title: Expression analysis of 24 endometrial stroma sarcoma

city: oslo

first: Francesca

last: Micci

address: Ullernchausseen 70

department: Institute for medical informatics

institute: Oslo Universitetssykehus

summary: The whole-gene expression profile of 24 endometrial stroma sarcol was used to identify genes that were deregulated in the tumors genome.

overall_design: The analysis was performed comparing the high-grade to the low-grade tumors.

first: Sverre

last: Heim


title: Gene expression profiling of HOS (human osteosarcoma) cells exposed to fluoride

status: Public on Jun 30 2016

city: Nagpur

first: Dr. saravana

last: devi

state: Maharashtra

department: Environmental Health Division

country: India

institute: CSIR-National Environmental Engineering Research Institute

summary: Though fluoride is considered an essential trace element, chronic exposure to fluoride is known to cause toxic effects. Chronic exposure of high concentration of fluoride may leads to fluorosis. To understand the molecular mechanism of fluoride induced toxicity gene expression profiling was performed on osteosarcoma cells (HOS). Cells were exposed to sub-lethal concentration of fluoride (8 ppm) for 30 days. Our result demonstrates that fluoride alters multiple biological pathways including bone development, osteoblast differentiation and apoptotic pathways.

overall_design: HOS cells grown in MEM were treated with fluoride and total RNA was isolated from cells after 30 days exposure. Three replicates per group were used for the experiment.

first: Deepa

last: Gandhi

first: S

middle: S

last: Devi

first: K

last: Krishnamurthi


title: Therapeutic targets of a new treatment for osteoarthritis composed by curcuminoids extract, hydrolyzed collagen and green tea extract

city: Liege

first: Fanny

last: Comblain

address: avenue Hippocrate 13, CHU Sart Tilman

country: Belgium

institute: University of Liege

summary: We have previously demonstrated that a mixture of curcuminoids extract, hydrolyzed collagen and green tea extract (COT) inhibited inflammatory and catabolic mediator’s synthesis by osteoarthritic (OA) human chondrocytes. The objectives of this study were to identify new targets of COT using genomic approaches. We compared gene expression profiles of chondrocytes treated with COT and/or with interleukin(IL)-1β. The proteins coded by the most important COT sensitive genes were then quantified by specific immunoassays.

overall_design: Cartilage specimens were obtained from 12 patients (10 women and 2 men; mean age 67 years old, range 54-76 years old) with knee OA. Primary human chondrocytes were cultured in monolayer until confluence and then incubated for 24 hours in the absence or in the presence of human IL-1β (10e-11M) and with or without COT, each compound at the concentration of 4 µg/ml. Microarray gene expression profiling between control, COT, IL-1β and COT IL-1β conditions was performed.

first: Yves

last: Henrotin


title: Mapping Variation in Cellular and Transcriptional Response to 1,25-dihydroxyvitamin D3 in Peripheral Blood Mononuclear Cells

status: Public on Jul 01 2016

city: Chicago

first: Silvia

last: Kariuki

state: IL

department: Human Genetics

country: USA

institute: University of Chicago

summary: This study characterizes the genetic basis of variation in the immunomodulatory effects of the active form of vitamin D, 1,25-dihydroxyvitamin D3 (1,25D). This was done by mapping  quantitative traits of 1,25D response both at the cellular and transcriptional level in peripheral blood mononuclear cells (PBMCs).

overall_design: Total RNA extraced from peripheral blood mononuclear cells from 85 healthy individuals of African-African ancestry treated with 1,25D or the vehicle control, ethanol, for 6 hours.

middle: N

first: Joseph

middle: C

last: Maranville

first: Shaneen

last: Baxter

first: Choongwon

last: Jeong

first: Shigeki

last: Nakagome

first: Cara

middle: L

last: Hrusch

first: David

middle: B

last: Witonsky

first: Anne

middle: I

last: Sperling

first: Anna

last: Di Rienzo


title: Plasmablast response to influenza vaccines

city: palo alto

first: weiqi

last: wang

state: ca

address: 1291 welch road

institute: stanford

summary:
To study the plasmablast response to influenza vaccines
We want to test and see that LAIV, TIV and ID TIV induced different plasmablast response

overall_design: We take peripheral plasmablast and test its response to influenza vaccines at day 7 after vaccination. This array data set is for day 0 (before vaccines)

first: Harry

last: Greenberg


title: Characterization of expression quantitative trait loci in extensively phenotyped pedigrees from Colombia and Costa Rica

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: The observation that variants regulating gene expression (expression quantitative trait loci, eQTL) are at a high frequency among SNPs associated with complex traits has made the genome-wide characterization of gene expression an important tool in genetic mapping studies of such traits. As part of a study to identify genetic loci contributing to bipolar disorder and a wide range of BP-related quantitative traits in members of 26 pedigrees from Costa Rica and Colombia, we measured gene expression in lymphoblastoid cell lines derived from 786 pedigree members. The study design enabled us to comprehensively reconstruct the genetic regulatory network in these families, provide estimates of heritability, identify eQTL, evaluate missing heritability for the eQTL, and quantify the number of different alleles contributing to any given locus.

overall_design:
Lymphoblastoid cell lines (LCLs) were established by in vitro infection of peripheral blood mononuclear cells with Epstein Barr virus, and RNA was extracted from these cell lines and its expression quantified using Illumina Human HT-12 v4.0 Expression BeadChips. Expression values were background corrected, quantile normalized, log2 transformed, and corrected for major known batch effects. The outcome of these procedures is what we refer to as ‘probe expression’ for all subsequent analyses. After quality control filters, the 34,030 probes included in the final set were uniquely aligned to hg19, contained no common SNPs (as defined in dbSNP 137 or 138), queried 24,385 unique genes, and their expression was detected in at least one individual.  For a detailed description of the processing steps used at each site and the RNA quantification, normalization, and quality control procedures, see the supplementary note.

Please note that charateristics FID, IID and DiagnosisBP1 represents family ID, individual ID and BP1 diagnosis (0= no BP1, 2= BP1), respectively.

first: C

last: Peterson

last: Service

first: A

middle: J

last: Jasinska

first: F

last: Gao

first: I

last: Zelaya

first: T

last: Teshiba

last: Bearden

first: V

last: Reus

first: G

last: Macaya

last: López-Jaramillo

first: M

last: Bogomolov

first: Y

last: Benjamini

first: E

last: Eskin

first: N

last: Freimer

last: Sabatti


title: Oncogenic EGFR Represses the TET1 DNA Demethylase to Induce Silencing of Tumor Suppressors in Cancer Cells

status: Public on Jun 23 2016

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: Oncogene-induced DNA methylation-mediated transcriptional silencing of tumor suppressors frequently occurs in cancer, but the mechanism and functional role of this silencing in oncogenesis is not fully understood. Here, we show that oncogenic epidermal growth factor receptor (EGFR) induces silencing of multiple unrelated tumor suppressors in lung adenocarcinomas and glioblastomas by inhibiting DNA demethylase TET oncogene family member 1 (TET1) via the C/EBPα transcription factor. After oncogenic EGFR inhibition, TET1 binds to tumor suppressor promoters and induces their re-expression via active DNA demethylation. Ectopic expression of TET1 potently inhibits lung and glioblastoma tumor growth, and TET1 knockdown confers resistance to EGFR inhibitors in lung cancer cells. Lung cancer samples exhibited reduced TET1 expression or TET1 cytoplasmic localization in a majority of cases. Collectively, these results identify a conserved pathway of oncogenic EGFR-induced DNA methylation-mediated transcriptional silencing of tumor suppressors, which may have therapeutic benefit for oncogenic EGFR-mediated lung cancers and glioblastomas.

overall_design: HCC827-Del (EGFR L747-S752) and HCC827-Del-TM (EGFR L747-S752/T790M) cell lines were treated with Decitibine (2.5 μM) and Vorinostat (1μM) or as a control cells that were treated with DMSO for 72 hrs. Expression profiling was performed using 3 biological replicates for each condition for a total of 12 samples analyzed.

first: Matteo

last: Forloni

first: Romi

last: Gupta

first: Shaillay

last: Dogra

first: Arvindhan

last: Nagarajan


title: Transcriptional profiling of shoots and roots in japonica and indica rice seedlings under salt stress and recovery stage

city: Taipei

first: Men-Chi

last: Chang

address: No. 1, Section 4, Roosevelt Road

department: Agronomy

country: Taiwan

institute: National Taiwan University

summary: Rice seedlings at 3-leaf stage were used for expression analysis in control and salt stressed (incloudling salt treatment for 3, 24hrs and recovery from salt stress for 24hrs) samples. Samples of shoots and roots from biological replicates of both genotypes were generated and the expression profiles were determined using Phalanx Rice OneArray＠ v1.

overall_design: Control and treated biological replicates of salt-tolerant cultivar TNG67 (japonica) and salt-sensitive cultivar TCN1 (indica) were analyzed

first: Yang

last: Yun-Wei

first: Chang

last: Men-Chi


title: miR-130b drives activation of a metastatic CDC42-PAK1-AP1 positive feedback loop in Ewing sarcoma by directly targeting Arhgap1

status: Public on Jun 21 2016

city: Houston

first: Jason

last: Yustein

state: Texas

address: 1102 Bates Street Suite 1025.07

department: Cancer Center Hemotology/Oncology

institute: Texas Children's Hospital

summary: Analysis of miR-130b regulated genes in TC71 Ewing Sarcoma cells. The hypothesis tested being that overexpression of miR-130b increases metastasis in Ewing Sarcoma.

overall_design: Total RNA obtained from Tc71 cells expressing a scramble control of miR-130b mimic after 48hrs.

first: Laura

last: Satterfield


title: Expression profile of PBMCs following decitabine treatment

city: bei jing

first: Jing

last: Nie

state: bei jing

address: 28 fuxing road

country: China

institute: PLA General Hospital

summary:
The epigenetic regulation, for example, DNA methylation, controls the development and differentiation of both tumor cells and immunocytes. Treatment with DNA demethylating agent (such as decitabine) has shown a dramatic clinical benefit in hematological malignancies and solid tumors.
However, the influence of epigenetic therapy on host immune system remains unclear.

overall_design: To investigate the effects of low-dose decitabine therapy on T cells, We collected whole blood samples from two solid tumor patients pre and post low-dose decitabine therapy, and detected the expression profiles of PBMCs.

first: Weidong

last: Han


title: A human pluripotent stem cell model of FSHD-affected skeletal muscles

city: Singapore

first: Kian Leong

last: LEE

state: Singapore

address: #07-21, 8 College Road

department: Duke-NUS Medical School

country: Singapore

institute: National University of Singapore (NUS)

summary: Facioscapulohumeral muscular dystrophy (FSHD) represents a majorunmet clinical need arising from the progressive weakness and atrophy of skeletal muscles. The dearth of adequate experimental models has severely hampered our understanding of the disease. To date, no treatment is available for FSHD. Human embryonic stem cells (hESCs) potentially represent a renewable source of skeletal muscle cells (SkMCs) and provide an alternative to invasive patient biopsies.Wedeveloped a scalable monolayer system to differentiate hESCs into mature SkMCs within 26 days, without cell sorting or genetic manipulation. Here we show that SkMCs derived from FSHD1-affected hESC lines exclusively express the FSHD pathogenic marker double homeobox 4 and exhibit some of the defects reported in FSHD. FSHD1 myotubes are thinner when compared with unaffected and Becker muscular dystrophy myotubes, and differentially regulate genes involved in cell cycle control, oxidative stress response and cell adhesion. This cellularmodelwill be a powerful tool for studying FSHDandwill ultimately assist in the development of effective treatments for muscular dystrophies.

overall_design: 21 samples consisting of skeletal muscle cells differentiated in triplicate experiments from 3 normal, 3 facioscapulohumeral muscular dystrophy (FSHD1) and 1 Becker Muscular Dystrophy (BMD) hESCs.

first: Leslie

last: Caron

first: Devaki

last: Kher

first: Kian

last: Lee

first: Robert

last: McKernan

first: Biljana

last: Dumevska

first: Alejandro

last: Hidalgo

first: Jia

last: Li

first: Henry

last: Yang

first: Heather

last: Main

first: Giulia

last: Ferri

first: Lisa

middle: M

last: Petek

first: Lorenz

last: Poellinger

first: Daniel

middle: G

last: Miller

first: Davide

last: Gabellini

first: Uli

last: Schmidt


title: Comprehensive Analysis of Recurrence-Associated Small Non-Coding RNAs in Esophageal Cancer  [clinical study, Illumina]

city: HOUSTON

first: Hyun-Sung

state: TX

address: One Baylor Plaza

department: Surgery

institute: BAYLOR COLLEGE OF MEDICINE

summary: Targeted cancer therapy for squamous cell carcinoma (SCC) has made little progress largely due to a lack of knowledge of the driving genomic alterations. Small non-coding RNAs (sncRNAs) as a potential biomarker and therapeutic target to SCC remain a challenge. We analyzed sncRNAs microarray in 108 fresh frozen specimens of esophageal squamous cell carcinoma (ESCC) as discovery set and assessed associations between sncRNAs and recurrence-free survival. SncRNA signature identified was externally validated in two independent cohorts. We investigated the functional consequences of sncRNA identified and its integrative analysis of complex cancer genomics. We identified 3 recurrence-associated sncRNAs (miR-223, miR-1269a and nc886) from discovery set and proved risk prediction model externally in high and low volume centers. We uncovered through in vitro experiment that nc886 was down-regulated by hypermethylation of its promoter region and influences splicing of pre-mRNAs with minor introns by regulating expression of minor spliceosomal small nuclear RNAs (snRNAs) such as RNU4atac. Integrative analysis from lung SCC data in The Cancer Genome Atlas revealed that patients with lower expression of nc886 had more genetic alterations of TP53, DNA damage response and cell cycle genes. nc886 inhibits minor splicing to suppress expression of certain oncogenes such as PARP1 and E2F family containing minor introns. We present risk prediction model with sncRNAs for ESCC. Among them, nc886 may contribute to complete minor splicing via regulation of minor spliceosomal snRNAs supporting the notion that aberrant alteration in minor splicing might be a key driver of ESCC.

overall_design:
Clinical study
ESCC tumor samples.

first: Ju-Seog


title: Comprehensive Analysis of Recurrence-Associated Small Non-Coding RNAs in Esophageal Cancer

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

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Transcriptional and functional characterization of dendritic cell differentiation induced by CD137 ligand reverse signaling in human monocytes

first: Kaibo

last: Duan

address: 8A Biomedical Grove, Immunos Building, Level 4

institute: Singapore Immunology Network

summary: The contribution of monocyte-derived dendritic cells (DC) to an immune response is essential for the elimination of pathogens. In vitro DC can be generated by treatment of monocytes with GM-CSF + IL-4 but it is unknown what stimuli induce the differentiation of monocytes to DC in vivo. CD137L-DC are human monocyte-derived DC that are generated by CD137 ligand (CD137L) signaling. Since CD137 is only expressed at sites of inflammation it would be a suitable signal for the induction of monocyte-derived DC. Here we report on gene expression analysis of CD137L-DC, immature and mature classical DC, monocytes and macrophages which indicates that CD137L-DC have a gene signature that is most similar to that of classical DC. Additionally, CD137L-DC signature genes are highly enriched in monocyte-derived DC which were isolated from sites of inflammation. Also cell surface marker expression and cytokine secretion of CD137L-DC are highly similar to that of inflammatory monocyte-derived DC. CD137L-DC express high levels of adhesion molecules, display strong attachment and employ the adhesion molecule ALCAM to stimulate T cell proliferation. This study identifies a physiological stimulus for the generation of monocyte-derived DC in vivo.

overall_design: A total of 30 expression profiles were obtained, on 6 APC subtypes from 5 different donors

first: Zulkarnain

last: Harfuddin

first: Bhushan

last: Dharmadhikari

first: Siew

last: Wong

first: Michael

last: Poidinger

first: Shaqireen

last: Kwajah

first: Herbert

last: Schwarz


title: Transcriptomic analysis of Human Umbilical Vein Endothelial Cells (HUVEC) in response to compound treatment

city: Athens

first: Olga

last: Papadodima

address: 48, Vasileos Konstantinou av.

country: Greece

institute: National Hellenic Research Foundation

summary: Human Umbilical Vein Endothelial Cells were treated with three newly synthesized compounds and DMSO as vehicle. Total RNA was isolated 6 and 24h after treatment and gene expression analysis was performed. Three independent experiments were performed, corresponding to rep1, rep2 and rep3. Experiment 1 (rep1) contained all substances at both time points tested. Experiment 2 (rep2) contained two of the compounds and control DMSO at both time points. Experiment 3 (rep3) contained the third compound and control DMSO at both time points.

overall_design: 18 samples were analyzed

first: Mary

last: Michailidou

first: Georgia

last: Kontogianni

first: Vassilis

last: Kotsikoris

first: Aristotelis

last: Chatziioannou

first: Heleni

last: Loutrari


title: Human pluripotent stem cells as a model of trophoblast differentiation in both normal development and disease

status: Public on Jun 16 2016

city: La Jolla

first: Mana

last: Parast

state: California

address: 9500 Gilman drive #0695

department: Pathology

institute: University of California San Diego

summary: Trophoblast is the primary epithelial cell type in the placenta, a transient organ required for proper fetal growth and development. We have identified a CDX2+/p63+ cytotrophoblast (CTB) subpopulation in the early post-implantation human placenta, which is significantly reduced later in gestation. CTB differentiate into different trophoblast subtypes, which are responsible for gas/nutrient exchange (syncytiotrophoblast/STB) and invasion and maternal vascular remodeling (extravillous trophoblast/EVT). Study of early human placental development is severely hampered by lack of a representative trophoblast stem cell (TSC) model, with the capacity for self-renewal and the ability to differentiate into both STB and EVT. We describe a reproducible protocol, using defined media containing BMP4, by which human embryonic stem cells (hESC) can be differentiated into CDX2+/p63+ CTB-like cells. These cells can be replated to further differentiate into STB- and EVT-like cells, based on marker expression, hormone secretion and invasive ability. Differentiation of hPSC-derived CTB in hypoxia leads to reduced hCG secretion and STB-associated gene expression, instead inducing EVT differentiation in a hypoxia-inducible factor-dependent manner.

overall_design: Human embryonic stem cells (hESC) (WA09/H9) were maintained on Geltrex-coated plates (BD Biosciences ) in StemPro (Thermo Fisher) + bFGF (12 ng/ml). Undifferentiated hESC (D-2) were switched to minimal media (EMIM (Erb et al., 2011) containing KO DMEM/F12 (Gibco), 1% Insulin-Transferrin-Selenium Mix (Sigma-Aldrich), 1% NEAA (Gibco), 2mM L-Glutamine (Corning), 0.1mM 2-mercaptoethanol (Gibo), and 2% BSA (Gemini Bio Products)) for 2 days then treated with BMP4 (StemRD, 10ng/ml) for 3 days in minimal media+BMP4 (D3). At D3, cells were replated onto Geltrex in Feeder Conditioned Media +BMP4 and cultured in normoxia (20% O2) or hypoxia (2% O2) for 2 days (D3+2) to assess the effect of hypoxia. Cells were infected with lentiviral shRNA for shScramble (control) or shARNT, the beta subunit of the Hypoxia Inducible Factor (HIF) complex to assess the effect of ARNT knockdown. Each sample includes biological triplicates.

first: Mariko

last: Horii

first: Yingchun

last: Li

first: Anna

middle: K

last: Wakeland

first: Francesca

last: Soncin

first: Matteo

last: Moretto-Zita

first: Donald

last: Pizzo

first: Katharine

last: Nelson

first: Karen

last: Sabatini

first: Louise

last: Laurent

first: Ying

last: Liu


title: Comprehensive Analysis of Recurrence-Associated Small Non-Coding RNAs in Esophageal Cancer [Illumina]

first: Hyun-Sung

last: Lee

summary: Targeted cancer therapy for squamous cell carcinoma (SCC) has made little progress largely due to a lack of knowledge of the driving genomic alterations. Small non-coding RNAs (sncRNAs) as a potential biomarker and therapeutic target to SCC remain a challenge.  We analyzed sncRNAs microarray in 108 fresh frozen specimens of esophageal squamous cell carcinoma (ESCC) as discovery set and assessed associations between sncRNAs and recurrence-free survival. SncRNA signature identified was externally validated in two independent cohorts. We investigated the functional consequences of sncRNA identified and its integrative analysis of complex cancer genomics.  We identified 3 recurrence-associated sncRNAs (miR-223, miR-1269a and nc886) from discovery set and proved risk prediction model externally in high and low volume centers. We uncovered through in vitro experiment that nc886 was down-regulated by hypermethylation of its promoter region and influences splicing of pre-mRNAs with minor introns by regulating expression of minor spliceosomal small nuclear RNAs (snRNAs) such as RNU4atac. Integrative analysis from lung SCC data in The Cancer Genome Atlas revealed that patients with lower expression of nc886 had more genetic alterations of TP53, DNA damage response and cell cycle genes. nc886 inhibits minor splicing to suppress expression of certain oncogenes such as PARP1 and E2F family containing minor introns.   We present risk prediction model with sncRNAs for ESCC. Among them, nc886 may contribute to complete minor splicing via regulation of minor spliceosomal snRNAs supporting the notion that aberrant alteration in minor splicing might be a key driver of ESCC.

overall_design:
Pre-clinical study
Analysis of Esophageal Squamous Cell Carcinoma cell lines knocked-down for nc886 and vault RNA VTRNA1-1 via antisense oligonucleotide (ASO)-targeting.

first: Yong-Sun

first: Ju-Seog


title: Microarray analysis of 20 gene knockdowns (including each three replicates and 12 controls) of EGFR mutated H1650 cell line in order to unravel AMPK signal transduction

status: Public on Jun 20 2016

city: Heidelberg

first: Ruprecht

last: Kuner

address: Im Neuenheimer Feld 460

department: Molecular Genetics

country: Germany

institute: German Cancer Research Center and National Center of Tumor Diseases

summary: Identification of a AMPK-relevant gene network hierarchy based on transcriptome data upon gene knockdown

overall_design: Knockdown of 20 genes in H1650 cell line following transcriptome analyses

first: Holger

last: Sültmann

last: Fröhlich

first: Helen

last: Hülsmann


title: Human iPSC-based model for Duchenne muscular dystrophy

city: Baltimore

first: Gabsang

state: MD

address: 733 North Broadway

department: School of Medicine

institute: The Johns Hopkins University

summary: We developed a novel somite-based step-wise strategy for the efficient derivation of functional human myocytes, suggesting that past failures were due to incomplete specification. Treatment with two small molecules inhibiting glycogen synthase kinase 3β (GSK-3β) and the Notch signaling pathway in undifferentiated hPSCs results in the formation of somite-like cells by Day 4 and, subsequently contractile myotubes in vitro around Day 25 with the ability to engraft and actively participate in muscle repair in vivo. Antibody-based purification can enrich homogenous myocyte populations exhibiting genuine myogenic molecular and cellular characteristics, including extraocular muscle-like features. Furthermore, hPSCs derived from patients with multiple neuromuscular diseases successfully give rise to patient-specific skeletal muscle cells bearing signature phenotypes.

overall_design: Human embryonic stem cell were differentiated to skeletal muscle and compared to non-differentiated cells in triplicate biological replicates. For the confirmation of differentiated cell's characteristics and the global mRNA profiles, We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process. Further more, we used microarrys for the comparing control and disease gene expression profiles, again in triplicate.

first: In-Young

last: Choi

first: Hotae

last: Lim


title: ERRalpha mediates metabolic adaptations that drive lapatinib resistance in breast cancer (gene expression profiles)

status: Public on Jun 15 2016

city: Montréal

first: Vincent

last: Giguère

state: QC

address: 1160 Pine Ave West, McIntyre Bldg Room 710

department: Goodman Cancer Centre

country: Canada

institute: McGill University

summary: Ablation of ERRalpha significantly delays ERBB2-induced mammary tumorigenesis and ERRalpha regulates genes of the ERBB2 amplicon. To further investigate the relationship between ERRalpha activity and RTK signaling, we depleted ERRalpha in SKBr3 cells upon serum starvation, EGF treatment or heregulin treatment.  Inhibition of ERBB2 signaling using the RTK inhibitor lapatinib impacts on ERRalpha stability. Since we have shown that the development of lapatinib-resistance restaures the expression of ERRalpha in breast cancer cells, we performed depletion of ERRalpha in SKBr3 cells that have developped resistance to lapatinib treatment in order to identify a potential reprogramming of ERRa transcriptional activity associated to lapatinib resistance,

overall_design: For the study of growth factor effec on ERRalpha activity,  total RNA was obtained from human SKBr3 breast cancer cells cultured in DMEM deprived of FBS (starved) for 24 hours and treated with PBS, EGF (100uM) or Heregulin (100uM) for an additional 24h. Cells were transfected with siRNA against ERRalpha or with siControl for 60 hours prior to harvesting. For the effect of ERRalpha in lapatinib resistance cells, parental SKBr3 cells (pSKBr3) and Lapatinib-resistant cells (LRSKBr3, maintained in 2uM lapatinib) were transfected with siControl (siC) or siERRalpha for 60 hours prior to harvesting and RNA extraction

last: Giguere


title: Expression data from ELK3 knocked down MDA-MB-231 cell line.

city: SungNam

first: Jae

middle: Yong

address: 335, Pangyo-ro

country: South Korea

institute: Cha Unniversity

summary:
Triple-negative breast cancer is a highly aggressive tumor subtype that lacks effective therapeutic targets. Here, we show that ELK3 is overexpressed in a subset of breast cancers, in particular basal-like and normal-like/claudin-low cell lines. Suppression of ELK3 in MDA-MB-231 cells led to transdifferentiation from an invasive mesenchymal phenotype to a non-invasive epithelial phenotype both in vitro and in vivo.
Suppression of ELK3 results in the extensive changes in genome expression profiles. Among these, GATA3, a master suppressor of metastasis, was epigenetically activated and we found that suppression of GATA3 led to the restoration of migration and invasion. These results suggest that the ELK3-GATA3 axis is a major pathway that promotes metastasis of MDA-MB-231 cells.

overall_design: Retrovirus expressing shRNA of ELK3 was transduced into MDA-MB-231 cell line and stable cell line of which ELK3 is suppressed more than 50% was selected by the drug selection (Puromycin).

first: Kyung-Soon

last: Park

first: Kwang-Soo

last: Kim


title: Characterization of aldehyde dehydrogenase 1 high ovarian cancer cells: Towards targeted stem cell therapy [SKOV3]

status: Public on Jun 07 2016

first: Richard

last: Jones

address: 1650 Orleans St.

institute: Johns Hopkins University School of Medicine

summary: Objective: The cancer stem cell (CSC) paradigm hypothesizes that successful clinical eradication of CSCs may lead to durable remission for patients with ovarian cancer.  Despite mounting evidence in support of ovarian CSCs, their phenotype and clinical relevance remain unclear.  We and others have found high aldehyde dehydrogenase 1 (ALDHhigh) expression in a variety of normal and malignant stem cells, and sought to better characterize ALDHhigh cells in ovarian cancer.  Methods: We compared ALDHhigh to ALDHlow cells in two ovarian cancer models representing distinct subtypes: FNAR-C1 cells, derived from a spontaneous rat endometrioid carcinoma, and the human SKOV3 cell line (described as both serous and clear cell subtypes).  We assessed these populations for stem cell features then analyzed expression by microarray and qPCR.  Results: ALDHhigh cells displayed CSC properties, including: smaller size, quiescence, regenerating the phenotypic diversity of the cell lines in vitro, lack of contact inhibition, nonadherent growth, multi-drug resistance, and in vivo tumorigenicity.  Microarray and qPCR analysis of the expression of markers reported by others to enrich for ovarian CSCs revealed that ALDHhigh cells of both models showed downregulation of CD24, but inconsistent expression of CD44, KIT and CD133.  However, the following drugable targets were consistently expressed in the ALDHhigh cells from both models: mTOR signaling, her-2/neu, CD47 and FGF18 / FGFR3.  Conclusions: Based on functional characterization, ALDHhigh ovarian cancer cells represent an ovarian CSC population.  Differential gene expression identified drugable targets that have the potential for therapeutic efficacy against ovarian CSCs from multiple subtypes.

overall_design: SKOV3 human ovarian cancer cells were sorted into Aldefluor high and Aldefluor low populations.  Analysis was performed in triplicate.  Aldefluor low cells served as the reference cells for fold-change analysis.

first: Allison

last: Sharrow

first: Wayne

last: Yu


title: Impact of tRNA-Glu(UUC) and tRNA-Arg(CCG) on mRNA stability

city: San Francisco

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

institute: UCSF

summary: Stable expression of tRNA-Glu(UUC) and tRNA-Arg(CCG) followed by whole-genome transcript stability measurements using a-amanitin mediated inhibition of RNA Pol II.

overall_design: Transfer RNA loci chr1.trna5 (Glu-TTC) and chr16.trna1 (Arg-CCG) were stably over-expressed in MDA-MB-231 cells. Cells were treated with a-amanitin (10ug/mL)  and samples were collected at 0- and 9-nr. The RNA samples were then profiled.

first: H

last: Nguyen

first: S

last: Zhang

middle: F

last: Tavazoie


title: Characterization of aldehyde dehydrogenase 1 high ovarian cancer cells: Towards targeted stem cell therapy

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus


title: Impact of tRNA-Glu(UUC) and tRNA-Arg(CCG) on mRNA abundance

summary: Stable expression of tRNA-Glu(UUC) and tRNA-Arg(CCG) followed by transcriptomic profiling to measure transcripts.

overall_design: Transfer RNA loci chr1.trna5 (Glu-TTC) and chr16.trna1 (Arg-CCG) were stably over-expressed in MDA-MB-231 cells. The cells were then subjected to transcripome profiling in comparison to mock-transfected cells.


title: caArray_nelso-00262: Gene expression profiling of gliomas strongly predicts survival

status: Public on Jun 14 2016

city: Rockville

first: Mervi

last: Heiskanen

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

summary: Migrated from 1.6 id: 1015897590491013 GEDP id: 760 In current clinical practice, histology-based grading of diffuse infiltrative gliomas is the best predictor of patient survival time. Yet histology provides little insight into the underlying biology of gliomas and is limited in its ability to identify and guide new molecularly targeted therapies. We have performed large-scale gene expression analysis using the Affymetrix HG U133 oligonucleotide arrays on 85 diffuse infiltrating gliomas of all histologic types to assess whether a gene expression-based, histology-independent classifier is predictive of survival and to determine whether gene expression signatures provide insight into the biology of gliomas. We found that gene expression-based grouping of tumors is a more powerful survival predictor than histologic grade or age. The poor prognosis samples could be grouped into three different poor prognosis groups, each with distinct molecular signatures. We further describe a list of 44 genes whose expression patterns reliably classify gliomas into previously unrecognized biological and prognostic groups: these genes are outstanding candidates for use in histology-independent classification of high-grade gliomas. The ability of the large scale and 44 gene set expression signatures to group tumors into strong survival groups was validated with an additional external and independent data set from another institution composed of 50 additional gliomas. This demonstrates that large-scale gene expression analysis and subset analysis of gliomas reveals unrecognized heterogeneity of tumors and is efficient at selecting prognosis-related gene expression differences which are able to be applied across institutions.

overall_design:
nelso-00262
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HG-U133A, HG-U133B
Organism: Homo sapiens (ncbitax)
Material Types: total RNA, synthetic_RNA, organism_part, whole_organism
Disease States: Glioma, Glioblastoma, Oligodendroglial Tumor, astrocytomas


title: Acute Appendicitis: Transcript Profiling of blood identifies promising biomarkers and potential underlying processes

status: Public on Jun 08 2016

city: Washington

first: Ian

middle: V

last: Toma

state: DC

address: 2300 Eye Str., NW, Ross Hall, Rm. 443D

department: Medicine

institute: The George Washington University

summary: Background: The diagnosis of acute appendicitis can be surprisingly difficult without computed tomography, which carries significant radiation exposure. Genome-wide expression profiling was applied to whole blood RNA of acute appendicitis patients versus patients with other abdominal disorders, in order to identify biomarkers of appendicitis. From a large cohort of emergency patients, a discovery set of patients with surgically confirmed appendicitis, or abdominal pain from other causes, was identified. RNA from whole blood was profiled by microarrays, and RNA levels were filtered by a combined fold-change (>2) and p value (<0.05). A separate set of patients, including patients with respiratory infections, was used to validate a partial least squares discriminant (PLSD) prediction model. Results: Transcript profiling identified 37 differentially expressed genes (DEG) in appendicitis versus abdominal pain patients. The DEG list contained 3 major ontologies: infection-related, inflammation-related, and ribosomal processing. Appendicitis patients had lower level of neutrophil defensin mRNA (DEFA1,3), but higher levels of alkaline phosphatase (ALPL) and interleukin-8 receptor-ß (IL8RB), which was confirmed in a larger cohort of 60 patients using droplet digital PCR (ddPCR). Conclusions: Patients with acute appendicitis have detectable changes in the mRNA expression levels of factors related to neutrophil inate defense systems. The low defensin mRNA levels suggest that appendicitis patient's immune cells are not directly activated by pathogens, but are primed by diffusible factors in the microenvironment of the infection. The detected biomarkers are consistent with prior evidence that biofilm-forming bacteria in the appendix may be an important factor in appendicitis.

overall_design: 40 samples were grouped into Discovery and Validation sets based on their clinical dx and analyzed for differential gene expression within groups by conditions

first: Lakhmir

last: Chawla

first: Danielle

last: Davison

first: Khashayar

last: Vaziri

first: Juliet

last: Lee

first: Raymond

last: Luca

first: Michael

last: Seneff

first: Aoibhim

last: Nyhan

first: Timothy

last: McCaffrey


title: An inhaled dose of budesonide induces genes involved in transcription and signaling in human airways

status: Public on Jun 11 2016

city: Calgary

first: Robert

last: Newton

state: Alberta

address: 3330 Hospital Dr NW

department: Snyder Institute for Chronic Diseases

institute: University of Calgary

summary:
Inhaled corticosteroids (ICS) control airway inflammation in mild to moderate asthma by reducing inflammatory gene expression. However, incomplete understanding of the molecular mechanisms underpinning corticosteroid action hinders development of improved therapies for more severe disease.
Microarray analysis was performed on RNA from biopsies taken from healthy individuals after receiving single dose of ICS to characterize corticosteroid-induced modulation of gene expression in the human airways.

overall_design: Healthy male, non-smoker, non-allergic volunteers (age 18-50 years) with normal lung function were recruited into a prospective, double-blind, placebo-controlled, randomized, two-period crossover study involving an initial screening visit, followed by two intervention visits. Participants were screened at visit 1 for fulfilment of the study eligibility criteria. At visit 2, volunteers were randomized to receive inhaled budesonide (1600 µg) or placebo, both via Turbuhaler. Two to three weeks later, at visit 3, participants received either budesonide or placebo, as appropriate to complete both study arms. Six hours after placebo or a budesonide inhalation, bronchial biopsies were obtained via bronchoscopy.

first: Mahmoud

last: Mostafa

first: Christopher

last: Rider


title: Deleterious assembly of the lamin A/C mutant p.S143P causes ER stress in familial dilated cardiomyopathy

status: Public on Jun 10 2016

city: Turku

first: Gun

last: West

address: Tykistökatu 6B6

country: Finland

institute: Turku University

summary: Mutation of the LMNA gene, encoding nuclear lamin A and lamin C (hereafter lamin A/C), is a common cause of familial dilated cardiomyopathy (DCM). Among Finnish DCM patients, the founder mutation c.427T>C (p.S143P) is the most frequently reported genetic variant. Here, we show that p.S143P lamin A/C is more nucleoplasmic and soluble than wild-type lamin A/C and accumulates into large intranuclear aggregates in a fraction of cultured patient fibroblasts as well as in cells ectopically expressing either FLAG- or GFP-tagged p.S143P lamin A. In fluorescence loss in photobleaching (FLIP) experiments, non-aggregated EGFP-tagged p.S143P lamin A is significantly more dynamic. In in vitro association studies, p.S143P lamin A failed to form appropriate filament structures but instead assembled into disorganized aggregates similar to those observed in patient cell nuclei. A whole genome expression analysis revealed an elevated unfolded protein response (UPR) in cells expressing p.S143P lamin A/C. Additional endoplasmic reticulum (ER) stress induced by tunicamycin reduced the viability of mutant lamin expressing cells further. In summary, p.S143P lamin A/C affects normal lamina structure and influences the cellular stress response, homeostasis and viability.

overall_design: Total RNA obtained from 4 control and 7 patient cell lines

first: Josef

last: Gullmets

first: Laura

last: Virtanen

first: Song

middle: P

last: Li

first: Anni

last: Keinänen

first: Takeshi

last: Shimi

first: Monika

last: Mauermann

first: Tiina

last: Heliö

first: Maija

last: Kaartinen

last: Ollila

first: Johanna

last: Kuusisto

first: John

middle: E

last: Eriksson

middle: D

last: Goldman

first: Harald

last: Herrmann

first: Pekka

last: Taimen


title: Endothelial Inflammatory Transcriptional Responses to an Altered Serum Exposome Following Inhalation of Diesel Emissions

status: Public on Jun 05 2016

city: Chapel Hill

first: Jonathan

last: Schisler

state: NC

address: MBRB, Rm 2340C

department: McAllister Heart Institute

institute: The University of North Carolina at Chapel Hill

summary: Air pollution, especially emissions derived from traffic sources, is associated with adverse cardiovascular outcomes.  However, it remains unclear how inhaled factors drive an extrapulmonary pathology, as the lung is an effective barrier for solid particulates and many gases. Previously, using plasma from healthy human subjects exposed to diesel exhaust under controlled conditions, we found that canonical inflammatory response transcripts of interleukin-8 (IL-8), intracellular adhesion molecule-1 (ICAM-1), and vascular cell adhesion molecule-1 (VCAM-1) were elevated in endothelial cells treated wih plasma obtained after exposure compared with pre-exposure samples or filtered air (sham) exposures. While the findings confirmed the presence of bioactive factor(s) in the plasma after diesel inhalation, we wanted to better examine the complete genomic response to investigate 1) major responsive transcripts and 2) collected response pathways and ontogeny that may help to refine this method. Thus, we assayed previousy collected RNA with microarray chips, examining the responses of cultured endothelial cells to plasma obtained from 6 healthy human subjects exposed to 100 μg/m3 diesel exhaust or filtered air for 2 h on separate occasions. In addition to pre-exposure baseline samples, we investigated samples obtained immediately post and 24h post exposure.  Primary human coronary artery endothelial cells were grown to confluence and treated with 10% plasma for 24 h, followed by isolation of RNA for microarrays. Microarray analysis of the coronary artery endothelial cells challenged with plasma identified 855 probes that change over time following diesel exhaust exposure. Over-representation analysis identified inflammatory cytokine pathways were upregulated both at the 2 and 24 h condition. These outcomes are consistent with our recent findings that plasma contains bioactive and inflammatory factors following pollutant inhalation and provide a novel pathway to explain the well-reported extrapulmonary toxicity of ambient air pollutants.

overall_design: There are 48 total samples representing three time points from two different conditions (air or diesel emissions) from eight study subjects.

first: Michael

last: Madden

first: Matthew

last: Campen

first: Monte

last: Willis


title: Genome-wide analysis of fatty acid synthase (FASN) gene silenced normal liver cells (THLE 2) using cDNA microarray analysis

status: Public on Jun 02 2016

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

institute: Theomics International Private Limited

summary: Fatty acid synthase is a major enzyme involved in de novo lipogenesis, associated with energy homeostasis, lipid storage and signalling in normal liver cells. The effect of fatty acid synthase knockdown in normal liver cells (THLE 2) using siRNA mediated gene silencing were assesed for global gene deregulations. The deregulated metabolism, cell signalling and cell cycle pathway related gene expressions were analysed. Statistical significance values were also recorded. This expermental analysis clearly points to a important biochemical role for FASN in normal liver cell physiology.

overall_design: Total RNA was extracted from the THLE 2 cells transfected with FASN siRNA at 48h, along with its untransfected control cells. cDNA converted samples were run on microarray platform- Illumina HumanHT-12 V4.0 expression beadchip

first: M

last: Sangeetha

first: P

middle: R

last: Deepa

first: S

last: Krishnakumar


title: PIWI-interacting RNAs in gliomagenesis: Evidence from post-GWAS and functional analyses

status: Public on Jun 04 2016

city: New Haven

first: Yong

last: Zhu

state: Connecticut

address: 60 College St

institute: Yale School of Public Health

summary:
Background: PIWI-interacting RNAs (piRNAs), the largest class of noncoding RNAs in mammals, cooperate with PIWI proteins to safeguard the genome from insertional mutations during germline development. Although a growing number studies have linked the PIWI-piRNA pathway to carcinogenesis, the role of piRNAs in glioma has not been explored.

Methods: Utilizing directly measured and imputed genotypes from the GliomaScan genome-wide association study (1,840 cases and 2,401 controls), genetic variants in 1,428 piRNAs were analyzed for association with glioma risk. In vitro assays were performed to interrogate the functional impact of a top identified piRNA and its variant allele.

Results: Variants in five piRNAs were considered to be associations of interest and four of these showed narrow clusters of enhanced association signals surrounding the index variant. Functional analyses of one of these piRNAs, piR-598, revealed that transfection of the wild-type piRNA impacted expression of genes involved in cell death/survival, and reduced glioma cell viability and colony formation. However, upon delivery of piR-598 containing the variant allele at rs147061479 (OR=1.80; 95% CI: 1.33-2.46; P=1.69 x 10-4), cell proliferation was sharply increased.

Conclusions: These findings suggest that variant rs147061479 in piR-598 increases glioma risk by abolishing the tumor-suppressive function of piR-598, instead conferring growth-promoting properties that may result from a shift in piRNA targets.

Impact: This transdisciplinary study demonstrates a role of piRNAs in gliomagenesis by evidence from both post-GWAS and in vitro functional analyses, and supports expanded investigation into the link between the PIWI-piRNA pathway and cancer.

overall_design: Expression profiling was performed for piR-598- and NC-transfected U87 cells in biological duplicate

first: Daniel

last: Jacobs


title: Anti-cancer agent ONC201 activates early ATF4/DR5 upregulation, and cell death associated with XIAP inhibition

status: Public on Jun 01 2016

city: Hershey

first: Penn State

last: COM

state: PA

address: 500 University Drive

department: Genome Sciences Facility

institute: Penn State College of Medicine

summary: Two experiments were performed with ONC201/TIC10 in human colon cancer cell lines. The first experiment is TIC10-induced transcriptional changes at 48hrs in HCT116 p53-null cells (10uM). The second experiment is RKO cells, with and without acquired resistance to ONC201, treated with with ONC201 (10uM) for 48 hrs.

overall_design: For the first experiment, six samples of HCT116 p53-null cells with TIC10 (10uM) or DMSO treatment. Three replicates each. For the second experiment, six samples of wild-type RKO cells with ONC201 (10uM) or DMSO treatment and the same treatments for RKO cells with acquired resistance to ONC201.

first: Joshua

last: Allen

first: Pieter

last: van den Huevel

first: Leah

last: Kline

first: Wafik

middle: S

last: El-Deiry


title: Periostin cooperates with mutant p53 to mediate invasion

city: Houston

first: Sangbae

last: Kim

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

summary: Periostin, a matricellular protein, has been reported to be important in supporting tumor cell dissemination. However, the molecular mechanisms underlying periostin function within the tumor microenvironment are poorly understood. In this study, we observe that loss of periostin decreases esophageal squamous cell carcinoma (ESCC) tumor growth in vivo and demonstrate that periostin cooperates with a conformational missense p53 mutation to enhance invasion.  Pathway analyses reveal that invasive esophageal cells expressing periostin and p53R175H mutation display activation of signal transducer and activator of transcription 1 (STAT1) target genes, suggesting that the induction of STAT1 and STAT1-related genes could foster a permissive microenvironment that facilitates invasion of esophageal epithelial cells into the extracellular matrix (ECM). Genetic knockdown of STAT1 in transformed esophageal epithelial cells underscores the importance of STAT1 in promoting invasion and potentiate tumor resistance to genotoxic stress. Furthermore, we find that STAT1 is activated in ESCC xenograft tumors but this activation is attenuated with inducible knockdown of periostin in ESCC tumors. Overall, these results highlight the molecular mechanisms supporting the capacity of periostin in mediating tumor invasion during ESCC development.

overall_design:
Pre-clinical study
hTERT: EPC cells immortalized by expression of hTERT
hTERT_p53: EPC cells expressing hTERT and mutant P53
hTERT_p53_POSTN: EPC cells expressing hTERT, mutant P53, and POSTN.

first: Gabrielle

last: Wong

first: Ju-Seog

last: Lee

first: Yun-Yong

last: Park

first: Anil

last: Rustgi


title: Ornithine decarboxylase is sufficient for prostate tumorigenesis via androgen receptor signaling

status: Public on Jun 03 2016

city: New York

first: Weijia

last: Zhang

state: NY

address: 1425 Madison Avenue

department: Department of Medicine

institute: Mount Sinai School of Medicine

overall_design: Normal prostate epithelial cells (RWPE1) were transfected with a plasmid to overexpress ODC1 (RWPE1_ODC) and the gene expression analyses of RWPE1 and RWPE1_ODC was perfromed to identify which pathways were altered with this genetic modification

first: Amita

last: Shukla-Dave

first: Mireia

last: Castillo-Martin

first: Ming

last: Chen

first: Jose

last: Lobo

first: Nataliya

last: Gladoun

first: Ana

last: Collazo Lorduy

first: Faisal

last: Khan

first: Vladimir

last: Ponomarev

first: Zhengzi

last: Yi

first: Pier

last: Paolo Pandolfi

first: Hedvig

last: Hricak

first: Carlos

last: Cordon-Cardo


title: PIWI-interacting RNAs function as novel tumor suppressors in glioblastoma multiforme

first: Yong

last: Zhu

summary: PIWI-interacting RNAs (piRNAs) are small non-coding RNAs that partner with PIWI proteins to protect germline tissues from destabilizing transposon activity. While the aberrant expression of PIWI proteins has been linked with poor outcomes for many cancers, less is known about the expression or function of piRNAs in cancer. We performed array-based piRNA expression profiling in seven pairs of normal and glioblastoma multiforme (GBM) tissue specimens and identified expression of ~350 piRNAs in both tissues and a subset with dysregulated expression in GBM. Several down-regulated piRNAs inhibited proliferation when transfected into glioma cell lines while those equivalently expressed in tumor and normal tissues did not, consistent with piRNA-specific tumor-suppressive roles. Upregulation of the most underexpressed piRNA, piR-8041, was found to induce cell cycle arrest and apoptosis and to alter transcriptional levels of several genes involved in stress and cell survival pathways. Additionally, the volume of intracranial mouse xenograft tumors was significantly reduced for approximately ten days after pre-implantation transfection with piR-8041. Taken together, our study reveals a previously unidentified functional role for piRNAs as tumor suppressors in gliomagenesis, and suggests that restoration of piRNA levels may be a potential strategy for GBM therapy.

overall_design: Expression profiling was performed for [1] piR-8041- and NC-transfected U87 cells in biological duplicate [2] pooled RNA samples from seven GBM and seven normal brain tissue specimens in biological duplicate.

first: Daniel

last: Jacobs


title: Transcriptional response to drug-induced oligomerization of the AIM2-like receptors IFI16, PYHIN1, and MNDA.

status: Public on May 31 2016

city: Seattle

last: Stetson

state: WA

address: 750 Republican St

department: Immunology

institute: University of Washington

summary:
We explored ALR function in a ligand-independent manner using a drug-inducible dimerization system in which ALRs were tagged with two FV domains that rapidly oligomerize upon addition of the drug AP1
We found that oligomerization of IFI16, PYHIN1, or MNDA did not result in any significant gene expression changes.

overall_design: Total RNA was isolated from BFP, IFI16-2xFV, PYHIN1-2xFV, or MNDA-2xFV-expressing THP1 cells mock-treated or treated with 30nM AP1 dimerizer drug for 4 or 12 hours.

first: Elizabeth

last: Gray


title: Genome-wide analysis of RAF inhibition in HCT116 cells in culture

status: Public on May 28 2016

city: Kolkata

first: Gaurisankar

last: Sa

state: West Bengal

address: p-1/12, CIT Scheme VII M

department: Molecular Medicine

institute: Bose Institute

summary:
gene expression profile of HCT116 p53+/+ cells in response to RAF inhibition
Total RNA obtained from HCT116 cells treated with or without 10nM SB590885

overall_design: Gaurisankar, Sa


title: CD147 and downstream ADAMTSs promote the tumorigenesis of Kaposi sarcoma-associated herpesvirus

city: New Orleans

first: Zhiqiang

last: Qin

state: LA

address: 1700 Tulane Ave

institute: LSUHSC-NO

summary: The Kaposi’s Sarcoma-associated Herpesvirus (KSHV) is the etiologic agent of several human cancers, including Kaposi’s Sarcoma (KS), which preferentially arise in immunocompromised patients but lack of effective therapeutic options. We have previously shown that KSHV or viral protein LANA can upregulate the glycoprotein CD147 (Emmprin) to induce primary endothelial cell invasiveness, which also requires PI3K/Akt and MAPK activation of VEGF production. In the current study, we first time identify the global network controlled by CD147 in KSHV-infected endothelial cells using Illumina microarray analysis. Among these downstream genes, ADAMTS1 and 9, two specific metalloproteases are strongly expressed in AIDS-KS tissues and contributed to KSHV-infected cell invasiveness through regulation of related cytokines production and respective receptors expression. By using a nude mice KS-like model, we found that targeting CD147 and downstream ADAMTSs proteins significantly suppressed KSHV-related tumorigenesis in vivo, which is potentially through impairing extracellular matrix (ECM) formation in tumor microenvironment. Taken together, we think that targeting CD147 and related proteins may represent a promising therapeutic strategy against KSHV-related malignancies.

overall_design: HUVEC cells were infected by KSHV or transduced by a CD147 recombinant adenoviral vector and the gene expression signature was compared to respective controls

first: Lu

last: Dai

first: Jimena

last: Trillo-Tinoco

first: Jianhai

last: Jiang

first: Yihan

first: Luis

last: Del Valle

first: Jovanny

last: Zabaleta

first: Bryan

last: Toole


title: Transcriptomic signatures of risk genes implicated in psychiatric disorders during neuronal differentiation

city: Frankfurt am Main

first: Andreas

last: Chiocchetti

address: Deutschordenstr 50

department: Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy

institute: JW Goethe University

summary: Susceptibility genes for Autism Spectrum Disorder (ASD), Fragile X Syndrome (FXS), monogenetic disorders with intellectual disabilities (ID) or schizophrenia (SCZ) converge on processes related to neuronal function and differentiation. Furthermore, ASD risk genes are enriched for FMRP (Fragile X Mental Retardation Protein) targets and for genes implicated in ID. In addition, a significant co-heritability was observed between ASD and SCZ. The genetic overlap between ASD, FXS, ID and SCZ together with the symptomatic differences gives rise to the question if pathomechanisms impair the same or different regulatory patterns activated during neuronal differentiation (ND). To test this idea, we performed transcriptome analysis of in-vitro differentiation of the neuroblastoma cell line model SH-SY5Y and identified genes that were differentially expressed, dynamically regulated, and coordinately expressed. The identified genetic modules activated during ND are enriched for genetic risk factors for these four disorders. Although risk genes for the disorders significantly overlap, we observed disorder specific enrichments: ASD or FXS implicated genes were likely to be positive regulators of ND whereas ID implicated genes were related to negative regulation. ASD and SCZ genes were specifically enriched among cholesterol and fatty acid associated modules. ID genes were overrepresented among cell cycle modules. In addition, we show that ASD genes are likely to be hub genes. We hypothesize that knowledge about genetic variants of an individual combined with network and pathway context of the related genes will allow differentiating between psychiatric disorders.

overall_design: 21 samples, consisting of 3 replicates harvested at 7 different time-points of RA+BDNF-induced neuronal differentiation

first: Denise

last: Haslinger

first: Jason

last: Stein

last: de la Torre-Ubieta

first: Enrico

last: Cocchi

first: Silvia

last: Lindlar

first: Regina

last: Waltes

first: Simone

last: Fulda

middle: H

last: Geschwind

first: Christine

last: Freitag


title: Transcriptomic profiling of rhesus macaques vaccinated with ALVAC-SIV/gp120 adjuvanted in Alum or MF59.

status: Public on May 29 2016

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

institute: Northwestern University

summary: The Canarypox/gp120/Alum vaccines decreased the risk of HIV acquisition in humans. We demonstrate here the efficacy of this vaccine regimen also in the SIVmac251 macaque model when we used the alum but not the MF59 adjuvant. Analysis of innate and adaptive cell responses, envelope antibodies Fc profiles and glycoforms demonstrated a lower inflammatory response with alum than MF59. Alum elicited mucosal V2 peptide-specific IgG associated with vaccine efficacy whereas the MF59 induced mucosal V2 peptide-specific IgG associated with increased risk of infection. Alum modulated the expression of 12 genes, 7 of which are part of the RAS pathway, that correlates with vaccine efficacy and were linked to innate responses that preserve mucosal integrity and adaptive mucosal antibody response to V2. Thus, activation of the RAS pathway, preservation of mucosal integrity and mucosal antibody to V2 in concert, reduce the risk of SIVmac251 acquisition.

overall_design:
Fifty-four (54) rhesus macaques were randomized into two vaccination groups. One group (n=27) was primed twice with ALVAC-SIV (at week 0 and week 4) and boosted twice with ALVAC-SIV/gp120 in MF59 adjuvant (at week 12 and week 24). The second group (n=27) was primed twice with ALVAC-SIV (at week 0 and week 4) and boosted twice with ALVAC-SIV/gp120 in Alum adjuvant (at week 12 and week 24). Blood samples were taken pre-vaccination, 24 hours after the first prime (post-1st imunization at week 0) and 24 hours after the first boost (post-3rd immunization at week 12). All the samples were taken before SIV challenge. Blood samples were conserved in PAXgene tubes. RNA was extracted and hybridized to Illumina beadchips.
technical replicate: P162_P382_post1st, P162_P382_post1st_rep1

first: Monica

last: Vaccari

first: Shari

middle: N

last: Gordon

first: Rafick-Pierre

last: Sékaly

first: Genoveffa

last: Franchini


title: Genome-wide expression microarray analysis of PRAME knock down TCam-2 cells with and without ATRA treatment

status: Public on May 22 2016

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Universitätsstr. 1

department: Urology

institute: University Hospital Düsseldorf

summary: Illumina expression microarray analysis of shRNA-mediated PRAME knock down TCam-2 cells with and without all trans retinoic acid (ATRA) treatment for 8 days, of TCam-2 cells with and without ATRA (8d) and of in vitro cultivated GCC cell lines TCam-2, 2102EP, NCCIT and JAR.  These data are part of the article 'The Cancer / Testis-Antigen PRAME supports the pluripotency network and represses somatic and germ cell differentiation programs in seminomas'.

overall_design: Total RNA was isolated from TCam-2 PRAME shRNA cells (sh)  treated for 8 days with (n = 3, sh+A) and without (n = 3, sh-A) ATRA (20 micromolar). Additionally, total RNA from TCam-2 cells treated with ATRA for 8 days was isolated (n = 1, TCam-2 +A). As controls, TCam-2 cells were infected with empty pSUPER.retro-vector (n = 1, TCam-2 pS.r) or treated with the ATRA-solvent DMSO (n = 1, TCam-2 DMSO). Stable PRAME shRNA knock down cells were generated by infecting TCam-2 cells with retroviral particles coding for PRAME shRNA (in pRETRO.super-vector). Stable clones were selected by Puromycin selection. Additionally, RNA was isolated from in vitro cultivated TCam-2 (n = 1), 2102EP (n = 1), NCCIT (n = 1) and JAR (n =1) cells. For more details, see Nettersheim et al. 2016, British Journal of Cancer (to be added upon publication).

first: Hubert

last: Schorle


title: Long non-coding RNA expression profiling in normal B-cell subsets and Hodgkin lymphoma reveals Hodgkin and Reed-Sternberg cell specific long non-coding RNAs

status: Public on May 26 2016

city: Groningen

first: Masoumeh

last: Tayari

address: Hanzeplein 1, , The Netherlands

department: pathology

country: Netherlands

institute: University of medical center Groningen

summary: Hodgkin lymphoma (HL) is a malignancy of germinal center (GC) B-cell origin. To explore the role of long non-coding RNAs (lncRNAs) in HL, we studied lncRNA expression patterns in normal B-cell subsets, HL cell lines and tissues. Naive and memory B-cells showed a highly similar lncRNA expression pattern, distinct from GC-B cells. Significant differential expression between HL and normal GC-B cells was observed for 475 lncRNA loci. For two validated lncRNAs an enhanced expression was observed in HL, diffuse large B cell lymphoma and lymphoblastoid cell lines. For a third lncRNA, increased expression levels were observed in HL and part of Burkitt lymphoma cell lines. RNA-FISH on primary HL tissues revealed a tumor cell-specific expression pattern for all three lncRNAs. A potential cis-regulatory role was observed for 107 differentially expressed lncRNA-mRNA pairs localizing within a 60kb region. In line with a cis-acting role, we showed a preferential nuclear localization for two selected candidates. Thus, we showed dynamic lncRNA expression changes during the transit of normal B-cells through the GC reaction and widely deregulated lncRNA expression patterns in HL. Three lncRNAs showed a tumor cell-specific expression pattern in HL tissues and might therefore be of value as a biomarker.

overall_design: Expression of all known mRNAs and >10 000 lncRNAs was assessed in normal B-cell subsets and HL cell lines.

first: Melanie

last: Winkle

first: Gertrud

last: Kortman

first: Jantine

last: Sietzema

first: Debora

last: de Jong

first: Martijn

last: Terpstra

first: Pieter

last: Mestdagh

first: Frans

last: Kroese

first: Lydia

last: Visser

first: Arjan

last: Diepstra

first: Klaas

last: Kok

first: Anke

last: van den Berg

first: Joost

last: Kluiver


title: Gene expression profile analysis of HepG2 cells upon PSTAR or hnRNP K knockdown

city: Beijing

first: Jin

last: Song

address: No.38 shengmingyuan Road

institute: Beijing Institute of Radiation Medicine

summary: We discovered  lncRNA PSTAR as a novel hepatocellular carcinoma (HCC) - associated lncRNA, which could interact with hnRNP K protein. To explore the function of PSTAR in HCC and underlying molecular mechanism, we examined the global gene expression change in HepG2 cells with PSTAR knockdown. The gene expression profile of HepG2 with hnRNP K knockdown was also analyzed to investigate the correlationship between PSTAR and hnRNP K. Further, doxorubicin (DOX) was applied to induce DNA damage, and the effect of PSTAR and hnRNP K under DNA damage was also investigated.

overall_design: HepG2 cells transfected with si-PSTAR, si-hnRNP K or si-scramble RNAs were treated with 400 nM DOX for sixteen hours, and then, the total RNA was extracted from above cells

first: Xinyi

last: Tu

first: Xi

last: Chen

first: Gangqiao

last: Zhou

first: Fuchu

last: He


title: Genome-wide analysis of gene expression by miR-204/211 in normal breast cell line MCF10A and breast cancer cell line MCF7

status: Public on May 23 2016

city: goyang

first: seungyeon

last: lee

address: dongguk-ro 32

department: life science

institute: dongguk unversity

summary: Genome-wide expression analysis of MCF-10A and MCF-7 where miR-204 and miR-211 are overexpressed.  The characteristics of differentially expressed genes in both cell lines derives the cells toward being oncogenic.

overall_design: Total RNA is obtained from MCF-10A and 7 where miR-204/211 are overexpressed using lipofectamine RNAiMAX

first: Hyunkung

last: Lee

first: Seungyeon

first: Sunjung

last: Kim


title: LNCRHOXF1: a long noncoding RNA from the X-chromosome that suppresses viral response genes during development of the early human placenta

status: Public on May 27 2016

city: Philadelphia

first: daniel

last: beiting

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania

summary: Long noncoding RNAs (lncRNAs) can regulate gene expression in a cell-specific fashion during development.  Here we identify a novel lncRNA from the X-chromosome that we named lncRHOXF1 and which is abundantly expressed in trophectoderm and primitive endoderm cells of human blastocyst-stage embryos. LncRHOXF1 is a spliced and polyadenylated lncRNA about 1 kb in length, found in both the nuclear and cytoplasmic compartments of in vitro differentiated human trophectoderm progenitor cells. Gain of function experiments in human embryonic stem cells, which normally lack lncRHOXF1 RNA, revealed that lncRHOXF1 reduced proliferation and favored cellular differentiation. LncRHOXF1 knockdown using siRNAs in human trophectoderm progenitors increased expression of viral response genes, including type I interferon.  Sendai virus infection of human trophectoderm progenitor cells increased lncRHOXF1 RNA levels and siRNA-mediated disruption of lncRHOXF1 during infection reduced the expression of viral response genes leading to higher virus replication. Thus, lncRHOXF1 RNA is the first example of a lncRNA that regulates the host response to viral infections in human placental progenitor cells, and we propose that it functions as a repressor of the viral response during early human development.

overall_design: Undifferentiated human embryonic stem cells (HUES9) containing the lncRHOXF1 and rtTA3 cDNAs inserted into the AAVS locus of chromosome 19 were used in overexpression experiments RNA was isolated from triplicate wells for analysis by Illumina microarray.

first: Daniel

last: Beiting

first: Ian

last: Penkala

first: Montserrat

last: Anguera

first: Camille

last: Syrett


title: Cholesterol biosynthesis pathway as a novel mechanism of resistance to estrogen deprivation in estrogen receptor positive breast cancer

status: Public on May 20 2016

city: London

first: Alice

last: Gao

state: London

address: 237 Fulham Road

department: Breast Cancer Now

country: United Kingdom

institute: The Institute of Cancer Research

summary: Therapies targeting estrogenic stimulation in estrogen receptor positive (ER+) breast cancer (BC) reduce mortality, but resistance remains a major clinical problem. Molecular studies have shown few high frequency mutations to be associated with endocrine resistance. In contrast, expression profiling of primary ER+ BC samples has identified several promising signatures/networks for targeting.  In this study, the cholesterol biosynthesis pathway was the common upregulated pathway in the ER+ LTED but not ER- LTED cell lines, suggesting a potential mechanism dependent on continued ER expression. Targeting the individual genes of the cholesterol biosynthesis pathway with siRNAs caused a 30-50% drop in proliferation. Further analysis showed increased expression of 25-hydroxycholesterol (HC) in the MCF7 LTED cells. Exogenous 25-HC or 27-HC increased ER mediated-transcription and expression of the endogenous estrogen-regulated gene TFF1 in ER+ LTED cells but not in the ER-negative LTED. Additionally, recruitment of the ER and CREB-binding protein (CBP) to the TFF1 promoter was increased upon treatment with 25-HC and 27-HC. In silico analysis of 704 primary ER+ BC patients treated with adjuvant tamoxifen showed increased expression of MSMO1 (p=0.047), EBP (p=0.043), SQLE (p=0.000009), and IDI1 (p=0.0005), enzymes required for cholesterol synthesis and increased in our in vitro models of endocrine resistance, to be associated with poor relapse-free survival. In contrast, no association was identified in over 700 patients with ER-negative BC. Taken together, these data provide support for the role of cholesterol biosynthesis enzymes and the cholesterol metabolites, 25-HC and 27-HC, in a novel mechanism of resistance to endocrine therapy in ER+ BC that has potential as a therapeutic target.

overall_design: To identify common adaptive mechanisms associated with resistance to aromatase inhibitors (AI), we assessed changes in global gene expression during adaptation to long-term estrogen deprivation (LTED) in a panel of ER+ BC cell lines cultured in 2D on plastic (MCF7, T47D, HCC1428, SUM44 and ZR75.1) or 3D on collagen (MCF7) to model the stromal compartment. Furthermore, dimethyl labelling followed by LC-MS/MS was used to assess global changes in protein abundance. The role of target genes/proteins on proliferation, ER-mediated transcription and recruitment of ER to target gene promoters was analysed

first: Qiong


title: NHDF Cells (Normal Human Dermal Fibroblasts): Control (unstimulated fibroblasts) vs. Borrelia infected cells

city: Strasbourg

first: Frédéric

last: Schramm

address: 3, rue Koeberlé

department: University of Strasbourg

country: France

institute: EA 7290 Early Bacterial Virulence

summary: Transcriptional profiling of NHDF Cells comparing control untreated fibroblasts with fibroblasts coincubated with three different species of the Borrelia burgdorferi sensu lato group.

overall_design: Four-conditions experiment (unstimulated NHDF; NHDF stimulated by Borrelia burgdorferi sensu stricto strain IBS19; NHDF stimulated by Borrelia garinii strain IBS6; NHDF stimulated by Borrelia garinii strain IBS17).  There is 6 Biological replicates for each condition (i.e. 6 different batches of NHDF cells from 6 independent human donor), independently grown and harvested.

first: Mariam

last: Meddeb

first: Wassila

last: Carpentier

first: Nicolas

last: Cagnard


title: Effects of model chylomicron remants on gene expresssion in human aortic endothelial cells (HAEC)

status: Public on May 19 2016

first: Caroline

last: Wheeler-Jones

address: Royal College Street

department: CBS

institute: Royal Veterinary College

summary: Global gene experssion study of the HAEC transcriptional response to artificial chlyomicron remnant-like particles (A-CRLPs) prepared with triglycerides extracted from four natural dietary oils: fish, DHASCO, corn and palm oils.  We hypothesised that A-CRLPs could differentially regulate HAEC gene expression according to thier triglyceride content.  These data provide an important starting point for investigations into the effects of A-CRLPs on endothelial cells, particulary genes involved in redox balance and inflammatory processes.

overall_design: Six experimental conditions: PBS (extra control), Primary/main  control remnant control (RC), Fish, DHASCO, Corn or Palm A-CRLPs  n = 4 biological replicates (i.e. 4 HAEC batches from different donors)

first: Sally

last: Latham Birt

first: Kathleen

last: Botham

first: Jayne

last: Dennis


title: caArray_mille-00271: Uppsala cohort

city: Rockville

first: Mervi

last: Heiskanen

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

summary: breast cancer

overall_design:
mille-00271
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HG-U133A, HG-U133B
Organism: Homo sapiens (ncbitax)


title: Genome-wide expression microarray analysis of SOX2-deficient TCam-2 cells in vivo

last: Nettersheim

summary: Illumina expression microarray analysis of seminoma-like TCam-2 cells depleted for SOX2 by CRISPR/Cas9. Cells were xenografted in nude mice. 2120EP embryonal carcinoma and parental TCam-2 cells were xenograted as controls. Tumors were recovered after 1 (1w) and 6 weeks (clone 1 - 5) of in vivo growth. Additionally, in vitro cultivated TCam-2 were analyzed as control. The data set is part of the study 'SOX2 is essential for in vivo reprogramming of seminoma-like TCam-2 cells to an embryonal carcinoma-like fate' (Nettersheim et al., 2016, Oncotarget).

overall_design: Total RNA was isolated from in vitro cultivated TCam-2 and from tumors of TCam-2 (parental and SOX2-deficient clones) and 2102EP cells xenografted for 1 or 6 weeks. 1x10^7 cells were xenografted in 500 microliter Matrigel. RNA was analyzed by an Illumina HT12 expression bead chip. For more details see the related publication.

first: Hubert

last: Schorle


title: HLA sensitization study

status: Public on May 17 2016

city: palo alto

first: weiqi

last: wang

state: ca

address: 1291 welch road

institute: stanford

summary:
Immune profiles were performed retrospectively in highly sensitized kidney transplant candidates
Our hypothesis was that baseline differences in immune profiles could help identify candidates that respond to desensitization therapy.

overall_design: Single-cell mass cytometry by time-of-flight (CyTOF) phenotyping, gene arrays, and phosphoepitope flow cytometry were performed in 20 highly sensitized kidney transplant candidates undergoing desensitization therapy.

first: Julie

last: Yabu


title: Characterization of gene expression profiling of mouse tissues obtained during the postmortem interval

status: Public on May 13 2016

city: Kasugai

first: Masatoshi

last: Ichihara

state: Aichi

address: 1200 Matsumoto-cho

country: Japan

institute: Chubu University

summary: Attempts to establish a tissue bank from autopsy samples have led to uncovering of the secrets of many diseases. Here, we examined the length of time that the RNA from postmortem tissues is available for microarray analysis and reported the gene expression profile for up- and down-regulated genes during the postmortem interval (PMI). We extracted RNA from fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) brains and livers of three different groups of mice: 1) mice immediately after death, 2) mice that were stored at room temperature for 3 h after death, and 3) mice that were stored at 4°C for 18 h after death, as this storage resembles the human autopsy process in Japan. Based on the microarray analysis, we selected genes that were altered by >1.3-fold or <0.77-fold and classified these genes using hierarchical cluster analysis following DAVID (database for annotation, visualization, and integrated discovery) gene ontology analysis. These studies revealed that cytoskeleton-related genes were enriched in the set of up-regulated genes, while serine protease inhibitors were enriched in the set of down-regulated genes. Interestingly, although the RNA quality was maintained, up-regulated genes were not validated by quantitative PCR, suggesting that these genes may become fragmented or modified by an unknown mechanism.

overall_design: We extracted RNA from fresh-frozen (FF) brains and livers from mice under three different conditions: 1) mice just after death as a control, 2) mice that were stored at room temperature for 3 h after death, and 3) mice that were stored at 4°C for 18 h after death to resemble the human autopsy process. We also created formalin-fixed paraffin-embedded (FFPE) tissue blocks at the same time using mouse organs obtained under the three conditions described above. We then purified RNA from the FFPE tissue blocks. Furthermore, we performed microarray analysis to examine changes in the gene expression profiles during the postmortem interval in FF samples and to compare ene expression profiles between FF and FFPE samples at three different postmortem times as described for the FF samples.

first: Sayaka

last: Sobue


title: Global gene expression analysis of development and progression of colorectal carcinoma

city: South San Francisco

first: Omar

last: Kabbarah

state: California

address: 1 DNA Way

department: Oncology Biomarker Development

institute: Genentech Inc

summary:
Colorectal cancer (CRC) tumorigenesis proceedes through well defined clinical stages assoicated with charateristic mutations. To get a better understanding of CRC progression at the transcriptional level, we performed transcriptome profiling on samples from normal colonic tissues, pre-malignant adenomas, carcinomas and metatases.
We used Affymatrix microarry to get a broad view of gene expression during colorectal cancer progression and identified significantly differentially expressed genes between different stages

overall_design: A total of 58 laser capture micro-dissected tissues that cover the major stages of colorectal cancer progression were collected from the Department of Pathology at the University of Virginia under the supervision of an experienced pathologist. DNA was extracted and run on Affymetrix microarrys. Gene-expression profiles were collected on Affymetrix HG-U133A GeneChips according to the manufacturer’s instructions.

first: Henry

last: Frierson Jr

first: Thomas

last: Sandmann

first: Garret

last: Hampton

first: Xueping

last: Qu

first: Richard

last: Bourgon


title: Transcriptional Profiling of Human Endocervical Tissues Reveals Distinct Gene Expression in the Follicular and Luteal Phases of the Menstrual Cycle

status: Public on May 12 2016

last: Kim

state: IL

address: 303 E. Superior St

department: Obstetrics and Gynecology

summary: The goal of this study was to identify genes differentially expressed in the follicular and luteal phases of the menstrual cycle in the human endocervix and to identify significantly represented biological pathways and processes.  This was done in order to better understand mechanisms associated with hormonal regulation of endocervix function which has implications in susceptibility to infections.

overall_design: Total RNA obtained from human endocervix tissues obtained from hysterectomy specimens that were separated into either follicular or luteal phases by endometrial dating.

first: Sevim

middle: Y

last: Arslan

first: J


title: Gene expression microarray of RMEL3-silenced A375-SM melanoma cell lines

status: Public on May 08 2016

city: Ribeirão Preto

first: Enilza

middle: Maria

last: Espreafico

state: São Paulo

address: Av. Bandeirantes, 3900

department: Cell and Molecular Biology

country: Brazil

institute: University of São Paulo

summary: Previous work identified RMEL3 as a lncRNA with enriched expression in melanoma. Analysis of The Cancer Genome Atlas (TCGA) data confirmed RMEL3 enriched expression in melanoma and demonstrated its association with the presence of BRAFV600E. RMEL3 siRNA-mediated silencing markedly reduced (95%) colony formation in different BRAFV600E melanoma cell lines. Multiple genes of the MAPK and PI3K pathways found to be correlated with RMEL3 in TCGA samples were experimentally confirmed. RMEL3 knockdown led to downregulation of activators or effectors of these pathways, including FGF2, FGF3, DUSP6, ITGB3 and GNG2. RMEL3 knockdown induces gain of protein levels of tumor suppressor PTEN and the G1/S cyclin-Cdk inhibitors p21 and p27, as well as a decrease of pAKT (T308), BRAF, pRB (S807, S811) and cyclin B1. Consistently, knockdown resulted in an accumulation of cells in G1 phase and subG0/G1 in an asynchronously growing population. Thus, TCGA data and functional experiments demonstrate that RMEL3 is required for MAPK and PI3K signaling, and its knockdown decrease BRAFV600E melanoma cell survival and proliferation.

overall_design: Total RNA obtained from RMEL3-silenced A375-SM melanoma cells (3 biological replicates) in 72 hours after siRNA transfection compared to control siRNA transfection (3 biological replicates).

first: Lucas

last: Goedert

first: Cristiano

last: Pereira

first: Jason

last: Roszik

first: Jessica

last: Plaça

first: Cibele

last: Cardoso

first: Guo

last: Chen

first: Wanleng

last: Deng

first: Vashisht

last: Yennu-Nanda

first: Wilson

middle: A

last: Silva Jr

first: Michael

last: Davies


title: Prox1 haploinsufficiency sensitizes the pancreas to KrasG12D-induced transformation

status: Public on May 09 2016

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary: Oncogenic mutations in Kras initiate neoplastic transformation in the pancreas through a process that hijacks the activity of developmental regulators and induces an inflammatory microenvironment.  We report that the homeodomain transcription factor Prox1 is a novel component of a progenitor signature that is activated in acinar cells undergoing dedifferentiation and ductal metaplasia conversion. Also, the conditional deletion of a single Prox1 allele markedly accelerates early transformation and significantly enhances features of inflammation in pancreatic tissues carrying a Kras oncogene. By using in vitro and in silico approaches, we demonstrate that Prox1 negatively regulates the expression of proinflammatory genes and genes implicated in malignant transformation in pancreatic cells.

overall_design: We used microrrays to identify gene expression profiles and pathways that are differentially activated after conditional expression of an oncogenic form of Kras and deletion of one allele of Prox1 in the pancreas

first: Yiannis

last: Drosos

first: Beatriz

last: Sosa-Pineda


title: Transcriptome profiling of SW480 cells treated or untreated with Floxuridine (FUdR)

status: Public on May 06 2016

city: Kolkata

first: Susanta

last: Roychoudhury

address: 4, Raja S. C. Mullick Road

department: Cancer Biology and Inflammatory Disorder Division

institute: CSIR-Indian Institute of Chemical Biology

summary: Colorectal cancer cells with TP53 mutation are highly resistant to chemotherapeutics. In order to identify potential chemo-resistance signatures, here; we explored the global gene expression profiles of drug resistant colorectal cancer cell line SW480 upon Floxuridine (FdUrd) treatment using  Illumina Human HT-12 v4.0 Expression Beadchip Array. Further, significantly altered genes were subjected to the pathway analysis in GeneCodis3 and crucial signaling pathways were found to be enriched. Upon further functional validations, these pathways could be targeted to enhance therapy in human cancers harboring mutant p53.

overall_design: Identification of potential  signature genes of chemoreistance in colorectal cancer cells harboring mutant p53


title: Expression data from mice CD11c circulating T lymphocytes

status: Public on May 04 2016

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

summary:
CD11c T cells remain an unknown cell population. Among up regulated genes related to the specific immune responseof CD11c T cells we aimed to detect adhesion molecules, chemokines receptors and other molecules associated with migration to genital tract.
We used microarrays to detail the global set of gene expression underlying CD11c T cells and identified distinct classes of up-regulated genes that distinct this cell population.

overall_design: Circulating TEM cells were sorted from three female mice. Blood samples (≈500µl) were immediately lysed using a RBC lysis buffer. Each sample was sorted into two subsets, CD3+ CD62L- CD44High CD11c+ and CD3+ CD62L- CD44High CD11c-.  Total RNA from each of the six samples was analyzed with an individual Affymetrix  HT MG-430 PM Strip Array. Thus the study compared CD11c positive versus CD11c negative T cells, 3 paired sample sets each derived from one of the three different individual mice.

first: Jamal

last: Qualai

first: Meritxell

last: Genesca


title: The Common Stress Responsive Transcription Factor ATF3 Binds Active Enhancers and Bookmarks Genomic Sites for Transcriptional Regulation [array]

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

institute: Emory University

summary: Comprehensive analysis of global ATF3-binding profiles in the human genome under quiescent and stressed (DNA damage) conditions. Although expressed at a low level, quiescent ATF3 was found to bind a large number of genomic sites that are often associated with genes required for cellular stress responses. While these ATF3-binding sites often contained motifs for other transcription factors (TFs), we found that ATF3 bound a large portion of active enhancers characterized by p300 binding, and as a consequence, ATF3 often regulates expression of the genes proximal to these enhancers. While DNA damage elicited by camptothecin dramatically altered the ATF3 binding profile, most of the genes regulated by ATF3 upon DNA damage were pre-bound by ATF3 before the stress. Moreover, we demonstrated that ATF3 was co-localized with the major stress responder p53 at genomic sites, thereby contributing to induction of p53 target gene expression upon DNA damage. Therefore, our results suggest that ATF3 bookmarks genomic sites and interacts with other TFs for transcriptional regulation under quiescent and stressed conditions.

overall_design: Wild-type HCT116 (HCT116 WT) and ATF3-knockout cells (HCT116 E11) were treated with DMSO or 1.5 uM of camptothecin for 4 h. Total RNAs were prepared for microarray analyses.

first: Chunhong

last: Yan

first: Jonathan

last: Zhao


title: Microarray analysis of cell types exposed to alpha particle radiation

city: Ottawa

first: Vinita

last: Chauhan

state: Ontario

address: 775 Brookfield Rd

institute: Health Canada

summary:
Four human-derived cell types: transformed monocytes (THP-1), transformed lung epithelial cells (A549), normal human pulmonary endothelial cells (HPEAC) and normal lung fibroblasts (HFL-1)
Cell types were independently exposed to alpha particle radiation using Americium-241 discs (0.9Gy/hr) at a dose range from 0-1.5 Gy. Twenty-four hours post-exposure cells were harvested and RNA was extracted and subjected to microarray analysis.

overall_design: Expression profiling by array analysis-Sample set, 0, 0.5, 1.0, 1.5 Gy ( n=5), analysed 24h post exposure, for THP-1 cells analysis was also conducted 72 h post-exposure

first: Matthew

last: Howland


title: Combination of the MEK inhibitor pimasertib with BTK or PI3K-delta inhibitors is active in pre-clinical models of aggressive lymphomas

status: Public on May 05 2016

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

summary: assess the efficacy of Pimasertib to characterize its mechanism of action

overall_design: GEP analysis of one lymphoma cell line with and without treatment with Pimasertib

first: Eugenio

last: Gaudio

first: Tarantelli

last: Chiara

first: Bernasconi

last: Elena

first: Andrea

last: Rinaldi


title: Gene expression profiling of immortalized normal fibroblasts from a breast cancer patient after transient transfection with miR-9 or control.

status: Public on May 15 2016

city: Mexico

first: Sandra

middle: Lorena

last: Romero-Cordoba

state: Mexico

address: Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan. México, D.F.

department: Cancer Genomics

country: Mexico

institute: National Instute of Genomic Medicine

summary: To clarify the molecular alterations triggered by miR-9 to induce the conversion of breast normal fibroblasts to a CAF-phenotype, gene expression profile of normal fibroblasts transiently transfected with miR-9 or control was performed.

overall_design: We performed a gene expression profiling of immortalized normal fibroblasts taken from a noncancerous region of the breast at least 2 cm from the outer tumor margin. Fibroblasts were transiently transfected with miR-9 or control for 24 hours. 3 independent biological replicates for each treatment.

first: Sara

last: Baroni

first: Loris

last: De Cecco

first: Marilena

last: Iorio


title: In vitro model of tumor-associated macrophages

status: Public on May 02 2016

first: Geoffrey

last: Neale

country: USA

summary: The tumor microenvironment is highly complex and consists af many non-tumor cells and factors. To simplify the complexity, we developed a simple in vitro system where tumor (neuroblastoma) 'spheres' ~1-2 mm in diameter were generated on concave surfaces of noble agar. After sphere development, bone marrow-derived macrophages were added to the well. Many macrophages crawled into the spheres (as shown by live cell microscopy). After 24-28 h, the macrophages were isolated from inside or outside the tumor spheres using tissue digestion and anti-CD11b MACs beads. The macrophages from inside or outside the spheres were then subject to microarray analysis.

overall_design: We used microarrays to measure gene expression profiles in macrophages isolated from tumor spheres, or the macrophages from the same cultures that did not enter the spheres. Two timepoints were chosen, in three replicates. Each replicate is an independent experiment where macrophages were pooled from multiple wells to obtain sufficient material for array analysis.

first: Joseph

last: Qualls

first: Peter

last: Murray


title: Genome-wide gene expression analysis of WERI-Rb-1 (retinal cells) infected with Toxoplasma gondii over time

status: Public on May 03 2016

city: Subiaco

first: Genevieve

last: Syn

state: Western Australia

address: 100 Roberts Road

country: Australia

institute: Telethon Kids Institute

summary: Analysis of gene expression patterms following infection of the parasite Toxoplasma gondii in a clinically relevant retinal cell line over a time course of 2 hours, 6 hours and 24 hours. Parasites were washed off after 2 hours to ensure that gene expression changes are truly reflective of an on-going infection, and not on-going parasite invasion.

overall_design: Total RNA extracted from Toxoplasma gondii infected for 2, 6 and 24 hours post-infected compared to mock-infected cells at the same time points

first: Denise

last: Anderson

first: Jenefer

middle: M

last: Blackwell

first: Sarra

last: Jamieson


title: Expression profiling of human early myotubes after exposure to RXF or SKR conditioned media

status: Public on May 01 2016

city: Singapore

first: Shyh-Chang

last: Ng

address: 60 Biopolis St

institute: Genome Institute of Singapore

summary: Cachexia is a devastating muscle wasting syndrome that occurs in patients suffering from chronic diseases, most commonly observed in 80% of advanced cancer patients. One of the primary causes of cachexia-associated morbidity and mortality is involuntary muscle wasting. And while many cachexia patients show hypermetabolism, its causative role in muscles had remained unclear. To understand the molecular basis of this muscle wasting, accurate models of cachexia are necessary. Using transcriptomics and cytokine profiling of human muscle stem cell-based models and human cancer-induced cachexia models in mice, we found that cachectic cancer cells secreted many inflammatory factors which rapidly led to higher levels of fatty acid metabolism and the activation of a p38 stress response signature, before the cachectic muscle wasting is manifested. Metabolomics profiling revealed that factors secreted by cachectic cancer cells rapidly induce excessive fatty acid oxidation in human myotubes, leading to oxidative stress, p38 activation, and impaired muscle growth. Pharmacological blockade of fatty acid oxidation not only rescued human myotubes, but also significantly improved muscle mass and total weight in cancer cachexia models in vivo. Therefore, fatty acid-induced oxidative stress could be targeted to prevent cancer cachexia.

overall_design: Primary human myoblasts were exposed to RXF or SKR conditioned media for 6 d, by which time they grew and differentiated into early myotubes. Human early myotubes were harvested and total RNA was extracted with the Trizol reagent (Ambion) for each sample, processed with the Total Prep RNA for Illumina kit (Ambion), and hybridized to an Illumina HumanHT-12 v4.0 beadchip, then scanned on the Illumina Beadarray Reader. Array normalization was performed with Illumina Genome Studio Gene Expression module 1.9.0 using quantile normalisation.

first: Yan-Jiang

middle: B

last: Chua

first: Jun-Hao

last: Tan


title: Knocking down fibroblastic core TFs and/or Overexpressing monocytic core TFs in human dermal fibroblasts

status: Public on Apr 27 2016

city: Yokohama

first: Jing-Ru

last: Li

state: Kanagawa

address: 1-7-22 Suehiro-cho,

department: Devision of Genomic Technology

institute: RIKEN Center for Life Science Technologies,

summary: we simultaneously deconstructed fibroblastic TRNW and reconstituted monocytic TRNW, and analyzed its monocytic and fibroblastic gene expression in comparison with that of fibroblastic TRNW deconstruction only or monocytic TRNW reconstitution only. This study provides an explicit example demonstrating how two networks together regulate gene expression during cell reprogramming processes.

overall_design: Total RNA obtained from human dermal fibroblasts(FIB), human CD14+ monocytes(Mon), knocking down fibroblastic only (KD-only),monocytic core TFs transduced (OE-only), and knocking down plus overxpression (KDOE)

first: Jing-ru

first: Takahiro

last: Suzuki

first: Hajime

last: Nishimura

first: Mami

last: Kishima

first: Shiori

last: Maeda

first: Harukazu


title: Transcriptome analysis of human airway stem cells at their early and late passages expanded in dual SMAD signaling inhibitors

status: Public on Apr 19 2016

city: Boston

first: Hongmei

last: Mou

state: MA

address: 55 Fruit Street, Jackson 1402

department: The Mucosal Immunology & Biology Research Center

institute: Massachusetts General Hospital

summary: SUMMARY of the associated publication: Many adult epithelial stem cells cannot undergo prolonged expansion. This may be due to a cell autonomous limitation or a lack of necessary culture conditions. Thus far, the long-term culture of adult stem cells has required the use of Matrigel organoid culture or feeder co-culture systems. We demonstrate that the TGFbetaBMP/SMAD signaling pathway is highly active in the luminal cells of diverse p63+ basal cell-containing epithelia. Indeed, the activation of SMAD signaling in airway stem cells causes their differentiation, while conversely, inhibition of SMAD signaling leads to stem cell hyperplasia and compromised differentiation. Consistently, TGFbetaBMP/SMAD signaling activation prevents mature cell dedifferentiation. Using pharmacologic dual SMAD inhibition, we developed a feeder-free culture system that allows the cloning of single airway basal stem cells and the expansion of airway stem cells from clinical non-invasively obtained samples with high efficiency. Furthermore, the expansion protocols are applicable not only to human cells but also to those of mouse, ferret, and pig. When differentiated epithelia are produced from expanded cells, they exhibit proper epithelial physiology, and respond to clinically relevant pharmacologic agents. Most remarkably, a very wide variety of functional adult epithelial basal stem cells can be expanded despite their differing origins. The goal of this microarray analysis: It has been shown that inhibition of TGFbeta signaling leads to tumorigenesis (e.g. Guasch et al., 2007, and others). It will be important to show whether the dual inhibited population assumes a tumorigenic status in the same or different manner compared to directly isolated progenitor cells. To address this concern, we have done comprehensive transcriptome analysis comparing gene expression signature of airway stem cells at their early and late passages. We do not find tumor-associated gene signatures during stem cell expansion.

overall_design: Sample: Human airway stem cells (normal without known lung diseases) at their passage 2 (P2), passage 8 (P8) and passage 14 (P14) are analyzed. Total number of sample: 9 (3 replicates at each passage). Microarray analysis condition: Total RNA is isolated from human airway stem cells from early to late passages using TRIzol (Invitrogen) and the miRNeasy mini kit (Qiagen) according to manufacturer’s instructions. RNA is hybridized on Illumina Human HT-12 (Translational Genomics Core, MGH). After normalization of probe intensities, annotated oncogenes and cancer suppressors are analyzed for their differential gene expression.

first: Mou

last: Hongmei

first: Rajagopal

last: Jayaraj