title: Human induced pluripotent stem cells (iPSCs) derived from T-cell compared with that from adult dermal fibroblast (aHDF) [gene expression]

city: Shinjuku-ku

first: Takuya

last: Matsumoto

address: 35 Shinanomachi

institute: Keio University School of Medicine

summary: In this study we determine the transcriptional profile by microarray of iPSCs and iPSC-derived neurospheres generated from T-cells or aHDF by using direct neurosphere method.

overall_design: iPSCs and iPSC-derived tertiary neurospheres generated from T-cells or aHDF subjected to the gene expression microarray analysis.

first: T

first: K

last: Fujimori

first: W

last: Akamatsu

first: H

last: Okano


title: eHSP70 promotes osteogenesis of hMSCs through activating ERK signaling pathway

status: Public on Jan 01 2016

city: Hangzhou

first: Erman

last: Chen

state: Zhejiang Province

address: No.88, Jiefang road

department: Department of Orthopedics

country: China

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

summary:
Heat shock proteins are highly conserved proteins that, when produced intracellularly, protect stress exposed cells. It has been suggested that extracellular Hsp70 has both protective and deleterious effects. Our study showed eHSP70 increased the ALP activity, promoted mineralization and up-regulated osteogenesis-related markers.
We used microarrays to determine the differentially expressed genes and identify revelant pathways through pathway enrichment analysis.

overall_design: hMSCs were selected for RNA extraction and hybridization on Affymetrix microarrays  after 3-day culture. The experimental group was treated with HSP70 (200ng/ml) during osteogenic differentiation and control group without it.

first: Zhijun

last: Pan

first: Deting

last: Xue

first: Wei

last: Zhang

first: Feng

last: Lin


title: DNA methylation profiling of placental villi from karyotypically normal recurrent miscarriage

status: Public on Jan 02 2016

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

summary: Miscarriage occurs in 15-20% of clinical pregnancies. While chromosomal errors are observed in over 50%, causes of karyotypically normal losses are poorly understood. DNA methylation undergoes reprogramming during development and must be appropriately set to maintain a healthy pregnancy. We hypothesize that aberrant DNA methylation may cause karyotypically normal miscarriage, particularly among women experiencing recurrent miscarriage (RM). DNA methylation in first trimester chorionic villi was assessed in chromosomally normal miscarriages from women with RM (N=33) or isolated miscarriage (M, N=21), and elective terminations (TA, N=16). Differentially methylated candidate loci were identified using the Illumina Infinium HumanMethylation27 BeadChip array by comparing 10 RM to 10 TA samples. Follow up showed a significant increase in methylation in RM and M compared to TA placentae at the CYP1A2 (p=0.002) and AXL (p=0.02) promoters and decrease at the DEFB1 (p=0.008) promoter. Gene function analysis showed an enrichment of imprinted genes (p=9.53E-10) and genes previously associated with RM (p=9.51E-06). DNA methylation was evaluated at 7 imprinted loci using bisulfite pyrosequencing. An increase of outliers at these loci was observed in RM (3.9%) compared to M (0%) and TA (0.9%) (p=0.02), with increased average methylation at the H19/IGF2 ICR1 in M samples (p<0.0001). Altered DNA methylation in the placenta at specific loci, as well as global dysregulation in specific cases, may contribute to or be a consequence of placental insufficiency in karyotypically normal miscarriage.

overall_design: First-trimester placental villi samples from karyotypically normal miscarriages from recurrent miscarriage patients (N, N=10) and chromosomally normal elective terminations (PZET, N=10).

first: C

middle: W

last: Hanna

first: D

middle: E

last: McFadden

middle: P


title: Integrated DNA methylation and RNA expression in Small Intestinal neuroendocrine tumors

city: London

first: Andrew

last: Feber

address: Division of Surgery & Interventional Science, Charles Bell House, 43-45 Foley Street

country: United Kingdom

institute: University College London

summary:
Background and Aims Small intestinal neuroendocrine tumours (SINETs) are the commonest malignancy of the small intestine; however underlying pathogenic mechanisms remain poorly characterised. Whole genome and exome sequencing has demonstrated that SINETs are mutationally quiet with the most frequent known mutation in the cyclin dependent kinase inhibitor 1B gene (CDKN1B) occurring in only ~8% of tumours, suggesting that alternative mechanisms may drive tumourigenesis. The aim of this study is to perform genome-wide molecular profiling of SINETs in order to identify pathogenic drivers based on molecular profiling. This study represents the largest unbiased integrated genomic, epigenomic, and transcriptomic analysis undertaken in this tumour type. Methods Here we present data from integrated molecular analysis of SINETs (n=97) including whole exome or targeted CDKN1B sequencing (n=29), HumanMethylation450 BeadChip (Illumina) array profiling (n=69), methylated DNA immunoprecipitation sequencing (n=16), copy number variance analysis (n=47) and Whole Genome-DASL (Illumina) expression array profiling (n=43). Results Based on molecular profiling SINETs can be classified in to three groups which demonstrate significantly different progression-free survival after resection of primary tumour (not reached at 10 years vs 56 months vs 21 months, p=0.04). Epimutations were found at a recurrence rate of up to 85% and 21 epigenetically dysregulated genes were identified, including CDX1 (86%), CELSR3 (84%), FBP1 (84%) and GIPR (74%). Conclusions This is the first comprehensive integrated molecular analysis of SINETs. We have demonstrated that these tumours are highly epigenetically dysregulated. Furthermore, we have identified novel molecular subtypes with significant impact on progression free survival.
Background and Aims Small intestinal neuroendocrine tumours (SINETs) are the commonest malignancy of the small intestine; however underlying pathogenic mechanisms remain poorly characterised. Whole genome and exome sequencing has demonstrated that SINETs are mutationally quiet with the most frequent known mutation in the cyclin dependent kinase inhibitor 1B gene (CDKN1B) occurring in only ~8% of tumours, suggesting that alternative mechanisms may drive tumourigenesis. The aim of this study is to perform genome-wide molecular profiling of SINETs in order to identify pathogenic drivers based on molecular profiling. This study represents the largest unbiased integrated genomic, epigenomic, and transcriptomic analysis undertaken in this tumour type. Methods Here we present data from integrated molecular analysis of SINETs (n=97) including whole exome or targeted CDKN1B sequencing (n=29), HumanMethylation450 BeadChip (Illumina) array profiling (n=69), methylated DNA immunoprecipitation sequencing (n=16), copy number variance analysis (n=47) and Whole Genome-DASL (Illumina) expression array profiling (n=43). Results Based on molecular profiling SINETs can be classified in to three groups which demonstrate significantly different progression-free survival after resection of primary tumour (not reached at 10 years vs 56 months vs 21 months, p=0.04). Epimutations were found at a recurrence rate of up to 85% and 21 epigenetically dysregulated genes were identified, including CDX1 (86%), CELSR3 (84%), FBP1 (84%) and GIPR (74%). Conclusions This is the first comprehensive integrated molecular analysis of SINETs. We have demonstrated that these tumours are highly epigenetically dysregulated. Furthermore, we have identified novel molecular subtypes with significant impact on progression free survival.

overall_design: This study included 97 tumour samples from 85 individuals, this included both primary and metastatic tumour samples. 25 normal small intestinal samples were analysed.

first: Anna

last: Karpathakis

first: Harpreet

last: Dibra

first: Chrisodoulos

last: Pipinikas

first: Tiffany

last: Morris

first: Joshua

middle: M

last: Francis

first: Dahmane

last: Oukrif

first: Dalvinder

last: Mandair

first: Marinos

last: Pericleous

first: Mohammad

last: Mohmaduvesh

first: Stefano

last: Serra

first: Olagunju

last: Ogunbiyi

first: Marco

last: Novelli

first: Tu-Vinh

last: Luong

first: Sylvia

middle: L

last: Asa

first: Matthew

middle: H

last: Kulke

first: Christos

last: Toumpanakis

first: Timothy

last: Meyer

first: Martyn

last: Caplin

last: Meyerson

first: Stephan

last: Beck

first: Christina

last: Thirlwell


title: TMEM45A, SERPINB5 and p16INK4A transcript levels are predictive for development of high-grade cervical lesions

city: Tuebingen

first: Frank

last: Stubenrauch

address: Elfriede-Aulhorn-Str. 6

department: Institute for Medical Virology

country: Germany

institute: University Hospital Tuebingen

summary: Women persistently infected with human papillomavirus (HPV) type 16 are at high risk for development of cervical intraepithelial neoplasia grade 3 or cervical cancer (CIN3+). We aimed to identify biomarkers for progression to CIN3+ in women with persistent HPV16 infection. In this prospective study, 11,088 women aged 20–29 years were enrolled during 1991-1993, and re-invited for a second visit two years later. Cervical cytology samples obtained at both visits were tested for HPV DNA by Hybrid Capture 2 (HC2), and HC2-positive samples were genotyped by INNO-LiPA. The cohort was followed for up to 19 years via a national pathology register. To identify markers for progression to CIN3+, we performed microarray analysis on RNA extracted from cervical swabs of 30 women with persistent HPV16-infection and 11 HPV-negative women. After further validation, we found that high mRNA expression levels of TMEM45A, SERPINB5 and p16INK4a were associated with increased risk of CIN3+ in persistently HPV16-infected women.

overall_design: We aimed at identifying genes differentially expressed in women with persistent HPV16 infection that either progressed to CIN3+ or not. As a test of principle we first compared HPV16 persistently infected women with HPV-negative women.

first: Anna

last: Manawapat-Klopfer

first: Rainer

last: Russ

first: Hans

last: Gmuender

first: Susanne

middle: K

last: Kjaer

first: Thomas

last: Iftner


title: Gene expression profile of splenic CD19 cells from NTg, PTPROt Tg, TCL1 Tg and PTPROt/TCL1 double Tg mice

status: Public on Jan 04 2016

city: Columbus

first: Tasneem

last: Motiwala

address: 420 W. 12th Ave

country: USA

institute: The Ohio State University

summary: TCL1 is an an oncogene and transgenic (Tg) mice expressing TCL1 specifically in B-cells are well-characterized models for chronic lymphocytic leukemia. On the contrary, PTPROt is a phosphatase with tumor suppressor characteristics in many cancers including leukemia. Our hypothesis was that transgenic expression of PTPROt in the B-cells of TCL1 Tg mice will alleviate disease phenotype and allow the study of the in vivo mechanism of action of PTPROt. To test this we have generated Tg mice with B-cell specific expression of PTPROt and crossed these mice with the TCL1 Tg mice.

overall_design: Single-channel experiment. Four replicates for each of the four groups (NTg, PTPROt Tg, TCL1 Tg, PTPROt/TCL1 double Tg) of mice at 4 months of age.

first: Xiaokui

last: Mo

first: Samson

middle: T

last: Jacob


title: Expression data of SHSY5Y cells after cocaine exposure

city: Barcelona

first: Noelia

last: Fernandez-Castillo

address: Avda Diagonal 643. Edifici Prevosti 3r pis.

department: Genetics

country: Spain

institute: Universitat de Barcelona

summary:
The aim of the study was to evaluate cocaine-induced changes in gene expression in a dopaminergic model.
Cocaine reward and reinforcing effects are mediated mainly by dopaminergic neurotransmission. In this study we aimed at evaluating gene expression changes induced by acute cocaine exposure on SH-SY5Y differentiated cells, which have been widely used as a dopaminergic neuronal model. Expression changes and a concomitant increase in neuronal activity were observed 6 hours after a 5 uM cocaine exposure, whereas no changes in gene expression nor in neuronal activity took place at 1 uM cocaine. A total of 756 differentially expressed genes, mainly related to regulation of transcription and gene expression, cell cycle, adhesion and cell projection, as well as MAPK, CREB, neurotrophin and neuregulin signaling pathways. Genes displaying altered expression were subsequently targeted with predicted functional SNPs in a case-control association study in a sample of 806 cocaine-dependent patients and 817 controls. This study highlighted associations between cocaine dependence and five SNPs predicted to alter microRNA binding at the 3’UTR of the NFAT5 gene. The association of SNP rs1437134 with cocaine dependence survived the Bonferroni correction for multiple testing. A functional effect was confirmed for this variant by a luciferase reporter assay, with lower expression observed for the rs1437134G allele, which was more pronounced in the presence of hsa-miR-509. However, brain volumes in regions of relevance to addiction, as assessed with MRI, did not correlate with NFAT5 variation. These results suggest that the NFAT5 gene, which is up-regulated a few hours after cocaine exposure, may be involved in the genetic predisposition to cocaine dependence.

overall_design: for each condition, 9 dishes containing SH-SY5Y were used. Pools of RNA from three dishes were used for each replicate in the microarray.

first: Noèlia

last: Fernàndez-Castillo

first: Bru

last: Cormand


city: Montréal

first: Mathieu

last: Vernier

state: Quebec

address: 2900 Edouard Montpetit

department: Biochemistry

institute: Université de Montréal

summary:
Expression data from xenograft in BALB/c 6-wk-old nude mice with PC3 prostate cancer cells stably expressing PML or a vector control after treatment of the mice with palbociclib (100mg/kg/day diluted in sodium lactate 50mM pH4 given by gavage) during 5 consecutive days
PML plays a role in the senescence tumor suppressor response of normal cells to oncogenic stress. PML also mediates therapy-induced senescence in acute promyelocytic leukemia cells after treatment with retinoic acid. However, many tumor cell lines fail to engage a complete senescence response to PML activation. Interestingly, in vivo and in vitro combination of PML overexpression with CDK inhibition induce senescence in PC3 prostate cancer cells. We used microarray to characterize the gene expression profile of PC3 stably expressing PML or a control vector after subcutaneous injection in BALB/c 6-wk-old nude mice and treatment of the mice with palbociclib (100mg/kg/day) during 5 consecutive days..

overall_design: PC3 cells were infected with a retroviral vector that express PML or an empty vector before subcutaneous injection of 10^6 cells in both flanks of BALB/c 6-wk-old nude mice. Then, mice were treated for 5 consecutive days with  palbociclib (100mg/kg/day diluted in sodium lactate 50mM pH4 given by gavage)

first: Mariana

last: Acedevo

last: vernier

first: Lian

last: Mignacca

first: Geneviève

last: Huot

first: Olga

last: Moiseeva

first: Véronique

last: Bourdeau

first: Gerardo

last: Ferbeyre

first: Frédéric

last: Lessard


title: Repeated monthly epicutaneous challenges with diphenylcyclopropenone (DPCP).

city: Copenhagen N

first: Atul

last: Anand

address: Ole Maaløes Vej 5, building 2, 3 floor

department: Department of Pathology

country: Denmark

institute: Rigshospitalet

summary: The level of reactivity in pre-sensitized individuals following repeated epicutaneous challenges with diphenylcyclopropenone (DPCP) remains unknown. We studied the kinetics and time-course of the developing reactivity to this potent contact sensitizer using genome-wide gene expression data

overall_design: Ten healthy human volunteers were sensitized to DPCP. Five or six elicitation challenges were performed and punch biopsies were selected from vehicle control and challenge sites for RNA extraction and hybridization on Affymetrix microarrays.

first: Kristian

middle: F

last: Mose

first: Mark

last: Burton

first: Mads

last: Thomassen

first: Flemming

last: Andersen

first: Torben

middle: A

last: Kruse

first: Qihua

last: Tan

first: Lone

last: Skov

last: Røpke

last: Litman

first: Ole

last: Clemmensen

first: Bjarne

last: Kristensen

first: Peter

middle: S

last: Friedmann

first: Klaus


title: Genome-wide profiling of PARP1 reveals an interplay with gene regulatory regions and DNA methylation

city: Grand Rapids

first: Yvonne

middle: Nsokika

last: Fondufe-Mittendorf

state: MI

address: 333 Bostwick Ave NE

department: Epigenetics

institute: Van Andel Institute

summary:
To address the global impact of PARP-1 on DNA methylation, we treated cells with PJ34 (PARylation inhibitor) and isolated genomic DNA from vehicle and PJ34 treated cells. This DNA was bisulfite treated and hybridized to the Illumina infinium Methylation 450 Beadchip. We next used these RNA-seq data sets (control, PARP-1 KD and PARylation inhibited) to assess whether PARP plays a role in DNA methylation by assessing differential methylation patterns.
PARP1 mediates methylation patterns.

overall_design: DNA from vehicle and PJ34 (PARylation inhibited) cells. 750ng of geneomic DNA was bisulfite converted and used for the Illumia infinium HD methylation assay.

first: Narasinharao

last: Nalabothula

first: Al-jumaily

last: Taha

first: Xiaorong

last: Shao


title: Regulation of ER Homeostasis and Cell Cycle by Pax4 Enhances β-Cell Survival and Protects Mice Against Experimental Autoimmune Diabetes

city: Seville

first: Benoit

middle: Raymond

last: Gauthier

state: Seville

address: Americo Vespucio Avenue

department: Stem Cells

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

summary: Strategies to enhance islet b-cell survival and regeneration while refraining inflammation through manipulation of molecular targets would provide means to stably replenish the deteriorating functional b-cell mass detected in both Type 1 and Type 2 Diabetes Mellitus (T1DM and T2DM). Herein we report that over expression of the islet enriched transcription factor Pax4 refrains development of hyperglycemia in the RIP-B7.1 mouse model of T1DM through reduced insulitis, decreased b-cell apoptosis correlating with diminished DNA damage and increased proliferation. Transcriptomics revealed up regulation of genes involved in immunomodulation, cell cycle and ER homeostasis in islets over expressing Pax4 as compared to the T2DM-linked mutant variant Pax4R129W. Pax4 but not Pax4R129W protected islets from thapsigargin-mediated ER-stress apoptosis. Collectively, Pax4 is a critical signaling hub coordinating regulation of distinct molecular pathways resulting in improved b-cell fitness whereas Pax4R129W sensitizes to death under stress. More importantly we highlight potential common pharmacological targets for the treatment of DM.

overall_design: 4 groups of 3 samples each. Primary isolated islets of langerhans from either Pax4/rtTA or Pax4R121W/rtTA mice treated or not with Doxicycline.

first: Ana

middle: I

last: Alvarez-Mercado

first: José

last: Gil

first: Carmen

last: Jiménez-Moreno

first: Alejandro

last: Martin-Montalvo

first: Nadia

last: Cobo-Vuilleumier

first: Petra

last: Lorenzo

first: Irene

last: de Gracia Herrera Gómez

first: Livia

last: Noriega

first: Javier

last: Pérez-Florido

last: Santoyo-López

first: Paolo

last: Meda

first: Andreas

last: Spyrantis

first: Bernhard

middle: O

last: Boehm

middle: R


title: Methylome study in Nasopharyngeal Carcinoma (NPC)

city: Hong Kong

first: Maria

middle: Li

last: Lung

address: 21 Sassoon Road

department: Clinical Oncology

country: Hong Kong

institute: The University of Hong Kong

summary: Aberrant methylation at the promoter region of tumor suppressors is frequently reported in NPC; however, genome-wide methylation changes have not been comprehensively investigated. Therefore, we systematically analyzed methylome data in 25 primary NPC tumors and non-tumor counterparts using Illumina HumanMethylation450 BeadChip.

overall_design: Bisulphite converted DNA from 50 samples were hybridized to the Illumina HumanMethylation450 BeadChip. Bisulphite pyrosequencing was used as an independent method to validate the BeadChip results.

first: Wei

last: Dai


title: Comparison of cultured chondrocytes from knee and proximal interphalangeal joints

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

summary: Osteoarthritis (OA) of the hand is a common disease resulting in pain and impaired function.  The pathogenesis of hand OA (HOA) is elusive and models to study it have not been described so far. Culture of chondrocytes is a model to study the development of cartilage degeneration, which is a hallmark of OA and well established in OA of the knee and hip. In the current study we investigated the feasibility human chondrocyte culture derived from proximal interphalangeal (PIP) finger joints of dissecting room cadavers. Index and middle fingers without signs of osteoarthritis were obtained from 30 cadavers using two different protocols.  Hyaline cartilage from both articulating surfaces of the proximal interphalangeal (PIP) joint was harvested and digested in collagenase. Cultured chondrocytes were monitored for contamination, viability, and expression of chondrocyte specific genes. Chondrocytes derived from knee joints of the cadavers were cultured under identical conditions. Gene expression comparing chondrocytes from PIP and knee joints was carried out using Affymetrix GeneChip Human 2.0 ST arrays. The resulting differentially expressed genes were validated by real-time PCR and immunohistochemistry.Chondrocytes harvested up to 101 hours after death of the donors were viable. mRNA expression of collagen 2A1, aggrecan and Sox9 was significantly higher in chondrocytes as compared to cultured fibroblasts.  Comparison of gene expression by chondrocytes from PIP and knee joints yielded 528 differentially expressed genes. Chondrocytes from the same joint region had a higher grade of similarity than chondrocytes of the same individual. These results were validated using real-time PCR and immunohistochemistry.We demonstrate for the first time a reliable method for culture of chondrocytes derived from PIP joints. PIP chondrocytes show a specific gene expression pattern and could be used as tool to study cartilage degeneration in HOA.

overall_design: Three samples of cultured chondrocytes from knee and proximal interphalangeal finger joints were compared. Gene expression of the four most differentially regulated genes was confirmed by real-time PCR in 10 independent samples.

first: Martin

last: Stradner


title: Expression data from primary term human decidual cells treated with interleukin-1-beta for 6 hours.

first: Douglas

last: Kniss

state: Ohio

address: 395 W. 12th Ave

department: Obstetrics and Gynecology

institute: Ohio State University

summary: Preterm birth is an important unsolved clinical problem.  Despite advanced treatments, infants who survive prematurity remain at increased risk for permanent disabilities.  In approximately one-third of cases, prematurity is related to infection and/or inflammation, which renders hostile the normally receptive intrauterine environment.  Proinflammatory cytokines provoke up-regulation of genes that promote uterine contractions.  Using monolayer cultures of human decidual cells as a model, we profiled the global pattern of gene expression in response to cytokine challenge.

overall_design: Decidualized human endometrial stromal cells were treated with 1 ng/ml of interleukin-1-beta for 6 hours, while control cells were treated with 0.1% PBS containing 0.1% bovine serum albumin (vehicle).  The cells were subjected to RNA extraction, quantification, and evaluation, followed by hybridization on Affymetrix Human Gene 2.0 ST Arrays (Platform GPL16686). Three biological replicates were used (6 total samples).

first: Sherrine

last: Ibrahim

first: William

last: Ackerman

first: Taryn

last: Summerfield

first: Charles

middle: J

last: Lockwood


title: Expression data of caerulein-treated wild-type mice and KrasG12D-mutated mice at different stages of pancreatic regeneration after inflammatory injury

city: Neuherberg

first: Philipp

last: Bruns

address: Ingolstädter Landstr. 1

department: ICB

institute: Helmholtz Zentrum München

summary:
Consecutive caerulein injections induce an acute pancreatitis in mice. Here, we recorded gene expression levels at different stages of  pancreatic regeneration in wild-type mice as well as
KrasG12D-mutated mice. Tissue was collected from mice pancreata, cell sorting was not performed. t=0h refers to the time where caerulein was injected. control referes to NaCl-treated samples (no caerulein).

overall_design: 13 time points were used for wild-type mice, 9 time points were used for KrasG12D-mutated mice. Multiple replicates were generated for each time point. We used Affymetrix GeneChip Mouse Gene 1.0 ST arrays.

first: B

last: Kong

first: P

first: N

last: Behler

first: S

last: Fritzsche

last: Valkovska

first: M

last: Irmler

first: J

last: Beckers


title: Sphere-Derived Multipotent Progenitor Cells Obtained From Human Oral Mucosa Are Enriched in Neural Crest Cells.

city: Itabashi-ku, Tokyo

first: Shigehiro

last: Abe

address: 30-1 Oyaguchikami-cho

department: Oral Surgery

country: Japan

institute: Nihon University

summary: The purpose of this study was to isolate NCSCs from oral mucosa using the neurosphere technique.

overall_design: Total RNA from human oral mucosa stromal cells and sphere-formig oral mucosa stromal cells was collected and compared at their gene expression level. Samples from 3 patients were analysed.

first: Satoshi

last: Yamaguchi

first: Yutaka

last: Sato

first: Kiyoshi

last: Harada


title: Delayed Cardiomyocyte Response to Total Body Particle Radiation Exposure – Identification of Regulatory Gene Network [proton]

city: Livermore

first: Matthew

last: Coleman

state: CA

address: 7000 East Ave.

institute: Lawrence Livermore National Laboratory

summary: We examined molecular responses using transcriptome profiling in isolated left ventricular murine cardiomyocytes to 90 cGy, 1 GeV proton (1H) and 15 cGy, 1 GeV/nucleon (n) proton (56Fe) particles 1, 3, 7, 14 and 28 days after exposure.  Unsupervised clustering analysis of gene expression segregated samples according to the radiation (IR) response, and time after exposure with 56Fe-IR showing the greatest level of gene modulation. 1H-IR exposures showed little differential transcript modulation. Network analysis categorized the major differentially expressed genes into cell cycle, oxidative responses and transcriptional regulation functional groups. Transcriptional networks identified key nodes regulating expression. Individual transcription factors were inferred to be active at 1, 3, 7, 14 and 28 days after exposure.  Validation of the signal transduction network by protein analysis showed that particle IR clearly regulates a long lived signaling mechanism for p38 MAPK signaling and NFATc4 activation. Electrophoresis mobility shift assays supported the role of additional key transcription factors GATA-4, STAT-3 and NF-κB as regulators of the response at specific time points. These data suggest that the molecular response to 56Fe-IR is unique and shows long-lasting gene expression in cardiomyocytes, up to 28 days after exposure.  Additionally, proteins involved in signal transduction and transcriptional activation via DNA binding play a role in the response to high charge (Z) and energy (E) particles (HZE).  Our study may have implications for NASA’s efforts to develop heart disease risk estimates for astronauts safety via identification of specific HZE-IR molecular markers and for patients receiving conventional and particle radiotherapy.

overall_design: Transcriptome profiling in isolated left ventricular murine cardiomyocytes to 90 cGy, 1 GeV proton (1H) and 15 cGy, 1 GeV/nucleon (n) proton (56Fe) particles 1, 3, 7, 14 and 28 days after exposure.

first: David

last: Goukassian


title: Delayed Cardiomyocyte Response to Total Body Particle Radiation Exposure – Identification of Regulatory Gene Network [iron]

summary: We examined molecular responses using transcriptome profiling in isolated left ventricular murine cardiomyocytes to 90 cGy, 1 GeV proton (1H) and 15 cGy, 1 GeV/nucleon (n) iron (56Fe) particles 1, 3, 7, 14 and 28 days after exposure.  Unsupervised clustering analysis of gene expression segregated samples according to the radiation (IR) response, and time after exposure with 56Fe-IR showing the greatest level of gene modulation. 1H-IR exposures showed little differential transcript modulation. Network analysis categorized the major differentially expressed genes into cell cycle, oxidative responses and transcriptional regulation functional groups. Transcriptional networks identified key nodes regulating expression. Individual transcription factors were inferred to be active at 1, 3, 7, 14 and 28 days after exposure.  Validation of the signal transduction network by protein analysis showed that particle IR clearly regulates a long lived signaling mechanism for p38 MAPK signaling and NFATc4 activation. Electrophoresis mobility shift assays supported the role of additional key transcription factors GATA-4, STAT-3 and NF-κB as regulators of the response at specific time points. These data suggest that the molecular response to 56Fe-IR is unique and shows long-lasting gene expression in cardiomyocytes, up to 28 days after exposure.  Additionally, proteins involved in signal transduction and transcriptional activation via DNA binding play a role in the response to high charge (Z) and energy (E) particles (HZE).  Our study may have implications for NASA’s efforts to develop heart disease risk estimates for astronauts safety via identification of specific HZE-IR molecular markers and for patients receiving conventional and particle radiotherapy.

overall_design: Transcriptome profiling in isolated left ventricular murine cardiomyocytes to 90 cGy, 1 GeV proton (1H) and 15 cGy, 1 GeV/nucleon (n) iron (56Fe) particles 1, 3, 7, 14 and 28 days after exposure.


title: Expression data in mouse liver expressing or not the adapter Grb14

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

summary:
Grb14 is an endogenous inhibitor of insulin signaling
We used microarrays to investigate gene expression patterns after Grb14 silencing in mouse liver

overall_design: Ten week old mice were injected intraveinously with recombinant adenovirus expressing a control sh RNA (sh scramble) or a sh targetting Grb14 (shGrb14), and liver were studied in the fed state 7 days after the infection

first: Lucie

last: Popineau

first: Anne-Francoise

last: Burnol


title: Shp2 transcriptome in melanoma

city: Rochester

first: Glynis

middle: Aileen

last: Scott

state: New York

address: 601 Elmwood Ave

department: Dermatology

institute: University of Rochester School of Medicine

summary: 1205Lu Metastatic Human melanoma cell lines with knockdown of Shp2 (PTPN11) were grown as xenograft tumors in NSG mice. RNA was extracted from the tumors and analyzed on [HuGene-2_0-st] Affymetrix Human Gene 2.0 ST Array [transcript (gene) version]

overall_design: Shp2 knockdown compared with non-target controls


title: LATS2 regulated genes in human colon cancer cell line

city: Los angeles

first: Xiangming

last: Ding

address: 650 Charles E Young Dr S, Los Angeles, CA 90095

institute: UCLA

summary: To investigate how LATS2 affect Wnt target genes expression, we performed gene expression profiling and comparison in control, LATS2 and LATS2N (1-625, kinase domain deletion) overexpression in human colorectal cancer SW480 cells.

overall_design: In SW480 cell line, the stable expression of LATS2 or LATS2N was generated. Total RNA was extracted from these 2 samples and control cell line

first: Jiong

last: Li

first: Cun-yu

last: Wang


title: Expression data from five independent murine BM MSC

city: Rehovot

first: Sarit

last: Levin

address: 234 Herzel st.

department: Department of Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

summary:
Data collected in our laboratory show that independent murine MSC cultures react in a heterogeneous manner to Toll-like receptors (TLRs) activation.
This array aims to investigate the molecular basis for the heterogeneity in the response of MSCs to TLR activation and its origin.

overall_design: For this array, 5 MSC preparation, all from BM of female C57BL/6J 6-8 weeks old, were studied in two replicates.

first: Meirav

middle: P

last: Fischer

first: Gilgi

last: Friedlander

first: Dov

last: Zipori


title: Array-based determination of DNA methylation in children born small for gestational age

city: Ulm

first: Ole

last: Ammerpohl

address: Albert-Einstein-Allee 11

institute: UK Ulm

summary: Genome wide DNA methylation profiling of peripheral blood samples obtained from normal controls and children born SGA. Illumina's HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across approximately 450.000 CpGs.

overall_design: Bisulphite converted DNA from the 110 samples were hybridised to the Illumina HumanMethylation450 Beadchip.

first: Julia

last: Kolarova


title: Induced Pluripotency of Human Prostatic Epithelial Cells

city: Stanford

first: Hongjuan

last: Zhao

address: 300 Pasteur Dr

department: Urology

institute: Stanford

summary: Induced pluripotent stem (iPS) cells are a valuable resource for discovery of epigenetic changes critical to cell type-specific differentiation. Although iPS cells have been generated from other terminally differentiated cells, the reprogramming of normal adult human basal prostatic epithelial (E-PZ) cells to a pluripotent state has not been reported.  Here, we attempted to reprogram E-PZ cells by forced expression of Oct4, Sox2, c-Myc, and Klf4 using lentiviral vectors and obtained embryonic stem cell (ESC)-like colonies at a frequency of 0.01%.  These E-PZ-iPS-like cells with normal karyotype gained expression of pluripotent genes typical of iPS cells (Tra-1-81, SSEA-3, Nanog, Sox2, and Oct4) and lost gene expression characteristic of basal prostatic epithelial cells (CK5, CK14, and p63).  E-PZ-iPS-like cells demonstrated pluripotency by differentiating into ectodermal, mesodermal, and endodermal cells in vitro, although lack of teratoma formation in vivo and incomplete demethylation of pluripotency genes suggested only partial reprogramming.  Importantly, E-PZ-iPS-like cells re-expressed basal epithelial cell markers (CD44, p63, MAO-A) in response to prostate-specific medium in spheroid culture.  Androgen induced expression of androgen receptor (AR), and co-culture with rat urogenital sinus further induced expression of prostate-specific antigen, a hallmark of secretory cells, suggesting that E-PZ-iPS-like cells have the capacity to differentiate into prostatic basal and secretory epithelial cells.  Finally, when injected into mice, E-PZ-iPS-like cells expressed basal epithelial cell markers including CD44 and p63.  When co-injected with rat urogenital mesenchyme, E-PZ-iPS-like cells expressed AR and expression of p63 and CD44 was repressed. DNA methylation profiling identified key pathways and regulators of prostatic differentiation including Wnt5a, BPM7, PTEN, and NKx3.1 using E-PZ-iPS-lke cells. Our results suggest that iPS-like cells can be derived from prostatic epithelial cells.  These cells are pluripotent and capable of prostatic differentiation, and therefore provide a novel model for investigating epigenetic changes involved in prostate cell lineage specification.

overall_design: Bisulphite converted DNA from the 10 samples were hybridised to the Illumina Infinium HumanMethylation450K Beadchip v1.2

first: Donna

middle: M

last: Peehl


title: Dual roles of RNF2 in melanoma progression [expression]

city: Houston

first: Kadir

middle: Caner

last: Akdemir

state: TX

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

summary:
Epigenetic regulators have emerged as critical factors governing the biology of cancer. Here, in the context of melanoma, we show that RNF2 is prognostic, exhibiting progression-correlated expression in human melanocytic neoplasms.
Through a series of gain of function and loss of function studies, we establish that RNF2 is oncogenic and pro-metastatic. Mechanistically, RNF2-mediated invasive behavior is dependent on its ability to mono-ubiquitinate H2AK119 at the promoter of LTBP2, resulting in silencing of this negative regulator of TGFβ signaling. In contrast, RNF2's oncogenic activity did not require its catalytic activity nor derives from its canonical gene repression function, rather RNF2 drives proliferation through direct transcriptional up-regulation of the cell cycle regulator CCND2. In summary, RNF2 regulates distinct biological processes in the genesis and progression of melanoma via distinct molecular mechanisms, underscoring the complex and multi-faceted actions of epigenetic regulators in cancer.

overall_design: RNF2 is overexpressed in immortalized human melanocytes HMEL-BRAFV600E to address impact of RNF2 overexpression in melanoma. GFP was overexpressed in HMEL-BRAFV600E cells as a control cell line. Expression profiling using microarray was performed and compared between RNF2 overexpressing versus GFP overexpressing HMEL-BRAFV600E cells.

middle: C

first: Kunal

last: Rai

first: Lynda

last: Chin


title: Expression data from POLG1 patients and control subjects muscle

city: Hasselt

first: An

last: Voets

address: Martelarenlaan 42

department: BIOMED

country: Belgium

institute: Hasselt University

summary:
Pathogenic mutations in the catalytic DNA polymerase gamma (POLG1) gene result in the accumulation of mtDNA mutations, deletions and/or decrease of mtDNA copy number. These features interfere with proper functioning of the electron transport chain, mostly affecting metabolically active tissues such as the brain, the heart and the liver. So far, mechanisms underlying POLG pathogenesis are not fully understood.
To identify general pathways influenced by mutant polymerase gamma, skeletal muscle gene expression profiles of six POLG1 patients and twelve controls were compared.

overall_design: Patient and control subject from three age categories (<10; 11-49; >50) were selected. RNA was extracted from skeletal muscle biopsies and hybridized on Affymetrix microarrays.

first: Bianca

last: van den Bosch

first: Patrick

last: Lindsey

first: Rob

last: Verdijk

first: Kees

last: Schoonderwoerd

first: Sabina

last: Vanherle

first: John

last: Esseling

first: Werner

last: Koopman

first: Peter

last: Willems

first: C

middle: E

last: de Die-Smolders

first: B

last: Poll-The

middle: G

last: Faber

first: Irineus

last: de Coo

first: Hubert

last: Smeets


title: The Histone Deacetylase Inhibitor Trichostatin A Promotes Totipotency in Cultured Pollen

city: Wageningen

first: Kim

last: Boutilier

address: Droevendaalsesteeg 1

country: Netherlands

institute: Plant Research International

summary: The haploid multicellular male gametophyte of plants, the pollen grain, is a terminally differentiated structure whose function ends at fertilization. Unlike pollen grains, the immature gametophyte retains its capacity for totipotent growth when cultured in vitro. Haploid embryo production from cultured immature male gametophytes is a widely used plant breeding and propagation technique that was described nearly 50 years ago, but one that is poorly understood at the mechanistic level. Using a chemical approach, we show that the switch to haploid embryogenesis is controlled by the activity of histone deacetylases (HDACs). Blocking HDAC activity with trichostatin A (TSA) in cultured immature male gametophytes of Brassica napus leads to a large increase in the proportion of cells that switch from pollen to embryogenic growth. Embryogenic growth is enhanced by, but not dependent on, the high temperature stress that is normally used to induce haploid embryogenesis in B. napus. The immature male gametophyte of Arabidopsis thaliana, which is recalcitrant for haploid embryo development in culture, also forms embryogenic cell clusters after TSA treatment. TSA treatment of immature male gametophytes for as little as eight hours was accompanied by hyperacetylation of histones H3 and H4, and by the upregulation of genes involved in cell-cycle progression, the auxin pathway and cell wall catabolism pathways. We propose that the totipotency of the immature male gametophyte in planta is kept in check by an HDAC-dependent mechanism, and that high temperature or other stresses used to induce haploid embryo development in culture impinge on this HDAC-dependent pathway.

overall_design: 8 samples were analyzed. We generated the following pairwise comparisons between treatment and the corresponding mock treatment: TSA+CHX (2 replicates) vs CHX (2 replicates); TSA (2 replicates) vs DMSO (2 replicates).

first: Li

last: Hui

first: Mercedes

last: Soriano

first: Jan

last: Cordewener

first: Jose

last: Muino

first: Hiroyuki

last: Fukuoka

first: Gerco

last: Angenent


title: Response of  human corneal epithelial cells to the secretomes of wild-type Serratia marcescens and an eepR mutant strain

status: Public on Dec 31 2015

city: Pittsburgh

first: Stephen

middle: Alan Kenneth

last: Harvey

state: PA

address: 203 Lothrop St

department: Ophthalmology

institute: University of Pittsburgh School of Medicine

summary:
The bacterium Serratia marcescens is a common contaminant of contact lens cases and lenses. Serratamolide is one of the secreted hemolytic/cytotoxic  factors which contribute to the virulence of this opportunistic pathogen (PMID 22615766).
A newly identified transcription factor (eepR) is essential for serratamolide production (PMID 25897029). In the present study, we used immortalized human corneal-limbal epithelial (HCLE) cells (PMID 12766048) as targets for the secreted products of either wild-type (WT) S. marcescens or an isogenic eepR mutant.
Microarray data showed that at sub - cytotoxic levels, the secretome of WT bacteria stimulated a > 2-fold response in 712 unique characterized genes.  Analysis showed that immune/inflammatory response pathways are significantly enriched in these genes.
The scaled response of eepR, ((eepR - control)/(WT – control)), was < 0.5 for 418 of these 712 genes (59%). Pathway analysis of these 2-fold attenuated genes confirmed that they too represented immune/inflammatory responses.
These data demonstrate that the serratamolide-deficient eepR mutant evokes a much weaker immune/inflammatory response from a clinically relevant cellular target than does the wild-type bacterium.

overall_design: A common batch of HCLE cells was used. Independent preparations of Serratia marcescens secretomes were made for each experiment.

first: Kimberly

last: Brothers

first: Robert

last: Shanks


title: Negative-Pressure Induces p120-Catenin Dependent Adherens Junction Disassembly

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

summary:
Background: Negative-pressure wound therapy has become widely available in modern chronic wound cares. Accelerated keratinocyte (HaCaT cell) movements and decreased E-cadherin expressions induced by the applied negative pressure gradient of 125 mmHg (NP) have been reported in previous studies. However, the molecular mechanism for E-cadherin regulations under NP remains unexplored. We highlighted the signal transduction involved in NP-induced E-cadherin regulation for keratinocytes in the study.
Results: Microarray results showed that catenin 1 (CTNND1) gene, the gene encoding the p120-catenin (p120ctn) in cell-cell junctions, was significantly (p = 0.0005) upregulated in HaCaT cells under NP for 12 hours in comparison with those at ambient pressure (AP). Cell fractionations and immunoblotting data showed that NP increased p120ctn phosphorylation, and resulted in p120ctn translocation from the plasma membrane to the cytoplasm. Fluorescent stains suggested that NP diminished the co-localization of p120ctn and E-cadherin on the plasma membrane. Similar phenomenon was also observed in the cells with overexpressed p120ctn at NP. Interestingly, overexpression of dN- p120ctn, a deletion mutant of p120ctn without the N-terminal phosphorylation sites, restored the adherens junctions (AJ) at NP. Knockdown of p120ctn with lentiviral small hairpin RNA not only diminished E-cadherin expressions but also accelerated cell movement at AP.  Conclusions: Phosphorylation of p120ctn is endowed to respond rapidly to NP and contributes to the AJ disassembly. This NP-induced E-cadherin downregulation can possibly accelerate wound-healing process. Conclusions: Phosphorylation of p120ctn is endowed to respond rapidly to NP and contributes to the AJ disassembly. This NP-induced E-cadherin downregulation can possibly accelerate wound-healing process.

overall_design: HaCaT cells under negative pressure (NP) gradient of 125 mmHg for 12 hours in comparison with those at ambient pressure (AP) were tested for RNA extraction and hybridization on Affymetrix microarrays. The experiments have been biological replicated three times. The differential expression gene between NP and AP were selected and validated with qPCR method.

first: Ching-Hui

last: Huang

first: Chih-Yi

last: Chien

first: Carl

last: Chen

first: Shu-Er

last: Chow

first: Jong-Shyan

last: Wang

first: Yu-Shien

first: Chih-Chin

last: Hsu


title: Synergistic activity of BET protein antagonist-based combinations in Mantle Cell Lymphoma cells sensitive or resistant to ibrutinib

first: Kapil

last: Bhalla

department: Leukemia

summary:
To determine the global transcriptome changes in mantle cell lymphoma cells following treatment with the BET bromodomain antagonist, JQ1
Mantle Cell Lymphoma (MCL) cells exhibit increased B cell receptor and NFkB activities. The BET protein BRD4 is essential for the transcriptional activity of NFkB. Here, we demonstrate that treatment with the BET protein bromodomain antagonist (BA) JQ1 attenuates MYC and CDK4/6, inhibits the nuclear RelA levels and the expression of NFκB target genes including Bruton’s Tyrosine Kinase (BTK) in MCL cells. While lowering the levels of the anti-apoptotic BCL2 family proteins, BA treatment induces the pro-apoptotic protein BIM and exerts dose-dependent lethality against cultured and primary MCL cells. Co-treatment with BA and the BTK inhibitor ibrutinib synergistically induces apoptosis of MCL cells. Compared to each agent alone, co-treatment with BA and ibrutinib markedly improved the median survival of mice engrafted with the MCL cells. BA treatment also induced apoptosis of the in vitro isolated, ibrutinib-resistant MCL cells which overexpress CDK6, BCL2, Bcl-xL, XIAP and AKT, but lack ibrutinib resistance-conferring BTK mutation. Co-treatment with BA and panobinostat (pan-histone deacetylase inhibitor) or palbociclib (CDK4/6 inhibitor) or ABT-199 (BCL2 antagonist) synergistically induced apoptosis of the ibrutinib-resistant MCL cells. These findings highlight and support further in vivo evaluation of the efficacy of the BA-based combinations with these agents against MCL, including ibrutinib-resistant MCL.

overall_design: MO2058 cells treated with vehicle, 250 nM or 1000 nM JQ1 for 8 hours. Samples were acquired and analyzed in duplicate.

middle: N

first: Warren

last: Fiskus


title: Deletion of Pten leads to liver steatosis and tumor formation

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: We found that deleting Pten in Albumin expressing cells results in liver steatosis as early as 1 month of age.  The mice develop hyperplasia and tumor phenotypes starting at 7-8 months of age.  At 12 months and beyond, all mice develope spontanous liver tumors of mixed lineage phenotypes  dihydrocollidine (DDC) shows that the primary effect of AKT2 loss is attenuation of hepatic injury and not inhibition of progenitor cell proliferation in response to injury.

overall_design: Pten is deleted specifically in the liver (Pten loxP/loxP; Alb-Cre+).  Liver tissues were analyzed at 3 months (steatosis stage) and 15 months (tumor stage)

first: Bangyan

last: Stiles

first: Lina

last: He

first: Ni

last: Zeng

first: Vivian

last: Galicia


title: Delayed Cardiomyocyte Response to Total Body Particle Radiation Exposure - Identification of Regulatory Gene Network

first: Matthew

last: Coleman

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

overall_design: Refer to individual Series


title: Molecular Evidence for a Dimensional Basis of Depression

city: San Diego

first: YING

last: DING

address: 10777 Science Center Dr.

department: Computational Biology

institute: Pfizer

summary: Here we identified a set of genes with frequent expression changes in the postmortem brain of MDD subjectsand show that this gene set is genetically related to brain and organ illnesses frequently associated with MDD. Specifically, we performed a meta-analysis of eight gene array studies in three corticolimbic brain regions and identified ~450 genes frequentlyderegulated in MDD (n=103 subjects, 50.5%MDD). These “MetaA-MDD” genes includepreviously-implicated neuroplasticity- and stress-related genes (CRH, BDNF, VGF), encompass multiple synaptic and signaling pathways, and suggests complex changes in cell structure and function. MetaA-MDD genes display low connectivity andhubnessin coexpression networks andare evenly distributed throughout the genome. However, MetaA-MDD genesare significantly over-represented in gene sets identified by the genome-wide association studies for brain disorders and organ diseases sharing clinical co-morbidity with MDD (e.g., cardiovascular, metabolic syndrome), but not for other diseases or body functions. Together, this study describes a robustmolecular characterization of altered brain function in MDD, and provides evidence for a shared genetic structure linking MDD andrelated illnesses, together biologically defining abroader dimensional definition ofa depressive-like syndrome.

overall_design: 14 pairs of human postmotem AMY samples of MDD patients and control

first: Etienne

last: Sibille


title: Circadian regulation of gene expression in the SCN (gene expression)

city: Philadelphia

first: Heather

last: Ballance

address: 3400 Civic Center Blvd. Building 421

institute: University of Pennsylvania

summary: We performed a circadian RNA expression profile of the mammalian biological clock, the suprachiasmatic nucleus (SCN) in C57/BL6 mice, at 2-hour resolution using microarrays, and at 6-hour resolution using RNA-seq.

overall_design: 24 samples total covering 24 time points, with no replicates. SCN samples from mouse brains collected every 2 hours for 2 days (24 samples total).

first: Daquan

middle: T

last: Daly

first: Nicholas

middle: F

last: Lahens

first: Katharina

last: Hayer

first: Jacqueline

last: Growe

first: Gang

first: John

middle: B

last: Hogenesch


title: Hypervulnerability to sound-exposure through impaired adaptive proliferation of peroxisomes

city: Paris

first: Sedigheh

last: Delmaghani

address: 25 rue du Dr Roux

institute: Institut Pasteur

summary: A deficiency of pejvakin, a protein of unknown function, causes a strikingly heterogeneous form of deafness. Pejvakin-deficient (Pjvk-/-) mice also exhibited variable auditory phenotypes. Correlation between their hearing thresholds and the number of pups per cage suggested a possible harmful effect of pup vocalizations. Direct sound or electrical stimulation showed that the cochlear sensory hair cells and auditory pathway neurons of Pjvk-/- mice and patients were exceptionally vulnerable to sound. Pjvk-/- cochleas displayed features of marked oxidative stress and impaired anti-oxidant defenses. We showed that pejvakin is associated with peroxisomes, and is required for the oxidative stress-induced proliferation of these organelles. In Pjvk-/- hair cells, peroxisomes displayed structural abnormalities after the onset of hearing. Noise-exposure of wild-type mice rapidly upregulated Pjvk cochlear transcription, and triggered peroxisome proliferation in hair cells and primary auditory neurons. Our results reveal that the anti-oxidant activity of peroxisomes protects the auditory system against noise-induced damage.

overall_design: Three RNA samples was extracted from dissected organ of Corti (OC) for each genotype (Pjvk-/- and Pjvk+/+ mice) and analyzed (triplicate OCmm-1, OCmm-2, and OCmm-3 for Pjvk-/-, and triplicate OCpp-1, OCpp-2, and OCpp-3 for Pjvk+/+).

first: Guillaume

last: Soubigou

first: Christine

last: Petit

first: Paul

last: Avan


title: Effect of ruxolitinib treatment on gene expression in triple-negative breast cancer cell lines

city: Nashville

first: Justin

last: Balko

state: TN

address: 777 Preston Research Building

department: Medicine

institute: Vanderbilt University

summary: HCC1143, HCC70, HCC38, and SUM159PT cells were treated for 4 or 24 hrs with 1uM ruxolitinib.  Control cells were treated for 24 hrs with DMSO (0.1%). The purpose was to determine changes in gene expresison patterns following inhibition of JAK1/2 in the cells.

overall_design: Three independent experiments were conducted for three biological replicates at each time point, for each cell line


title: The histone H3 lysine 4 presenter WDR5 induces N-Myc target gene transcription and promotes neuroblastoma [gene expression]

city: Randwick

first: Tao

last: Liu

state: NSW

address: Lowy Cancer Research Centre

country: Australia

institute: Children's Cancer Institute Australia

summary:
WDR5 is an important co-factor for N-Myc-regulated transcriptional activation and tumorigenesis
We analysed whether WDR5 siRNAs modulate gene expression

overall_design: Neuroblastoma BE(2)-C cells were treated with control siRNA, WDR5 siRNA-1, and WDR5 siRNA-2 for 40 hours, and subjected to differential gene expression studies with Affymetrix microarrays.

first: Liu

last: Tao

first: Sun

last: Yuting


title: BCOR controls maintenance of haematopoietic stem cell quiescence and regulates myeloid cell proliferation and differentiation [Affymetrix]

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

summary: BCOR is a component of a variant Polycomb group repressive complex 1 (PRC1) complex. Recently, we and others reported recurrent somatic BCOR loss-of-function mutations in myelodysplastic syndrome and acute myelogenous leukaemia (AML). However the role of BCOR in normal hematopoiesis is largely unknown. Here, we explored the function of BCOR in myeloid cells using myeloid murine cell models with Bcor conditional loss-of-function or overexpression alleles. Bcor mutant bone marrow cells showed significantly higher proliferation and differentiation rates with reduced protein levels of RING1B, a ubiquitin ligase subunit of PRC1 family complexes. Global RNA expression profiling in murine cells and AML patient samples with BCOR loss-of-function mutation suggested that loss of BCOR expression is associated with proliferation and myeloid differentiation and decreased stem cell quiescence. Further, we used a MLL-AF9 murine model of AML and found that loss of Bcor increased serial replating efficiency, enhanced MLL-AF9 in blocking cell differentiation, and increased expression of Evi1 which is associated with leukemic transformation. Our results strongly suggest that BCOR plays an indispensable role in maintaining hematopoietic stem cell (HSC) quiescence by inhibiting myeloid stem cell proliferation and differentiation and offer a mechanistic explanation for how BCOR regulates gene expression such as Hox genes.

overall_design: Normal karyotype AML primary cells with either wild type BCOR (6 cases) or destructive mutated BCOR (6 cases) were collected and subjected to RNA expression microarray study

first: Qi

last: Cao

first: Micah

middle: D

last: Gearhart

first: Sigal

last: Gery

first: Seyedmehdi

last: Shojaee

first: Wenwen

last: Chien

first: Haibo

last: Sun

first: Monica

last: Mead

first: Zhiqiang

last: Zhao

first: Dechen

last: Lin

last: Chen

first: Serhan

last: Alkan

first: Torsten

last: Haferlach

first: Markus

last: Müschen

first: Vivian

last: Bardwell

first: H

last: Koeffler


title: BCOR controls maintenance of haematopoietic stem cell quiescence and regulates myeloid cell proliferation and differentiation

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Expression data among esophageal cancer cell sublines with different migration ability

city: Beijing

first: Zhihua

last: Liu

address: No.17, Panjiayuannanli, Chaoyang District

department: Cancer Institute & Hospital

country: China

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

summary:
Cellular directed migration is critical to invasion-metastasis cascade of cancer cells. We used in vitro transwell model to screen two esophageal cancer cell lines (KYSE30/180) and obtained two pairs of subpopulations with distinct motility ability.
Then we used microarrays to detail the differentially expressed genes and microRNAs between these two cell sublines (30U/D and 180U/D) to identify those responsible for ESCC motility.

overall_design: KYSE30/180 cells were subject to four successive selections using transwell (CORNING, USA). Subpopulations penetrated through membrane (D) or not (U) were harvested respectively for RNA extraction and hybridization on Affymetrix genome and LC Sciences microRNA microarrays simultaneously.

first: Gang

last: Ma

first: Chao

last: Jing


title: Esophageal cancer cell sublines with different migration ability

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


title: Expression data from the inducible expression of EWS-FLI1 (EF) in embryoid bodies

city: Iowa City

first: David

middle: Jon

last: Gordon

state: Iowa

address: 25 S Grand Ave

department: Pediatric Hematology/Oncology

institute: University of Iowa

summary: Oncogenic transformation in Ewing sarcoma tumors is driven by the fusion oncogene EWS-FLI1. The inducible expression of EWS-FLI1 (EF) in embryoid bodies, or collections of differentiating stem cells, generates cells with properties of Ewing sarcoma tumors, including characteristics of transformation.  These cell lines exhibit anchorage-independent growth, a lack of contact inhibition and a strong Ewing sarcoma gene expression signature. These cells also demonstrate a requirement for the persistent expression of EWS-FLI1 for cell survival and growth.

overall_design:
We used microarrays to detail the effects of doxycycline-inducible expression of EWS-FLI1 on the gene expression signature of cells derived from differentiating stem cells, or embryoid bodies.
Triplicate biological replicates were collected and analyzed.

last: Pellman

first: Mona

last: Motwani


title: Changes in gene expression associated with overexpression of a novel oncogene

city: Boston

first: Manish

last: Neupane

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary:
Oncogenic drivers are still not obvious in a number of human cancers. Identification of oncogenes that contribute to tumorigenic transformation when overexpressed in their wild-type form, either because of gene amplification or due to some other epigenetic changes, is particularly challenging.
This study was carried out to understand the gene expression changes associated with overexpression of a novel oncogene, Methyl CpG Binding Protein 2 (MECP2), that we recently uncovered from a genome-scale screen.

overall_design: Immortalized but non-transformed derivatives of human mammary epithelial cells (HMECs) carrying catalytic subunit of human telomerase and  SV40 large T and small t antigens, were used as recipient cells for these experiments. We compared changes in gene expression among four different experimental groups: (1) recipient cells overexpressing EGFP (negative control); (2) recipient cells overexpressing MECP2 (our oncogene-of-interest); (3) recipient cells overexpressing activated HRASV12 (which is a classical oncogene); (4) recipient cells overexpressing OTX2 (another known oncogene is medulloblastoma). There were biological duplicates of each experimental group (therefore, with 8 samples in total).

first: Daniel

last: Silver


title: Prediction of isolated central nervous system relapses in pediatric acute lymphoblastic leukemia

city: Rotterdam

first: Vincent

middle: HJ

last: van der Velden

address: Wytemaweg 80

department: Immunology

institute: Erasmus MC

summary: Background   In childhood acute lymphoblastic leukemia (ALL), central nervous system (CNS) involvement is rare at diagnosis (1-4%), but more frequent at relapse (~30%). Minimal residual disease diagnostics predict  most bone marrow (BM) relapses, but likely cannot predict isolated CNS relapses. Consequently, CNS relapses may become relatively more important. Because of the significant late sequelae of CNS treatment, early identification of patients at risk of CNS relapse is crucial.     Methods  Gene expression profiles of ALL cells from cerebrospinal fluid (CSF) and ALL cells from BM were compared and differences were confirmed by real-time quantitative PCR. For a selected set of overexpressed genes, protein expression levels of ALL cells in CSF at relapse and of ALL cells in diagnostic BM samples were evaluated by 8-color flow cytometry.     Results  CSF-derived ALL cells showed a clearly different gene expression profile than BM-derived ALL cells, with differentially-expressed genes (including SCD and OPN) involved in survival and apoptosis pathways and linked to the JAK-STAT pathway. Flowcytometric analysis showed that a subpopulation of ALL cells (>1%) with a “CNS signature” (SCD positivity and increased OPN expression) was already present in BM at diagnosis in ALL patients who later developed a CNS relapse, but was <1% or absent in virtually all other patients.     Conclusions  The presence of a subpopulation of ALL cells with a “CNS signature” at diagnosis may predict isolated CNS relapse. Such information can be used to design new diagnostic and treatment strategies that aim at prevention of CNS relapse with reduced toxicity.

overall_design: We compared gene expression profiles of ALL cells obtained from cerebrospinal fluid (n=8) with profiles of ALL cells obtained from bone marrow at diagnosis (n=22) or at relapse (n=20)

middle: H

first: Daphne

last: de Launaij

first: Jeltje

last: de Vries

first: Valerie

last: de Haas

first: Edwin

last: Sonneveld

first: Jane

middle: S

last: Voerman

first: Maaike

last: de Bie

first: Tom

last: Revesz

first: Smadar

last: Avigad

first: Allan

last: Yeoh

first: Sigrid

last: Swagemakers

first: Connie

last: Eckert

first: Rob

last: Pieters

first: Jacques

last: van Dongen


title: The dynamics of chromatin accessibility during EMT

city: Los Angeles

first: Xiaojing

last: Yang

address: 1441 Eastlake Ave, Room 7336

institute: USC/Norris Comprehensive Cancer Center

type: Methylation profiling by genome tiling array

summary:
The power of our genome-wide survey lies in that we were able to query chromatin accessibility changes concurrently with those in DNA methylation. We identified both opening and closing events, predominantly independent of DNA methylation, in both systems.
Our results have powerful implications for future basic and clinical research on this developmental process and its resurfacing during cancer cell metastasis.

overall_design: To address epigenetic changes that mediate EMT, we used two models in the human system: EMT induced by the transcriptional repressor Twist as well as EMT induced by TGF-beta. We performed AcceSssIble on these cells at several time points through the course of the transition and identified genes that need to be repressed to allow for the process.

first: Jueng

last: You

first: Kurinji

last: Pandian

first: Gangling

last: Liang

first: Peter

middle: A

last: Jones


title: Expression data from BM-CD138+, obtained from newly diagnosed Multiple Myeloma patients [response to VTD therapy]

city: Bologna

first: Carolina

last: Terragna

address: Via Massarenti, 9

department: Department of Experimental, Diagnostic and Specialty Medicine - DIMES

country: Italy

institute: Institute of Hematology "L.A.Seràgnoli"

summary:
The prime focus of the current therapeutic strategy for Multiple Myeloma (MM) is an early and deep tumour burden reduction; this characterizes and defines the complete response (CR). To date, no description of the characteristics of the plasma cells (PC) prone to achieve CR has been reported. This study aimed at the molecular characterization of PC derived from MM patients who achieved CR after bortezomib-thalidomide-dexamethasone (VTD) first line therapy.
One hundred and eighteen MM primary tumours obtained from homogeneously treated patients were globally profiled both for gene expression and for single nucleotide polymorphism genotype. Genomic results were used to obtain a predictor of sensitivity to VTD induction therapy, as well as to describe both the transcription and the genomic profile of PC derived from patients with MM who will respond optimally to primary induction therapy.
By analysing the gene profiles of CR patients, we identified a 5-gene signature predicting CR with an overall median accuracy of 75% (range: 72%-85%). In addition, we highlighted the differential expression of a series of genes, whose deregulation, accordingly to their reported functions, might explain the CR patients’ sensitivity to VTD therapy. We also showed that a small copy number loss, covering 606Kb on chromosome 1p22.1 was the most significantly associated with CR patients.
The study provides insights into the genomic landscape of PC obtained from newly diagnosed MM patients achieving CR after VTD and shows that patients might be accurately stratified according to their sensitivity to VTD.

overall_design:
118 samples have been analyzed; the homogeneity of samples has been ensured by the immunomagnetic enrichment procedure: only >90% pure CD138+ cells have been employed.

Response to vtd therapy (provided in each sample record);
CR: complete response
nCR: near complete response
VGPR: Very good partial response
PR: partial response
SD: Stable disease

first: Marina

last: Martello

first: Flores

last: Dico


title: Gene Expression and HD-SNP6.0 data from Primary Testicular (PTL), Primary Central Nervous System Lymphoma (PCNSL) and Primary Mediastinal B-cell Lymphoma (PMLBCL)

first: Björn

last: Chapuy

address: 450 Brookline Ave.

department: Medical Onology

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

summary: We obtained gene expression data and HD-SNP6.0 copy number data from PTL, PCNSL and PMLBCL samples and performed an integrative analysis on them. RNA was whole genome amplified using Nugen.

overall_design:
Gene expression profiles (GEP) and copy number (CN) data were obtained from 7 PTL. GEP was obtained from 15 PCNSL and CN from 23 PCNSL (overlap of 11). The PMLBCL series contained GEP of 9 and CN data from 11 cases (overlap of 9).
180 samples from GSE34171 provide the framework for the CN analysis and are therefore added to the segmented CN file (input_to_gistic.seg.txt).

first: Bjoern

first: Stefano

last: Monti

first: Margaret

last: Shipp


title: CD138+ expression and genomic profile obtained from newly diagnosed Multiple Myeloma patients up-front treated with VTD induction therapy

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


title: Gene expression profile from short-term caloric restriction in mouse adipose tissue

city: Seoul

first: Cheol-Koo

last: Lee

address: Korea University, Biotechnology #318 West building, Anam-dong, Seongbuk-gu

department: Biotechnology

country: South Korea

institute: Korea University

summary:
To provide a robust understanding of a transcriptomic change by short-term CR at body fat of mice, we applied three serial strengths of CR to mice including 15%, 30%, and 45% reduction of carbon source. Using Affymetrix mouse 1.0 ST array platform, we obtained and analyzed the transcriptome data for significantly changed genes in expression.
Here, we identified 446 genes and categorized the genes based on their biological roles. We observed gradual down-regulation of several signaling pathways including insulin/insulin-like growth factor (IGF) 1, epidermal growth factor (EGF), transforming growth factor beta (TGF-β) and canonical Wingless-type mouse mammary tumor virus integration site (Wnt) signaling according to the CR strengths. Many genes related to structural feature including extracellular matrix (ECM), cell adhesion and cytoskeleton were also down-regulated with a strong correlation to the serial CR treatments. Furthermore, genes for cell cycle and adipogenesis were down-regulated. According to previous studies, these are target functions of the aforementioned four signaling pathways. On the other hand, the genes for specific metabolic features including tricarboxylic acid (TCA) cycle and electron transport chain (ETC) exhibited a transcriptional increase. In addition, adipose tissue expansion markers such as leptin, Mesoderm specific transcript (Mest) and Secreted frizzled-related sequence protein 5 (Sfrp5), and most genes for transport and immune response showed a down-regulation by CR.

overall_design: Comparing gene expression profiles to understand transcriptomic changes of adipose tissue by serial strength (15%, 30%, and 45%) of short-term (10 weeks) caloric restriction to young age (18 weeks) mice (n=3 in each group).

first: Seung-Soo

last: Kim


title: Effect of electromagnetic fields on the chondrogenic differentiation under microgravity conditions

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

country: Germany

institute: Ludwig-Maximilian University

summary: A combination therapy of electromagnetic fields (EMF) and simulated microgravity (SMG) has not been examined in regenerative medicine of cartilage. In the present study, a bioreactor system using extremely low-frequency EMF and SMG was applied during the chondrogenic differentiation of human mesenchymal stem cells (hMSCs). It was hypothesized that a beneficial effect of EMF regarding chondrogenesis (COL2A) could be combined with an avoiding effect of SMG regarding hypertrophy (COLXA1) of cartilage. Pellet cultures of hMSCs formed cartilaginous tissue under the addition of growth factors (FGF; TGF-β3). Pure SMG reduced COLXA1 expression but also COL2A expression of hMSCs. Pure EMF showed no gene expression changes of hMSCs during chondrogenic differentiation. Combining EMF/SMG resulted in a re-increase of COL2A but did not reach control levels. The COL2A to COLXA1 ratio of combined EMF/SMG was not significantly different from control levels. The combination therapy of EMF/SMG did not significantly improve the chondrogenic potential of hMSCs.

overall_design: chondrogenic differentiation, electromagnetic stimulation-control, 1 timepoint with/without stimulation

first: Susanne

last: Mayer-Wagner

first: Florian

last: Hammerschmid

first: Helmut

last: Blum

first: Julia

middle: I

last: Redeker

first: Boris

last: Holzapfel

first: Volkmar

last: Jansson

last: Müller


title: ZEB1 expression prevents DNA replication stress in cancer stem cells and delays chromosomal instability [Affymetrix]

city: Lyon

first: Anne

last: Wierinckx

state: select a state

address: 8, av Rockefeller

institute: University Lyon1

summary: Aberrant cell proliferation, a hallmark of most cancers, requires the escape from intrinsic antitumour barriers. Primary among these is the DNA damage response (DDR). In both cell culture-models and in early stages of tumorigenesis in vivo, activated oncogenes induce DNA replication stress and DNA double-strand breaks (DSBs), leading to DDR activation and p53-dependent apoptosis and/or senescence. The means by which tumour-initiating cells, also termed cancer stem cells (CSCs), circumvent this oncosuppressive response is unknown. Here we demonstrate that the ZEB1 transcription factor provides breast CSCs with the ability to withstand an aberrant mitogenic activity. Its forced expression in human mammary epithelial cells is sufficient to alleviate DNA replicative stress and to decrease the production of reactive oxygen species, an important contributor to DDR and oncogene-induced senescence. Consistently, human breast cancer cells with endogenous ZEB1 expression show two characteristic features: low levels of DSBs and DDR markers, reflecting mitigation of the DNA replication stress, and a low p53 mutation frequency, reflecting a weak selective pressure for inactivation. Using high-throughput sequencing analysis of controlled cellular models, we further demonstrate that ZEB1 delays the onset of structural chromosomal instability (CIN), a known consequence of replicative stress and prevents the emergence of chromosome 8p deletions and 8q amplifications, two prevalent abnormalities in high-grade breast cancers. Supporting these findings, ZEB1 expression discriminates human breast tumours by their copy number alterations (CNAs) and chromosome 8 aberrations. We propose that the tumorigenic potential of CSCs relies upon their unique capacity to tolerate oncogenic stimuli through the alleviation of DNA replication stress.

overall_design: Immortalized human mammary epithelial cells were infected with retrovirus expressing H-RASV12 with or without a retrovirus expressing ZEB1.

middle: P

last: Morel

first: Alain

last: Puisieux

first: Fréderique

last: Fauvet

first: Christelle

last: Lamblot

first: Christiane

last: Pinatel

first: Séverine

last: Croze

first: Joël

last: Lachuer


title: Targeted Bmi1 inhibition impairs tumor growth in pulmonary adenocarcinomas defined by low CEBPa levels

first: Henry

last: Yang

summary: A new subset of pulmonary NSCLC patients can be defined as negative for C/EBP alpha and positive for Bmi-1 expression, which are mimicked by our lung-specific C/EBP alpha null mice. Bmi-1 activity is required for both tumor initiation and maintenance in the C/EBP alpha null background and pharmacological inhibition of Bmi-1 exhibits anti-tumor effect. Overall, we show that C/EBP alpha is a tumor-suppressor gene in lung, and that Bmi-1 is involved in mediating the oncogenic process downstream of C/EBP alpha, implying that Bmi-1 inhibition may offer a therapeutic advantage for the subset of patients with low levels of C/EBP alpha expression.

overall_design: A316 cebp alpha knock out primary adenocarcinoma line cells treated with Bmi inhibition through compound PTC-209 were used for RNA extraction and hybridization on Affymetrix microarrays. We compared the microarray samples with the corresponding the control treatment (0.5% DMSO).

first: Elena

last: Levantini

first: Daniela

last: Basseres

first: Kol

middle: J

last: Yong

first: Robert

last: Welner

first: Wen

last: Zhang

first: Junrong

last: Yan

first: Meritxell

last: Alberich-Jorda

first: Junyan

first: Lorena

middle: L

last: de Figueiredo-Pontes

first: Chiara

last: Battelli

first: Christopher

last: Hetherington

first: Min

last: Ye

first: Karen

last: O’Brien

first: Hong

first: Maria

last: Magli

last: Borczuk

first: Lyuba

last: Varticovski

first: Olivier

last: Kocher

first: Pu

first: Young

last: Moon

first: Nadiya

last: Sydorenko

first: Liangxian

last: Cao

first: Thomas

middle: W

last: Davis

first: Bhavin

middle: M

last: Thakkar

first: Ross

last: Soo

first: Atsushi

last: Iwana

first: Bing

last: Lim

first: Balazs

last: Halmos

first: Daniel

last: Tenen


title: Gene expression signature associated with BRAFV600E mutation in human papillary thyroid carcinoma based on transgenic mouse model

city: Warsaw

first: Michal

last: Swierniak

address: Banacha 2C

department: Centre of New Technologies

country: Poland

institute: University of Warsaw

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

overall_design: Refer to individual Series


title: Gene expression signature associated with BRAFV600E mutation based on transgenic mouse model (mouse)

summary:
BRAFV600E mutation is the most frequent molecular event in papillary thyroid carcinoma. The relation of this genetic alteration with the factors od poor prognosis has been reported as well as its influence on PTC gene signature. However human material disables distinction of cancer causes from its effect.
We used our transgenic mouse model of papillary thyroid carcinoma induced by the BRAFV600E mutation to select BRAFV600E-specific gene signature

overall_design: The transgenic mouse model was obtained by the microinjection of the transgene, composed of the human BRAF cDNA with V600E mutation under the control of bovine thyroglobulin, into the ferilized mice egg cells. Three lines were derived and mice after 4-24 months were sacrificed and histopathological evaluation of thyroids was carried out. In order to find BRAFV600E-specific gene signature microarray analysis was performed. The analysis invloved 38 mice thyroid samples: 10 mice papillary thyroid carcinomas, 10 borderline lesions (all being BRAF-positive), 10 apparently asymptomatic thyroids (5 BRAF-positive and 5 BRAF-negative) and 8 benign hyperplastic lesions (4 BRAF-positive and 4 BRAF-negative). Multofactoral analyses were performed in order to define some additional factors that could have impact on the gene expression profile.

first: Dagmara

last: Rusinek

first: Barbara

last: Jarzab


title: Microarray analysis of thyrospheres from human THJ-11T cells

city: St Louis

first: Reigh-Yi

last: Lin

state: MO

address: 1100 South Grand Blvd

department: Otolaryngology

country: USA

institute: Saint Louis University

summary: We used an Affymetrix Human Genome HG-U133 Plus 2.0 Array to analyze the differential expression of genes in thyrospheres and monolayer cells from the THJ-11T cells in an attempt to identify the molecular signature of thyroid cancer stem cells.

overall_design: Gene expression levels in thyrospheres were compared with that of the parental monolayer cells on a total of six arrays, three arrays for each of the thyrospheres versus monolayer cells from three independent experiments.


title: Differential gene expression in neuroblastoma cells after treatment with vehicle control, JQ1, panobinostat, or combination of JQ1 and panobinostat

first: Tao

last: Liu

summary:
The bromodomain inhibitor JQ1 and the histone deacetylase inhibitor panobinostat induce synergistic anticancer effects
We analyzed whether JQ1 and panobinostat synergistically modulate gene expression

overall_design: Neuroblastoma SK-N-BE(2) cells were treated with vehicle control, 1 microM JQ1, 10 nM panobinostat, or combination of JQ1 and panobinostat for 6 hours, and subjected to differential gene expression studies with Affymetrix microarrays.

first: Liu

last: Tao


title: ZEB1 expression prevents DNA replication stress in cancer stem cells and delays chromosomal instability

first: Anne

last: Wierinckx

type:
Expression profiling by array
Genome variation profiling by array


title: HIV-1 TAT SUPPRESSES THE TCR/CD3 MACHINERY IN HUMAN CD4+ T CELLS [HIV]

city: Brussels

first: Chunyan

last: GU

address: Bld de Waterloo 127

department: Medecine (Jules Bordet Institute)

institute: Free University of Brussels

summary:
Our previous work demonstrated that HIV-1 infection progressively reduces TCR/CD3 expression due to a defect in CD3g gene transcripts. We further found that knocking down expression of the viral tat and/or nef genes was correlated with CD3g transcript and TCR/CD3 surface receptor levels on HIV-1 infected cells. This study was undertaken to investigate the direct effect of HIV-1 Tat expression on the TCR/CD3 machinery. Progressive downregulation from TCR/CD3hi to TCR/CD3lo to TCR/CD3− was observed on Tat expressing cells in a manner that emulated HIV-1 infection, with a lack of CD3g transcripts again responsible for the defect. When Tat cell cultures containing a mixture of TCR/CD3 surface densities were separated into TCR/CD3hi and TCR/CD3lo/− populations, they quickly reverted to a mixed CD3 phenotype. Thus, the progression TCR/CD3hi to TCR/CD3lo to TCR/CD3− is an active, reversible process with receptor levels fluctuating in response to intracellular dynamics. Examination of tat mutants found that the regions involved in Tat-mediated transactivation and TAR binding are required for TCR/CD3 downregulation while the lysine at position 28 and Tat exon 2 are dispensable. Global gene expression, assessed in association with TCR/CD3 downregulation in HIV-1 infected and Tat expressing cells, detected broad suppression of TCR/CD3 signaling, co-stimulation and negative regulatory genes along with target transcription factors, ligands and receptors. A significant subset of the genes altered in HIV-1 infected cells was specifically targeted by Tat in association with TCR/CD3 loss. Our finding that Tat negatively regulates many facets of the TCR/CD3 machinery has important implications for disease pathogenesis.
We used microarrays to investigate changes in CD4+ T cell gene expression induced by HIV-1 infection for comparison with the Tat expressing cells.

overall_design: Examine changes in gene expression in TCR/CD3 negative HIV-1 infected cells compared to TCR/CD3 positive uninfected controls.

first: Karen

last: Willard-Gallo


title: HIV-1 TAT SUPPRESSES THE TCR/CD3 MACHINERY IN HUMAN CD4+ T CELLS [Tat]

summary:
Our previous work demonstrated that HIV-1 infection progressively reduces TCR/CD3 expression due to a defect in CD3g gene transcripts. We further found that knocking down expression of the viral tat and/or nef genes was correlated with CD3g transcript and TCR/CD3 surface receptor levels on HIV-1 infected cells. This study was undertaken to investigate the direct effect of HIV-1 Tat expression on the TCR/CD3 machinery. Progressive downregulation from TCR/CD3hi to TCR/CD3lo to TCR/CD3− was observed on Tat expressing cells in a manner that emulated HIV-1 infection, with a lack of CD3g transcripts again responsible for the defect. When Tat cell cultures containing a mixture of TCR/CD3 surface densities were separated into TCR/CD3hi and TCR/CD3lo/− populations, they quickly reverted to a mixed CD3 phenotype. Thus, the progression TCR/CD3hi to TCR/CD3lo to TCR/CD3− is an active, reversible process with receptor levels fluctuating in response to intracellular dynamics. Examination of tat mutants found that the regions involved in Tat-mediated transactivation and TAR binding are required for TCR/CD3 downregulation while the lysine at position 28 and Tat exon 2 are dispensable. Global gene expression, assessed in association with TCR/CD3 downregulation in HIV-1 infected and Tat expressing cells, detected broad suppression of TCR/CD3 signaling, co-stimulation and negative regulatory genes along with target transcription factors, ligands and receptors. A significant subset of the genes altered in HIV-1 infected cells was specifically targeted by Tat in association with TCR/CD3 loss. Our finding that Tat negatively regulates many facets of the TCR/CD3 machinery has important implications for disease pathogenesis.
We used microarrays to investigate changes in CD4+ T cell gene expression induced by expression of the HIV-1 Tat protein.

overall_design: Examine changes in gene expression in HIV-1 Tat transduced cells compared with cells transduced with an antisense Tat sequence used as a control.


title: HIV-1 TAT SUPPRESSES THE TCR/CD3 MACHINERY IN HUMAN CD4+ T CELLS

summary:
Our previous work demonstrated that HIV-1 infection progressively reduces TCR/CD3 expression due to a defect in CD3g gene transcripts. We further found that knocking down expression of the viral tat and/or nef genes was correlated with CD3g transcript and TCR/CD3 surface receptor levels on HIV-1 infected cells. This study was undertaken to investigate the direct effect of HIV-1 Tat expression on the TCR/CD3 machinery. Progressive downregulation from TCR/CD3hi to TCR/CD3lo to TCR/CD3? was observed on Tat expressing cells in a manner that emulated HIV-1 infection, with a lack of CD3g transcripts again responsible for the defect. When Tat cell cultures containing a mixture of TCR/CD3 surface densities were separated into TCR/CD3hi and TCR/CD3lo/? populations, they quickly reverted to a mixed CD3 phenotype. Thus, the progression TCR/CD3hi to TCR/CD3lo to TCR/CD3? is an active, reversible process with receptor levels fluctuating in response to intracellular dynamics. Examination of tat mutants found that the regions involved in Tat-mediated transactivation and TAR binding are required for TCR/CD3 downregulation while the lysine at position 28 and Tat exon 2 are dispensable. Global gene expression, assessed in association with TCR/CD3 downregulation in HIV-1 infected and Tat expressing cells, detected broad suppression of TCR/CD3 signaling, co-stimulation and negative regulatory genes along with target transcription factors, ligands and receptors. A significant subset of the genes altered in HIV-1 infected cells was specifically targeted by Tat in association with TCR/CD3 loss. Our finding that Tat negatively regulates many facets of the TCR/CD3 machinery has important implications for disease pathogenesis.

This SuperSeries is composed of the SubSeries listed below.


title: The transcriptional landscape of early pancreatic development

city: Neuherberg

first: Nikola

last: Müller

address: Ingostädter Landstr. 1

institute: Helmholtz Zentrum München

summary: Pancreas organogenesis is a highly dynamic process where neighbouring tissue interactions lead to dynamic changes in gene regulatory networks that orchestrates endocrine, exocrine and ductal lineage formation. To understand the spatio-temporal regulatory logic we have used the Forkhead transcription factor Foxa2-Venus fusion (FVF) knock-in reporter mouse to separate the FVF+ pancreatic epithelium from the FVF- surrounding mesenchyme and blood vessels to perform a whole genome-wide mRNA expression profiling at embryonic day (E)12.5-15.5. This allowed us to annotate genes and molecular processes differentially regulated in these cell types and compartments of the pancreas to generate a dynamic transcriptional landscape.

overall_design: Time-resolved profiling across four embryonic development days. Pancreata were FAC sorted by Foxa2-Venus Fusion (FVF) for each day with each 2-3 biological replicates.

first: Heiko

last: Lickert


title: Expression data in HK-2 cells following exposure to non_tox representatives

city: Dublin

first: Peadar

last: O'Gaora

address: Belfield

country: Ireland

institute: UCD

summary:
Background: The development of a new drug from candidate to market is a complex process requiring vast resources of time, money and personnel. The rate of failure in the development pipeline is enormous, leading to wasted resources that could have been better employed on alternative candidates. The requirement for early stage prediction of toxicity is, then, of paramount importance to expedite the introduction of new therapies to clinical practice. To date, most transcriptomics efforts to solve this problem have applied Support Vector Machine techniques to data derived from in vivo studies in rats.

Results: We applied a toxicogenomics approach to determine whether known renal toxicants could be identified as such from their effects on the transcriptome of the human renal proximal tubular epithelial cell line, HK-2. Based on clustering of differentially expressed genes, we identified 3 toxicity groups within the set of compounds. We used Random Forest to generate a classifier to accurately place compounds in groups. The classifier is based on a signature biomarker comprising 21 genes identified by Random Forest and could differentiate between the groups with high accuracy. Furthermore, we could correctly classify external samples from a dataset exhibiting a marked ‘batch effect’.

Conclusions: No toxicity-associated gene expression alterations could be identified across a set of toxic compounds. Random Forest is a suitable technique for the classification of compounds into toxicity groups. Using a measure of differential expression rather than expression level per se generates a robust classifier that can potentially be applied in a platform-independent manner.

overall_design:
Gene expression changes in HK-2 cells were measured following exposure to 9 different compounds over a range of doses and time-points with the aim of finding biological signatures of toxicity. Clustering of the resulting gene expression data revealed 3 groups of nephrotoxic compounds (Tox 1, Tox 2 and Tox 3), each exhibiting their own distinct effect on HK-2 cells.

This study measures gene expression changes following exposure to controls over 12 hrs or 48 hrs. Three biological replicates per compound/time-point.

first: Leonhard

last: Gruber

first: Mohamed

middle: R

last: Daha

first: Michael

last: Ryan


title: PARVB overexpression increases migration capability and defines high risks for endophytic growth and metastasis in tongue squamous cell carcinoma.

city: Tokyo

first: Afsaneh

last: Eslami

state: Tokyo To

address: 45-5-1, Yushima, Bunkyo Ku

institute: Tokyo Medical and Dental University

summary: Tongue squamous cell carcinoma (TSCC) varies in characteristics even in early stages and is mainly classified into three subtypes, which are superficial, exophytic and endophytic types, based on a macroscopic appearance of tumor growth.Of these subtypes, endophytic tumor has a poorer prognosis because of its invasive feature and higher frequency to have metastasis. To understand a molecular mechanism of endophytic subtype and identify biomarkers, we performed comprehensive microarray analysis for mRNAs from clinical biopsy sampleswhich were classified into subtypes and found overexpression of parvin-beta (PARVB) gene significantly related to endophytic type. PARVB is known to play a critical role in actin reorganization and focal adhesions. Knocking down PARVB expression in vitrocaused apparent decreases in cell migration and wound healing, implying that PARVB has a crucial role in cellular motility. Moreover, metastasis-free survival was significantly lowered in patients with higher PARVB expression. Therefore overexpression of PARVB is a candidate biomarker for endophytic tumor and metastasis and may be clinically applicable for decision making of an adjuvant therapy in TSCC.

overall_design: Twenty seven OCT embedded tissues were used to extract total RNA. Then RNAs were amplified, biotinylated, fragmented and hybridized on GeneChip Human Genome U133 plus 2.0 arrays.

first: Ken

last: Miyaguchi

first: Kaoru

last: Mogushi

first: Hiroshi

last: Watanabe

first: Norihiko

last: Okada

first: Hitoshi

last: Shibuya

last: Mizushima

first: Masahiko

last: Miura

last: Tanaka


title: Expression data in HK-2 cells following exposure to Tox 3 compounds: Ota and Aa

overall_design:
Gene expression changes in HK-2 cells were measured following exposure to 9 different compounds over a range of doses and time-points with the aim of finding biological signatures of toxicity. Clustering of the resulting gene expression data revealed 3 groups of nephrotoxic compounds (Tox 1, Tox 2 and Tox 3), each exhibiting their own distinct effect on HK-2 cells.

This study measures gene expression changes following exposure to Ota, Aa, or control over 24 hrs, 48 hrs, and/or 72 hrs. Three biological replicates per compound/time-point.

middle: N


title: Expression data in HK-2 cells following exposure to Ota_ld

summary:
Background: The development of a new drug from candidate to market is a complex process requiring vast resources of time, money and personnel. The rate of failure in the development pipeline is enormous, leading to wasted resources that could have been better employed on alternative candidates. The requirement for early stage prediction of toxicity is, then, of paramount importance to expedite the introduction of new therapies to clinical practice. To date, most transcriptomics efforts to solve this problem have applied Support Vector Machine techniques to data derived from in vivo studies in rats.

Results: We applied a toxicogenomics approach to determine whether known renal toxicants could be identified as such from their effects on the transcriptome of the human renal proximal tubular epithelial cell line, HK-2. Based on clustering of differentially expressed genes, we identified 3 toxicity groups within the set of compounds. We used Random Forest to generate a classifier to accurately place compounds in groups.  The classifier is based on a signature biomarker comprising 21 genes identified by Random Forest and could differentiate between the groups with high accuracy. Furthermore, we could correctly classify external samples from a dataset exhibiting a marked ‘batch effect’.

Conclusions: No toxicity-associated gene expression alterations could be identified across a set of toxic compounds. Random Forest is a suitable technique for the classification of compounds into toxicity groups. Using a measure of differential expression rather than expression level per se generates a robust classifier that can potentially be applied in a platform-independent manner.

overall_design:
Gene expression changes in HK-2 cells were measured following exposure to 9 different compounds over a range of doses and time-points with the aim of finding biological signatures of toxicity. Clustering of the resulting gene expression data revealed 3 groups of nephrotoxic compounds (Tox 1, Tox 2 and Tox 3), each exhibiting their own distinct effect on HK-2 cells.

This study measures gene expression changes following exposure to a low dose of Ota or a control over 24 hrs or 72 hrs. Three biological replicates per compound/time-point.


title: Expression data in HK-2 cells following exposure to all conditions

overall_design:
Gene expression changes in HK-2 cells were measured following exposure to 9 different compounds over a range of doses and time-points with the aim of finding biological signatures of toxicity. Clustering of the resulting gene expression data revealed 3 groups of nephrotoxic compounds (Tox 1, Tox 2 and Tox 3), each exhibiting their own distinct effect on HK-2 cells.

In this study, all data were normalized together.


title: Expression data in HK-2 cells following exposure to Tox 1 compounds: CsA, Fk, Nnm and Ra

overall_design:
Gene expression changes in HK-2 cells were measured following exposure to 9 different compounds over a range of doses and time-points with the aim of finding biological signatures of toxicity. Clustering of the resulting gene expression data revealed 3 groups of nephrotoxic compounds (Tox 1, Tox 2 and Tox 3), each exhibiting their own distinct effect on HK-2 cells.

This study measures gene expression changes following exposure to CsA, Fk, Nnm, Ra, or control over 12 hrs, 24 hrs, and/or 48 hrs. Three biological replicates per compound/time-point.


title: Expression data in HK-2 cells following exposure to Tox 2 compounds: CdCl, Di, and Kbr

overall_design:
Gene expression changes in HK-2 cells were measured following exposure to 9 different compounds over a range of doses and time-points with the aim of finding biological signatures of toxicity. Clustering of the resulting gene expression data revealed 3 groups of nephrotoxic compounds (Tox 1, Tox 2 and Tox 3), each exhibiting their own distinct effect on HK-2 cells.

This study measures gene expression changes following exposure to CdCl, Di, Kbr, or control over 12 hrs, 24 hrs, and/or 48 hrs. Three biological replicates per compound/time-point.


title: Expression data in HK-2 cells following exposure to Ra

overall_design:
Gene expression changes in HK-2 cells were measured following exposure to 9 different compounds over a range of doses and time-points with the aim of finding biological signatures of toxicity. Clustering of the resulting gene expression data revealed 3 groups of nephrotoxic compounds (Tox 1, Tox 2 and Tox 3), each exhibiting their own distinct effect on HK-2 cells.

This study measures gene expression changes following exposure to Ra or control over 12 hrs or 48 hrs. Three biological replicates per compound/time-point.


title: Expression data in HK-2 cells following exposure to Ota_hd

overall_design:
Gene expression changes in HK-2 cells were measured following exposure to 9 different compounds over a range of doses and time-points with the aim of finding biological signatures of toxicity. Clustering of the resulting gene expression data revealed 3 groups of nephrotoxic compounds (Tox 1, Tox 2 and Tox 3), each exhibiting their own distinct effect on HK-2 cells.

This study measures gene expression changes following exposure to a high dose of Ota or a control over 24 hrs or 72 hrs. Three biological replicates per compound/time-point.


title: Expression data in HK-2 cells following exposure to Nnm_hd

overall_design:
Gene expression changes in HK-2 cells were measured following exposure to 9 different compounds over a range of doses and time-points with the aim of finding biological signatures of toxicity. Clustering of the resulting gene expression data revealed 3 groups of nephrotoxic compounds (Tox 1, Tox 2 and Tox 3), each exhibiting their own distinct effect on HK-2 cells.

This study measures gene expression changes following exposure to high doses of Nnm or a control over 24 hrs or 48 hrs. Three biological replicates per compound/time-point.


title: Expression data in HK-2 cells following exposure to Kbr_ld

overall_design:
Gene expression changes in HK-2 cells were measured following exposure to 9 different compounds over a range of doses and time-points with the aim of finding biological signatures of toxicity. Clustering of the resulting gene expression data revealed 3 groups of nephrotoxic compounds (Tox 1, Tox 2 and Tox 3), each exhibiting their own distinct effect on HK-2 cells.

This study measures gene expression changes following exposure to a low dose of Kbr or a control over 24 hrs or 48 hrs. Three biological replicates per compound/time-point.