study sampled seven tissues at four ages in rats to measure genome-scale gene expression, which allows global insight into coordination, specificity and/or commonness among different tissues with aging progress.

overall_design: We sampled seven different tissues or organs of male Sprague Dawley rats including hypothalamus, pituitary, adrenal gland, spleen lymphocytes, liver, kidney, and bone at successive ages of 4, 10, 18, and 24 months. For each age, ten individual rats were obtained, seven tissues from each individual rat were isolated, 5µg of each extracted RNA sample of the same tissue from ten individual rats was equally mixed, and then a total amount of 15 µg RNA from this mixture was hybridized to an Affymetrix RAE230A GeneChip.

first: Jianhua

last: Huang

first: Xinmin

last: Zhang

first: Ziyin

last: Shen


title: ChIP-chip for histone modifications in hESCs and differentiated hESCs

status: Public on Jul 23 2011

city: Dallas

first: Gary

middle: Chung

last: Hon

address: 5323 Harry Hines Blvd.

department: OB/GYN

institute: UT Southwestern

summary: The objective of this study was to identify how histone modifications are differentially marked at promoter and enhancer elements in hESCs before and after differentiation to understand the regulatory mechanisms that defined pluripotency and early differentiation.

overall_design: ChIP for promoter and enhancer histone modifications were conducted relative to input DNA in hESCs and hESCs treated with BMP4

first: R

last: Hawkins

first: Bing

last: Ren


title: SW480 Signaling Hub Inhibition

status: Public on Jun 03 2011

first: Markus

last: Morkel

address: Ihnestr. 73

department: Developmental Genetics

summary: In tumor cells, stepwise oncogenic deregulation of signaling cascades induces alterations of cellular morphology and promotes the acquisition of malignant traits. Using a panel of small molecular inhibitors, we established associated gene expression signatures of key signaling hubs.

overall_design: SW480 cells were grown in DMEM, 10% FCS, and treated for 24h with the following inhibitors or with solvent (DMSO): SU5402 (42uM); U0126 (10uM), SP600125 (20uM), LY294002 (20uM)

first: M

last: Leushacke


title: Gene expression analysis of colorectal tumors and matched adjacent non-tumor colorectal tissues.

first: Toshinori

last: Hinoue

address: 1450 Biggy Street, NRT G511

institute: USC Epigenome Center

summary: We performed gene expression profiling of 26 colorectal tumors and matched histologically normal adjacent colonic tissue samples using the Illumina Ref-8 whole-genome expression BeadChip. We performed an integrated analysis of promoter DNA methylation and gene expression data to investigate the effects of DNA hypermethylation on gene expression.

overall_design: Total RNA was isolated from 26 pairs of fresh frozen colorectal tumor and matched adjacent non-tumor tissue samples. Their gene expression profiles were obtained using the Illumina Ref-8 whole-genome expression BeadChip (HumanRef-8 v3.0, 24,526 transcripts).

first: Daniel

last: Weisenbuerger

last: Van Den Berg

first: Peter

middle: W

last: Laird


title: Deregulation of Gene Expression induced by Environmental Tobacco Smoke Exposure in Pregnancy

status: Public on Jul 20 2011

first: Hana

last: Bruchova

department: Molecular Genetics

institute: Institute of Hematology and Transfusion

summary: Passive smoke intake by pregnant women may have detrimental effects such as spontaneous abortion, lower birth weight, stillbirth, and reduced infant lung function. To extend our knowledge on molecular effects of tobacco smoke exposure in pregnancy, we analyzed transcriptome alterations in passive smokers (PS) and compared them to those in active smokers (AS).   Using Illumina Expression Beadchip with 24,526 transcript probes, gene expression patterns were assayed in placentas from PS (N=25) exposed to environmental tobacco smoke (ETS) throughout pregnancy and non-exposed (NS) counterparts (N=35), and in cord blood cells from their newborns. The ETS exposure was evaluated by questionnaire disclosure and cotinine measurement in maternal and cord bloods. A total of 196 genes were significantly deregulated in placentas of PS compared to NS. These genes were primary associated with extracellular matrix, apoptosis, blood clotting, response to stress, embryonic morphogenesis, and lipid metabolism. Cord blood of newborns of PS displayed differential expression of 116 genes encoding mainly neuronal factors, regulators of immunologic response, and protooncogenes. Gene ontology analyses highlighted some important biological processes that might be associated with placental insufficiency and fetal growth restriction in PS, such as fatty acid catabolism, coagulation, regulation of growth, and response to steroid hormone stimulus.   The study demonstrates that even low dose exposure to ETS during pregnancy leads to the significant deregulation of transcriptional regulation in placental and fetal cells. The data suggest the effect of ETS on the fetus is primary indirect, mediated via deregulation of placental functions. Comparison of PS and AS indicated that ETS exposure and active smoking in pregnancy partly employ the same molecular mechanisms.

overall_design: A total of 60 women who gave birth to a baby in the Faculty Hospital Motol (Czech Republic)  were enrolled into the study approved by the local Institutional Review Board. The participants signed written informed consent and self-reported information on tobacco smoke exposure (type of exposure, number of cigarettes per day, exposure period) and life style during pregnancy (alcohol drinking, diet, area of residency etc.). Further, the women completed the questionnaire on pregnancy/delivery course (complications, diseases, medication, and delivery mode) and newborn characteristics (physical parameters, Apgar score) with the assistance of gynecologist. Only women without any health complications during pregnancy and their newborns without manifestation of pathological abnormalities were included in the study. Based on self-reported tobacco smoke exposure, the women were divided into two groups, non-smokers (NS, N=35) and passive smokers (PS, N=25). Former and active smokers were excluded from the study.  Exposure to tobacco smoke was further evaluated by measurement of plasma cotinine levels in maternal peripheral blood and newborn cord blood using radioimmunoassay.

last: Votavova

first: Michaela

last: Merkerova-Dostalova

first: Zdenek

last: Krejcik

first: Kamila

last: Fejglova

first: Alzbeta

last: Vasikova

first: Nana

last: Tabashidze

first: Anna

last: Pastorkova

first: Jan

last: Topinka

first: Ivan

last: Balascak

first: Radim

last: Sram

last: Brdicka


title: Cell of origin strongly influences genetic selection in a mouse model of T-ALL.

status: Public on Aug 21 2011

city: Iowa City

first: Adam

last: Dupuy

address: 51 Newton Road

institute: University of Iowa

summary: Thymic lymphomas were generated by inducing Sleeping Beauty transposon mutagenesis at different stages of T-cell development.

overall_design: This dataset includes exon array results from 14 tumor samples from two different Sleeping Beauty models of T-ALL (7 Vav-SB and 7 CD4-SB samples).

first: A


title: Gene profiling using archival formalin-fixed paraffin-embedded breast cancer specimens can generate informative microarray data: A comparison with matched fresh fine needle aspiration biopsy samples (FNA samples)

status: Public on Jun 22 2011

first: Dong-Yu

last: Wang

address: 610 University Ave

institute: UHN-PMH-OCI

summary: The Formalin-Fixed Paraffin-Embedded (FFPE) samples on selected breast cancer subtypes (ER+/Her2-, ER+/Her2+, ER-/Her2+, and ER-/Her2-) and their paired fresh fine needle aspirated biopsies (FNA) were investigated. The cases represented different subtypes of breast cancers based on their clinical receptors ER (E) and Her2 (H) status to demonstrate the ability of gene profiles to differentiate these tumors. Compared to FNA specimens, FFPE samples yielded relatively more degraded RNA, and 80% of the samples deemed suitable for cDNA-mediated annealing, selection, extension and ligation (DASL) assay. It is able to demonstrate that gene profiles from FFPE microarrays were reproducible and correlated well with the corresponding gene profiles from FNA microarrays. The gene profiles from both FNA and FFPE could differentiate the four breast cancer subtypes, and the expression levels of corresponding gene set were consistent with qRT-PCR and correlated to the clinical outcomes on published microarray data. It supports the use of FFPE specimens to develop a prognostic tool for breast cancers which can obviate the need for fresh specimens.

overall_design: 25 FNA specimens were processed for direct hybridization assays using Illumina Human-Ref8 version 3 BeadChips. Invasive ductal carcinoma (IDC)-type subtypes ER+/Her2-, ER+/Her2+, ER-/Her2+, and ER-/Her2- (ER: estrogen receptor, HER2: human epidermal growth factor receptor 2) were analyzed.

first: Dong

middle: Y

first: Al

last: Sadi

first: Wey

last: Leong


title: Modeling the functional genomics of autism using human neurons.

status: Public on Jun 01 2011

first: Genevieve

last: Konopka

department: Neuroscience

institute: UT Southwestern Medical Center

summary: We examined whether a human neuronal culture system could be used to assess the transcriptional program involved in human neural differentiation and in modeling some of the molecular features of a neurodevelopmental disorder such as autism.

overall_design: Primary normal human neuronal progenitors differentiation for 0, 2, 4, or 8 weeks.

first: Fuying

last: Gao

first: Daniel

middle: H

last: Geschwind


title: Genome-wide gene expression analysis during endotoxin tolerance in PBMCs.

status: Public on May 17 2011

first: Christopher

last: Fjell

address: Room 166 - 1081 Burrard Street

department: Medicine

institute: University of British Columbia

summary: Genome-wide gene expression was measured in peripheral blood mononuclear cells (PBMC) from healthy humans donors, four hours post stimulation of  a single or double treatment of LPS and compared to untreated control PBMCs. We show that a second treatment with LPS induces endotoxin tolerance, with a transcription profile similar to that seen during alternative polarization (M2) of mononuclear cells. Microarray processing was performed by the Genome BC Microarray Platform.

overall_design: Total RNA obtained from PBMCs from blood from healthy humans after single treatment with LPS, two treatments with LPS, or untreated. Comparison of LPS or LPS/LPS to untreated cells shows the gene expression pattern of endotoxin tolerance.

first: Olga

last: Pena

first: Robert

last: Hancock


title: Overexpression of the lung cancer-prognostic miR-146b microRNAs has a minimal and negative effect on the malignant phenotype of A549 lung cancer cells

status: Public on May 24 2011

city: Buffalo

first: Santosh

middle: Kumar

last: Patnaik

address: Elm and Carlton Streets

department: Thoracic Surgery

institute: Roswell Park Comprehensive Cancer Center

summary: Biological effects of overexpression of miR-146b microRNAs in the A549 human lung cancer cell-line was studied. A549 cells were engineered to express the precursor RNA (pre-miR-146b) that generates the miR-146b microRNAs. Control cells were engineered using the same gene expression plasmid (pLemiR, Open Biosystems®) but without the pre-miR-146b insert. The Trans-Lentiviral GIPZ™ packaging system (Open Biosystems®) was used to generate stable transfectant populations of the engineered cells.

overall_design: Gene expression was compared between A549 stable transfectants of empty pLemiR plasmid (A549/vec cells) or of the pLemiR plasmid containing an insert for overexpressing human pre-miR-146b (A549/146b cells). Two different cell cultures were used for each cell-line (for biological replicates).

middle: K

first: Eric

last: Kannisto

first: Reema

last: Mallick

first: Sai

last: Yendamuri


title: The comparison of gene expression profile in the amygdalae between the wild-type and neuropsin knock-out mice

status: Public on May 13 2011

city: Krakow

first: Marcin

last: Piechota

address: Smetna 12

department: Molecular Neuropharmacology

country: Poland

institute: Institute of Pharmacology PAS

summary: Extracellular proteolysis contributes to fear-associated responses by facilitating neuronal plasticity at the neuron-matrix interface. A serine protease neuropsin is critical for stress-related plasticity in the amygdala by regulating the strength of EphB2/NMDA receptor interaction controlling the expression of fear-related genes and anxiety-like behavior. To look for downstream effects of neuropsin-mediated disassembly of the EphB2/NR1 complex we analyzed gene expression in the amygdalae of wild-type and neuropsin-/- mice.

overall_design: Wild-type control and neuropsin-/- mice were anaesthetised and perfused transcardially with ice cold PBS. The brains were removed and dissected using a vibrating microtome. Amygdalae were dissected from a coronal slice and were stored in RNAlater until processed. The amygdalae have been isolated from 15 brains of neuropsin-/- and 15 wild-type control animals. RNA pulled from 3 animals has been reverse transcribed and hybridized with GeneChip Mouse Exon 1.0 ST Affymetrix Array.

last: Pawlak


title: Effect of Medroxyprogesterone Acetate on Transcript Profile of Human Pregnant Myometrium

status: Public on Jun 08 2011

first: D. Stephen

last: Charnock-Jones

address: The Rosie Hospital

department: Obstetrics and Gynaecology

institute: University of Cambridge

summary:
Context: Progesterone is important physiologically and therapeutically to maintain uterine quiescence during pregnancy. It acts in part through controlling myometrial gene expression.

Objective: To use expression microarray and qRT-PCR validation to determine the changes in gene expression induced by prolonged exposure to a synthetic progestogen.

Design: Myometrial explants, obtained at elective Caesarean section (n=9 patients), were maintained in culture, under 0.6g tension, for 3 days in the presence or absence of medroxyprogesterone acetate (MPA, 100nM). Expression array was performed using Illumina human-8 v3 beadchip arrays. Approximately 30% of differentially expressed transcripts were validated in biological replicates (n=10) using qRT-PCR.

Results: Transcripts from 114 genes were significantly differentially expressed. These were significantly enriched in inflammatory response (P=0.00001), growth factor activity (P=0.0004) and cytokine activity genes (P=0.008). 34 transcripts were validated using qRT-PCR using an additional independent sample set obtained from 10 further women. There was very close agreement in the fold changes obtained by array and qRT-PCR analysis (r2=0.9, P<0.0001). We confirmed significant down-regulation of a number of genes which have been well characterized as progesterone sensitive, such as IL1B, IL6, PTGS2 and GJA1. However, the top and 6th most down-regulated genes encoded two cytokines, IL11 and IL24, respectively, not previously implicated in mediating the effects of progesterone in myometrium. Both were validated by qRT-PCR (4.3-fold and 2.2-fold down-regulated, both P<0.001).

Conclusions: Progestogens control expression of multiple genes in myometrium, including many with no previously recognised role, including IL11 and IL24. It is plausible that proteins encoded by some of these genes may have important, but as yet uncharacterized effects in controlling human parturition.

overall_design: 9 paired samples of human myometrium treated with MPA (10-7M) or vehicle

first: Y

last: Cordeaux

first: M

last: Tattersall

first: D

first: G

middle: C

last: Smith


title: Activator protein-2γ is a critical determinant of estrogen receptor interactome formation and gene transcription in breast cancer [expression]

status: Public on Jun 02 2011

first: SI KEE

last: TAN

address: 60 Biopolis Street #02-01 Genome

department: Cancer biology and Pharmacology

institute: Genomic Institute of Singapore

summary: Estrogen receptor α (ERα) is key player in the progression of breast cancer. ERα binds to DNA and mediates long-range chromatin interactions throughout the genome, but the underlying mechanism in this process is unclear. Here, we show that AP-2 motifs are highly enriched in the ERα binding sites (ERBS) identified from the recent ChIA-PET of ERα. More importantly, we demonstrate that AP-2γ (also known as TFAP2C), a member of the AP-2 family which has been implicated in breast cancer oncogenesis, is recruited to chromatin in a ligand-independent manner and co-localized with ERα binding events. Furthermore, pertubation of AP-2γ expression disrupts ERα DNA binding, long-range chromatin interactions, and gene transcription. Using ChIP-seq, we show that AP-2γ and ERα binding occurs in close proximity on a genome-wide scale. The majority of these shared genomic regions are also occupied by the pioneer factor, FoxA1. AP-2γ is required for efficient FoxA1 binding and vice versa. Finally, we show that most ERBS associated with long-range chromatin interactions are co-localized with both AP-2γ and FoxA1. Together, our results suggest AP-2γ is an essential factor in ERα-mediated transcription, primarily working together with FoxA1 to facilitate ERα binding and long-range chromatin interactions.

overall_design: Gene expression profiling of negative control (NC) and AP-2γ siRNA transfected MCF-7, with and without E2 (estradiol) stimulation using microarray.

first: Si

last: Tan

first: Zhenhua

last: Lin

first: Cheng

last: Chang

first: Edwin

last: Cheung


title: Gene Expression Profiling of Human Whole Blood Samples with the Illumina WG-DASL Assay

status: Public on Apr 01 2011

city: Grand Rapids

first: Mary

last: Winn

state: MI

address: 333 Bostwick Ave NE

institute: Van Andel Research Institute

summary: Microarray-based gene expression analysis of peripheral whole blood is a common strategy in the development of clinically relevant biomarker panels for a variety of human diseases. However, the results of such an analysis are often plagued by decreased sensitivity and reliability due to the effects of relatively high levels of globin mRNA in whole blood. Globin reduction assays have been shown to overcome such effects, but they require large amounts of total RNA and may induce distinct gene expression profiles. The Illumina whole-genome DASL (WG-DASL) assay can detect gene expression levels using partially degraded RNA samples and has the potential to detect rare transcripts present in highly heterogeneous whole blood samples without the need for globin reduction. We therefore assessed the utility of the WG-DASL assay in the analysis of peripheral whole blood gene expression profiles. We find that gene expression detection is significantly increased with the use of WG-DASL compared to the standard in vitro transcription-based direct hybridization (IVT), while globin-probe-negative WG-DASL did not exhibit significant improvements over globin-probe-positive WG-DASL. Globin reduction increases the detection sensitivity and reliability of both WG-DASL and IVT with little effect on raw intensity correlations: raw intensity correlations between total RNA and globin-reduced RNA were 0.970 for IVT and 0.981 for WG-DASL. Overall, the detection sensitivity of the WG-DASL assay is higher than the IVT-based direct hybridization assay, with or without globin reduction, and should be considered in conjunction with globin reduction methods for future blood-based gene expression studies.

overall_design: Peripheral whole blood samples were collected from eight human donors in PAXGene tubes. RNA was isolated after freezing and storage, and then prepared for gene expression analysis using the Illumina Human-Ref8 v3.0 BeadChip. Alpha and beta globin were reduced from a portion of the total RNA using the GLOBINclear assay (Ambion, Austin, TX, USA). Two methods of microarray target preparation were examined: Illumina IVT-based direct hybridization (IVT) and Illumina Whole-Genome DASL (WG-DASL). Two DASL Assay Oligo pools (DAP) were utilized for DASL target preparation: the DASL Assay Oligo Pool with globin probes (DAP +) and the DASL Asssay Oligo Pool without globin probes (DAP-).

first: Marian

last: Shaw

first: Craig

last: April

first: Brandy

last: Klotzle

first: Jian-Bing

last: Fan

first: Sarah

middle: S

last: Murray

first: Nicholas

last: Schork


title: Rapid induction and long-term self-renewal of primitive neural precursors from human embryonic stem cells by small molecule inhibitors

status: Public on Apr 28 2011

city: La Jolla

first: Li

last: Wenlin

address: 10550 North Torrey Pines Road

institute: The Scripps Research Institute

summary:
Here, we report synergistic inhibition of glycogen synthase kinase 3 (GSK3), transforming growth factor β (TGF β), and Notch signaling pathways by small molecules can efficiently convert monolayer cultured hESCs into homogenous primitive neuroepithelium within one week under chemically defined condition. These primitive neuroepithelia can stably self-renew in the presence of leukemia inhibitory factor, GSK3 inhibitor (CHIR99021) and TGF β receptor inhibitor (SB431542); retain high neurogenic potential and responsiveness to instructive neural patterning cues toward midbrain and hindbrain neuronal subtypes; and exhibit in vivo integration.
hESCs at about 20% confluence were treated with 3 μM CHIR99021, 2 μM SB431542, 0.1 μM Compound E (γ-Secretase Inhibitor XXI) in neural induction media containing Advanced DMEM/F12:Neurobasal (1:1), 1xN2, 1xB27, 1% Glutmax, 5 μg/ml BSA and 10 ng/ml hLIF, for 7 days. The culture was then split 1:3 for the next six passages using Accutase and cultured in neural induction media supplemented with 3 μM CHIR99021 and 2 μM SB431542 on X-ray inactivated MEF feeders or Matrigel-coated plates. After six passages, the cells were split 1:10 regularly.

overall_design: Global gene expression analysis of primitive neural stem cells

first: Wenlin

last: Li


title: Clinical relevance of DNA microarray analyses using archival formalin-fixed paraffin-embedded breast cancer specimens

city: Toronto

first: Dong-Yu

last: Wang

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

overall_design: Refer to individual Series


title: Transcriptomic Analysis of Autism Brain Reveals Convergent Molecular Pathology [array data]

status: Public on May 01 2011

city: Los Angeles

first: Irina

last: Voineagu

address: 695 Chrles E Young Dr

institute: UCLA

summary: Autism spectrum disorder (ASD) is a common, highly heritable neuro-developmental condition characterized by marked genetic heterogeneity. Thus, a fundamental question is whether autism represents an etiologically heterogeneous disorder in which the myriad genetic or environmental risk factors perturb common underlying molecular pathways in the brain. Here, we demonstrate consistent differences in transcriptome organization between autistic and normal brain by gene co-expression network analysis. Remarkably, regional patterns of gene expression that typically distinguish frontal and temporal cortex are significantly attenuated in the ASD brain, suggesting abnormalities in cortical patterning. We further identify discrete modules of co-expressed genes associated with autism: a neuronal module enriched for known autism susceptibility genes, including the neuronal specific splicing factor A2BP1/FOX1, and a module enriched for immune genes and glial markers. Using high-throughput RNA-sequencing we demonstrate dysregulated splicing of A2BP1-dependent alternative exons in ASD brain. Moreover, using a published autism GWAS dataset, we show that the neuronal module is enriched for genetically associated variants, providing independent support for the causal involvement of these genes in autism. In contrast, the immune-glial module showed no enrichment for autism GWAS signals, indicating a non-genetic etiology for this process. Collectively, our results provide strong evidence for convergent molecular abnormalities in ASD, and implicate transcriptional and splicing dysregulation as underlying mechanisms of neuronal dysfunction in this disorder.

overall_design: Total RNA was extracted from approximately 100mg of postmortem brain tissue representing Cerebellum (C), Frontal cortex (F), and Temporal cortex (T), from autistic and control individuals.


title: Effect of PITX2 knockdown on transcriptome of primary human trabecular meshwork cell cultures

city: Tehran

first: hassan

last: paylakhi

address: Jalale aleahmad

country: Iran

institute: Tarbiat Modares University

summary: To identify genes whose expressions in primary human trabecular meshwork (TM) cell cultures are affected by the transcription factor PITX2 and to identify genes that may have roles in glaucoma.  Expression profiles derived using microarrays were compared between TM control cells and cells treated with PITX2 siRNAs

overall_design: TM1 and TM2 cells were cultured in 6 well plates were transfected with either of two PITX2 specific siRNAs or scrambled siRNA (as control). The scrambled siRNA treatment was performed in duplicate for each TM.  Forty eight hours after exposure to siRNAs, cells were harvested and RNA was extracted. Considering the two siRNAs for PITX2 transcription factor, the two scrambled siRNA treatments, and the two TM primary cultures, we performed 8 array hybridizations.

first: Elahe

last: Elahi

first: Seyed

last: Paylakhi


title: Transcriptomic analysis of targets regulated by miR-125b in primary endothelial cells

status: Public on Apr 30 2011

city: Liege

first: Ingrid

last: Struman

address: Avenue de l'Hôpital, 1

department: BMGG

country: Belgium

institute: GIGA-R

summary: Human vein umbilical endothelial cells (HUVEC) were transfected with pre-miR control and pre-miR 125b (Ambion) in order to identify targets (direct and indirect) downregulated by miR-125b in endothelial cells. 317 transcripts were downregulated with a fold change ≥ 1.5, among which 99 are predicted direct targets of mir-125b. Computional approach performed with Ingenuity Pathway Knowledge shows that movement of cell and cell-to-cell signalling are the top two biological functions affected bewteen control and transfected cells. Experiments performed in zebrafish and in HUVEC confirmed that mir-125b mainly affects genes involved in cellular movements and junctions.

overall_design: Total RNA was obtained from cells transfected in HUVEC with pre-miR control and pre-miR 125b. Three independent transfections were performed for each condition.

first: Ludovic

last: Malvaux

first: Helene

last: Pendeville


title: Comprehensive Study of Tobacco Smoke-Related Transcriptome Alterations in Maternal and Fetal Cells

first: Hana

last: Bruchova

address: U nemocnice 1

summary: Maternal smoking has a severe negative effect on all stages of pregnancy that in consequence impairs fetal growth and development. Tobacco smoke-related defects are well established at the clinical level; however, little is known about molecular mechanisms underlying these pathological conditions. We thus employed a genomic approach to determine transcriptome alterations induced by maternal smoking  in pregnancy. We assayed gene expression profiles in peripheral blood (M) leukocytes and placentas (PL) of pregnant smokers and those without significant exposure, and in cord blood (D) leukocytes of their babies. Comparative analyses defined significant deregulation of 193 genes in M cells, 329 genes in placentas, and 49 genes in D cells of smokers. These genes were mainly involved in xenobiotic metabolism, oxidative stress, inflammation, immunity, hematopoiesis, trophoblast differentiation, and vascularization. Functional annotation of the deregulated genes outlined processes and pathways affected by tobacco smoke. In smoker newborns, we identified several deregulated pathways associated with autoimmune diseases. The study demonstrates a limited ability of placenta to modulate toxic effects of maternal tobacco use at the gene expression level.

overall_design: Blood and placental samples were obtained from 91 women who gave birth to a baby in the Ceske Budejovice Hospital from November 2008 to March 2009. The study was approved by the Local Institutional Review Board. All participants provided written informed consent and completed an extensive questionnaire on pregnancy history (medication, diseases), delivery course, newborn characteristics and life style (smoking, diet, alcohol drinking, area of residency). Only subjects who underwent vaginal delivery were included in the study. Based on smoking history, the women were divided into two groups, “smokers” (N=20) and “non-smokers” (N=52), while passive smokers (N=19) were excluded from the study. Smoking status was further confirmed by detection of excessive plasma levels of cotinine (the major nicotine metabolite) in maternal blood.

last: Votavova

first: Michaela

last: Merkerova Dostalova

first: Kamila

last: Fejglova

first: Alzbeta

last: Vasikova

first: Zdenek

last: Krejcik

first: Nana

last: Tabashidze

first: Milos

last: Veleminsky Jr.

first: Anna

last: Pastorkova

first: Jan

last: Topinka

first: Radim

last: Sram

last: Brdicka


title: CNVs in spermatogenic failure

status: Public on Mar 17 2011

city: Münster

first: Frank

last: Tüttelmann

address: Vesaliusweg 12-14

department: University of Münster

institute: Institute of Human Genetics

summary: To determine the involvement of Copy Number Variants (CNVs) in the origin of male infertility, patients with idiopathic severe oligozoospermia, Sertoli-cell-only syndrome and controls with normozoospermia were analysed by array CGH using the 244A/400K array sets (Agilent Technologies).

overall_design: Comparison of 89 infertile male patients with severe oligozoospermia (≤5 x Mill./ml sperm concentration and ≤10 Mill. total sperm count) and 37 with azoospermia due to complete, bilateral Sertoli-cell-only syndrome (SCOS) with 100 healthy controls with normal semen parameters (≥20 Mill./ml sperm concentration, ≥40 Mill. total sperm count, ≥2 ml semen volume, ≥50% of a+b or ≥25% a motility, high percentage of normal forms (≥10%)). Patients with recurring, patient-specific and mostly private, sex-chromosomal CNVs (29 with OAT and 17 with SCOS) are reported as possibly causing spermatogenic failure.

first: Albrecht

last: Röpke


title: P19 neuronal cell differentiation

status: Public on Mar 10 2011

city: Nomi

first: Hitoshi

last: Suzuki

state: Ishikawa

address: 1-1 Asahidai

department: CNMT

institute: JAIST

summary: We comprehensively investigated the neural-splicing using P19 cells, set up nine filtering conditions, and obtained 262 candidate exons (236 genes). Results of semi-quantitative RT-PCR in randomly selected 30 candidates suggested that 87% of the candidates were actually changed more than double compared with the undifferentiated and differentiated cells. GO analysis and pathway analysis also showed that these 236 candidate genes were highly involved in the neural events. These results suggested that our extraction of alternative exons was quite reasonable and successful.

overall_design: We have biological duplicates in this project. We essentially compared Day 7 (neural-differentiated) against Day0 (Undifferentiated)

first: Ken

last: Osaki

first: Toshifumi

last: Tsukahara