title: Seminoma and embryonal carcinoma footprints identified by analysis of integrated genome-wide epigenetic and expression profiles of germ cell cancer cell lines (gene expression data).

status: Public on Jun 01 2014

city: Rotterdam

first: Martin

middle: Anne

last: Rijlaarsdam

address: Wytemaweg 80

institute: Erasmus MC

summary:
Background: Germ Cell Cancers (GCC), originating from Primordial Germ Cells /gonocytes, are the most common cancer in young men, subdivided in seminoma (SE) and non-seminoma (NS, stem cell component: embryonal carcinoma (EC)). Somatic mutations are rarely found in GCC. It has been proposed that disruption of the epigenetic constitution, either primarily or secondary (e.g. environmental influences), is involved in cancer, and specifically in GCC.
Results: This study aims at identifying epigenetic footprints of SE and EC cell lines in genome-wide profiles by studying the interaction between gene expression, DNA CpG methylation and histone modifications, and their function in GCC and related disruption of germ cell maturation. Two well characterized GCC-derived cell lines were compared, one representative for SE (TCam-2) and the other for EC (NCCIT). Data was acquired using the Illumina HumanHT-12-v4 (gene expression) and HumanMethylation450 BeadChip (methylation) microarrays as well as ChIP sequencing (activating histone modifications (H3K4me3, H3K27ac)). The data show that known germ cell markers are not only present and differentiating between SE and NS at the expression level, but also in the epigenetic landscape.
Conclusion: The overall similarity between TCam-2 / NCCIT supports an erased embryonic gem cell arrested in early gonadal development as common origin. Subtle difference in the (integrated) epigenetic and expression profiles indicated TCam-2 to exhibit a more germ cell like profile (enrichment Androgen regulation) while NCCIT proved more pluripotent. The results provide insight into an integrated analysis of the functional genome in GCC cell lines.

overall_design: Two wildtype germ cell cancer (type II germ cell tumor) cell lines were analyzed. TCam-2 (representative for the seminomatous subtype of germ cell cancer) , [1, 2]) and NCCIT (representative of the non-seminomatous (embryonal carcinoma) subtype of germ cell cancer, [3]). Of each cell line two biological replicates were included.  1. Mizuno, Y., et al., [Establishment and characterization of a new human testicular germ cell tumor cell line (TCam-2)]. Nihon Hinyokika Gakkai Zasshi, 1993. 84(7): p. 1211-8.  2. de Jong, J., et al., Further characterization of the first seminoma cell line TCam-2. Genes Chromosomes Cancer, 2008. 47(3): p. 185-96.  3. Teshima, S., et al., Four new human germ cell tumor cell lines. Lab Invest, 1988. 59(3): p. 328-36.

first: Yvonne

middle: G

last: van der Zwan

middle: A

first: Ad

middle: J

last: Gillis

first: Lambert

last: Dorssers

first: Leendert

last: Looijenga


title: Differential blood biomarkers and PBMC transcriptome profiles in normal-weight and obese individuals

city: Daegu

first: Seo

last: Yu-Ri

address: 1370, Sankyuk-Dong, Buk-gu

country: South Korea

institute: uree

summary: The aim of study was to investigate correlation bewteen peripheral blood mononuclear cell (PBMC) transcriptome profiles and plasma lipid profiles of Korean adult with varying BMI. In Korean, BMI cut-off points are 18.5~22.9 kg/m2 (normal range), ≥ 23 kg/m2 (overweight), ≥ 25 kg/m2 (obese), ≥ 30 kg/m2 (severely obese). Thus, the obese group was subdivided into mildly obese (BMI 25~27 kg/m2, OA) and highly obese (BMI 27~30 kg/m2, OB). This study indicates that lipid, glucose and inflammation metabolism-related gene expressions were altered according to cahnge of varing phenotype biomarkers such as BMI, plasma total-C, TG, FFA and HDL-C. Thus, blood biomarkers and PBMC gene expression profiles identified in this study may be useful as indicative biomarkers for obese susceptibility in Korean adult as well as response to various intervention for treating obesity.

overall_design: Total RNA of PBMCs was obtained from normal weight, obese person and mRNA expression was measured.

first: Yu-Ri

last: Seo

first: Myung-Sook

last: Choi


title: A quantitative framework to evaluate modeling of cortical development by neural stem cells

city: Chapel Hill

first: Jason

middle: L

last: Stein

state: NC

address: Neuroscience Research Building 8109C, 115 Mason Farm Rd

department: Genetics

country: USA

institute: UNC Chapel Hill

summary: In vitro neural stem cell models are widely used to model a wide range of neuropsychiatric conditions. However, how well such models correspond to in vivo brain has not been evaluated in an unbiased, comprehensive manner. We used transcriptomic analyses to compare in vitro systems to developing human fetal brain and observed strong conservation of in vivo gene expression and network architecture in differentiating primary human neural progenitor cells (phNPCs). Conserved modules are enriched in genes associated with ASD, supporting the utility of phNPCs for studying neuropsychiatric disease. We also developed and validated a machine learning approach called CoNTExT that identifies the developmental maturity and regional identity of in vitro models. We observed strong differences between in vitro models, including hiPSC-derived neural progenitors from multiple laboratories. This work provides a framework for evaluating in vitro systems and supports their value in studying the molecular mechanisms of human neurodevelopmental disease. In this GEO submission, we upload data from 5 lines of phNPCs as well as hiPSCs cultured in two different laboratories all at multiple differentiation time points.

overall_design: phNPCs: For each of 5 lines generated from 3 donors (15-16 PCW), two independent differentiation experiments each containing two replicates were performed and harvested at four time points (1, 4, 8, 12 wks PD; ~16 samples per line; 77 total samples). We confirmed RNA integrity by RIN score with the Agilent 2100 Bioanalyzer (mean +/- sd: 9.16 +/- 0.78).   iPSC: Two hiPSC datasets were RNA profiled as part of this study.  hiPSCs grown in the Kosik lab was derived from two independent, non-isogenic IPS lines: one derived from a patient carrying a mutant Tau variant G55R and one reference control. For each of these lines, two samples were harvested at each of 0, 1, 4, and 8 weeks PD (total n=16 samples). hiPSCs grown in the Gage lab were from six samples derived from 3 control lines at each of two time points (0 and 4 wk PD, total n=12 samples).  Samples were randomized to microarray chip by all biological variables of interest (donor, line, passage, replicate number, differentiation week, plate date, and RIN) to control for potential batch effects.

first: Luis

last: de la Torre-Ubieta

first: Yuan

last: Tian

first: Neelroop

middle: N

last: Parikshak

first: Israel

last: Hernandez

first: Maria

middle: C

last: Marchetto

first: Dylan

middle: K

last: Baker

first: Daning

last: Lu

first: Cassidy

middle: R

last: Hinman

first: Jennifer

last: Lowe

first: Eric

middle: M

last: Wexler

first: Alysson

last: Muotri

first: Fred

middle: H

last: Gage

first: Kenneth

middle: S

last: Kosik

first: Daniel

last: Geschwind


title: Regulation of NF-κB signaling by miR-21-3p and miR-27a-5p in Response to Oxidized Phospholipids in Human Aortic Endothelial Cells

city: Los Angeles

first: Mete

last: Civelek

state: CA

address: 675 Charles E. Young Dr. S. MRL 3220

department: Medicine

institute: University of California Los Angeles

summary: The transition of the endothelium to a pro-inflammatory state is key to progression of chronic inflammatory diseases including rheumatoid arthritis, chronic bowel disease and atherosclerosis. In atherosclerosis it is hypothesized that low density lipoproteins (LDL) that become trapped in the intima of the blood vessels are oxidized to minimally modified LDL (mmLDL)  and that these serve as an important contributing factors to endothelial dysfunction.  Oxidized 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphatidylcholine (OX-PAPC), a model of the active phospholipid components of mmLDL affects the expression of hundreds of genes involved in inflammatory and other biological processes in human aortic endothelial cells (HAECs). We hypothesized that microRNAs (miRNAs) partially regulate this response. Using next generation sequencing, we identified miR-21-3p and miR-27a-5p to be induced 4-fold and 3-fold, respectively in response to OX-PAPC treatment compared to control treatment in HAECs. To identify the targets, we performed whole genome transcript profiling following transient over-expression of these two miRNAs followed by. In total, 1254 genes were down-regulated with 925 of them overlapping between the two miRNAs. Functional enrichment analysis using Gene Ontology predicted that the two miRNAs were involved in the regulation of NF-κB signaling. We characterized the Toll/interleukin-1 receptor (TIR) domain-containing adaptor protein TICAM2 as a direct target of miR-21-3p and miR-27a-5p. Furthermore, we showed that over-expression of miR-21-3p and miR-27a-5p lead to decreased p65 translocation to the nucleus and decreased the expression of known NF-κB downstream target genes confirming both miRNAs’ role in negatively regulating NF-κB signaling in endothelial cells.

overall_design: mRNA expression profiling of human aortic endothelial cells from two separate donors that were transfected with 1 nM microRNA mimics and negative control. The miRIDIAN mimics used were miR-21-3p (Catalog Number:C-301023-01-0005), miR-27a-5p (Catalog No: C-301028-01-0005), negative control (Catalog No: CN-001000-01-05)

first: Milagros

last: Romay

first: Judith

last: Berliner

first: Aldons

last: Lusis


title: Transcriptional profiling of human cancer cell lines upon ZMPSTE24 silencing

city: Oviedo

first: Jorge

last: de la Rosa

address: Avda. Jose Maria Richard

country: Spain

institute: Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA)

summary: Defining the aging-cancer relationship is a challenging task. Mice deficient in Zmpste24, a metalloproteinase mutated in human progeria and involved in nuclear prelamin A maturation, recapitulate many features of aging. However, their short lifespan and cell-intrinsic and -extrinsic alterations restrict the application and interpretation of carcinogenesis protocols. To circumvent these limitations we have generated Zmpste24 mosaic mice. Interestingly, these mice develop normally - revealing cell-extrinsic mechanisms are preeminent in progeria- and display decreased incidence of infiltrating oral carcinomas. Moreover, ZMPSTE24 knock-down reduces human cancer cell invasiveness. Our results disclose the ZMPSTE24-prelamin A system as an example of antagonistic pleiotropy on cancer and aging, support the potential of cell-based and systemic therapies for progeria, and highlight ZMPSTE24 as a new anticancer target.

overall_design: We used siRNAs to silence ZMPSTE24 in different human cancer cell lines (SCC-40, SCC-2, A549 and MDA-MB-231), and compared their RNA expression profiles with  those of mock treated cells. Each experimental condition (ZMPSTE24 or Scrambled siRNA) was performed in duplicate. Thus, a total of 16 array hybridizations were performed.

first: Roland

last: Rad

first: Allan

last: Bradley

first: Juan

last: Cadiñanos

first: Carlos

last: López-Otín


title: Broad-Spectrum Therapeutic Suppression of Metastatic Melanoma Through Nuclear Hormone Receptor Activation

city: New York

first: Nora

last: Pencheva

state: NY

address: 1230 York Avenue, Box 194

institute: Nora Pencheva

summary:
Melanoma metastasis is a devastating outcome in need of novel preventive therapies. We provide pharmacologic, nolecuar, and genetic evidence establishing the liver-X nuclear hormone receptor (LXR) as a therapeutic target in melanoma. Molecular and genetic experiments revealed these effects to be mediated by LXRb, which elicits these outcomes through transcriptional induction of tumoral and systemic apolipoprotein-E (ApoE).
LXRb agonism robustly suppressed tumor growth and metastasis across a wide spectrum of melanoma lines of diverse mutational subtypes established in xenograft, immunocompetent, and genetically-initiated model. We propose a path for the clinical testing of LXRb targeting-a therapeutic approach that uniquely acts by transcriptionally acivating a metastasis suppressor gene.

overall_design: In this experiment we analyzed the effect of GW3965 treatment on gene expression in the MeWo human melanoma cell line. The cells were treated either with DMSO or GW3965 at 1 micromolar for 48 hours, after which the RNA was extracted and gene expression was analyzed by transcriptomic profiling

first: Colin

last: Buss

first: Marija

last: Drobnjak

first: Taha

last: Merghoub

first: Sohail

middle: F

last: Tavazoie


title: Genome-wide analysis of miR-509-3p-mediated gene silencing in A549 lung cancer cells

status: Public on May 31 2014

city: Yongin

first: Young-Chul

last: Choi

state: Gyeonggi-do

address: 1 Seocheon-dong Giheung-gu

institute: Kyung Hee University

summary: Analysis of changes in gene expression after transfection with miR-509-3p mimic in A549 cells

overall_design: Total RNA was obtained from  A549 cells transfected with miR-509-3p and negative control mimics, and gene expression was compared using microarrays.

first: Kwanghee

last: Baek

first: Sena

last: Yoon


title: BCR-ABL1 and a dominant negative isoform of Ikaros cooperate to induce human acute myeloid leukemia

status: Public on May 23 2014

city: Cambridge

first: Elisa

last: Laurenti

address: Jeffrey Cheah Biomedical Centre

department: Haematology

country: United Kingdom

institute: University of Cambridge

summary: Analysis of lineage depleted human cord blood cells sequentially transduced with retro- (BCR-ABL1) and lentiviral (Ik6) vectors and the corresponding controls. Results provide important informations on the collaboration of BCR-ABL1 and Ik6 in human hematopoietic cells.

overall_design: Double-transduced lineage depleted human cord blood cells were puirifed according to GFP and LNGFR expression. RNA was extracted from purified cells.

first: Alexandre

middle: P

last: Theocharides

first: Stephanie

last: Dobson

first: John

middle: E

last: Dick


title: GRHL1 acts as a tumor suppressor in neuroblastoma and is negatively regulated by MYCN and HDAC3

status: Public on May 22 2014

city: Heidelberg

first: Johannes

last: Fabian

address: Im Neuenheimer Feld 280

department: CCU Pediatric Oncology

country: Germany

institute: German Cancer Research Center

summary: Neuroblastoma is an embryonic solid tumor of neural crest origin and accounts for 11% of all cancer-related deaths in children. Novel therapeutic strategies are therefore urgently required. MYCN oncogene amplification, which occurs in 20% of neuroblastomas, is a hallmark of high risk. Here we aimed to exploit molecular mechanisms that can be pharmacologically addressed with epigenetically modifying drugs, such as histone deacetylase (HDAC) inhibitors. GRHL1, a gene critical for Drosophila neural development, belonged to the genes most strongly responding to HDAC inhibitor treatment of neuroblastoma cells in a genome- wide screen. An increase in the histone H4 pan-acetylation associated with its promoter preceded transcriptional activation. Physically adjacent, HDAC3 and MYCN co-localized to the GRHL1 promoter and repressed its transcription. High-level GRHL1 expression in primary neuroblastomas correlated on transcriptional and translational levels with favorable patient survival and established clinical and molecular markers for favorable tumor biology, including lack of MYCN amplification. Enforced GRHL1 expression in MYCN-amplified neuroblastoma cells with low endogenous GRHL1 levels abrogated anchorage-independent colony formation, inhibited proliferation and retarded xenograft growth in mice. GRHL1 regulated 170 genes genome-wide, and most were involved in pathways regulated during neuroblastomagenesis, including nervous system development, proliferation, cell-cell adhesion, cell spreading and cellular differentiation. In summary, the data presented here indicate a significant role of HDAC3 in the MYCN-mediated repression of GRHL1 and suggest drugs that block HDAC3 activity and suppress MYCN expression as promising candidates for novel treatment strategies of high-risk neuroblastoma.

overall_design: Twelve samples were analyzed. Each 2 replicated of paired empty vector control and GRHL1 forced expression at 3 different time points.

first: Marco

last: Lodrini

first: Ina

last: Oehme

first: Marie

last: Schier

first: Theresa

last: Thole

first: Thomas

last: Hielscher

first: Annette

last: Kopp-Schneider

first: Lennart

last: Opitz

first: David

last: Capper

first: Andreas

last: von Deimling

first: Inga

last: Wiegand

first: Till

last: Milde

first: Ulrich

last: Mahlknecht

first: Frank

last: Westermann

first: Odilia

last: Popanda

first: Frederick

last: Roels

first: Barbara

last: Hero

last: Berthold

first: Matthias

last: Fischer

last: Kulozik

first: Olaf

last: Witt

first: Hedwig

last: Deubzer


title: Towards epigenetic understanding and therapy of insulin resistance by intranuclear insulin [human cell line gene expression]

city: Hangzhou

first: Yun

last: Xiao

address: Yuhangtang Road

country: China

institute: Zhejiang University

summary:
There is evidence indicating the involvement of DNA methylation memory in maintaining gene expression patterns associated with insulin resistance. Although the exact mechanism remains unknown, it has been proved that insulin resistance is correlated to low heat shock protein (HSP) expression.
We reveal that intranuclear insulin can reduce HSP DNA methylation level to up-regulate HSP protein expression and result in long term cure of hyperglycemia.

overall_design: Insulin resistance HepG2 cell were selected in our experiments.Three conditions were compared with three replicates each. These are:(1) Insulin resistance HepG2(R-HepG2) (2) Insulin treated HepG2(Insulin); (3) Biomineralized insulin treated HepG2 (BI).

first: Zheng

last: Li

first: Yiyu

last: Cheng

first: Ruikang

last: Tang


title: Biological effects of platelet-derived growth factor receptor alpha lockade in uterine cancer

status: Public on Jun 04 2014

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

summary: Platelet-derived growth factor receptor alpha (PDGFRα) expression is frequently observed in many kinds of cancer and is a candidate for therapeutic targeting. Here, we evaluated the biological significance of PDGFRα and PDGFRα blockade (using a fully humanized monoclonal antibody, 3G3) in uterine cancer. PDGFRα was expressed in uterine cancer cells, and its blockade with 3G3 resulted in inhibition of PDGFRα phosphorylation and of downstream signaling molecules, AKT and MAPK. Cell viability and invasive potential of uterine cancer cells were also inhibited by treatment of 3G3. Moreover, greater therapeutic effects were observed for 3G3 in combination with chemotherapy than for either drug alone in orthotopic mouse models of uterine cancer. These findings identify PDGFRα as an attractive therapeutic target for uterine cancer.

overall_design: Two groups of samples are included: 1.Hec-1A 2.Rl-95-2. Gene expression profiles of Hec-1A cells were compared to that of  RL95-2 cells.

first: Jie

last: Huang

first: Nicholas

middle: B

last: Jennings

first: Anil

last: Sood

first: Ju-Seog

last: Lee


title: Identifying the downstream effectors of E2F7 in squamous cell carcinoma (SCC) cells

status: Public on May 30 2014

city: Brisbane

first: Mehlika

last: Hazar-Rethinam

state: QLD

address: Translational Research Institute, 37 Kent Street, Woolloongabba

country: Australia

institute: The University of Queensland Diamantina Institute

summary: Advanced head and neck squamous cell carcinomas (HNSCC) are frequently drug resistant and have a mortality rate of 40%. We have previously shown that E2F7 may contribute to drug sensitivity. In the present study, we conducted an –omics screen to identify factors that were responsible for E2F7-dependent resistance to anthracyclines by HNSCC. We provide, in vitro, in vivo and patient data that identifies the existence of a novel E2F7/Sphingosine kinase 1/Sphingosine-1-phosphate/AKT axis that regulates sensitivity to anthracyclines in HNSCC. Specifically, we show that E2F7-dependent sensitivity to doxorubicin occurs via induction of the sphingosine kinase 1/AKT axis.  We also show that pharmacological inhibition of Sphingosine kinase 1 or AKT sensitizes SCC cells to the cytotoxic actions of doxorubicin in vitro and in vivo. Combined, these findings highlight a novel mechanism through which SCC cells acquire resistance to anthracyclines and identify specific pharmacological combinations that could be used to treat SCC.

overall_design: Duplicate total RNA  isolated from i) untreated, KJD cells, ii) 1µM doxorubicin-treated KJD cells, iii) control plasmid (pcDNA3) transfected, untreated KJD cells, iv) control plasmid (pcDNA3) transfected, 1µM doxorubicin-treated KJD cells, v) E2F7 expression plasmid transfected, untreated KJD cells, vi) E2F7 expression plasmid transfected, 1µM doxorubicin-treated  KJD cells, vii) untreated, SCC25 cells, viii) 1µM doxorubicin-treated SCC25 cells, ix) control siRNA (GFPsiRNA) transfected, untreated SCC25 cells, x) control siRNA (GFPsiRNA)  transfected, 1µM doxorubicin-treated SCC25 cells, xi) E2F7siRNA transfected, untreated SCC25 cells, xii) E2F7siRNA transfected, 1µM doxorubicin-treated SCC25 cells were hybridised to an RNA microarray to identify genes which are downstream of E2F7 and regulate chemosensitivity in SCC.

last: Saunders


title: Genomic analysis of non-NF2 meningiomas reveals mutations in TRAF7, KLF4, AKT1, and SMO.

status: Public on May 29 2014

city: New Haven

first: Victoria

middle: Elizabeth

last: Clark

state: CT

address: 300 Cedar Street TAC S330

department: Departments of Neurosurgery and Genetics

institute: Yale University School of Medicine

summary: We report genomic analysis of 300 meningiomas, the most common primary brain tumors, leading to the discovery of mutations in TRAF7, a proapoptotic E3 ubiquitin ligase, in nearly one-fourth of all meningiomas. Mutations in TRAF7 commonly occurred with a recurrent mutation (K409Q) in KLF4, a transcription factor known for its role in inducing pluripotency, or with AKT1(E17K), a mutation known to activate the PI3K pathway. SMO mutations, which activate Hedgehog signaling, were identified in ~5% of non-NF2 mutant meningiomas. These non-NF2 meningiomas were clinically distinctive-nearly always benign, with chromosomal stability, and originating from the medial skull base. In contrast, meningiomas with mutant NF2 and/or chromosome 22 loss were more likely to be atypical, showing genomic instability, and localizing to the cerebral and cerebellar hemispheres. Collectively, these findings identify distinct meningioma subtypes, suggesting avenues for targeted therapeutics.

overall_design: Analysis of meningioma gene expression data for each mutation subtype. Includes gene expression data from 75 unique meningiomas and 39 replicates.

first: Akdes

last: Serin

first: Murat

last: Gunel


title: Expression data from human brain dorsolateral prefrontal cortex - including control samples and samples with major depression disorders (26 samples NY_BA9)

status: Public on May 16 2014

city: Pittsburgh

first: Etienne

last: Sibille

state: PA

address: 450 Technology Drive, Suite 231

department: Psychiatry

institute: University of Pittsburgh

summary: Major depressive disorder is a heterogeneous illness with a mostly uncharacterized pathology. Large scale gene expression (transcriptome) analysis and genome-wide association studies (GWAS) for single nucleotide polymorphisms have generated a considerable amount of gene- and disease-related information, but heterogeneity and various sources of noise have limited the discovery of disease mechanisms. As systematic dataset integration is becoming essential, we developed methods and performed meta-clustering of gene coexpression links in 11 transcriptome studies from postmortem brains of human subjects with major depressive disorder (MDD) and non-psychiatric control subjects. We next sought enrichment in the top 50 meta-analyzed coexpression modules for genes otherwise identified by GWAS for various sets of disorders. One coexpression module of 88 genes was consistently and significantly associated with GWAS for MDD, other neuropsychiatric disorders and brain functions, and for medical illnesses with elevated clinical risk of depression, but not for other diseases (See publication for details).

overall_design: 26 total samples in 13 pairs were analyzed in postmortem tissue from the dorsolateral prefrontal cortex.


title: Characterization of Gene Expression in ASS1-Deficient Breast Cancer Cells

status: Public on May 20 2014

city: Taipei City

first: Cheng-Ying

last: Chu

address: 250 Wu-Hsing Street

department: Center for Translational Medicine

country: Taiwan

institute: Taipei Medical University

summary: Analysis of mechanism underlying the metabolic effects of ADI-PEG20 at gene expression level. The hypothesis tested in the present study was that ASS1-deficient breast cancer cells would be arginine-auxotrophs and would therefore be sensitive to arginine starvation. Results provide important information of the response of ASS1-deficient breast cancer cells to ADI-PEG20-treatment, such as the suppression of mRNAs encoding mitochondrial respiratory chain proteins.

overall_design: Total RNA obtained from ADI-treated, or ADI- and L-arginine-treated 231 cells compared to untreated cells.

first: David

last: Ann

first: Hsing-Jien

last: Kung


title: Expression data from human brain orbital ventral prefrontal cortex - including control samples and samples with major depression disorders (24 samples NY_BA47)

overall_design: 24 total samples in 12 pairs were analyzed in postmortem tissue from the orbital ventral prefrontal cortex.


title: Genome-wide identification of expression quantitative trait loci (eQTLs) in human heart: gene expression

status: Public on May 21 2014

city: Amsterdam

first: Michiel

middle: Emanuel

last: Adriaens

address: Meibergdreef 15

department: Experimental Cardiology

country: Netherlands

institute: AMC

summary: In recent years genome-wide association studies (GWAS) have uncovered numerous chromosomal loci associated with various electrocardiographic traits and cardiac arrhythmia predisposition. A considerable fraction of these loci lie within inter-genic regions. Trait-associated SNPs located in putative regulatory regions likely exert their effect by modulating gene expression. Hence, the key to unraveling the molecular mechanisms underlying cardiac traits is to interrogate variants for association with differential transcript abundance by expression quantitative trait locus (eQTL) analysis. In this study we conducted an eQTL analysis of human heart. To this end, left ventricular mycardium samples from non-diseased human donor hearts were hybridized to Illumina HumanOmniExpress BeadChips for genotyping (n = 129) and Illumina Human HT12 Version 4 BeadChips (n = 129) for transcription profiling.

overall_design: To assess the gene expression levels of 129 human donor hearts from the study, genome-wide transcription profiling was carried out using Illumina Human HT12 Version 4 Beadchips interrogating over 47,000 unique transcripts (total of 47323 probes including controls).

first: Tamara

last: Koopmann

first: Connie

last: Bezzina


title: SPIB and BATF provide alternate determinants of IRF4 occupancy in Diffuse Large B-cell Lymphoma linked to disease heterogeneity.

status: Public on Jun 03 2014

city: York

first: Matthew

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

department: Department of Biology

institute: The University of York

summary: Gene expression from OCI-LY3 cells 48hrs after knock down of SPIB.

overall_design: 2 samples analysed (scramble and siRNA knock down), each with a single repeat.

first: Reuben

last: Tooze


title: Genome-wide identification of expression quantitative trait loci (eQTLs) in human heart

type:
Expression profiling by array
SNP genotyping by SNP array

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

overall_design: Refer to individual Series


title: Expression data from human brain amygdala - including control samples and samples with major depression disorders (42 samples MD3_AMY)

overall_design: 42 total samples in 21 pairs were analyzed in postmortem tissue from the amygdala.


title: Reciprocal leukemia-stroma VCAM-1/VLA-4-dependent activation 1 of NF-κB mediates chemoresistance

status: Public on May 19 2014

first: Wencai

last: Ma

address: 7455 Fannin st

institute: MD Anderson Cancer Center

summary: Bone marrow (BM) mesenchymal stromal cells (BM-MSC) upregulate their NF-κB signaling to protect leukemia cells from chemotherapy-induced apoptosis.

overall_design: To elucidate molecular mechanisms by which leukemia-stroma interactions within the BM microenvironment could confer chemoresistance to leukemia cells, we used genome-wide gene expression profiling (GEP) to examine human normal BM-MSC that had been co-cultured with the pre-B ALL REH cells and then separated by flow cytometry (FACS). GEP results for co-cultured cells of each type were compared to GEP results for cells of the corresponding type cultured alone, and taken through the same FACS purification procedure, to identify changes in gene expression profiles caused by co-culture.

first: Rodrigo

last: Jacamo

first: Zhiqiang

last: Wang

first: R.

last: Davis

first: Michael

last: Andreeff


title: The ETS family member GABPa mediates the development of castrate-resistant prostate cancer (BeadChip)

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

summary: In prostate cancer, the androgen receptor (AR) is a key transcription factor at all disease stages. We recently showed that during progression to castrate-resistant prostate cancer the AR acquires the ability to bind to a distinct set of genomic sites in tissue samples and that some of the genes that are regulated by the AR in these conditions correlate with poor prognosis. Based on this work we hypothesised that the AR is reprogrammed through interactions with other transcription factors. In the present study we show that GABPá, an ETS transcription factor which is upregulated in CRPC, is an AR-interacting transcription factor. Ectopic expression of GABPA in prostate cancer cell-lines enables them to acquire some of the molecular and cellular characteristics of CRPC tissues as well as more aggressive growth phenotypes.

overall_design: Cells were made to either overexpress GABPa or have it knocked down; these conditions also had empty vector and non-targetting controls respectively. All four treatments were carried out with and without androgen for the LNCaP and c42b cell lines. Biological and technical replicates were used.

first: Naomi

last: Sharma

first: Suraj

last: Menon


title: Expression data from human brain anterior cingulate cortex - including control samples and samples with major depression disorders (20 samples MD2_ACC)

first: Etienne

last: Sibille

overall_design: 20 total samples in 10 pairs were analyzed in postmortem tissue from the anterior cingulate cortex.


title: Expression profiling of Wnt3a-treated HeLa cells in G1 and G2/M phase

status: Public on May 15 2014

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

institute: Institute of Molecular Biology

summary: The early transcriptional response of HeLa cervical carcinoma cells to the canonical Wnt signalling pathway was investigated at two different cell cycle phases (G1 and G2/M) via microarray gene expression profiling.

overall_design: HeLa cells grown under standard conditions were treated for 3 h with either Control, Wnt3a- or Dkk1-conditioned media and then FACS-sorted into G1 and G2/M populations for microarray expression analysis with 4 independent replicates per group.

first: Birgit

last: Berger

first: Sergio

last: Acebron

first: Christof

last: Niehrs


title: The effect of androgens on CD4 T-cells

city: Boston

first: Haydn

last: Kissick

state: MA

address: 3 Blackfan Circle, CLS 4/430

institute: Beth Israel Deaconess Medical Ceter

summary: The hormonal milieu influences immune tolerance as well as the immune response against viruses and cancer, but the direct effect of androgens on cellular immunity remains largely uncharacterized. We therefore sought to evaluate the effect of androgens on murine CD4 T-cells by micro-array analysis

overall_design: Male mice were castrated, or received sham surgery. Four weeks later, CD4 cells were sorted by FACS.  Splenocytes were pooled from 3 mice to be analysed on each micro-array chip. 2 micro-array chips were used for each group (containing samples from 6 mice total for each group)

first: Arredouani

last: Simo

first: Kissick

last: Haydn


title: Gene Expression Profiling on Stably Expressing Full Length (FL) JM-a CYT-1 or CYT-2 ERBB4 isoforms in  MCF10A cells

status: Public on May 07 2014

first: James

middle: T.

last: Platt

address: 333 Cedar ST

department: Medical Oncology

institute: Yale University

summary: Convergent and divergent effects of two FL ERBB4 isoforms on gene expression in normal-like MCF10A mammary epithelial cells lacking endogeneous ERBB4 expression.

overall_design: Control vector (VEC) and ERBB4 expression MCF10A cells(CYT1 or CYT2) were serum starved for 48 hours and incubated with or without ERBB4 ligand NRG1 for 2h.  RNA samples were collected and analyzed.

first: Vikram

last: Wali


title: Gene expression profiling of melanoma brain metastases and matched extracranial metastases

status: Public on May 08 2014

first: Guo

last: Chen

address: 7435 Fannin Street

department: Melanoma Medical Oncology

institute: The University of Texas MD Anderson Cancer Center

summary: An improved understanding of the molecular pathogenesis of brain metastases, one of the most common and devastating complications of advanced melanoma, may identify and prioritize rational therapeutic approaches for this disease. In particular, the identification of molecular differences between brain and extracranial metastases would support the need for the development of organ-specific therapeutic approaches. Hotspot mutations, copy number variations (CNV), global mRNA expression patterns, and protein expression and activation, quantitatively analyzed by molecular inversion probe arrays, microarrays and reverse phase protein array (RPPA) were evaluated in pairs of melanoma brain metastases and extracranial metastases from patients who had undergone surgical resection for both types of tumors.

overall_design: Seventy-two samples from 52 brain (except for patient 01, who had a spinal cord metastasis) and extracranial metastases of melanoma were analyzed. Available biological replicates (different parts of the same tumor) were included.

first: Kimberly

last: Aardalen

first: Nitin

last: Charkravarti

first: Alexander

middle: J

last: Lazar

middle: T

last: Tetzlaff

first: Bradley

last: Wubberhorst

first: Sang-Bae

last: Kim

first: Scott

last: Kopetz

first: Alicia

middle: A

last: Ledoux

first: Y

middle: V

last: Gopel

first: Cristiano

middle: G

last: Pereira

first: Wanleng

last: Deng

first: Ju-Seog

last: Lee

first: Katherine

last: Nathanson

first: Kenneth

middle: D

last: Aldape

first: Victor

last: Prieto

first: Darrin

last: Stuart

last: Davies


title: Gene Expression Profiling on Stably Expressing ICD JM-a CYT-1 or CYT-2 ERBB4 isoforms in  MCF10A cells

first: James

last: Platt

summary: Convergent and divergent effects of two ICD ERBB4 isoforms on gene expression in normal-like MCF10A mammary epithelial cells lacking endogeneous ERBB4 expression.

overall_design: Control vector (VEC) and ERBB4 expression MCF10A cells (ICD CYT1 or CYT2) maintained in regular medium containing 10% serum, were collected and RNA samples were collected and analyzed.

first: Maureen

last: Gilmore-Hebert

first: Vikram

last: Wali


title: Gene expression analysis of PST-Dox nanoparticles on isolated normal lymphocytes and in cancer cell lines

status: Public on May 02 2014

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

summary: Analysis of expression variation of PST-Dox nanoaprticles for elucidating the molecular mechanism of action in cancer cell lines and normal lymphocytes.

overall_design: Total RNA isolated from PST-Dox treated cells subjected to 24 hr treatment compared to untreated samples.

first: Manu

middle: M

last: Joseph

first: T

last: Sreelekha


title: Melanoma brain metastases and matched extracranial metastases

first: Guo

last: Chen

type:
Expression profiling by array
Genome variation profiling by SNP array
SNP genotyping by SNP array


title: Induced pluripotent stem cell derived neuronallineages as human cellular models for Herpes Simplex Virus, type 1 (HSV-1) infections

first: Leonardo

last: D'Aiuto

address: 3811 O’Hara Street

institute: UPMC

summary: Herpes simplex virus type 1 (HSV-1) is a 152 Kb double stranded DNA alpha-herpesvirus, which establishes long life latent infection in sensory neurons. Most of our knowledge regarding HSV-1 latency comes from in vivo studies using small animal models, mainly rodents and rabbits, which are not naturally infected by HSV-1. Furthermore, these animal models do not fully recapitulate the species specific effects of human HSV-1 infection. Human cellular models utilize trigeminal ganglia removed from cadavers or, alternatively, neuron-like cells derived from cancerous cell lines that do not fully reflect effects on normal human neurons. This limitation poses the need to develop an in vitromodel to investigate molecular details of  the mechanisms underlying quiescence and reactivation in human neurons. Induced pluripotent stem (iPS) celltechnologies offer an unprecedented opportunity  to generate unlimited supplies of neurons and the facility to manipulate such cells in vitro. In this study,  we developed an in vitro HSV-1 infection model in human iPS-derived neurons, which displays the main hallmarks of latency defined in animal models and in humans. Our results show for the first time that: i) persistent infection cannot be established in neural progenitor cells (NPCs); ii) the ability of HSV-1 to establish persistent infection is extended to glutamatergic neurons, and not limited to sensory neurons; iii) in neuronal cultures persistently infected with HSV-1, viral genome is localized at the nuclear periphery; iv) HSV-1 acute infection reduces RNA editing at the GluRB site. These results highlight the importance of iPS-based platforms to elucidate unknown aspects of HSV-1 quiescence in human neurons.

overall_design: NPCs were 70-80% confluence

first: Vishwajit

last: Nimgaonkar

first: Jadranka

last: Milosevic


title: Pouch transcriptional differences between UC and FAP indicate altered immune response.

status: Public on May 01 2014

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

summary:
A total proctocolectomy with ileal pouch-anal anastomosis (IPAA) is considered the surgery of choice for definitive management of familial adenomatous polyposis (FAP) and selected patients with ulcerative colitis (UC). However, this surgical treatment often associates with a long-term complication, pouchitis, which occurs mostly in UC patients.
To better define the molecular background of pouchitis, the microarray-based survey was performed using pouch mucosal samples collected from 28 and 8 patients operated for UC and FAP, respectively. A number of 4771 genes was significantly differentiating uninflamed from inflamed mucosal samples, and their functional features were represented mostly by alerted metabolic and cell proliferation pathways. In contrast, functional analyses of aberrantly expressed probe sets between UC and FAP samples, irrespectively of mucosal inflammation status, revealed multiple pathways and terms which were linked to changes in immune response. Noteworthy, the comparison of uninflamed UC and FAP samples distinguished a set of 26 altered mRNAs including inflammation-related transcript encoding a Charcot-Leyden crystal (CLC) protein. The most discrete changes in gene expression profiles differentiating uninflamed UC and FAP mucosal samples were attributed to a Gene Ontology category innate immune response.
Our study confirmed alterations of the immune responses as dominant in UC pouchitis which were earlier found in the studies using analyses of singular molecular elements. This observation may be important when managing IPAA patients.

overall_design: Each sample represents three biopsies taken from single patient, from the same areas of the lower part of the pouch mucosa (above the rectal cuff) during endoscopic examination. 28 patients underwent surgery for UC and 8 patients for FAP.

first: Agnieszka

last: Paziewska

first: Karolina

last: Horbacka

first: Michal

last: Mikula

first: Dorota

last: Jarosz

first: Michalina

last: Dabrowska

first: Piotr

last: Krokowicz

first: Jacek

last: Karon

first: Jerzy

last: Ostrowski


title: Expression data from human brain anterior cingulate cortex - including control samples and samples with major depression disorders (50 samples MD3_ACC)

first: Etienne

last: Sibille

overall_design: 50 total samples in 25 pairs were analyzed in postmortem tissue from the anterior cingulate cortex.


title: Pancreatic cancer stem-like cells display aggressive behavior mediated via activation of FoxQ1

city: Detroit

first: Aliccia

last: Bollig-Fischer

address: 4100 John R

department: Oncology

institute: Karmanos Cancer Institute & Wayne State University

summary: A microarray approach was used to measure and compare whole genome expression in non-sorted cell population and in subsets of cultured cells, including stem-like cancer cell and non-stem like cancer cell populations,

overall_design: MiaPaCa-2 pancreatic cancer cells from culture were sorted by Fluorescence Activated Cell Sorting (FACS) using 3 markers: CD44, CD133 and EpCAM. Three resulting populations, i.e., not sorted, sorted triple positive and sorted triple negative, were analyzed. 4 cultures were sorted independently to arrive at 4 biological replicates.

first: Bin

last: Bao


title: Gene expression analysis of FOXN1+ thymic endoderm cells derived from the in vitro differentiation of human embryonic stem cells

city: Melbourne

first: Ed

last: Stanley

state: Victoria

address: Flemington Road

department: Cell Biology

institute: Murdoch Childrens Research Institute

summary:
The goal of this study was to document the gene expression profile of FOXN1+ thymic endoderm cells derived from the in vitro differentiation of human pluripotent stem cells.
Thymic epithelial cells (TECs) play a critical role in T-cell maturation and tolerance induction. The generation of TECs from in vitro differentiation of human pluripotent stem cells (PSCs) would provide a platform for studying the mechanisms of this interaction and have implications for immune reconstitution. To facilitate analysis of PSC-derived TECs, we generated human embryonic stem cell (hESC) reporter lines in which sequences encoding GFP were targeted to FOXN1, a gene required for TEC development. Using this FOXN1GFP/w line as a read out, we developed a reproducible protocol for generating FOXN1-GFP+ thymic endoderm cells. Transcriptional profiling and flow cytometry identified Integrin-β4 (ITGB4, CD104) and HLA-DR as markers that could be used in combination with EpCAM to selectively purify FOXN1+ TEC progenitors from differentiating cultures of unmanipulated PSCs. Human FOXN1+ TEC progenitors generated from PSCs will facilitate the study of thymus biology and are a valuable resource for future applications in regenerative medicine

overall_design: Human embryonic stem cells were differentiated for 30 days using the protocol described by Soh et al, 2014. The hESCs used in this protocol had been genetically modified by targeting sequences encoding GFP to the FOXN1 locus, thus enabling FOXN1 expressing cells to be identified on the basis of GFP expression.  At differentiation day 30, differentiating cells were separated into three fractions using FACS. These fractions were the FOXN1+(GFP+)EpCAM+, FOXN1-(GFP-)EpCAM+, FOXN1-(GFP-)EpCAM-.

first: Chew-Li

last: Soh


title: Genome-wide transcriptional profiling of human PBMCs stimulated with Candida albicans and non-fungal inflammatory stimuli

first: Aylwin

last: Ng

address: 185 Cambridge Street

institute: CCIB, MGH

summary: Candida albicans is the most common human fungal pathogen causing mucosal and systemic infections, but human anti-fungal immunity remains poorly defined. Expression profiling of Candida-stimulated human peripheral blood mononuclear cells (PBMCs) provides new insights into Candida-specific host defense mechanisms in humans.

overall_design: Total RNA was extracted from PBMCs from healthy human volunteers. PBMCs were stimulated with heat-killed Candida albicans (10^6/ml), non-fungal inflammatory stimuli or RPMI control for 4 or 24 hours. A large number of biological replicates (>20) were included per stimulation condition and duration.

first: Sanne

last: Smeekens

first: Vinod

last: Kumar

first: Melissa

last: Johnson

first: Theo

last: Plantinga

first: Cleo

last: van Diemen

first: Peer

last: Arts

first: Eugène

last: Verwiel

first: Mark

last: Gresnigt

first: Karin

last: Fransen

first: Suzanne

last: van Sommeren

first: Marije

last: Oosting

first: Shih

middle: C

last: Cheng

first: Leo

last: Joosten

first: Alexander

last: Hoischen

first: Bart

last: Kullberg

first: William

middle: K

last: Scott

first: John

middle: R

last: Perfect

first: Jos

middle: W

last: van der Meer

first: Cisca

last: Wijmenga

first: Mihai

last: Netea

first: Ramnik

last: Xavier


title: Gene expression profile of PBMCs after intake of fish oil for seven weeks compared to high oleic sunflower oil

city: OSLO

first: Mari

last: Myhrstad

address: Postboks 4, St. Olavs plass

department: Department of health

country: Norway

institute: Oslo and Akershus University College

summary: Fish oil supplementation has been shown to alter gene expression of mononuclear cells both in vitro and in vivo. However, little is known about the total transcriptomic profile in healthy subjects after intake of fish oil compared to a control group. The objective was to examine the gene expression profile in peripheral blood mononuclear cells (PBMCs) in healthy subjects after intake of fish oil for seven weeks using whole-genome transcriptomic analysis. In a double-blinded randomized controlled study, healthy subjects received capsules containing either 8 g/d of fish oil (1.6 g/d EPA+DHA) (n=17) or 8 g/d of high oleic sunflower oil (n=19) for seven weeks. The results provide important information on how fish oil may modulate basic cellular processes involved in normal cell function and lymphocyte activation such as ER stress, cell cycle and apoptosis.

overall_design: The subjects were taking 16 capsules/d containing 8 g/d of either fish oil (FO) or high oleic sunflower oil (HOSO) for seven weeks. Subjects in the FO group received capsules containing 0.7 g/d EPA + 0.9 g/d DHA from cod liver oil (Gadidae sp., TINE EPADHA Oil 1200) provided by TINE SA (Oslo, Norway) and subjects in HOSO group received high oleic sunflower oil purchased from AarhusKarlshamn AB (Malmӧ, Sweden). Prior to the baseline visit (visit 2, wk 0), the subjects conducted a four-week washout period, where foods containing marine n-3 fatty acids were excluded from the diet. The first three weeks of the intervention period the subjects conducted a fully-controlled isocaloric diet, provided with all food and beverages at Akershus University College, Norway. During the last four weeks of the intervention the subjects returned to their habitual diet. Use of fish, fish products, marine n-3 enriched food or dietary supplements was not allowed during the entire study period of 11 weeks. The study was registered at www.clinicaltrial.gov (IDno. NCT01034423). The subjects met for four visits and blood samples for the transcriptome analyses were collected at wk 0, 3 and 7. After blood collection, PBMCs were isolated by using the BD Vacutainer Cell Preparation tubes according to the manufacturer's instructions (Becton, Dickinson and Company, NJ 07417, USA). Pellets were frozen and stored at -80o C for further RNA isolation.

first: Stine

last: Ulven

first: Clara

last: Günther

first: Inger

last: Ottestad

first: Marit

last: Holden

first: Einar

last: Ryeng

first: Grethe

middle: I

last: Borge

first: Achim

last: Kohler

first: Kirsti

last: Brønner

first: Magne

last: Thoresen

first: Kirsten

last: Holven


title: ICGC Pancreas: Genomewide DNA methylation patterns in pancreatic ductal adenocarcinoma (gene expression of 103 samples)

status: Public on May 05 2014

city: Sydney

first: Jianmin

last: Wu

state: NSW

address: 370 Victoria Street Darlinghurst

department: Cancer Division

institute: Garvan Institute of Medical Research

summary: This dataset includes gene expression data from 103 primary tumour samples. 86 samples from this dataset have already been deposited into GEO (GSE36924), and has been duplicated here since the data has been processed differently. This data is also available through the International Cancer Genome Consortium (ICGC) Data Portal (http://dcc/icgc.org), under the project code: Pancreatic Cancer (QCMG, AU). Access to the restricted clinical data must be made through the ICGC Data Access Compliance Office (http://www.icgc.org/daco).

overall_design: This dataset contains gene expression array data from 103 primary pancreatic ductal adenocarcinoma samples. All samples have 1 biological replicate. These data have corresponding methylation 450K array data (GSE49149).

first: Katia

last: Nones

first: Nic

last: Waddell

first: Sarah

last: Song

first: Ann-Marie

last: Patch

first: Karin

middle: S

last: Kassahn

first: David

last: Chang

first: Amber

last: Johns

last: Wood

first: Peter

last: Bailey

last: Miller

first: Suzanne

last: Manning

first: Angelika

last: Christ

first: Craig

last: Nourse

first: Darrin

last: Taylor

first: Conrad

last: Leonard

first: Marc

last: Jones

first: Michelle

last: Thomas

first: Clare

last: Watson

first: Mark

last: Pinese

last: Cowley

first: Ilse

last: Rooman

first: Marina

last: Pajic

first: Rita

last: Lawlor

first: Anthony

last: Gill

first: Aldo

last: Scarpa

last: Pearson

first: Andrew

last: Biankin

first: Sean

last: Grimmond


title: Genome wide transcriptional profiling of HIV positive and negative children with active tuberculosis, latent TB infection and other diseases

city: London

first: Michael

last: Levin

address: South Kensington Campus

department: Paediatrics

institute: Imperial College London

overall_design: Refer to individual Series


title: The orphan nuclear receptor NR4A1 (Nur77, TR3) regulates oxidative and endoplasmic reticulum stress in pancreatic cancer cells

status: Public on Apr 30 2014

first: Sangbae

last: Kim

address: 1 Baylor plaza

institute: Baylor Colleage of Medicine

summary: NR4A1 (Nur77, TR3) is an orphan nuclear receptor that is overexpressed in pancreatic cancer cells and tumors and exhibits pro-oncogenic activity. Knockdown of NR4A1 by RNA interference (siNR4A1) in Panc1 cells and analysis of the proteome resulted in induction of several markers of endoplasmic reticulum (ER) stress including glucose-related protein 78 (GRP78), CCAAT/enhancer-binding protein-homologous protein (CHOP), activating transcription factor-3 (ATF-3) and AFT-6. These effects were accompanied by induction of apoptosis and similar results were observed after treatment of pancreatic cancer cells with the known inactivator of NR4A1, 1,1-bis(3’-indolyl)-1-(p-hydroxyphenyl)methane (DIM-C-pPhOH). Both siNR4A1 (transfected) and DIM-C-pPhOH also induced reactive oxygen species (ROS) and induction of ROS and ER stress by these agents was attenuated after cotreatment with antioxidants. Transfection of Panc1 cells with siNR4A1 follow by analysis of gene expression by arrays identified ROS metabolism genes regulated by NR4A1. Knockdown of one of these genes, thioredoxin domain containing 5 (TXNDC5) also resulted in induction of ROS and ER stress demonstrating that NR4A1 regulates levels of ER stress and ROS in pancreatic cancer cells to facilitate cell proliferation and survival. Inactivation of this receptor by siNR4A1 or DIM-C-pPhOH decreases TXNDC5 resulting in activation of ROS/ER stress and pro-apoptotic pathways and represents a novel pathway for inducing cell death in pancreatic cancer cells.

overall_design: Two groups of samples are included: 1. siControl; 2. siNR4A1 treatment in PAC1 cell. Transfection of Panc1 cells with siNR4A1 follow by analysis of gene expression by arrays identified ROS metabolism genes regulated by NR4A1.

first: Syng-Ook

last: Lee

first: Ju-Seog

first: Stemphen

last: Safe


title: Whole-genome microarray analysis was performed on cells treated with 5 μM dTAT for 1h

status: Public on May 09 2014

city: College Station

first: Jean-Philippe

last: Pellois

state: Texas

address: 300 Olsen Blvd

department: Biochemistry and Biophysics

institute: Texas A&M university

summary: Analysis of the impacto of dTAT treatment on primary human dermal flibroblast at the gene expression level. Results show that dTAT cytosolic penetration has a minimal impact on mRNA expression and that cells rapidly recover from treatment with dTAT.

overall_design: Primary Human dermal Fibroblast (HDF) were treated with dTAT (5µM) for 1h. Total RNA was harvested from HDF cells immediately, 1h or 24h after treatment.

first: Alfredo

last: Erazo-Oliveras

first: Kristina

last: Najjar


title: Genome wide transcriptional profiling of HIV positive and negative children with active tuberculosis, latent TB infection and other diseases from Kenya

summary:
The study aimed to define transcriptional signatures for detection of active TB (TB) compared to latent TB infection (LTBI) as well as to other diseases (OD) with similar clinical phenotypes in patients with and without HIV in a paediatric cohort from Kenya
Transcriptional signatures were identified that distinguished active TB from LTBI, active TB from other diseases, and active TB from both LTBI and other diseases in HIV+/- patients.

overall_design: Children were recruited from 2 hospitals in Coast Province, Kenya (n=157) who were either HIV+  or HIV - with either active TB (culture confirmed), active TB (culture negative), LTBI or OD. Blood was collected into PAX gene tubes (PreAnalytiX). Total RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). Labeled cRNA was hybridized to Illumina Human HT-12 Beadchips. Data were analysed in R.

last: Brent

first: Victoria

last: Wright

first: Myrsini

last: Kaforou

first: Hemed

last: Twahir

first: Victor

last: Bandika

first: Joyce

last: Langat

first: Carole

last: Mulunda

first: Joshua

last: Wambua

first: John

middle: P

last: Odhiambo

first: Robert

last: Musyimi

first: Daisy

last: Mugo

first: Agnes

last: Mutiso

first: Susan

last: Morpeth

first: Ling

last: Ling

first: Martin

last: Hibberd

first: Jay

last: Berkley

first: Kath

last: Maitland

first: Charles

last: Newton

last: Scott

first: Lachlan

last: Coin


title: Genome wide transcriptional profiling of HIV positive and negative children with active tuberculosis, latent TB infection and other diseases from South Africa and Malawi

first: Michael

last: Levin

summary:
The study aimed to define transcriptional signatures for detection of active TB (TB) compared to latent TB infection (LTBI) as well as to other diseases (OD) with similar clinical phenotypes in patients with and without HIV in two African paediatric populations.
Transcriptional signatures were identified that distinguished active TB from LTBI, and active TB from other diseases.

overall_design: Children were recruited from Cape Town, South Africa (n=157) and Blantyre, Malawi (n=177) who were either HIV+  or HIV - with either active TB, LTBI or OD. Blood was collected into PAX gene tubes (PreAnalytiX). Total RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). Labeled cRNA was hybridized to Illumina Human HT-12 Beadchips. Data were analysed in R.

first: Suzanne

last: Anderson

first: Amelia

last: Crampin

first: Hazel

last: Dockrell

first: Brian

last: Eley

first: Neil

last: French

last: Heyderman

middle: L

first: Myrsini

last: Kaforou

first: Florian

last: Kern

first: Paul

last: Langford

first: Mike

last: Wilkinson

first: Victoria

last: Wright


title: Temporal gene regulation of human hepatocellular carcinoma HepG2 cells treated with obacunone

status: Public on Apr 29 2014

city: Seoul

first: Jong Min

last: Kim

address: 209, Neungdong-ro, Gwangjin-gu

department: Bioscience and Biotechnology

institute: Sejong University

summary: Obacunone treatment slightly changes gene expression of cholesterol metabolism-associated genes in HepG2 cells

overall_design: Total RNA obtained from HepG2 cells treated with 100 uM obacunone for 0.5, 1, 3, 6, or 12 h was compared to that of vehicle control cells.

first: Jong

last: Lee


title: Temporal gene regulation of human keratinocyte HaCaT cells treated with obacunone

summary: Obacunone treatment upregulates gene expression of cholesterol metabolism-associated genes in HaCaT cells

overall_design: Total RNA obtained from HaCaT cells treated with 100 uM obacunone for 0.5, 1, 3, 6, or 12 h was compared to that of vehicle control cells.


title: Whole blood gene expression profiling for coronary  in-stent restenosis: A Indian pilot case study.

city: Chandigarh

first: Dr. Yashpaul

last: Sharma

state: Chandigarh

department: Dept of Cardiology

institute: PGIMER, Chandigarh

summary:
Percutaneous coronary intervention (PCI) with stent placement is a standard treatment for coronary artery disease (CAD). Despite all medical advances, restenosis remains a challenging clinical problem. However, the molecular and biochemical pathways of restenotic process are not fully understood yet. Furthermore, as restenosis is assumed to be a multigenetic process and genetic predisposition is considered an important risk factor, analysis of the genome-wide gene expression is recommended for better insight of the phenomenon.
We used microarray technology to monitor thousands of genes expression simultaneously. The whole genome expression will be analyzed with this technique to identify cluster of up-regulated and down-regulated genes which may be involved in this complex pathological condition.

overall_design: Coronary restenosis after percutaneous coronary intervention remains a challenging problem, despite all medical advances. Molecular and biochemical pathways of restenotic process are not fully understood yet. Furthermore, as restenosis is assumed to be a multigenetic process. We used microarray technology to monitor thousands of genes expression simultaneously in restenosis postive group with reference restenosis negative group, which will unravel potentially modifiable pathways, possible targets and biomarkers for coronary restenosis.

first: YASHPAUL

last: SHARMA

first: Rakesh

last: Patyar

first: Ashsih

last: Trivedi

first: Sandeep

last: Kumar


title: Gene expression profiles of human keratinocytes and hepatocytes treated with obacunone

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


title: Gene expression profiling of CD34/CD38 sorted CML cells

status: Public on Apr 17 2014

city: Vienna

first: Martin

last: Bilban

country: Austria

institute: Medical University of Vienna

summary:
BACKGROUND: BCR-ABL1+ chronic myeloid leukemia (CML) is characterized by abnormal production of leukemic stem (LSC) and progenitor cells and their spread from the bone marrow into the blood resulting in extramedullary myeloproliferation. So far, little is known about specific markers and functions of LSC in CML.
METHODS: We examined the phenotype and function of CD34+/CD38─/Lin─ CML LSC by a multi-parameter screen approach employing antibody-phenotyping, mRNA expression profiling, and functional studies, including LSC repopulation experiments in irradiated NOD-SCID-IL-2Rgamma-/- (NSG) mice, followed by marker-validation using diverse control-cohorts and follow-up samples of CML patients treated with imatinib.
RESULTS: Of all LSC markers examined, dipeptidylpeptidase IV (DPPIV=CD26) was identified as specific and functionally relevant surface marker-enzyme on CD34+/CD38─ CML LSC. CD26 was not detected on normal CD34+/CD38─ stem cells or LSC in other hematopoietic malignancies. The percentage of CD26+ CML LSC decreased to undetectable levels during successful treatment with imatinib in all patients (p<0.001). Whereas the sorted CD26─ stem cells obtained from CML patients engrafted irradiated NSG mice with multilineage BCR-ABL1-negative hematopoiesis, CD26+ LSC engrafted NSG mice with BCR-ABL1+ cells. Functionally, CD26 was identified as target-enzyme disrupting the SDF-1alpha-CXCR4-axis by cleaving SDF-1alpha a chemotaxin for CXCR4+ stem cells. Whereas CD26 was found to inhibit SDF-1alpha-induced migration, CD26-targeting gliptins reverted this effect and blocked the mobilization of CML LSC in a stroma co-culture assay.
CONCLUSIONS: CD26 is a robust biomarker of LSC and a useful tool for their quantification and isolation in patients with BCR/ABL1+ CML. Moreover, CD26 expression may explain the extramedullary spread of LSC in CML.

overall_design: To define specific mRNA expression patterns and to identify specific LSC markers in CML LSC, gene array analyses were performed. RNA was isolated from sorted CD34+/CD45+/CD38─ CML LSC, CD34+/CD45+/CD38+ CML progenitor cells, CML MNC, sorted CD34+/CD38─ cord blood (CB) SC, CB-derived CD34+/CD38+ progenitor cells, and CB MNC. Total RNA was extracted from sorted cells using RNeasy Micro-Kit (Qiagen) and used (100 ng total RNA) for Gene Chip analyses. Preparation of terminal-labeled cRNA, hybridization to genome-wide human PrimeView GeneChips (Affymetrix, Santa Clara, CA, USA) and scanning of arrays were carried out according to the manufacturer's protocols (https://www.affymetrix.com). Robust Multichip Average (RMA) signal extraction and normalization were performed according to http://www.bioconductor.org/ as described.18 Differences in mRNA expression levels (from multiple paired samples) were calculated as mRNA ratio of i) CML LSC versus CB SC, ii) CML LSC versus CD34+/CD38+ CML progenitors, and normal cord blood SC versus cord blood progenitors. To calculate differential gene expression between individual sample groups where appropriate, we performed a statistical comparison using the LIMMA package as described previously. Briefly, LIMMA estimates the fold change between predefined sample groups by fitting a linear model and using an empirical Bayes method to moderate the standard errors of the estimated log-fold changes for each probe set.

first: Peter

last: Valent


title: Sorted Bulk and KK10-specific CD8+ T cells from HLA-B*2705 HIV elite controllers before and after KK10 peptide stimulation

status: Public on Apr 23 2014

city: Cambridge

first: Gaurav

middle: Das

last: Gaiha

address: 400 Technolology Square

department: Ragon Institute

institute: Massachusetts General Hospital

summary:
CD8+ T cells from HLA-B*2705 HIV+ elite controllers
Hi and Lo samples are CD8+ T cells bound by an HLA-B*2705 tetramer specific for the Gag p24 peptide KK10

overall_design: PBMCs were incubated in the presence and absence of KK10 peptide for 6 days, and CD8+ and KK10-specific CD8+ T cell were sorted by flow cytometry


title: Gene expression profiling study of VCaP xenograft tumors collected from intact and castrated athymic nude mice

status: Public on Apr 21 2014

city: Turku

first: Matias

last: Knuuttila

address: Kiinamyllynkatu 10

department: Department of Physiology

country: Finland

institute: University of Turku

summary: The purpose of the study was to characterize the properties of human prostate cancer VCaP tumors pre- and post-castration. The main focus was on androgen signaling, androgen metabolism and steroid synthesis. Results provide valuable information about how castration-resistant tumors (CRPC) are able grow in absence of gonadal androgens.

overall_design: One million VCaP cells were inoculated orthotopically into the dorsolateral prostate of nude mice through an abdominal incision. Tumor growth was followed by serum PSA measurements.  Intact mice were sacrificed and tumors were collected 3-14 weeks after inoculation (Intact 1, Intact 2). Mice in the remaining three groups (GNX, CRPC 1, CRPC 2) were castrated by removing the testes. Mice were sacrificed and tumors were collected one day after castration (GNX) or 3-14 weeks after castration (CRPC 1, CRPC 2) in castration-resistant stage.  4 tumors were selected from each study group, totally 20 tumors.

first: Emrah

last: Yatkin

first: Jenny

last: Kallio

first: Saija

last: Savolainen

first: Teemu

last: Laajala

first: Tero

last: Aittokallio

first: Riikka

last: Oksala

first: Merja

last: Häkkinen

first: Pekka

last: Keski-Rahkonen

first: Seppo

last: Auriola

first: Matti

last: Poutanen

first: Sari

last: Mäkelä


title: Breast Cancer Gene Expression Data from Hamburg Series

city: Frankfurt

first: Thomas

last: Karn

address: Theodor-Stern-Kai 7

summary: Gene expression profiling of surgical biopsies from 74 breast cancer patients of different subtypes from Hamburg dataset.

overall_design: Fresh frozen pre-treatment surgical biopsy samples from breast cancer patients were analyzed on Affymetrix HGU133A.

first: Volkmar

last: Müller


title: Induced pluripotent stem cell derived neuronal lineages as human cellular models for Herpes Simplex Virus, type 1 (HSV-1) infections

city: Pittsburgh

first: Leonardo

last: D'Aiuto


title: Hes6 expression is controlled by c-Myc and the AR to promote E2F1 activity and poor outcome in castrate-resistant prostate cancer (LNCaP)

first: Roslin

last: Russell

address: Robinson Way

institute: Cambridge Research Institute, Cancer Research UK

summary: Hes6 is a transcription co-factor that is associated with stem cell characteristics in neural tissue, but its role in cancer remains uncertain. Here we show that Hes6 is controlled by c-Myc and the AR and can drive castration resistance in xenografts of the androgen-dependent LNCaP prostate cancer cell line model. Hes6 activates a cell cycle enhancing transcriptional network that maintains tumour growth in the absence of circulating androgen but with maintained nuclear AR. We demonstrate interaction between E2F1, the AR and Hes6 and show the co-dependency of these factors in the castration-resistant setting. In the clinical setting, we have discovered a Hes6-associated signature that predicts poor outcome in prostate cancer, which could be pharmacologically targeted.

overall_design: LNCaP cells with stable Hes6-overexpression and empty vector controls were grown in RPMI & 10% FBS for 3 days before lysis and extraction of RNA.

first: Alastair

last: Lamb

first: Antonio

last: Ramos-Montoya


title: Hes6 expression is controlled by c-Myc and the AR to promote E2F1 activity and poor outcome in castrate-resistant prostate cancer (xenografts)

overall_design: LNCaP-LM (luciferase expressing) cells with stable Hes6-overexpression and empty vector controls injected dorso-subcutaneously into NOD SCID gamma (NSG) mice. Mice were castrated when average graft size reached 100mm3 . Mice were culled after 12 weeks growth and grafts harvested.


title: Sorted Bulk and KK10-specific CD8+ T cells from HLA-B*2705 HIV chronic progressors before and after KK10 peptide stimulation

status: Public on Apr 15 2014

first: Gaurav

last: Gaiha

summary:
CD8+ T cells from HLA-B*2705 HIV+ chronic progressors
Hi and Lo samples are CD8+ T cells bound by an HLA-B*2705 tetramer specific for the Gag p24 peptide KK10


title: Genome wide expression profiling of 30 urothelial cancer cells

first: Tiewei

last: Cheng

state: United States

address: 7777 Knight Rd.

institute: UT MD Anderson Cancer Center

summary: Expression profiling of a panel of urothelial cancer cells. The goal of the study is to exam the genome wide expression profile in each of the 30 urothelial cancer cells tested in our laboratory

overall_design: Each of the 30 cell lines was DNA fingerprinted to confirm its real identity. Total RNA was obtained from each cell line and subjected to illumina expression profiling microarray

first: Woonyoung

last: Choi

first: I-Ling

last: Lee

first: David

last: McConkey


title: Enrichment of inflammatory bowel disease and colorectal cancer risk variants in colon expression quantitative trait loci

city: Chicago

first: Sonia

last: Kupfer

state: IL

address: 900 East 57th Street, MB#9

department: Department of Medicine

institute: University of Chicago

summary: Genome wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with diseases of the colon including inflammatory bowel diseases (IBD) and colorectal cancer (CRC). However, the functional role of many of these SNPs is largely unknown and tissue-specific resources are lacking. Expression quantitative trait loci (eQTL) mapping identifies target genes of disease-associated SNPs. Here, we comprehensively map eQTLs in the human colon, assess their relevance for GWAS of colonic diseases and provide functional characterization.

overall_design: Subjects included 40 healthy African American individuals who had undergone colonoscopy at the University of Illinois Chicago for screening purposes. Distal colonic biopsies were obtained in all subjects at 20 cm from the anal verge at the recto-sigmoid junction and were immediately dispensed in RNAlater. Total mRNA was extracted from manually ground tissue with the Promega Maxwell 16 Tissue LEV Total RNA Purification Kit for automated purification on the Maxwell 16 Instrument and mRNA analysis was performed on Illumina HumanHT-12v4 Expression BeadChip arrays. Genomic DNA was obtained from whole-blood samples from the same individuals and genotyped using the Affymetrix Axiom Genome-wide Pan-African array. Cis- and trans-eQTL analyses were performed on the dataset of 8.4 million imputed SNPs and 16,252 expression probes corresponding to 12,363 unique autosomal genes in 40 subjects. Associations between SNPs and gene expression levels were examined with Matrix eQTL using linear regression. False discovery rate calculations were performed separately for cis- and trans-eQTLs.

first: Imge

last: Hulur

first: Eric

last: Gamazon

first: Andrew

last: Skol

first: Rosa

last: Xicola

first: Xavier

last: Llor

first: Kenan

last: Onel

first: Nathan

last: Ellis


title: CD4+ T cell gene expression in virologically suppressed HIV-infected patients during Maraviroc intensification therapy.

status: Public on Apr 16 2014

city: La Jolla

first: Nadejda

middle: S.

last: Beliakova-Bethell

address: 9500 Gilman Dr.

department: Medicine

institute: University of California, San Diego

summary:
Analysis of CD4+ T cell gene expression changes after 4 and 24 weeks of Maraviroc administration relative to baseline in 25 immunodiscordant patients with viral suppression.
Maraviroc elicited very modest changes in CD4+ T cell transcriptome.

overall_design: The goal of this study was to identify genes with a potential role in Maraviroc-induced CD4+ T cell recovery in immunodiscordant patients. The study measured gene expression in CD4+ T cells isolated from the whole blood of HIV-infected patients before and at two time points after addition of Maraviroc to the baseline antiretroviral therapy. Thirty two patients were recruited from 3 sites, University of California, San Diego (UCSD), University of California, Los Angeles (UCLA) and University of Southern California (USC), and peripheral blood samples were obtained at 3 visits, week 0 (baseline), week 4 and week 24 after initiation of Maraviroc therapy. Because of poor RNA quality and outliers on the microarrays, 7 patients were excluded from the study. Non-outlier week 0 and week 24 arrays from one of the patients (Patient ID 01-005) were used for array data normalization and processing, but were not included in the time course analysis since the week 4 sample was not available.

first: Christopher

last: Woelk

first: Michael

last: Dubé


title: Antiproliferative effects and mechanisms of liver X receptor ligands in pancreatic ductal adenocarcinoma cells

city: Houston

first: Nicholes

last: Candelaria

address: 3605 Cullen Boulevard SERC (Building 545), Rm 3023

department: Cellular and Molecular Biology

institute: University of Houston

summary: This microarray is an analysis of differentially expressed genes in three pancreatic ductal adenocarcinoma cell lines treated with LXR-agonist GW 3965. We first report that GW 3965 has antiproliferative effects in three PDAC cell lines. This microarray was designed to identify key mechanisms of the antiproliferative effect of LXR agonists within pancreatic cancer cell lines.

overall_design: Total RNA obtained from BxPC-3, MIA-PaCa-2, and PANC-1 pancreatic cancer cells grown in culture treated GW 3965 or ethanol (vehicle control) for 72 hours.

first: Chin-Yo

last: Lin


title: Pemetrexed and gemcitabine as combination therapy for the treatment of Group3 medulloblastoma

city: Memphis

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: We devised a high-throughput, cell-based assay to identify novel therapeutic compounds to treat Group3 medulloblastoma (G3 MB).  Mouse G3 MBs, grown as neurospheres, were screened against a library of approximately 7,000 compounds including FDA-approved drugs.  We identified two FDA-approved drugs, pemetrexed and gemcitabine that preferentially inhibited tumor proliferation in vitro compared to control neurospheres, and substantially inhibited tumor proliferation in vivo.  When combined, the two drugs significantly increased survival

overall_design: P7 Trp53-/-, Cdkn2c-/- neurospheres and MYC mouse cells were compared treated and untreated with drugs pemetrexed+gemcitabine

first: Marie

last: Morfouace

first: Anang

last: Shelat

first: Megan

last: Jacus

first: Burgess

middle: B

last: Freeman III

last: Turner

first: Sarah

last: Robinson

first: Frederique

last: Zindy

last: Wang

first: Laure

last: Bihannic

first: Stephanie

last: Puget

first: Olivier

last: Ayrault

first: Giles

first: Xiao-Nan

last: Li

first: Kip

last: Guy

first: Clinton

last: Stewart

first: Amar

last: Gajjar

first: Martine

middle: F

last: Roussel


title: Risk of T1D progression in islet autoantibody positive children can be further stratified using expression patterns of multiple genes implicated in peripheral blood lymphocyte activation and function

status: Public on Apr 10 2014

city: Augusta

first: Jin-Xiong

last: She

state: GA

department: Center for Biotechnology and Genomic Medicine

institute: Medical College of Georgia

summary: To identify genes with expression levels that are associated with T1D progression from AbP (islet autoantibody positive),   global gene expression changes were analyzed in AbP subjects with different T1D progression rate.

overall_design: Total RNA were obtained from peripheral blood mononuclear cells (PBMC) of total 36 AbP subjects with different T1D progression rate.   Microarray was carried out to analyze gene expression and Kaplan-Meier survival analysis and log-rank test were used to compare differences in diabetes-free survival between groups classified based on single gene expression.

first: Yulan

last: Jin

first: Ashok

last: Sharma

first: Shan

last: Bai

first: Colleen

last: Carey

first: Haitao

last: Liu

first: Diane

last: Hopkins

first: Kathy

last: Barriga

first: Marian

last: Rewers


title: PEA15 regulates the DNA damage induced cell cycle checkpoint and oncogene-directed transformation

status: Public on Apr 07 2014

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

summary: Regulation of the DNA damage response and cell cycle progression is critical for maintaining genome integrity. Here we report that in response to DNA damage, COPS5 deubiquitinates and stabilizes PEA15 in an ATM kinase-dependent manner. PEA15 expression oscillates throughout the cell cycle, and the loss of PEA15 accelerates cell cycle progression by activating CDK6 expression via the c-JUN transcription factor. Cells lacking PEA15 exhibit a DNA damage-induced G2/M checkpoint defect due to increased CDC25C activity and consequentially higher CDK1/Cyclin B activity and accordingly have an increased rate of spontaneous mutagenesis. We find that oncogenic RAS inhibits PEA15 expression and ectopic PEA15 expression blocks RAS-mediated transformation, which can be partially rescued by ectopic expression of CDK6. Finally, we show that PEA15 expression is down regulated in colon, breast and lung cancer samples. Collectively, our results demonstrate that tumor suppressor PEA15 is a regulator of genome integrity and is an integral component of the DNA damage response pathway that regulates cell cycle progression, the DNA-damage-induced G2/M checkpoint and cellular transformation.

overall_design: HCT116 cells stably expressing a non-silencing shRNA or two individual shRNAs against PEA15 were used to prepare the total RNA, which was then used to analyze for gene expression using Illumina expression array.

first: Arvindhan

last: Nagarajan

first: Shaillay

last: Dogra

first: Alex

middle: Y

first: Michael

last: Green


title: Genome-wide analysis of EGFR inhibitor erlotinib treatment in Head and neck, squamous cell carcinoma's FADU, SQ20B and Cal 27

status: Public on Apr 08 2014

city: Iowa City

first: Thomas

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

summary: Chronic inflammation plays a significant role in tumor promotion, migration and invasion. Using microarray analysis, we observed a profound increase in genes involved in pro-inflammatory pathways in epidermal growth factor receptor inhibitor (EGFRI)-treated head and neck squamous cell carcinoma (HNSCC) cell lines compared to their respective vehicle-treated cell lines. We hypothesized that the efficacy of EGFRIs may be offset by the pro-inflammatory response that these drugs produce in HNSCC tumor cells. We found that clinical EGFRIs such as erlotinib, cetuximab, lapatinib and panitumumab induced the secretion of pro-inflammatory cytokines such as IL-2, IL-4, IL-6, IL-8, GM-CSF, TNFα and IFNγ. Focusing on IL-6, we found that erlotinib induced a time-dependent increase in IL-6 mRNA and protein expression and exogenous IL-6 was able to protect HNSCC cells from erlotinib-induced cytotoxicity. Conversely, an IL-6 receptor antagonist tocilizumab, sensitized HNSCC cells to erlotinib in vitro and in vivo. Inhibitors of NFκB, p38 and JNK suppressed erlotinib-induced IL-6 expression, suggesting an important role of NFκB and MAPK pathways in IL-6 expression. Furthermore, knockdown of NADPH oxidase 4 (NOX4) suppressed erlotinib-induced pro-inflammatory cytokines expression. Taken together, these results suggest that clinical EGFRIs induce the expression of pro-inflammatory cytokines via NOX4. Therefore, the anti-tumor activity of EGFRIs may be partially reduced by activation of NOX4-mediated pro-inflammatory pathways in HNSCC.

overall_design: Total RNA was isolated from Head and Neck Squamous Cell Carcinoma cell lines FADU, SQ20B and Cal 27 subjected to 48 hours of 0.01% DMSO or 5uM EGFR inhibitor, erlotinib treatment.

first: Andrean

last: Simons

first: Laurie

last: Love-Homan

first: Elise

middle: V

last: Fletcher

first: Arya

last: Sobhakumari

first: Charlotte

last: Feddersen

first: Apollina

last: Goel


title: Role of TCR:peptide/MHC Class I Affinity in Directing Different Maturation Phenotypes of Dominant and Subdominant Epitope-Specific CD8+ T Cells in Mamu-A*01+ Rhesus Monkeys

status: Public on Apr 24 2014

city: Boston

first: Hsun-Hsien

last: Chang

address: 300 Longwood Ave

department: Children's Hospital Informatics Department

institute: Harvard Medical School

summary: CD8+ T cells that bind different regions of proteins derived from a virus are often present at different frequencies. It is thought that those virus-specific CD8+ T cells that are present at the highest frequency are predominantly responsible for control of viral infections. While the number of virus-specific CD8+ T cells is undoubtedly important, the functionality of these cells may also play a role in their anti-viral capacity. It was not known if virus-specific CD8+ T cells present at high frequencies are more functionally effective against viral infection than those present at low frequencies. In this study, we characterized the functional differences between the SIV-specific cells present at high frequencies to those present at low frequencies in the blood of rhesus monkeys infected with simian immunodeficiency virus (SIV). We found that the high-and low-frequency SIV-specific cells had different functional capacities both during acute and chronic SIV infection. We also found that the strength with which a cell interacts with the proteins derived from the virus may contribute to the functional differences between the high- and low-frequency cells. These findings further our understanding of anti-viral responses and may inform HIV vaccine design.

overall_design: Peripheral blood was collected on days 14, 21, 28, 35, 42, 56, 70, and and 210 after inoculation with SIVmac251. Plasma viral RNA from these samples was measured using an ultra-sensitive branched DNA amplification assay (Siemens Diagnostics, Berkeley, CA). PBMC were stained with p11C and p54AS tetramers and CD3 and CD8 antibodies at 4°C. Tetramer-positive single CD3+CD8+ lymphocytes were sorted to greather than 95% purity into RNAprotect (Qiagen) at 4°C. RNA was isolated using a Trizol (Invitrogen) extraction protocol. Briefly, 0.8 ml of Trizol were added to the cell pellet and incubated for 5 minutes at room temperature and 0.16 ml of chloroform were added, shaken vigorously by hand for 15 seconds, incubated at room temperature for 2-3 minutes and centrifuged at 13,000 rpm for 15 minutes at 4ºC. The colorless upper aqueous phase was carefully collected and transferred to a new tube containing 2 ?l of linear acrylamide for mixing. An equal volume of isopropyl alcohol was then added and mixed. The mixture was incubated at room temperature for 10 minutes and centrifuged at 13,000 rpm for 10 minutes at 4ºC. The supernatant was collected and the RNA was washed with 1 ml of 70% ethanol and centrifuged at 10,500 rpm for 5 minutes at 4ºC. The supernatant was completely removed and the RNA pellet was allowed to air-dry. The RNA was then resuspended in RNase-free water and stored at -80ºC. RNA integrity was tested using an Agilent Bioanalyzer. RNA was then amplified using the TargetAmp 2-Round Biotin-aRNA Amplification Kit 3.0 (Epicentre Biotechnologies) according the manufacturer’s instructions. Amplified biotinylated antisense-RNA (aRNA) was resuspended in RNase-free water and stored at -80ºC. Nanodrop ND-1000 was used to determine the biotinylatedaRNA concentration and an Agilent Bioanalyzer was used to determine its integrity.Amplified aRNA was hybridized to Illumina Human HT-12 Expression BeadChips according to the manufacturer instructions and was stained with Streptavidin Cy3 for detection (Illumina, San Diego, CA, USA).

first: Letvin

last: Norman


title: Initiation of an inflammatory response in resident intestinal lamina propria cells -use of a human organ culture model

status: Public on Apr 03 2014

city: Heidelberg

first: Judith

last: Gras

address: INF 305

institute: University Hospital Heidelberg

summary: Resident human lamina propria immune cells serve as powerful effectors in host  defense. Molecular events associated with the initiation of an intestinal inflammatory  response in these cells are largely unknown. Here, we aimed to characterize  phenotypic and functional changes induced in these cells at the onset of intestinal  inflammation using a human intestinal organ culture model.  In this model, healthy human colonic mucosa was depleted of epithelial cells by EDTA  treatment. Following loss of the epithelial layer, expression of the inflammatory  mediators IL-1β, IL-6, IL-8, IL-23p19, TNF-α, CXCL2 and the surface receptors CD14,  TLR2, CD86, CD54 was rapidly induced in resident lamina propria cells in situ as  determined by qRT-PCR and immunohistology. Gene microarray analysis of lamina  propria cells obtained by laser-capture microdissection provided an overview of global  changes in gene expression occurring during the initiation of an intestinal inflammatory  response in these cells. Bioinformatic analysis gave insight into signalling pathways  mediating this inflammatory response. Furthermore, comparison with published  microarray datasets of inflamed mucosa in vivo (ulcerative colitis) revealed a significant  overlap of differentially regulated genes underlining the in vivo relevance of the organ  culture model.   The organ culture model characterized may be useful to study molecular mechanisms  underlying the initiation of an intestinal inflammatory response in normal mucosa as  well as potential alterations of this response in inflammatory bowel disease.

overall_design: Gut specimens were derived from individuals undergoing resection for localized colon cancer. Microscopically normal colonic mucosa was dissected from the surgical specimen near the resection margin and immediately subjected to the experimental procedures.  After extensive washing, healthy human colonic mucosa was depleted of epithelial cells by EDTA  treatment.   Samples were collected prior to culturing and washing (control, t = 0 h, total mucosa, TM) as well as after loss of the epithelial layer (t = 5 h, mucosa after loss of epithelial layer, LEL-M) and snap frozen in liquid nitrogen. Lamina Propria (LP) was subsequently isolated via Laser Capture Microdissection (LMD) followed by RNA isolation. Microarray analysis of TM-LP (control) and LEL-LP samples was performed using the WG-DASL Human HT_12 V4 Expression BeadChip Assay from Illumina employing a minimum of 200 ng total RNA per sample. Four replicates from individual experiments were measured for each time point.

first: Jutta

last: Schröder-Braunstein


title: Modular repertoire analyses identify dynamic type I and type II interferon transcriptional signatures in adult SLE patients

status: Public on Apr 01 2014

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

summary: Gene expression profiling (compared to healthy controls) to identify patients with active SLE disease and patients with quiescent disease

overall_design: 157 “SLE” and 20 “Healthy controls of SLE were followed up for up to 3 years. Clinical assessment, current treatment, laboratory results and SLEDAI score were collected at each visit (V1, V2...). SLE patients are compared to control groups.

first: Laurent

last: Chiche

first: Noemie

last: Jourde-Chiche


title: Microarray analysis of human pre-eclamptic placenta

city: Amsterdam

first: Remco

last: Keijser

address: Meibergdreef 9

department: Reproductive Biology Laboratory

institute: Amsterdam UMC

summary: RNA was extracted from placentas selected based on normotensive pregnancy with low GBA messenger RNA expression and hypertensive pregnancy with relatively high expression of GBA messenger RNA.

overall_design: Total RNA was extracted from placental tissue biopsies stored in RNALater within 2 hours after delivery.

first: R

first: G

last: Afink

first: C

last: Ris-Stalpers


title: The enzymatic activities of CD38 enhance CLL growth and trafficking: implications for therapeutic targeting

city: Turin

first: SILVIA

last: DEAGLIO

address: Via Nizza 52

department: Medical Sciences

country: Italy

institute: University of Torino & Human Genetics Foundation

summary: The ecto-enzyme CD38 is a marker of unfavorable prognosis for chronic lymphocytic leukemia (CLL) patients and an indicator of activation and proliferation of leukemic cells. Here we show that CD38 is enzymatically active in primary CLL cells and that its forced expression increases disease aggressiveness in a xenograft model. The effect is completely lost when using an enzyme deficient version of CD38 with a single amino-acid mutation. Through the enzymatic conversion of NAD, CD38 increases cytoplasmic Ca2+ concentrations, positively influencing proliferation, chemotaxis, adhesion and matrix digestion. Inhibition of the enzymatic activities of CD38 using the flavonoid kuromanin blocks CLL homing. In a short-term xenograft model using primary cells, kuromanin treatment traps CLL cells in the blood, increasing responses to chemotherapy.

overall_design: Microarrays were performed comparing genetic signature derived from Mec-1 cell line variants, generated infecting cells by lentiviruses carrying the genetic material for a wild-type (CD38WT ) or an enzymatically-inactive form of CD38 (CD38M), grown in vitro and in vivo in NSG mice. GFP+ Mec-1 clones (Mec-1/GFP) were generated with the same protocol and used as control.

first: Tiziana

last: Vaisitti

first: Valentina

last: Audrito

first: Sara

last: Serra

first: Roberta

last: Buonincontri

first: Giovanna

last: Sociali

first: Elena

last: Mannino

first: Andrea

last: Pagnani

first: Antonella

last: Zucchetto

first: Erika

last: Tissino

first: Candida

last: Vitale

first: Marta

last: Coscia

first: Cesare

last: Usai

first: Chris

last: Pepper

first: Valter

last: Gattei

first: Santina

last: Bruzzone

first: Silvia

last: Deaglio


title: Genome-wide analysis of genes regulated by p44/wdr77 and PRMT5 in lung and prostate cancer cells

status: Public on Apr 14 2014

first: Wencai

last: Ma

address: 7455 Fannin st

institute: MD Anderson Cancer Center

summary: Analysis of gene expression in lung and prostate cancer cells expressing non-target (NT), p44/wdr77. or PRMT5 shRNA.  Results provide important information on how p44/wdr77 and PRMT5 control cellular proliferation.

overall_design: Total RNA obtained from cells expressing NT, p44/wdr77, or PRMT5 shRNA.

first: Zhongping

last: Gu

first: Zhiqiang

last: Wang

first: R

middle: E

last: Davis

first: Zhengxin


title: Pharmacological levels of Withaferin A (Withania somnifera) trigger clinically relevant anticancer effects specific to triple negative breast cancer cells

city: Edegem

first: Ken

last: Op de Beeck

address: Universiteitsplein 1

country: Belgium

institute: University Of Antwerp

summary: Withaferin A isolated from Withania somnifera (Ashwagandha) has recently become an attractive phytochemical under investigation in various preclinical studies for treatment of different cancer types. In the present study, a comparative pathway-based transcriptome analysis was applied in epithelial-like MCF-7 and triple negative mesenchymal MDA-MB-231 breast cancer cells exposed to concentrations of Withaferin A (WA) which can be detected systemically in in vivo experiments. Whereas WA revealed attenuation of multiple cancer hallmarks the withanolide analogue Withanone (WN), did not exert any of the described effects in these cells at comparable concentrations. Pathway enrichment analysis identified that WA targeted relevant cancer programs related to cell death, cell cycle and proliferation, which could functionally be validated flow cytometrically and by real-time proliferation xCELLigence assay. With respect to cell motility, invasion and metastasis processes, WA was found to strongly decrease MDA-MB-231 invasion as determined by single-cell collagen invasion assay. This is further supported by gene expression changes which demonstrate increased expression of a validated breast cancer metastasis suppressor gene (BRMS1) and concomitant decreased expression of extracellular matrix-degrading proteases (PLAU, PLAT, ADAM8), cell adhesion molecules (integrins, laminins) as well as pro-inflammatory mediators of the metastasis-promoting tumor microenvironment (TNFSF12, IL6, ANGPTL2, CSF1R). Subsequent in silico network analysis listed key node transcription factors regulating these processes (p53, E2F1, CDKN2A, NRF2) and revealed the role of chromatin modifying enzymes (p300, JARID1B) as central master switches, linking multiple anticancer activities of WA. Furthermore, hierarchical clustering analysis of 84 chromatin writer-reader-eraser enzymes revealed that WA treatment of invasive mesenchymal MDA-MB-231 cells reprogrammed their transcription levels more similarly towards the pattern observed in non-invasive MCF-7 cells. In conclusion, taking in account that sub-cytotoxic concentrations of WA target multiple metastatic effectors in therapy resistant triple negative breast cancer, WA based therapeutic strategies hold promise for further (pre)clinical development to defeat aggressive metastatic breast cancer.

overall_design: Total RNA from 2 different cell lines treated with WA, are compared to their untreated states

first: Katarzyna

last: Szarc vel Szic

first: Dariusz

last: Ratman

first: An

last: Wouters

first: Ilse

last: Beck

last: Declerck

first: Karen

last: Heyninck

first: Erik

last: Fransen

first: Marc

last: Bracke

first: Karolien

last: De Bosscher

first: Filip

last: Lardon

first: Guy

last: Van Camp

first: Wim

last: Vanden Berghe


title: Molecular pathways reflecting poor intrauterine growth are imprinted in Wharton’s jelly derived Mesenchymal Stem Cells [Set2]

status: Public on Mar 31 2014

city: Singapore

first: Dennis

address: 30 Medical Drive

country: Singapore

institute: Singapore Institute for Clinical Sciences

summary:
In order to identify gene-expression patterns in mesenchymal stem cells associated with different birth weights and intrauterine growth parameters,
we conducted comparative microarray gene expression experiments prior and post acute insulin stimulation

overall_design: Mesenchymal stem cells (MSC) were extracted from the Wharton's jelly of the umbilical cord of normal and SGA babies. The MSCs were expended in culture. The MSCs were subjected to acute insulin treatment for various time points. The RNA of these cells were collected for gene-expression study.

first: Walter

last: Stunkel


title: Molecular pathways reflecting poor intrauterine growth are imprinted in Wharton’s jelly derived Mesenchymal Stem Cells [set1]

overall_design: Samples were collected from umbilical cord derived mesenchymal stem cells (UC-MSC). 4 samples belong to SGA (Small for Gestational Age) and 4 samples belong to control group


title: Determination of genes affected by HERVH depletion

status: Public on Mar 30 2014

first: Xinyi

last: Lu

address: 60 Biopolis

institute: Genome Institute of Singpaore

summary: The unique cellular state of embryonic stem cells is maintained by pluripotency-associated transcription factors such as OCT4. The transcriptional regulatory circuitries between human and mouse pluripotent stem cells exhibit notable differences. Transposable elements have altered the pluripotency network by contributing new cis-regulatory elements to mammalian genomes. In our study, we found that the expression of HERVH is enriched in human embryonic stem cells (hESCs) and depletion of HERVH in hESCs induced differentiation. To confirm the differentiation phenotype and identify potential downstream target genes of HERVH, we conducted the microarray analysis on hESCs treated with control shRNA against Luciferase and shRNA against HERVH.

overall_design: Total RNA was extracted from cells treated with control shRNA or HERVH shRNA for 5 days. 3 replicates each.

first: Friedrich

last: Sachs

first: LeeAnn

last: Ramsay

first: Pierre-Étienne

last: Jacques

first: Jonathan

last: Göke

first: Guillaume

last: Bourque

first: Huck-Hui

last: Ng


title: Molecular pathways reflecting poor intrauterine growth are imprinted in Wharton’s jelly derived Mesenchymal Stem Cells [set3]

last: Wang


title: Finger-prick iPSCs Facilitate the Development of Stem cell banking

status: Public on Mar 28 2014

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

summary: Induced pluripotent stem cells (iPSCs) derived from somatic cells of patients can be a good model for studying human diseases and for future therapeutic regenerative medicine. Current initiatives to establish iPSC banking face challenges in recruiting large numbers of donors with diverse diseased, genetic and phenotypic representations. Here, we describe the derivation of transgene-free iPSCs from human finger-prick blood. Fingerprick samples collection can be performed “DIY (Do-it-yourself)” by donors and sent to the iPSC facility for reprogramming. We show that single drop volumes of finger-prick samples are sufficient for performing cellular reprogramming, DNA sequencing and blood serotyping in parallel. Our novel strategy will facilitate the development of large scale iPSC banking world-wide.

overall_design: Total RNA from PBMC, hES cells, or iPS cells from PBMC was labeled with biotin. Samples were hybridized to HumanHT-12v4 Beadchip (Illumina) according to manufacturer’s protocol.

first: Yuin-Han

last: Loh


title: Molecular pathways reflecting poor intrauterine growth are imprinted in Wharton's jelly derived Mesenchymal Stem Cells

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

overall_design: Refer to individual Series