title: Myeloid cell RelA/p65 promotes lung cancer proliferation

status: Public on Apr 01 2012

city: Homburg (Saar)

first: Christoph

last: Beisswenger

address: Kirrbergerstrasse

department: Department of Internal Medicine V – Pulmonology, Allergology and Respiratory Critical Care Medicine

institute: Saarland University Medical Center

summary:
Smoking is the most important risk factor for both lung cancer (LC) and chronic obstructive pulmonary disease (COPD). The aim of this study was to investigate the role of myeloid cell NF-kB in the regulation of tumor cell growth signaling. We subjected mice lacking myeloid RelA/p65 to a metastatic LC model. Cigarette smoke (CS) exposure significantly increased the proliferation of Lewis lung carcinoma cell (LLC) tumors in wild type mice. In CS exposed  mice lacking myeloid RelA/p65, the tumor growth was largely inhibited. Transcriptome and pathway analysis of cancer tissue revealed a fundamental impact of myeloid cells on various growth signaling pathways. Myeloid RelA/p65 is necessary to link smoke-induced inflammation with LC growth.

Keywords: Expression profiling by array

overall_design: Analysis of gene expression in lewis lung carcinoma cells resected from lungs of WT and RelA/p65 deficient mice exposed to smoke or air. Four different samples were analyzed (3 replicates each).

first: Li

last: Dong

first: Robert

last: Bals


title: Tetracycline-Inducible Cyr61 effect on LN229 glioma cells

status: Public on Apr 04 2012

city: Columbus

first: Amy

last: Haseley

state: OH

department: Neurological Surgery

country: USA

institute: The Ohio State University

summary:
Glioblastoma multiforme is the most common and aggressive form of brain cancer. The use of oncolytic HSV-1 (oHSV) to selectively target brain cancer cells leading to their lytic destruction has shown to be very promising in a preclinical setting, but is lacking efficacy in clinical trials. Cyr61, a secreted extracellular matrix protein which functions to promote angiogenesis, migration, proliferation and tumorigenesis, was found to be upregulated rapidly following oHSV infection. Here we show, using microarray analysis, that Cyr61 expression leads to the induction of several genes with type 1 interferon function. We show that Cyr61 mediated type 1 IFN induction is through its interaction with integrin alpha6beta1 on the cell surface and results in oHSV inhibition, reducing the efficacy of this therapy.
We used microarray to detail the global program of gene expression underlying Cyr61 mediated oncolytic HSV-1 inhibition and identified distinct classes of up-regulated genes during this process.

overall_design: Tetracycline-Inducible glioma cells expressing Cyr61 protein in the presence of doxycycline were treated with or without doxycycline for 24 hours. RNA was extracted and hybridized on Affymetrix microarray.  Two groups: ± dox to induce cyr61, performed in triplicate.

first: A

first: L

last: Yu

first: B

last: Kaur


title: Microarray analysis of a multiple myeloma cell line, MM1S, treated with adenosine A2A and Beta-2 Adrenergic Receptor agonists in combination with dexamethasone

city: Cambridge

first: Winnie

middle: F

last: Tam

state: MA

address: 245 First Street

department: Oncology

institute: Zalicus, Inc

summary:
We have used an agnostic approach to identify drug combinations by using combination high throughput screening (cHTS) technology and make the surprising discovery that adenosine A2A and beta-2 adrenergic receptor agonists are highly synergistic, selective and novel agents that enhance glucocorticoid activity in B-cell malignancies.
We used the microarray study to understand the synergistic mechanism between dexamethasone and A2A receptor agonist or Beta-2 Adrenergic receptor agonist in a multiple myeloma cell line, MM1S.

overall_design: MM1S cells were treated with CGS-21680 or Salmeterol alone, or in combination with dexamethasone for six hours for RNA extraction and hybridization on Affymetrix microarrays.

first: Richard

last: Rickles

first: Margaret

last: Lee


title: Expression data from murine beta thalassemia erythroblasts

city: Philadelphia

first: Mitchell

middle: J

last: Weiss

state: PA

address: 3615 Civic Center Blvd

department: Hematology

institute: Children's Hospital of Philadelphia

summary: This study analyzes gene expression in beta-thalassemic fetal liver erythroblasts in the Th3 murine model. FACS-purified wild-type, heterozygous, and homozygous stage-matched erythroblasts from E14.5 fetal livers are compared.

overall_design: We used FACS to purify CD71+Ter119+FSChigh matched populations from E14.5 fetal livers of wild-type, Th3/+, and Th3/Th3 embryos


title: In vitro and in vivo evidences of osteocytes involvement in myeloma-induced osteoclast formation and bone disease

status: Public on May 22 2012

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

summary: The involvement of osteocytes in multiple myeloma (MM)-induced osteoclast formation and the occurrence of bone lesions are still unknown. Osteocytes regulate bone remodeling at least in part through the cell death and apoptosis triggering osteoclast recruitment and formation. In this study, firstly we shown that MM cells increased osteocyte death and affect their transcriptional profile evaluated by microarray analysis up-regulating osteoclastogenic cytokines as interleukin (IL)-11. Consistently we show that the conditioned media of human pre-osteocytes co-cultured with MM cells significantly increased osteoclastogenesis. To translate into a clinical perspective such in vitro evidences, we then performed histological analysis on bone biopsies obtained from MM patients, MGUS and healthy controls. We found a significant reduction in the number of viable osteocytes in MM patients as compared to controls. A significant negative correlation between the number of viable osteocytes and that of osteoclasts was also demonstrated. Moreover, as regards the skeletal involvement, we found that MM patients with bone lesions have a significant lower number of viable osteocyte than those without. Overall, our data suggest a role of osteocytic cell death in MM-induced osteoclast formation in vitro and MM bone disease in vivo in MM patients.

overall_design: This series of microarray experiments contains the gene expression profiles of HOB-01 osteocytes cultured alone and co-cultured with the JJN3 human myeloma cell line. 5 micrograms of total RNA was processed, and in accordance with the manufacturer's protocols, the fragmented biotin-labelled cRNA were hybridized on GeneChip Human Genome U133 Plus 2.0 Arrays (Affymetrix Inc.). The arrays were scanned using the Agilent GeneChip Scanner 3000 7G. The images were acquired using Affymetrix GeneChip Operating System (GCOS) 1.1 software and the probe level data converted to expression values using default GCOS1.1 scaling. Natural-scaled data are provided.

first: Nicola

last: Giuliani

first: Marina

last: Bolzoni

first: Marzia

last: Ferretti

first: Paola

last: Storti

first: Mirca

last: Lazzaretti

first: Benedetta

last: Dalla Palma

first: Eugenia

last: Martella

first: Antonino

last: Neri

first: Vittorio

last: Rizzoli

first: Carla

last: Palumbo


title: The General Transcription Factor TAF7 is Essential for Embryonic Development but Not Essential for the Survival or Differentiation of Mature T Cells (T cell 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: The T cells are purified spleen CD4+ T cells coming either from TAF7f/- 8EIII-cre+ (TAF7 -/-) or TAF7 f/- 8EIII-cre - (TAF7+/-). The cells were purified by FACS based on cell surface marker expression: high TCRbeta and CD4 expression. The cells are enriched in naive CD4 T cells based on their low level of CD44 surface expression. All RNAs were extracted using shredders and the Qiagen RNeasy mini kit and their quality assayed before using for hybridization. Total RNA 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: Expression data from in vitro-induced non-hypoxic tumour associated macrophages (TAMs)

city: Tokyo

first: Yurai

last: Okaji

address: Bunkyo-ku, Hongo 7-3-1

country: Japan

institute: The University of Tokyo

summary: Active immunotherapy is a promising strategy for anti-angiogenic cancer therapy. Recently, we have reported that a vaccine using human umbilical vein endothelial cells (HUVECs) induced specific anti-endothelial immune responses in the most of immunized patients, and resulted in tumor regression in some patients with recurrent malignant brain tumors, whereas not in colorectal cancer patients. In this study, we hypothesized that non-hypoxic perivascular tumor associated macrophages (TAMs) in colorectal cancer, but not in glioblastoma, might negatively alter the therapeutic efficacy of anti-angiogenic active immunotherapy. To test this hypothesis, we examined global gene expression profiles of non-hypoxic macrophages stimulated in vitro by soluble factors released from tumor cells of human glioblastoma U-87MG (‘brain TAMs’) or colorectal adenocarcinoma HT-29 (‘colon TAMs’).

overall_design: Murine non-hypoxic TAMs were induced in vitro by incubation with soluble factors released from human cancer cell lines U-87MG ('brain TAMs') or HT-29 ('colon TAMs'), for RNA extraction and subsequent hybridization on Affymetrix microarrays. To evaluate homogeneous macrophage populations at different tumour developmental stages, RNA aliquots of control macrophages and TAMs obtained at five different time-points, i.e. 8h, 16h, 24h, 32h and 40h, were pooled and used for screening of differentially expressed genes. The experiments for TAMs as well as for control unstimulated macrophages were performed in triplicates.

first: Nelson

middle: H

last: Tsuno

first: Minoru

last: Tanaka

first: Eiji

last: Sunami

first: Joji

last: Kitayama

first: Katsushi

last: Tokunaga

first: Hirokazu

last: Nagawa

first: Koki

last: Takahashi


title: Expression data comparing Huh7 CD133+ and CD133- HCC cells

status: Public on Apr 05 2012

city: Hong Kong

first: Stephanie

last: Ma

address: Rm 47, 1/F, Lab Block, Faculty of Medicine Bldg, 21 Sassoon Rd, Pok Fu Lam

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

summary:
To identify candidate genes involved in enhanced tumorigenicity of CD133+ liver tumor-initiating cells
Affymetrix Human Genome U133 Plus GeneChip 2.0

overall_design: HCC cell line Huh7 was sorted into CD133+ and CD133- populations by flow cytometry


title: Expression data from the mouse liver with constitutively active NF-kB

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

country: Germany

institute: Ulm University

summary:
Activation of hepatic NF-kB signaling induces inflammation and ultimately fibrosis.
To investigate the underlying mechanism, we used microarrays to detail the global programme of gene expression which is regulated by hepatic NF-kB signaling.

overall_design: We generated transgenic mice which express a constitutively active IKK2 controlled under the LAP promotor. The liver samples were collected from transgenic mice as well as from control animals at the age of 4 weeks. RNA extraction was performed from these liver samples and hybridized on Affymetrix microarrays.

first: Yoshiaki

first: Pavel

last: Strnad

first: Thomas

last: Wirth


title: Expression data from mouse neural cells and tumors

status: Public on Mar 31 2012

city: Minato-ku

first: Hideto

last: Koso

state: Tokyo

address: 4-6-1 Shirokanedai

institute: Institute of Medical Science, The University of Tokyo

summary:
Neural stem cells (NSCs) are considered to be the cell-of-origin of brain tumor stem cells. To identify the genetic pathways responsible for the transformation of normal NSCs to brain-tumor-initiating cells, we used Sleeping Beauty (SB) transposons, to mutagenize NSCs. Mobilized SB transposons induced the immortalization of NSCs. Immortalized NSCs induced tumors upon subcutaneous transplantation in immunocompromized mice. To further classify the immortalized cells and mouse tumors, we performed Gene Set Enrichment Analysis (GSEA) using DNA microarray data.

Ten immortalized NSC lines (four WT and six p53 mutant lines) and two normal NSCs were used for RNA extraction and hybridization on Affymetrix microarrays. CEL files were processed using the RMA algorithm to normalize the data. Unsupervised hierarchical clustering was applied to the normalized gene expression data across samples using the R module pvclust (Suzuki and Shimodaira, Bioinformatics 22, 1540-1542, 2006). Hierarchical clustering showed a close similarity in gene expression between all ten immortalized lines, compared with two normal NSCs. We then compared their gene expression profiles to those present in the brain transcriptome database (Cahoy et al., J Neurosci 28, 264-278, 2008). Using five gene sets that are associated with neurons, oligodendrocytes, OPCs, astrocytes and cultured astroglial cells, GSEA enrichment scores were calculated for the ten immortalized NSCs lines against two control normal NSCs. GSEA enrichment analysis was performed using GSEA software v. 2.07 (http://www.broadinstitute.org/gsea). We found a strong enrichment for genes that are differentially expressed in the cultured astroglial cells.

Twelve tumors (six WT and six p53 mutant tumors) and three control subcutaneous tissues were used for RNA extraction and hybridization on Affymetrix microarrays. CEL files were processed using the RMA algorithm to normalize the data. Unsupervised hierarchical clustering was applied to the normalized gene expression data across samples using the R module pvclust (Suzuki and Shimodaira, Bioinformatics 22, 1540-1542, 2006). Hierarchical clustering of 12 tumors showed a close similarity between the tumors, compared with three control subcutaneous tissues. We next performed GSEA analysis on the tumors. Using gene sets specific to the four defined GBM subtypes (Verhaak et al., Cancer Cell 17, 98-110, 2010), a GSEA enrichment score was then calculated for the twelve tumor samples against three control subcutaneous tissue samples. GSEA enrichment analysis was performed using GSEA software v. 2.07 (http://www.broadinstitute.org/gsea). This analysis showed that the mouse tumors were significantly enriched for genes specific for the mesenchymal GBM.

overall_design: Immortalized cell lines and tumors were used for RNA extraction and hybridization on Affymetrix microarrays. Ten immortalized lines (Line 3, 28, 31, 59, 95, 116, 119, 120, 123, 331) were compared with two normal NSCs. Twelve tumors were generated from four lines (1, 31, 59, 123) and compared with three subcutaneous tissues (SubQ).

first: Neal

middle: G

last: Copeland


title: Comparison of transcriptomes between Marf1+/+ (WT) and Marf1 ENU/ENU (Mutant) fully-grown oocytes (FGO)

city: Bar Harbor

first: You-Qiang

last: Su

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary:
Marf1 (MUT) female mice are infertile and the meiosis of the oocytes are arrest at prophase I. We thought to identify the potential causes of the meiotic arrest phenotype in the mutant oocytes by comparing the transcriptomes of the WT and mutant fully-grown oocytes (from 23-d old mice) that are transcriptional silent.
We compared the transcriptomes of WT and MUT FGOs.

overall_design: 3 individual oocyte samples of each genotype (WT and MUT).

first: John

last: Eppig


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

first: Dinah

last: Singer

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

overall_design: Refer to individual Series


title: Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin

status: Public on Apr 03 2012

city: State College

middle: K.

last: Wood

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

summary: Persisters are a subpopulation of metabolically-dormant cells in biofilms that are resistant to antibiotics; hence, understanding persister cell formation is important for controlling bacterial infections. Previously we discerned that MqsR and MqsA of Escherichia coli are a toxin/antitoxin pair that influence persister cell production via their regulation of Hha, CspD, and HokA. Here, to gain more insights into the origin of persisters, we used protein engineering to increase the toxicity of toxin MqsR by reasoning it would be easier to understand the effect of this toxin if it were more toxic. We found that two mutations (K3N and N31Y) increase the toxicity four fold and increase persistence 73 fold compared to native MqsR by making the protein less labile. A whole transcriptome study revealed that the MqsR variant represses acid resistance genes (gadABCEWX and hdeABD), multidrug resistance genes (mdtEF), and osmotic resistance genes (osmEY).  Corroborating these microarray results, deletion of rpoS as well as the genes that the master stress response regulator RpoS controls, gadB, gadX, mdtF, and osmY, increased persister formation dramatically to the extent that nearly the whole population became persistent. Therefore, the more toxic MqsR increases persistence by decreasing the ability of the cell to respond to antibiotic stress through its RpoS-based regulation of acid resistance, multidrug resistance, and osmotic resistance systems.

overall_design: For the whole-transcriptome study of BW25113 mqsR/pBS(Kan)-mqsR 2-1 versus BW25113 mqsR/pBS(Kan)-mqsR, planktonic cells were grown to a turbidity of 0.5 at 600 nm in LB medium with 1 mM IPTG at 37 °C, adjusted the turbidity to 1, and exposed to 20 μg/mL ampicillin with 1 mM IPTG for 1 h.  Cells were isolated by centrifuging at 0°C, and RNALater® buffer (Ambion, Cat# AM7021) was added to stabilize RNA during the RNA preparation steps.  Total RNA was isolated from cell pellets with Qiagen RNeasy mini Kit (Cat# 74104) using a bead beater.  cDNA was synthesized and fragmented to obtain 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP, and hybridization was performed at 45°C with 60 rpm for 16 hours. The probe array was washed, stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS)”, and scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS). Data were processed with MAS 5.0 Expression Analysis Default Setting. Genes were identified as differentially expressed if the expression ratio was higher than the standard deviation: 4.0 fold (enriched and differentially degraded) cutoff for the DNA microarrays (standard deviation 1.3 fold), and if the p-value for comparing two chips was less than 0.05.

first: SeokHoon

last: Hong

first: Xiaoxue

last: Wang

middle: K


title: Profiling of gene expression in TLR2 and TLR3 activated macrophages

status: Public on Mar 28 2012

city: Birmingham

first: Gang

last: Liu

state: Alabama

address: 901 19TH ST S

department: Medicine

institute: University of Alabama at Birmingham

summary: We have identified more than 50 genes that have upregulated expression in TLR3 activated (PMI-1,2), but have downregulated expression in TLR2 activated (PMP-1,2) macrophages, as compared to control cells (PMC-1,2)

overall_design: identify genes that have upregulated expression in TLR3 activated (PMI-1,2), but have downregulated expression in TLR2 activated (PMP-1,2) macrophages, as compared to control cells (PMC-1,2)


title: Expression data from primary breast tumors (Auckland)

city: Auckland

first: Cris

last: Print

address: Grafton Campus, Park Rd

country: New Zealand

institute: Auckland University

summary:
Frozen tissue specimens from primary breast tumors were collected and profiled using Affymetrix U133 plus 2 expression microarrays.
A publication describing the generation of these data is not yet available. However, these data can be used alongside other Affymetrix breast tumour data sets to form large meta-cohorts for breast cancer research, as was done in Lasham et. al. J Natl Cancer Inst. 2012 Jan 18;104(2):133-146.

overall_design: Frozen tumor tissues comprising of >60% tumor cellularity were extracted for total RNA and hybridized on Affymetrix microarrays.

first: Cristin

first: Lance

last: Miller

first: Mik

last: Black


title: Expression data from primary breast tumors


title: Regulation of Autophagy by VEGF-C axis in cancer

city: Rochester

first: Alexey

middle: Aleksandrovich

last: Leontovich

state: MN

address: 200 First street

department: Health Science Research

institute: Mayo Clinic

summary: A major contributor to cancer mortality is recurrence and subsequent metastatic transformation following therapeutic intervention. In order to develop new treatment modalities or improve the efficacy of current ones it is important to understand the molecular mechanisms that promote therapy-resistance to cancer cells. One pathway that has been demonstrated to therapy resistance is autophagy, a self-digestive process that can eliminate unnecessary or damaged organelles to protect cancer cells from necrosis. Effective targeting of this pathway could lead to the development of new therapies. In our studies, we found that the VEGF-C/NRP-2 axis is involved in the activation of autophagy, which is essential for the survival of cancer cells following chemotherapy treatment. Furthermore, we identified two VEGF-C/NRP-2-regulated genes, LAMP-2 and WDFY-1 that have previously been suggested to participate in autophagy and vesicular trafficking. The upregulation of WDFY-1 upon depleted level of VEGF-C contributed to cytotoxic drug-mediated cell death. Altogether, these data suggest a link between VEGF-C/neuropilin-2 axis and cancer cell survival despite the presence of chemotherapy-induced stress.

overall_design: Human prostate cancer cell lines PC3, Du145 and pancreatic cancer cell line CaPan1 were cultured at 37οC either in RPMI 1640 with L-glutamine or in DMEM media with 10% fetal bovine serum and supplemented with penicillin/streptomycin. PC3 stable transfected cell line was growing in presence of 1µg/ml puromycin selection pressure. Cells were transfected with SmartPool cocktail siRNA for NRP-2, VEGF-C, LAMP-2, and WDFY-1, using DharmaFECT 1-4. siRNA transfection was allowed to proceed 72 h before collection of whole-cell extract or total RNA.To identify potential pathways involved in this VEGF-C-mediated cell survival, we performed a microarray study comparing cells depleted in either VEGF-C or NRP-2 using SmartPool siRNA to PC-3 cells treated with scrambled siRNA. Upon comparison of the two data sets, we found 34 gene-tags that were commonly up- or down-regulated in both NRP-2- and VEGF-C-depleted cells.

middle: A

first: Kaustubh

last: Datta


title: Expression data from MDSCs at different time points during tumor progression

status: Public on Mar 30 2012

city: Seoul

first: Chang-Yuil

last: Kang

address: 29-102, Seoul National University, Shillim-dong, Gwanak-gu

country: South Korea

institute: Seoul National University

summary: Myeloid-derived suppressor cells (MDSCs) are increased by tumor-derived factors and suppress anti-tumor immunity. MDSCs obtained at a late time point after tumor injection had stronger suppressive activity than MDSCs obtained at an early time point, as measured by T cell proliferation assays. To find factors in MDSCs that change during tumor growth, we analyzed gene expression profiles from MDSCs at different time points after tumor injection.  We found that immune response-related genes were down-regulated, but pro-tumor function-related genes were up-regulated in both Mo-MDSCs and PMN-MDSCs at the late time point. Among differentially expressed genes, FK506 binding protein 51 (FKBP51), which is a member of the immunophilin protein family and plays a role in immunoregulation, was increased in the Mo- and PMN-MDSCs isolated from the late time points. Experiments using siRNA and a chemical inhibitor of FKBP51 revealed that FKBP51 contributes to the regulation of the suppressive function of MDSCs by increasing iNOS, ARG1, and ROS levels and enhancing NF-kappaB activity. Collectively, our data suggest that FKBP51 is a novel molecule that can be targeted to regulate the immunosuppressive function of MDSCs.

overall_design: To identify the factors that licensed MDSCs to be more suppressive as tumors grow, we analyzed gene expression profiles in the two subsets of MDSCs at different time points (3wks, 6wks) during tumor progression. CD11b+Ly-6C(high)Ly-6G(low) Mo-MDSCs and CD11b+Ly-6C(low)Ly-6G(high) PMN-MDSCs were sorted from pooled spleens of naïve mice and Her-2/CT26 tumor-bearing mice.  Total RNA was purified and gene expression was analyzed by the Affymetrix GeneChip® Mouse Gene 1.0 ST Array.

first: Yeon-Jung

last: Kim

first: Yun-Sun


title: Altered Gene Expression Profile of Microvascular Endothelium in Placentas from IUGR/Preeclamptic Pregnancies

city: Toronto

first: Brian

middle: Joseph

last: Cox

state: Ontario

address: 1 King's College Circle, Rm 3360

department: Physiology

country: Canada

institute: University of Toronto

summary: The placental microvasculature of the human fetus is essential for the efficient transfer of gases, nutrients and waste between the mother and fetus. Microvascular hypoplasia of the terminal villi is associated with the placental pathology observed in cases of severe Intra Uterine Growth Restriction (IUGR). We used novel methods to isolate a pure population of placental microvascular endothelial cells from control preterm placentas (n=3) and placenta complicated by severe IUGR (n=6) with superimposed preeclampsia (n=5). Distal placental villous tissue was collected to enrich for terminal villi. Tissue was minced, digested and placental microvascular endothelial cells (PlMEC) were positively selected using tocosylated magnetic Dynabeads labeled with Human Endothelial Antigen lectin. The purity of the PlMEC (95%) was assessed by CD31 immunocytochemistry. RNA was extracted from the PlMEC samples and also from 3 term placenta and subjected to Affymetrix microarray analysis (U133Plus2 array chips). Data from the 3 term placentas and 3 preterm PlMEC arrays was used to generate an endothelial cell specific gene profile. This profile was used to identify the endothelial genes differentially regulated in all 6 IUGR cases. BTNL9 and NTRK2 transcripts were upregulated and SAA1, GNAS and SLAMF1 transcripts were downregulated as relative to the preterm controls. These changes were validated by Real time PCR in the PlMEC samples. This novel study is the first to identify endothelial candidate genes that may play a role in the villous hypoplasia of severe IUGR. This work advances our understanding of the molecular defects in placental microvascular endothelial cells in normal and pathologic pregnancies.

overall_design: Three normal control placentas were compared against endothelial cells isolated from IUGR, IUGR and preeclampsia and normal pregancies. In this way enrichment of endothelial genes could be determined as well as changes in the expression pattern of endothelial genes due to different pathologies.

first: Anne

middle: M

last: Roggensack

first: Jonathan

middle: E

last: Perkins

first: Sarah

last: Keating

first: Rosanna

last: Weksberg

middle: C

last: Kingdom

first: S

middle: L

last: Adamson

first: Caroline

last: Dunk


title: Clonal competition with alternating dominance in multiple myeloma [GEP]

city: Phoenix

last: Keats

state: Arizona

address: 445 N. Fifth Street

department: Integrated Cancer Genomics

institute: Translational Genomics Research Institute (TGen)

summary:
Copy number and  expression profiling of multiple myeloma patients at multiple stages of their individual clinical course
Identification of evolutionary patterns in multiple myeloma

overall_design: Gene expression analysis of individual CD138 purified tumor populations using Affymertix U133Plus2.0 GeneChips

first: P

last: Bergsagel


title: Expression data from ACC xenografts and normal salivary glands

status: Public on Mar 27 2012

city: Frederick

first: Sudhir

middle: R

last: Chowbina

state: MD

address: Frederick

department: Advanced Biomedical Computing Center

institute: SAIC-Frederick

summary: Adenoid cystic carcinoma (ACC) is an uncommon malignant neoplasm (incidence of 0.35 per 100,000) that occurs in different body sites. It most often arises in salivary glands and other secretory glands in the head and neck region. To find the gene expression signatures of ACC, we performed microarray experiments to compare ACC xenograft tumor models and normal tissue samples. We used microarrays to detail the global program of gene expression underlying adenoid cystic carcinoma and identified distinct classes of up- and down-regulated genes compared to non-neoplastic salivary tissue.

overall_design: Viable tumor tissue samples from human patients were used to establish xenograft tumor models in nude/nude immunodeficient mice. Tissue from these tumor models were compared to tissue samples of normal human salivary glands. Tissue samples were frozen, examined by cryostat histologic sectioning and macrodissected to obtain samples that represented at least 70% epithelial cells.

first: Christopher

last: Moskaluk

first: Jason

last: Papin

first: Alyson

last: Prorock

first: Yongde

last: Bao


title: Expression analysis of doxycycline inducible secondary fibroblasts reprogramming under adherent and suspension conditions

status: Public on Mar 25 2012

first: David

last: Fluri

address: 160 College Street

summary: Samples of adherent and suspension cells undergoing reprogramming were collected at day 0, day2, day6, day15 (with doxycycline) and day25 (without doxycycline).

overall_design: Reprogramming under adherent and suspension conditions was compared by PCC analysis, non-hierarchical clustering and by functional criteria for differentially expressed genes.


title: Expression data from BAC transgenic mice overexpressing Glo1

city: Chicago

first: Margaret

middle: Gail

last: Distler

state: IL

department: Department of Human Genetics

institute: University of Chicago

summary:
We generated mice with a transgenic BAC on a B6 background. The BAC contains Glo1, and the transgenic mice were found to overexpress Glo1.
We performed a microarray on whole-brain RNA of adult mice to identify differentially expressed genes resulting from Glo1 overexpression.

overall_design: Wild type (WT) and transgenic (Tg) littermates were used. Mice were adult males, and RNA was extracted from whole brains.

first: Abraham

last: Palmer


title: Time-course transcriptome measure of HoxB4-mediated HSC development from ES cells

status: Public on Mar 23 2012

city: La Jolla

first: Kai

last: Tan

state: CA

address: 9500 Gilman Drive

department: Bioengineering

institute: University of California San Diego

summary: Efficient in vitro generation of hematopoietic stem cells (HSCs) from embryonic stem cells (ESCs) holds great promise for cell-based therapies of hematological diseases. To date, HoxB4 remains to be the most effective transcription factor (TF) whose over-expression in ESCs confers long-term repopulating ability to ESC-derived HSCs. Despite its importance, the components and dynamics of the HoxB4 transcriptional regulatory network is poorly understood, hindering efforts to develop a more efficient protocol for in vitro derivation of HSCs. Towards this goal, we performed global gene expression profiling and chromatin immunoprecipitation coupled with deep sequencing (ChIP-Seq) at four stages of the HoxB4-mediated HSC development. Joint analyses of ChIP-Seq and gene expression profiles unveil a number of global features of the HoxB4 regulatory network.

overall_design: Cells from four time points of the developmental processes were collected, including days 0, 6, 16, and 26. Triplicate microarray hybridizations were done for cells from each time point.


title: Clonal competition with alternating dominance in multiple myeloma

type:
Genome variation profiling by array
Expression profiling by array


title: Gene expression profiling of peripheral blood mononuclear cells in the setting of peripheral arterial disease

status: Public on Mar 22 2012

first: Iftikhar

last: Kullo

state: Minnesota

address: 200, First Street Southwest

department: Division of Cardiovascular Diseases

summary: Peripheral arterial disease (PAD) is a relatively common manifestation of systemic atherosclerosis that leads to progressive narrowing of the lumen of leg arteries. Circulating monocytes are in contact with the arterial wall and can serve as reporters of vascular pathology in the setting of PAD. We performed gene expression analysis of peripheral blood mononuclear cells (PBMC) in patients with PAD and controls without PAD to identify differentially regulated genes. We identified 87 genes differentially expressed in the setting of PAD; 40 genes were upregulated and 47 genes were downregulated. We employed an integrated bioinformatics pipeline coupled with literature curation to characterize the functional coherence of differentially regulated genes. Notably, upregulated genes mediate immune response, inflammation, apoptosis, stress response, phosphorylation, hemostasis, platelet activation and platelet aggregation. Downregulated genes included several genes from the zinc finger family that are involved in transcriptional regulation. These results provide insights into molecular mechanisms relevant to the pathophysiology of PAD.

overall_design: PAD was defined as an ankle brachial index (ABI) <= 0.9 (n = 19) while age and gender matched controls had an ABI > 1.0 (n = 18). Microarray analysis was performed using Affymetrix HG-U133 plus 2.0 gene chips and analyzed using GeneSpring GX 11.0. Gene expression data was normalized using Robust Multichip Analysis (RMA) normalization method, differential expression was defined as a fold change [greater than or equal to]1.5, followed by unpaired Mann-Whitney test (P < 0.05) and correction for multiple testing by Benjamini and Hochberg False Discovery Rate. Meta-analysis of differentially expressed genes was performed using an integrated bioinformatics pipeline with tools for enrichment analysis using Gene Ontology (GO) terms, pathway analysis using Kyoto Encyclopedia of Genes and Genomes (KEGG), molecular event enrichment using Reactome annotations and network analysis using Ingenuity Pathway Analysis suite. Extensive biocuration was also performed to understand the functional context of genes.

first: Rizwan

last: Masud

first: Khader

last: Shameer

first: Aparna

last: Dhar

first: Keyue

last: Ding

first: Kullo

last: Iftikhar


title: Gene expression profile of human embryonic stem cells growth in low concentrations of nitric oxide

status: Public on Mar 20 2012

city: Seville

first: Rafael

middle: A.

last: Tapia Limonchi

state: Seville

address: Av. Américo Vespucio s/n-Edif. CABIMER Parque Científico y Tecnológico Cartuja 93

department: Department of Cell Therapy and Regenerative Medicine

country: Spain

institute: Andaluzian Center for Molecular Biology and Regenerative Medicine (CABIMER)

summary: Identification of genes regulated in human embryonic stem cells by the effect of low concentrations of nitric oxide. The transcriptome of cells treated with NO were compared with that of cells cultured in abscense of LIF, and undifferentiated ES cells cultured in presence of LIF. The H181 hES cell line was used for the experiments. These data complement a previous study realized in mES cells under the same NO conditions . The aim of the work is to know how NO modify transcriptome of ES cells and how participate in the modulation of self renewal and differentiation.

overall_design: Passages between 72 and 74 of the H181 cell line were cultured on Matrigel-coated tissue culture plates in presence of 8ng/ml of bFGF for maintain them undifferentiated (control). For treatments, cells were cultured in the absence of bFGF to induce differentiation and treat cells with 2uM of DETA/NO. Cells were grown for 6 days mantaining the conditions of the treatment each 19 hours. Dietilentriamine-NO (DETA-NO) (Sigma) was used as donor of nitric oxide.  Expression data of cells treated with NO in absence of bFGF were compared with cells cultured in absence of this, in order to observe how the treatment affects the transcriptome, and if there is some similarity with undifferentiated condition in presence of bFGF.

first: Juan

last: Tejedo

last: Tapia-Limonchi

first: Gladys

last: Cahuana

first: Sergio

last: Castilla

first: Bernat

last: Soria

first: Francisco

last: Bedoya


title: Expression data for mouse hypothalamus

city: Memphis

first: Khyobeni

last: Mozhui

state: TN

address: 66 N. Pauline Street, #631

department: Preventive Medicine

institute: University of Tennessee Health Science Center

summary:
Strain differences in gene expression in the hypothalamus of BXD recombinant inbred mice
We used microarrays to evaluate genetic and sex-specific differences in gene expression in the hypothalamus

overall_design: Hypothalamus was dissected from adult male and female mice and process for expression analysis

first: K

first: R

middle: W

last: Williams


title: Genetic perturbations direct the development of distinct brain tumor types from postnatal neural stem/progenitor cells

status: Public on Mar 21 2012

city: Lund

first: Ulrike

last: Nuber

address: Klinikgatan 26

country: Sweden

institute: Lund University

summary:
Primary brain tumors are classified and treated based on their histological features, however the factors which specify these tumor types remain largely unknown.  We demonstrate that the over-expression of HRAS (V12) and MYC alone or in combination directs the development of glioma, CNS PNET, and atypical  teratoid/rhabdoid (AT/RT)-like tumors from postnatal murine p53-deficient neural stem/progenitor cells.
Microarray analyses were performed to investigate the gene expression profile of the tumor cells generated by the different genetic perturbations.

overall_design: Murine brain tumors were generated by overexpressing different oncogenes in cultured neurosphere cells from the postnatal lateral ventricle wall region (LVW) of Trp53-deficient mice. Neurosphere cultures were established from isolated cells of the generated tumors, which still expressed the transgene/fluorescent marker gene cassette. Total RNA was isolated and used for gene expression analyses using the Affymetrix Gene 1.0 ST array platform.

first: Falk

last: Hertwig


title: Transcriptomal effects of four-day exposure to estradiol on mouse primary culture urogenital sinus mesenchymal cells of fetal mouse prostate

city: Charlestown

first: Toshihiro

last: Shioda

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

summary: Developmental exposure of mouse fetuses to estrogens results in dose-dependent permanent effects on prostate morphology and function. Fetal prostatic mesenchyme cells express estrogen receptor alpha (ERα) and androgen receptors and convert stimuli from estrogens and androgens into signaling to regulate epithelial cell proliferation and differentiation. To obtain mechanistic insight into the role of different doses of estradiol (E2) in regulating mesenchymal cells, we examined E2-induced transcriptomal changes in primary cultures of fetal mouse prostate mesenchymal cells. Urogenital sinus mesenchyme cells were obtained from male mouse fetuses at gestation day 17 and exposed to 10 pM, 100 pM or 100 nM E2 in the presence of a physiological concentration of dihydrotestosterone (0.69 nM) for four days. Gene ontology studies suggested that low doses of E2 (10 pM and 100 pM) induce genes involved in cell adhesion, morphological tissue development, and sterol biosynthesis but suppress genes involved in growth factor signaling and cell adhesion. Genes showing inverted-U-shape dose responses (enhanced by E2 at 10 pM E2 but suppressed at 100 pM) were identified, and their enrichment in the glycolytic pathway was demonstrated. At the highest dose (100 nM), E2 induced genes enriched not only for cell adhesion but also steroid hormone signaling and metabolism, cytokines and their receptors, cell-to-cell communication, Wnt signaling, and TGF-β signaling. These results suggest that prostate mesenchymal cells may regulate epithelial cells through direct cell contacts when estrogen level is low whereas soluble growth factors might play significant roles when estrogen level is high.

overall_design: Primary culture urogenital sinus mesenchymal cells were isolated from prostate glands of gestation day 17 CD1 male mouse fetuses. Cells were then exposed to 10 pM or 100 pM 17beta-estradiol or vehicle (0.05% ethanol) for four days in the presence of 690 pM 5alpha-dihydrotestosterone. Total cellular RNA was then isolated for determination of transcriptomal profiles by Affymetrix mouse gene 1.0 ST array.

first: Julia

last: Taylor

first: Catherine

last: Richter

first: Karhryn

last: Coser

first: Frederick

middle: S

last: vom Saal


title: Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm

city: Gyeongsan-Si

first: Jintae

last: Lee

state: Gyeongsangbuk-Do

address: 214-1 Daedong

department: Chemical engineering

institute: Yeungnam University

summary: Honey has been widely used against bacterial infection for centuries.  Previous studies suggested that honeys in high concentrations inhibited bacterial growth due to the presence of anti-microbial compounds, such as methylglyoxal, hydrogen peroxide, and peptides.  In this study, we found that three honeys (acacia, clover, and polyfloral) in a low concentration as below as 0.5% (v/v) significantly suppress virulence and biofilm formation in enterohemorrhagic E. coli O157:H7 affecting the growth of planktonic cells while these honeys do not harm commensal E. coli K-12 biofilm formation.  Transcriptome analyses show that honeys (0.5%) markedly repress quorum sensing genes (e.g., AI-2 import and indole biosynthesis), virulence genes (e.g., LEE genes), and curli genes (csgBAC). We found that glucose and fructose in honeys are key compounds to reduce the biofilm formation of E. coli O157:H7 via suppressing curli production, but not that of E. coli K-12. Additionally, we observed the temperature-dependent response of honeys and glucose on commensal E. coli K-12 biofilm formation; honey and glucose increase E. coli K-12 biofilm formation at 37°C, while they decrease E. coli K-12 biofilm formation at 26°C.  These results suggest that honey can be a practical tool for reducing virulence and colonization of the pathogenic E. coli O157:H7, while honeys do not harm commensal E. coli community in the human.

overall_design: For the microarray experiments, E. coli O157:H7 EDL933 was inoculated in 250 ml of LB in 1000 ml flasks with overnight cultures that were diluted at 1:100. Cells were shaken with 10g of glass wool at 100 rpm and 37°C for 7 hrs.  Cells were immediately chilled with dry ice and 95% ethanol (to prevent RNA degradation) for 30 sec before centrifugation in 50 ml centrifuge tubes at 13,000 g for 2 min; cell pellets were frozen immediately with dry ice and stored -80°C.  RNA was isolated using Qiagen RNeasy mini Kit (Valencia, CA, USA). To eliminate DNA contamination, Qiagen RNase-free DNase I was used to digest DNA. RNA quality was assessed by Agilent 2100 bioanalyser using the RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, The Netherlands), and quantity was determined by ND-1000 Spectrophotometer (NanoDrop Technologies, Inc., DE, USA).

first: Jin-Hyung

first: Moo

last: Cho


title: Expression comparison between SMC4 and conventional cultures

status: Public on Mar 16 2012

city: San Diego

first: Dave

last: Robbins

address: 3535 General Atomics Court Ste. 200

institute: Fate Therapeutics

summary: The undifferentiated state of pluripotent stem cells depends heavily on the culture conditions.  We show that a unique combination of small molecules, SMC4, added to culture conditions converts primed pluripotent stem cells to a more naïve state.  By conducting Affymetix analysis we show of majority of lineage markers are repressed in SMC4 culture.

overall_design: Human embryonic stem cells were compared to human induced pluripotent stem cells cultured in either primed or naïve conditions.

first: David


title: Screening for Epigenetically Masked Genes in Colorectal Cancer using 5-aza-2’-deoxycytidine treatment, Microarray and Gene Expression Profile

city: Bunkyo-ku

first: Kaoru

last: Mogushi

address: 2-1-1 Hongo

department: Intractable Disease Research Center

institute: Juntendo University

summary: Unearthing of silenced genes in colorectal cancer (CRC) is of great importance. We employed oligonucleotide microarray to find changes in global gene expression of five CRC cell lines. These were analyzed before and after treatment with the 5-aza-2'-Deoxycitidine. Expression of the responding genes was integrated with gene expression profiling generated by microarray analysis of matched colorectal tissue samples. Selected candidates were subjected to methylation-specific PCR (MSP) and real-time quantitative reverse transcription-PCR using CRC cell lines and paired tumor and normal samples from CRC patients. Sixty eight genes were re-expressed after 5-aza-2'-Deoxycitidine treatment and over-expressed in normal colorectal mucosa, including genes that were known to be methylated in CRC. After applying study selection criteria, we identified 16 potential genes. Two candidates were selected (ASPP1 and SCARA5). Among 15 CRC cell lines, methylation was identified in SCARA5 (20%). The methylation status of SCARA5 was subsequently investigated in 23 paired colorectal tissue samples; methylation was detected in 17%, respectively. Observed promoter methylation showed a tendency towards methylation in tumor-derived samples, in SCARA5 gene. Significant down expression of SCARA5 mRNA was observed in CRC cell lines and tumor tissues compared to adjacent normal tissues (P < 0.001 and P = 0.001, respectively). The use of genome-wide screening led to the identification of a group of candidate genes. Among them, SCARA5 was methylated and markedly down-regulated in CRC. SCARA5 gene may have a role in CRC tumorigenesis.

overall_design: Gene expression profiles for 17 pairs of cancer and non-cancerous tissues from colorectal cancer patients were measured by Affymetrix HG-U133 Plus 2.0 arrays. Five cell lines were also used to investigate genes upregulated after 5-aza-2'-deoxycytidine treatment. Normalization was performed by robust multi-array average (RMA) method by Gene Expression Console (affymetrix). The normalization procedure was separately performed for each data set of clinical samples and the cellline samples. The normalized gene expression levels were presented as log2-transformed values by RMA.

first: Khamas

last: Ahmed

first: Ishikawa

last: Toshiaki

first: Shimokawa

last: Kazuro

first: Mogushi

last: Kaoru

first: Iida

last: Satoru

first: Ishiguro

last: Megumi

first: Mizushima

last: Hiroshi

first: Tanaka

first: Uetake

last: Hiroyuki

first: Sugihara

last: Kenichi


title: Expression data from Shh-driven mouse medulloblastoma and control adult wild-type mouse cerellum

status: Public on Mar 15 2012

city: San Francisco

first: Xi

last: Huang

address: 1550 4th Street, Room RH-481

institute: University of California, San Francisco

summary: Medulloblastoma is the most common pediatric CNS cancer. In order to identify important molecules important for deregulated tumor cell growth, we use microarray to detail the global gene expression profile in Shh-driven mouse medulloblastomas and determine the most differentially expressed genes compared to the control wild-type cerebellum.

overall_design: Medulloblastoma and control cerebellum tissues were dissected and processed for RNA extraction and microarray analyses using Affymetrix Mouse Gene 1.0 ST.  The mice were from a mixed genetic background  involving C57BL/6 and C3H strains.

first: Chin

last: Chiang


title: Differential RNAs in the sperm cells of asthenozoospermic patients

city: Barcelona

first: Rafael

last: Oliva

address: C/Casanova 143

department: Ciències Fisiològiques I

institute: University of Barcelona

summary:
Alterations in the presence of sperm RNAs have been identified using microarrays in teratozoospermic (abnormal morphology) or other types of infertile patients. However, so far no studies had been reported on the sperm RNA content using microarrays in asthenozoospermic patients (low motility).
We started the present project to with the goal to characterize the RNA expression in asthenozoospermic infertile patients as compared to normozoospermic fertile controls.

overall_design: We selected four normal fertile donors and four severe asthenozoospermic infertile patients. Equal amounts of RNA were extracted from the sperm samples, subjected to different quality controls and hybridized to the Affymetrix U133 Plus version 2 arrays.

first: Meritxell

last: Jodar

first: Susana

last: Kalko


title: Effects of DAC treatment

city: Ghent

first: Leander

last: Van Neste

address: Coupure Links 653

department: Molecular Biotechnology

country: Belgium

institute: Ghent University

type:
Expression profiling by array
Methylation profiling by array

summary: Reversal of gene promoter DNA hypermethylation and associated abnormal gene silencing is an attractive approach to cancer therapy. The DNA methylation inhibitor, decitabine (5-aza-2'-deoxycitidine), is proving efficacious for hematological neoplasms especially at lower, less toxic, doses. Experimentally, high doses induce rapid DNA damage and cytotoxicity, but these may not explain the prolonged time to response seen in patients. Transient exposure of leukemic and solid tumor cells to clinically-relevant nanomolar doses, without causing immediate cytotoxicity or apoptosis, produces sustained reduced tumorigenicity, and for leukemia cells, diminished long-term self-renewal. These effects appear triggered by cellular reprogramming and include sustained decreases in promoter DNA methylation with associated gene re-expression, and anti-tumor changes in multiple key cellular regulatory pathways, most of which are high priority targets for pharmacologic anti-cancer strategies. Thus, low dose decitabine regimens appear to have broad applicability for cancer management.

overall_design:
[Gene expression profiling] Leukemia cell lines Kasumi-1 and KG1A are treated with 10nM DAC during 72 hours and gene expression was assayed at day 3, 7 and 14 after the start of the treatment. Appropriate mock treated samples were used as control in each case. In addition, Kasumi-1 cells were also treated with a higher dose of DAC (500nM), 100nM ARA-C and 300 nM TSA, again controlled against mock treated Kasumi-1 cells, to separate dose and agent dependent effects.
MCF7 was studied as an example of a solid tumor cell line. Therefore MCF7 cells were treated with 100nM DAC and results were assayed at day 1, day 3 and day 10.

[Methylation profiling] The effects of the demethylating agent DAC were studied in the leukemia cell line Kasumi-1 over a 28 day time course. Intermediate time points were studied at days 3, 7, 14 and 21. These results were verfied in KG1A and KG1 leukemia cell lines, at one selected time point. The effects on one primary sample were also studied. Four normal leukemia samples (PL1, 2, 4 and 5) were used as general controls. The effect of DAC was compared to ARA-C, TSA. Both mock treated and day 3 DAC treated Kasumi-1 cells were repeated. These results were verified at one selected time point for the DAC treated MCF7 breast cancer cell line.

first: Hsing-Chen

last: Tsai

first: Huili

last: Li

first: Ray-Whay

last: Chiu Yen

first: Cynthia

last: Zahnow

first: Stephen

middle: B

last: Baylin


title: Gene expression profile in A375 melanoma cells after 45 functionally important molecules were knocked down using siRNA

city: Auckland

first: Li

last: Wang

address: 85 Park Rd

department: Molecular Medicine & Pathology

institute: University of Auckland

summary: Affymetrix microarray data were generated from A375 melanoma cells treated in vitro with siRNAs against 45 transcription factors and signalling molecules.

overall_design: 45 functionally important molecules were knocked down in A375 melanoma cells by siRNA. Then the gene expression profiles of these A375 cells, along with untreated cells and sRNA control treated cells were analysed by microarrays.

first: Cris

last: Print

first: Daniel

last: Hurley


title: Dissection of cancer cell and stromal cell-derived signals in melanoma xenografts following treatment with the stromal-targeting agent DMXAA

summary: 5,6-Dimethylxanthenone-4-acetic acid (DMXAA), a tumor vascular disrupting agent, is shown here to have substantial activity as a single agent against human A375 melanoma xenografts in nude mice (94 % hemorrhagic necrosis after 24 h, and 26 days growth delay following single dose at 25 mg/kg). CD45+ cells in tumor tissue increased 5-fold over the first 3 days after treatment, which was due largely to an influx of CD11b+ Ly6G+ neutrophils. Using murine and human multiplex cytokine assays to dissect the cytokines produced by host stromal cells or by the melanoma cells, it was shown that both the stromal cells and the A375 melanoma cells produced cytokines capable of attracting neutrophils into the tumor. The same xenografts were also analyzed using human and mouse Affymetrix microarrays to separately identify tumor cell-specific (human) and stromal cell-specific (mouse) gene expression changes. DMXAA induced numerous stromal cytokine mRNAs, including IP-10, IL-6, MIP-1α/β, MIP-2, KC, RANTES, MIG, MCP-1 and IL-1β, many of  which were also elevated at the protein level. Numerous human cytokine mRNAs were also induced including MCP-1, IL-8, GRO, VEGF, GM-CSF and IL-6, which again was in line with our protein data. Pathway analysis indicated that significant numbers of the stromal mRNAs induced by DMXAA are regulated downstream of TNF-α, interferon-β and NFκB. Our results suggest that DMXAA may have utility in combination therapy for human melanoma through the activation of pro-inflammatory signalling pathways and cytokine expression from both stromal and tumor cells, leading to haemorrhagic necrosis, neutrophil influx and growth inhibition.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Microarrays were used to identify separately the abundance of tumour cell and stromal cell RNA in A375 melanoma xenografts, with and without treatment by the stromal targetting drug DMXAA.

first: Cristin


title: Genome-wide association analysis of juvenile idiopathic arthritis identifies a new susceptibility locus at chromosomal region 3q13.

city: Cincinnati

first: Michael

last: Barnes

state: OH

address: 3333 Burnet Ave

department: Rheumatology

institute: Cincinnati Childrens Hospital Medical Center

summary: Juvenile idiopathic arthritis (JIA) is the most common chronic childhood rheumatic disease in the Western world.  To identify novel JIA predisposing loci, a genome-wide association study (GWAS) in 814 Caucasian JIA cases and 3058 Caucasian controls was completed.  After adjusting for the most significant HLA associations, the strongest novel associations included rs6479891 (10q21, odds ratio (OR)=1.59, P=1.3x10-8) and rs10761747 (OR=1.34, P=4.0x10-5) within JMJD1C; rs12719740 (15q26, OR=1.47, P=3.3x10-7) near FAM169B; rs4688011 (3q13, OR=1.33, P=1.1x10-4) within C3orf1 and rs4254850 (4q31, OR=0.85, P=7.8x10-3) near IL15.  Eleven SNPs were genotyped in Caucasian replication cohorts (1744 cases, 7010 controls) and meta-analysis continued to provide evidence for association with three of the SNPs (rs6479891, P=4.3x10-5; rs12719740, P=5.2x10-4; rs4688011, P=3.6x10-7).  Analysis of expression data from 68 JIA cases and 23 controls overlapping in the GWAS cohort1 and published lymphoblastoid cell lines (LCL)2 showed cis eQTL associations for JMJD1C SNPs (P=0.01 and P=1.6x10-6, respectively), and the C3orf1 SNP (P=5.7x10-6).

overall_design: Peripheral blood samples were obtained from 23 healthy children and 68 children with JIA.  RNA was purified from Ficoll-isolated mononuclear cells, fluorescently labeled and then hybridized to Affymetrix U133 Plus 2.0 GeneChips.  Data were imported using Robust Multi-Array Average pre-processing and Distance Weighted Discrimination normalization.  eQTL analysis were performed using genomewide association data.

first: Susan

middle: D

last: Thompson

first: Miranda

last: Marion

first: Marc

last: Sudman

first: Timothy

last: Howard

first: Paula

last: Ramos

first: Mimi

last: Ryan

first: Monica

last: Tsoras

first: Wendy

first: Anne

last: Hinks

first: J

middle: P

last: Hass

first: Sampath

last: Prahalad

first: John

last: Bohnsack

first: Carol

last: Wise

first: Marilynn

last: Punaro

first: Carols

last: Rosé

last: Spigarelli

first: Mehdi

last: Keddache

last: Wagner

first: Carl

first: David

middle: N

last: Glass


title: Human monocyte activation with NOD2L vs. TLR2/1L

city: Los Angeles

first: Mirjam

last: Schenk

address: 615 Charles E young Dr S

institute: UCLA

summary:
human blood monocytes were isolated, activated and harvested at several timepoints
In this study, we identified genes that were differentially expressed in human monocytes activated with eiter NOD2L and/or TLR2/1L.

overall_design: human blood monocytes were purified from healthy donors by Ficoll, Percoll and adherence. Monocytes were activated using NOD2L (MDP) and the TLR2/1L (19kD, triacylated peptide). Cells were harvested before activation (0h) and 6h and 24h after stimulation with ligands.

first: Robert

last: Modlin


title: Genome-wide profiling of E12.5 cardiomyocytes RNA expression in both heterozygous control and mutant

city: Boston

first: Michael

last: Hsing

state: MA

address: 300 Longwood Ave.

department: Cardiology

institute: Children's Hospital Boston

type: Expression profiling by high throughput sequencing

summary: Congenital heart disease is among the most frequent major birth defects. Epigenetic marks are crucial for organogenesis, but their role in heart development is poorly understood. Polycomb Repressive Complex 2 (PRC2) trimethylates histone H3 at lysine 27, establishing H3K27me3 repressive epigenetic marks that promote tissue-specific differentiation by silencing ectopic gene programs. We studied the function of the catalytic subunit of PRC2, EZH2, in murine heart development. Early EZH2 inactivation by Nkx2-5Cre caused lethal congenital heart malformations, but slightly later EZH2 inactivation by cTNT-Cre did not. To study how the cardiomyocytes gene expression program is properly established in the early heart development, we combined the technologies of RNA sequencing and chromatin immunoprecipitation sequencing to identify the functional target genes directly repressed by EZH2. Intriguingly, these were enriched for transcriptional regulators of non-cardiac expression programs, such as transcription factors that regulate neuronal (Pax6) and cardiac progenitor genes (Isl1 and Six1). EZH2 was also required to maintain spatiotemporal regulation of cardiac gene expression, as Hcn4, Mlc2a, and Bmp10 were inappropriately upregulated in ventricular RNA. Furthermore, EZH2 was required for normal cardiomyocyte proliferation, establishing H3K27me3 epigenetic marks at cell cycle inhibitors Ink4a/b and repressing their expression. Our study reveals a previously undescribed role of EZH2 in regulating heart formation and shows that perturbation of the epigenetic landscape early cardiogenesis has sustained disruptive effects at later developmental stages.

overall_design: 8 E12.5 heart apex were used for RNA preparation each group.

first: Aibin

last: He

first: William

middle: T

last: Pu


title: Gene expression profile in MCF7 breast cancer cells after 78 functionallly important molecules were knocked down using siRNA.

first: Li

last: Wang

summary: Affymetrix microarray data was generated from MCF7 breast cancer cells treated in vitro with siRNAs against 78 transcription factors and signalling molecules.

overall_design: Gene expresion of 78 functionally important molecules were knocked down in MCF7 breast cancer cells using siRNA. Then the gene expression profiles of these MCF7 cells, along with untreated cells and non-targetting control (SICONTROL) treated cells were analysed using microarrays.

first: Cris

last: Print

first: Anita

last: Muthukaruppan

first: Andrew

last: Shelling


title: Human cumulus cells

status: Public on Mar 10 2012

city: Montpellier

first: Said

last: Assou

address: 80, Av. Augustin Flich

country: France

institute: INSERM

summary:
Cumulus cells (CCs) are biologically distinct from other follicular cells and perform specialized roles, transmitting signals within the ovary and supporting oocyte maturation during follicular development. The Affymetrix 3’ IVT express protocol was used to prepare cRNA (one-cycle amplification) with a starting concentration of 100 ng of total RNA
To compare groups of CCs at different stages of oocyte nuclear maturation, a Significance Analysis of Microarrays (SAM) was performed.

overall_design: CC samples were issued from oocyte at germinal vesicle (CCGV), stage metaphase I (CCMI) and stage metaphase II (CCMII)

first: SAID

last: ASSOU

first: JOHN

last: DE VOS

first: SAMIR

last: HAMAMAH


title: Characterization and clinical evaluation of CD10+ stroma cells in the breast cancer microenvironment

city: Brussels

first: Sandeep

middle: K.

last: Singhal

state: Brussels

address: Boulevard de Waterloo, 125

institute: Institut Jules Bordet

summary:
Purpose: There is growing evidence that interaction between stromal and tumor cells is pivotal in breast cancer progression and response to therapy. Since the pioneer work of Allinen et al. suggested that during breast cancer progression striking changes occur in CD10+ stromal cells, we aimed to better characterize this cell population and its clinical relevance.
Results: This 12-gene CD10+ stroma signature includes among others genes involved in matrix remodeling (MMP11, MMP13, COL10A1) and genes related to osteoblast differentiation (periostin). The co-culture experiments demonstrated all three CD10+ cell types contribute to the CD10+ stroma signature.
Of interest, this signature demonstrated an important role in differentiating in situ from invasive breast cancer, in prognosis of the HER2+ subpopulation of breast cancer only, and potentially in non-response to chemotherapy for those patients.
Conclusions: Our results highlight the importance of CD10+ cells in breast cancer prognosis and efficacy of chemotherapy, particularly within the HER2+ breast cancer disease.

overall_design: We developed a CD10+ stroma gene expression signature (using HG U133 Plus 2.0) based on the comparison of CD10 cells isolated from tumoral (n=28) and normal (n=3) breast tissue. We further characterized the CD10+ cells by co-culture experiments of representative breast cancer cell lines with the different CD10+ stromal cell types (fibroblasts, myoepithelial and mesenchymal stem cells (MSC)). We then evaluated its clinical relevance in terms of in situ to invasive progression, invasive breast cancer prognosis and prediction of efficacy of chemotherapy using publicly available datasets.

first: Christine

last: Desmedt

first: Samira

last: Majjaj

first: Naima

last: Kheddoumi

middle: K

first: Benjamin

last: Haibe-Kains

first: Frank

last: El Ouriaghli

first: Carole

last: Chaboteaux

first: Stefan

last: Michiels

first: Françoise

last: Lallemand

first: Fabrice

last: Journe

first: Hughes

last: Duvillier

first: Sherene

last: Loi

first: John

last: Quackenbush

first: Sophie

last: Dekoninck

first: Cédric

last: Blanpain

first: Laurence

last: Lagneaux

first: Nawal

last: Houhou

first: Mauro

last: Delorenzi

first: Denis

last: Larsimont

first: Martine

last: Piccart

first: Christos

last: Sotiriou


title: Primary human hepatocytes treated with IFNalpha and IL28B

status: Public on Mar 09 2012

city: Bethesda

first: WeiPing

last: Chen

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: Recent identification of IL28B gene polymorphisms associated with hepatitis C virus (HCV) clearance suggests a role for type III interferons (IFNs) in hepatitis C infection. The function of type III IFNs in intrinsic antiviral immunity is poorly understood.  Here we show that HCV infection of primary human hepatocytes results in a robust induction of type III but not type I IFNs, leading to IFN- stimulated gene (ISG) expression.  In addition, HCV infection elicits a much broader range of gene expression alterations in addition to ISG induction. The induction of type III IFNs is mediated by IRF3 and NFkB- dependent pathways.  Type III IFN, aside from upregulating ISGs with a different kinetic profile, induces a distinct set of genes from type I IFN, potentially explaining the functional difference between the two types of IFNs. Chimpanzees undergoing experimental HCV infection demonstrated a prompt hepatic induction of IL28, associating with ISG upregulation, but minimal type I IFN induction. Analysis of liver biopsies from HCV-infected patients supported a close correlation among hepatic expression of IL28 and ISGs, but not with type I IFNs.    Our study demonstrates that HCV infection results predominantly in type III IFN induction in the liver and the level of induction correlates with hepatic ISG levels, thus providing a mechanistic explanation for the association between IL28, ISG levels and recovery from HCV infection as well as a potential therapeutic strategy for the treatment of non-responders.

overall_design: Microarray analysis of primary human hepatocytes treated samples with IFN, IL28b and T-PolyC after 6 or 24 hours respectively and with recombinant IL28B (25 ng/mL for 24 hours) and JFH1 (MOI of 5 for 36 hours) with three replications.

first: Emmanuel

last: Thomas

first: Yaron

last: Rotman

first: Veronica

last: Gonzalez

first: Jake

last: Liang

first: Qisheng

last: Li

first: Ankit

middle: A

last: Modi

first: Mazen

last: Noureddin


title: Expression data from primary human keratinocytes exposed to cytokines in vitro (IL-4, IL-13, IL-17A, IFN-alpha, IFN-gamma, TNF)

status: Public on Mar 07 2012

first: William

last: Swindell

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard University

summary:
The clinical features of psoriasis, characterized by sharply demarcated scaly erythematous plaques, are typically so distinctive that a diagnosis can easily be made on these grounds alone. However, there is great variability in treatment response between individual patients, and this may reflect heterogeneity of inflammatory networks driving the disease. In this study, whole-genome transcriptional profiling was used to characterize inflammatory and cytokine networks in 62 lesional skin samples obtained from patients with stable chronic plaque psoriasis. We were able to stratify lesions according to their inflammatory gene expression signatures, identifying those associated with strong (37% of patients), moderate (39%) and weak inflammatory infiltrates (24%). Additionally, we identified differences in cytokine signatures with heightened cytokine-response patterns in one sub-group of lesions (IL-13-strong; 50%) and attenuation of these patterns in a second sub-group (IL-13-weak; 50%). These sub-groups correlated with the composition of the inflammatory infiltrate, but were only weakly associated with increased risk allele frequency at some psoriasis susceptibility loci (e.g., REL, TRAF3IP2 and NOS2). Our findings highlight variable points in the inflammatory and cytokine networks known to drive chronic plaque psoriasis. Such heterogeneous aspects may shape clinical course and treatment responses, and can provide avenues for development of personalized treatments.
We used Affymetrix microarrays to evaluate genome-wide expression in primary human keratinocytes exposed to cytokines. Cytokine activity signatures were used to interpret the shifts in gene expression that occur in psoriasis plaques relative to normal uninvolved skin.

overall_design: Primary keratinocytes from three donors (subjects 1, 2,  and 3) were obtained and were either untreated (control) or exposed to cytokines (IL-4, IL-13, IFN-alpha, IFN-gamma and TNF). For the IL17A samples, primary keratinocytes were obtained from six donors, with cells derived from three donors treated with IL-17A and cells derived from the other three donors left untreated (i.e., unpaired control samples).

first: Andrew

last: Johnston

first: Johann

last: Gudjonsson


title: Expression analysis of mouse thyroid tumors

status: Public on Mar 14 2012

city: Bronx

first: Antonio

last: Di Cristofano

state: NY

address: 1301 Morris Park Ave Price 302

department: Developmental and Molecular Biology

institute: Albert Einstein College of Medicine

summary: Anaplastic thyroid carcinoma (ATC) is the most aggressive form of thyroid cancer, and often derives from pre-existing well-differentiated tumors.  We have engineered the first mouse model of ATC by combining in the mouse thyroid follicular cells two molecular hallmarks of human ATC: activation of PI3K (via Pten deletion) and inactivation of p53.  By 9 months of age, over 75% of the compound mutant mice develop aggressive, undifferentiated thyroid tumors that evolve from pre-existing follicular hyperplasia and carcinoma.  These tumors display all the features of their human counterpart, including pleomorphism, epithelial-mesenchymal transition, aneuploidy, local invasion and distant metastases.

overall_design: We have performed expression profiling of thyroids from control, single mutants, compound mutants, follicular tumors from Pten-/- mice and [Pten-/-,KrasG12D] mice, and anaplastic tumors from Pten, p53-/- mice.

first: Marika

last: Russo


title: Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM

city: Dallas

first: Jacqueline

middle: Wanjiku

last: Njoroge

address: 5323 Harry Hines Blvd

institute: UTSW medical center

summary: Analysis of effect of deletion of the two adrenergic kinases QseC and QseE on gene expression of EHEC 8624 in the absence and presence of epinephrine

overall_design: A double mutant of qseC and qseE in the EHEC 8624 was grown in the absence or presence of epinephrine to OD600=1.0 in DMEM then processed according to manufacturer's specifications: http//www.affymetrix.com/support/technical/manual/expression_manual.affx

first: Vanessa

last: Sperandio

first: David

last: Hughes

first: Nicola

last: Reading


title: Transcriptome study of hepatocytes isolated from transgenic mice expressing HCV core.

status: Public on Mar 03 2012

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

institute: university Paris Sud11

summary:
Hepatitis C Virus (HCV) core protein plays  a major role in HCV mediated liver pathologies. We have previously reported that HCV core variants isolated from tumoral (T) and non-tumoral (NT) livers were capable to alleviate Smad transcriptional activity and to shift TGF-β responses from tumor suppressor effects to tumor promotion.
To comprehensively appreciate the consequences of core-mediated deregulation of Smad signaling on TGF-b target gene expression, Affimetrix microarrays were performed.
Microarray analyses demonstrate that HCV core expression in hepatocytes modulates TGF-b target gene expression. Furthermore, most of the genes modulated in core expressing hepatocytes after TGF-b treatment were already regulated in these non treated cells suggesting that HCV core is capable to activate latent TGF-b.

overall_design: Transcriptome analysis was performed on primary hepatocytes from transgenic mice expressing  either Core T  or core NT or their control littermates treated  or not with TGF-b.

first: Nassima

last: Benzoubir

first: Christophe

last: Desterke

first: Serena

last: Battaglia

first: Barbara

last: Testoni

last: Benassi

first: Massimo

last: Levrero

first: Christian

last: Brechot

first: Marie-Françoise

last: Bourgeade


title: Transcriptomic analysis of human retinal detachment (RD) reveals both inflammation and photoreceptor death

status: Public on Mar 06 2012

city: Illkirch/Strasbourg

first: Wolfgang

last: Raffelsberger

address: 1 rue Laurent Fries

department: DBGS

institute: IGBMC

summary:
We have used surgical specimens to perform a differential analysis of the transcriptome of human retinal tissues following detachment.
Data analysis reveals major involvement of the immune response in the disease and interindividual variation was monitored to unravel a second crucial aspect of the pathological process, the death of photoreceptor cells.

overall_design: In total 38 surgical specimens (samples) were analyzed, 19 represent biopsies from patients with retinal detachment (RD) and 19 represent contral samples without retinal detachment.

first: Marie-Noëlle

last: Delyfer

last: Mercier

first: Jean-François

last: Korobelnik

first: Alain

last: Gaudric

middle: G

last: Charteris

first: Ramin

last: Tadayoni

first: Florence

last: Metge

first: Georges

last: Caputo

first: Pierre-Olivier

last: Barale

first: Raymond

last: Ripp

first: Jean-Denis

last: Muller

first: Olivier

last: Poch

first: Jose-Alain

last: Sahel

first: Thierry

last: Leveillard


title: Expression data from LCMV-infected P14 and Akt transgenic P14 CD8 T cells

status: Public on Mar 01 2012

city: Madison

first: Eui Ho

last: Kim

state: Wisconsin

address: 2015 Linden Dr.

department: Pathobiological Sciences

institute: University of Wisconsin-Madison

summary: The PI3K/Akt signaling pathway impacts various aspects of CD8 T cell homeostasis, such as effect versus memory cell differentiation, during viral infection. We used microarrays to determine which downstream molecules were affected and what other signaling pathways were interconnected with the Akt pathway by constitutive activation of Akt in LCMV-infected CD8 T cells.

overall_design: Splenocytes from naive P14/WT or P14/Akt mice were stained with anti-CD8 and anti-Ly5.1, and CD8 T cells were sorted using a FACSAria II instrument. Purified Ly5.1+ CD8 T cells from P14/WT or P14/Akt mice were transferred into B6 mice, which were subsequently infected with LCMV Armstrong. At day 8 post infection, splenocytes were stained with anti-CD8, anti-Ly5.1, anti-KLRG1, and anti-CD127. Following staining, short-lived effector cells (SLECs) and memory precursor effector cells (MPECs) were sorted using the FACSAria II instrument; the purity of the sorted cells was >95%.  A total of 5 samples were analyzed, including WT naive, WT SLEC, WT MPEC, Akt naive and Akt SLEC.

first: Eui

middle: H

first: M

last: Suresh


title: Genome-wide analysis revealed a crosstalk between p53 and the pluripotent gene networks in mouse embryonic stem cells (expression)

status: Public on Mar 05 2012

first: Jing

last: Huang

institute: National Cancer Institute

summary: The tumor suppressor p53 regulates the differentiation of embryonic stem (ES) cells upon DNA damage. However, our understanding of this critical tumor suppressive role of p53 in ES cells is limited, mainly because of the lack of molecular mechanism. Here, we report a widespread cross-regulation of p53-mediated DNA damage signaling and the pluripotent gene network in ES cells using chromatin-immunoprecipitation assay-based sequencing (ChIP-seq) and gene expression microarray. Upon DNA damage, p53 directly regulates the transcription of 3644 genes (p<0.005) in mouse ES cells. Genome-wide analysis revealed a dramatic difference between the regulation of p53-activated and -repressed genes. p53 mainly regulates the promoter regions of activated genes, whereas the main regulatory regions for repressed genes reside in distal regions. Among p53-repressed genes, many are pluripotent transcription factors of ES cells, such as Oct4, Nanog, Sox2, Esrrb, c-Myc, n-Myc and Sall4. Strikingly, these transcriptional factors also directly regulate the transcription of the Trp53 gene, highlighting a previously under-estimated transcriptional regulation of p53 in ES cells. Therefore, p53 signaling and ES pluripotent transcriptional networks form an intertwined circuitry. Together, our results provide mechanistic insights into the crosstalk of p53-mediated DNA damage and ES cell "stemness" transcriptional gene networks and shed light on the tumor suppressive function of p53 in ES cells.

overall_design:
The goal of this experiment is to identify the gene expression changes after adriamycin treatment in a p53-dependent manner.
Total six samples: triplicates for untreated mES cells and triplicates for mES cells treated with adriamycin.


title: Frequent driver mutations in histone H3.3 and chromatin remodeling genes in paediatric glioblastoma

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 580

department: Pediatric Neuro Oncology

institute: German Cancer Research Center

summary:
Whole exome sequencing identified frequent driver mutations in a series of paediatric glioblastomas
We used microarray-based profiling to investigate differences in gene expression according to mutational status of driver genes

overall_design: RNA from 27 primary tumor samples was subject to QC by Agilent BioAnalyser analysis and then hybridised to an Affymetrix U133 Plus2 gene expression array

first: Jeremy

last: Schwartzentruber

first: Andrey

last: Korshunov

first: Xiao-Yang

last: Liu

first: Jacek

last: Majewski

first: Stefan

middle: M

last: Pfister

first: Nada

last: Jabado


title: A genomic storm in critically injured humans

first: Wenzhong Xiao

address: 55 Fruit Street, GRV 1302

department: Department of Surgery

institute: Massachusetts General Hospital

summary:
Human survival from injury requires an appropriate inflammatory and immune response. We describe the circulating leukocyte transcriptome after severe trauma and show that the severe stress produce a global
reprioritization affecting >80% of the cellular functions and pathways, a truly unexpected “genomic storm.” In severe blunt trauma, the early leukocyte genomic response is consistent with simultaneously increased
expression of genes involved in the systemic inflammatory, innate immune, and compensatory antiinflammatory responses, as well as in the suppression of genes involved in adaptive immunity. Furthermore,
complications like nosocomial infections and organ failure are not associated with any genomic evidence of a second hit and differ only in the magnitude and duration of this genomic reprioritization.

overall_design:
Blood was sampled from 167 severe blunt trauma patients under the age of 55 yr who consented to blood sampling. The first blood sample was taken within 12 h of the injury and 1, 4, 7, 14, 21, and 28 d after injury.
Study subjects were treated under the guidance of standard operating procedures developed, implemented, and audited across all participating centers to minimize treatment variation. In addition, 37 healthy control
subjects were sampled.  Total blood leukocytes were isolated according to protocols published previously. Total cellular RNA was extracted and hybridized onto an HU133 Plus 2.0 GeneChip (Affymetrix) according to
the manufacturer’s recommendations.

first: Wenzhong

last: Xiao

first: Michael

last: Mindrinos

first: Junhee

last: Seok

first: Joseph

last: Cuschieri

first: Alex

last: Cuenca

first: Hong

last: Gao

first: Douglas

middle: L

last: Hayden

first: Laura

last: Hennessy

first: Ernest

middle: E

last: Moore

last: Minei

first: Paul

last: Bankey

first: Jeffrey

last: Johnson

first: Jason

last: Sperry

first: Avery

last: Nathens

first: Timothy

middle: R

last: Billiar

last: West

first: Bernard

last: Brownstein

first: Philip

last: Mason

first: Henry

middle: V

last: Baker

first: Celeste

middle: C

last: Finnerty

first: Marc

last: Jeschke

last: López

first: Matthew

last: Klein

first: Richard

last: Gamelli

first: Nicole

last: Gibran

first: Brett

last: Arnoldo

first: Weihong

last: Xu

first: Yuping

last: Zhang

first: Steven

last: Calvano

first: Grace

last: McDonald-Smith

first: David

last: Schoenfeld

first: John

last: Storey

first: J

last: Cobb

first: H


title: A new subtype of bone sarcoma defined by BCOR-CCNB3 gene fusion

city: Paris

first: Franck

last: Tirode

address: 26 Rue d'Ulm

department: Inserm U830

institute: Institut Curie

summary: The identification of subtype-specific translocations has revolutionized diagnostics of sarcoma and provided new insight into oncogenesis. We used RNA-Seq to investigate samples diagnosed as small round cell tumors of bone, possibly Ewing sarcoma, but lacking the canonical EWSR1-ETS translocation. A new fusion was observed between the BCL6 co-repressor (BCOR) and the testis specific cyclin B3 (CCNB3) genes on chromosome X. RNA-Seq results were confirmed by RT-PCR and cloning the tumor-specific genomic translocation breakpoints. 24 BCOR-CCNB3-positive tumors were identified among a series of 594 sarcomas. Gene profiling experiments indicate that BCOR-CCNB3-positive cases are biologically distinct from other sarcomas, particularly Ewing’s sarcoma. Finally, we show that CCNB3 immunohistochemistry is a powerful diagnostic marker for this group of sarcoma and that over-expression of BCOR-CCNB3 or of a truncated CCNB3 activates S-phase in NIH3T3 cells. Thus the intrachromosomal X fusion described here represents a new subtype of bone sarcoma caused by a novel gene fusion mechanism.

overall_design: Comparison of expression profiles of 10 BCOR-CCNB3 samples (plus 4 EWS-FLI1 Ewing sarcomas samples as control) with publicly available profiles of other tumor types.

first: Gaelle

last: Pierron

first: Carlo

last: Lucchesi

first: Stéphanie

last: Reynaud

first: Stelly

last: Ballet

first: Sarah

last: Cohen-Gogo

first: Virginie

last: Perrin

first: Jean-Michel

last: Coindre

first: Olivier

last: Delattre


title: DNA Methylation Profiling Defines Clinically Relevant Biological Subsets of Non-small Cell Lung Cancer

city: South San Francisco

middle: S

last: Shames

address: 1 DNA Way

department: Oncology Biomarker Development

institute: Genentech Inc

summary:
PURPOSE: Non-small cell lung cancers (NSCLC) comprise multiple distinct biological groups with different prognoses. For example, patients with epithelial-like (EL) tumors have a better prognosis and exhibit greater sensitivity to inhibitors of the epidermal growth factor receptor (EGFR) pathway than patients with mesenchymal-like (ML) tumors. Here we test the hypothesis that EL NSCLCs can be distinguished from ML NSCLCs on the basis of global DNA methylation patterns.

EXPERIMENTAL DESIGN: To determine whether phenotypic subsets of NSCLC can be defined based on their DNA methylation patterns, we combined microfluidics-based gene expression analysis and genome-wide methylation profiling. We derived robust classifiers for both gene expression and methylation in cell lines and tested these classifiers in surgically resected NSCLC tumors. We validate our approach using quantitative RT-PCR and methylation specific PCR in formalin-fixed biopsies from NSCLC patients who went on to fail front-line chemotherapy.

RESULTS: We show that patterns of methylation divide NSCLCs into EL and ML subsets as defined by gene expression and that these signatures are similarly correlated in NSCLC cell lines and tumors. We identify multiple DMRs, including ERBB2 and ZEB2, whose methylation status is strongly associated with an epithelial phenotype in NSCLC cell lines, surgically resected tumors, and formalin-fixed biopsies from NSCLC patients who went on to fail front-line chemotherapy.

CONCLUSIONS: Our data demonstrate that patterns of DNA methylation can divide NSCLCs into two phenotypically distinct subtypes of tumors and provide proof of principle that differences in DNA methylation can be used for predictive biomarker discovery and development.

first: Kim

last: Walter

first: Pan

last: Du

first: Richard

last: Bourgon


title: mRNA expression profiling of ERCP biliary brushings of malignant biliary strictures

city: London

first: michael

last: chapman

address: Rowland Hill St

department: HPB Cancer Group

country: United Kingdom

institute: Univeristy College London

summary: Identification of differential gene expression uging endoscopic biliary brushings

overall_design: Bile duct brishings of benign biliary strictures and malignant biliary strictures, samples snap frozen in liquid nitrogen

first: Mike

last: Chapman


title: A Robust Induction of  Type III Interferons and Chemokines Defines a Unique Pattern of Hepatic Innate Immunity in Response to Hepatitis C Virus Infection

first: WeiPing

last: Chen

overall_design: Samples were treated with IFN or IL28b after 6 or 24 hours with three replications

first: Emmanuel

last: Thomas

first: Veronica

middle: D

last: Gonzalez

first: Qisheng

last: Li

first: Ankit

last: Modi

first: Mazen

last: Noureddin

first: Yaron

last: Rotman

first: T

middle: J

last: Liang


title: Gene expression profiles of fibroblasts from childhood cerebral adrenoleukodystrophy patients and healthy controls

first: Joseph

middle: Gerard

last: Hacia

address: 2250 Alcazar Street, IGM 261

department: Biochemistry and Molecular Biology

institute: University of Southern California

summary:
Although not an affected cell type, skin fibroblasts from individuals with childhood cerebral adrenoleukodystrophy (CCALD), an early onset X-linked neurological disorder, show defects in very long chain fatty acid (VLCFA) metabolism that provide the basis for clinical diagnostic tests.
We report the gene expression profiles of fibroblasts from childhood cerebral adrenoleukodystrophy patients and healthy controls

overall_design: Primary dermal fibroblast cultures from 5 CC-ALD patients and 5 healthy controls were cultured in DMEM medium supplemented with 10% FBS at 37°C with 5% CO2 until confluence for RNA extraction. The overall goal was to identify genes that are differentially expressed between CCALD patients and healthy controls

first: Xiao-Ming

last: Wang

first: Patricia

last: Dranchak


title: Gene expression arrays on lung cancer cells exposed to  Notch inhibitor

city: Watertown

first: Mary

last: Simcox

address: 500 Arsenal St

institute: Forma Therapeutics

summary:
Genes responses in A549 and H460 cells after GSI (RO4929097-001-003 , 2 uM) treatment.
Notch signaling is an area of great interest in oncology. RO4929097 is a potent and selective inhibitor of gamma-secretase, producing inhibitory activity of Notch signaling in tumor cells. The RO4929097 IC50 in cell-free and cellular assays is in the low nanomolar range with >100-fold selectivity with respect to 75 other proteins of various types (receptors, ion channels, and enzymes). RO4929097 inhibits Notch processing in tumor cells as measured by the reduction of intracellular Notch expression by Western blot. This leads to reduced expression of the Notch transcriptional target gene Hes1. RO4929097 does not block tumor cell proliferation or induce apoptosis but instead produces a less transformed, flattened, slower-growing phenotype. RO4929097 is active following oral dosing. Antitumor activity was shown in 7 of 8 xenografts tested on an intermittent or daily schedule in the absence of body weight loss or Notch-related toxicities. Importantly, efficacy is maintained after dosing is terminated. Angiogenesis reverse transcription-PCR array data show reduced expression of several key angiogenic genes. In addition, comparative microarray analysis suggests tumor cell differentiation as an additional mode of action. These preclinical results support evaluation of RO4929097 in clinical studies using an intermittent dosing schedule. A multicenter phase I dose escalation study in oncology is under way.

overall_design: A549 and H460 cells were treated in quadruplicate with either vehicle or GSI (RP4929097-001-003, 2 uM) for 6 or 24 hours.

first: W

last: Berkofsky-Fessler

first: J

last: Cai


title: Identifying the molecular signature of the t(12;14) subgroup of uterine leiomyomata using a paired analysis

city: Rochester

first: Jennelle

last: Hodge

address: 200 First Street SW

department: Department of Laboratory Medicine and Pathology

institute: Mayo Clinic

summary: Uterine leiomyomata (UL), the most common neoplasm in reproductive age women, have recurrent cytogenetic abnormalities including t(12;14).  To develop a molecular signature, matched t(12;14) and non-t(12;14) tumors identified by FISH or karyotyping from each of 9 women were profiled using Affymetrix GeneChip U133 Plus 2.0 oligonucleotide arrays.  Model analysis demonstrated the necessity for a matched design to eliminate the confounding effect of genotype and environment that underlay patient to patient variation.

overall_design: Matched myometrium, t(12;14) fibroid tumors and non-t(12;14) fibroid tumors identified by FISH or karyotyping from each of 9 women were profiled using Affymetrix GeneChip U133 Plus 2.0 oligonucleotide gene expression arrays.

first: Tae-Min

last: Kim

first: Jonathan

last: Dreyfuss

first: Priya

last: Somasundaram

first: Nicole

last: Christacos

first: Marissa

last: Rousselle

first: Bradley

last: Quade

first: Peter

last: Park

first: Elizabeth

last: Stewart

first: Cynthia

last: Morton


title: Gene profile of Myeloid derived Suppressive Cells from the Bone Marrow of Lysosomal Acid Lipase Knock-out Mice

city: Indianapolis

first: Hong

last: Du

address: 635 Barnhill Drive

department: Pathology and Laboratory Medicine

institute: Indiana University School of Medicine

summary: Expression profile of MDSC isolated from Bone marrow of lysosomal acid Lipase mice compared to the WT counterpart

overall_design: four samples


title: Traffic-related Particulate Matter Upregulates Allergic Responses by a Notch-pathway Dependent Mechanism

city: Stanford

first: Sean

last: McGhee

address: 269 Campus Drive, CCSR Rm 2115

department: Pediatrics

institute: Stanford University

summary:
The mechanisms by which diesel exhaust particles act as an adjuvant are unknown. We hypothesized that these would be mediated through monocyte interactions with DEP.
We sought to identify pathways with a role in inflammation or other signaling mechanisms that might demonstrate the mechanism of response to DEP.

overall_design: Cultured human monocytes from healthy donors were cultured in the presence or absence of diesel exhaust particles. RNA was extracted following culture to determine changes in gene expression pathways.

first: Loida

last: Viera-Hutchins

first: Maria

last: Garcia-Lloret

first: Zena

last: Chatila

first: Schuyler

last: Girion

first: Reuben

last: Caja

first: Petra

last: Wise

first: Zhi

last: Ning

first: Costas

last: Sioutas

first: Talal


title: Immune-activation as a therapeutic direction for patients with high-risk ovarian cancer based on gene expression signature (1)

city: Niigata

first: Kosuke

last: Yoshihara

address: 1-757 Asahimachi-dori

department: Obstetrics and Gynecology

institute: Niigata University

summary:
The Japanese Serous Ovarian Cancer Study Group
Advanced-stage ovarian cancer is one of the most lethal gynecologic malignancies. To improve prognosis of patients with ovarian cancers, a predictive biomarkers leading to personalized treatments are required. In this large-scale cross-platform study of six microarray datasets consisting of 1054 ovarian cancer patients, we developed a novel risk classification system based on a 126-gene expression signature for predicting overall survival by applying elastic net7 and 10-fold cross validation to a Japanese dataset A (n = 260). We further validated its predictive ability with the five other datasets using multivariate analysis. Also, through gene ontology and pathway analyses of 1109 high-risk ovarian cancer specific transcripts, we identified a significant reduction of expression of immune-response related genes, especially on the antigen presentation pathway. Furthermore, an immunohistochemical analysis demonstrated that the number of CD8 T lymphocytes infiltrating into tumor tissue was significantly decreased in high-risk ovarian cancers. These predictive biomarkers based on the 126-gene expression signature will identify high-risk ovarian cancer patients who need novel immune-activating therapeutic approaches, leading to improved outcomes for such patients.

overall_design:
Two hundred sixty patients who were diagnosed as advanced-stage high-grade serous ovarian cancer were analyzed in this study.

Microaray data from 10 patients who were diagnosed as advanced-stage high-grade serous ovarian cancer were analyzed to investigate coefficient of correlation in each probes between Agilent Whole Human Genome Oligo Microarray and Affymetrix HG-U133Plus2.0.

first: Group


title: Transcriptomic Analysis of Placenta Affected by Antiphospholipid Antibodies: Following the TRAIL of trophoblast death

status: Public on Feb 27 2012

city: Auckland

first: Priyadarshini

last: Pantham

address: 85 Park Road

department: Obstetrics & Gynaecology

institute: The University of Auckland

summary: Antiphospholipid antibodies, a maternal risk factor for preeclampsia, increase shedding of necrotic trophoblast debris from the placenta, leading to endothelial dysfunction. Using Affymetrix HGU133 Plus 2 microarrays, we found changes in the transcriptome of placental explants treated with antiphospholipid antibodies including seven mRNAs encoding for genes BCL2L1, MCL1, PDCD2L, FASLG, SEMA6A, PRKCE and TRAIL that are involved in the regulation of apoptosis. Quantitative real-time RT-PCR and immunohistochemistry confirmed a reduction in TRAIL expression. These results may help to understand how antiphospholipid antibodies affect trophoblast cell death and how the antibodies could contribute to the pathogenesis of preeclampsia.

overall_design:
Three different first-trimester placentas (8-8.5 weeks gestation) were dissected into 6 explants each and cultured either with antiphospholipid antibodies (25ug/mL) or untreated media for 16h. RNA was extracted from treated placental explants and Affymetrix HGU133 Plus 2 arrays were conducted to investigate changes in mRNA expression.

Untreated: 1UNT, 2UNT, 3UNT
Antiphospholipid antibody treatment: 1APL, 2APL, 3APL
Biological replicates: 1, 2, 3

first: Roseanne

last: Rosario

first: Qi

last: Chen

first: Cristin

last: Print

first: Larry

middle: W

last: Chamley


title: Expression data from MDA-MB-231 parental and xenograft tumor cells treated with Smac mimetic SM-164.

city: ANN ARBOR

first: Shaomeng

last: Wang

address: 1150 E Med. Ctr. Dr.

institute: University of Michigan

summary:
Small-molecule Smac mimetics target inhibitor of apoptosis (IAP) proteins to induce TNFα-dependent apoptosis in cancer cells and several Smac mimetics have been advanced into clinical development as a new class of anticancer drugs. However, preclinical studies have shown that only a small subset of cancer cell lines are sensitive to Smac mimetics used as single agents and these cell lines are at risk of developing drug resistance to Smac mimetics. Thus, it is important to understand the molecular mechanisms underlying intrinsic and acquired resistance of cancer cells to Smac mimetics in order to develop effective therapeutic strategies to overcome or prevent Smac mimetic resistance.
We established Smac mimetic resistant sublines derived from MDA-MB-231 breast cancer cells, which exhibit exquisite sensitivity to the Smac mimetic SM-164, and used microarrays to detail the global programme of gene expression underlying SM-164 resistance in MDA-MB-231 cells and identified differentially expressed genes in SM-164-resistant and -sensitive  MDA-MB-231 cells.

overall_design: SCID mice with MDA-MB-231 xenograft tumors were treated with 5 mg/kg of SM-164 intravenously for 5 days/week for 2 weeks. SM-164-regressed MDA-MB-231 tumors regrew after treatment ended. Tumor cells from these regrown MDA-MB-231 tumors were isolated and total RNAs were prepared for microarray analysis.

first: Longchuan

last: Bai