title: Sema6A and Mical1 control cell growth and survival of BRAFV600E human melanomas

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: Therapeutic targeting of BRAFV600Eand of MEK has shown a significant impact on progression-free and overall survival in advanced melanoma, but only a fraction of patients benefit from these treatments, suggesting that additional signaling pathways involved in melanoma growth/survival need to be identified. To this end, we used whole genome microarray analysis to identify differentially expressed genes in a set of neoplastic clones, isolated from a single melanoma metastasis, and characterized by mututally exclusive expression of BRAFV600E or NRASQ61R. By this approach we identified two genes, SEMA6A and Mical-1 belonging to the semaphorin-plexin signaling pathway and higly expressed, at mRNA and protein level, in BRAF-mutant neoplastic clones. Real-time PCR, Western blot analysis and immunohistochemistry confirmed the preferential expression of SEMA-6A and Mical-1 in BRAFV600E neoplastic cells from melanoma clones, primary and metastatic cell lines and tissue sections from melanoma lesions. SEMA6A depletion, by specific RNA-interference experiments, led to cytoskeletal remodeling, loss of stress fibers, generation of actin-rich protrusion, and cell death, whereas SEMA6A overexpression, in NRASQ61R clones, promoted invasiveness. Mical-1 depletion, by siRNA, in BRAFV600E melanomas, did not alter the actin cytoskeleton organization but caused a strong NDR phosphorylation and NDR-dependent apoptosis. Overall, these results suggest that the SEMA and MICAL pathways contribute to promote survival of BRAFV600E melanomas.

overall_design: The human melanoma cell lines Me 4405, Me26635, Me665/2, Me10538; clones 2/33; 2/21; 2/4; 2/17; 2/14; 2/59 were established in our laboratory from a surgical specimens. Cells were routinely maintained in RPMI medium 1640 supplemented with 10% FBS and 2 mM glutamine. Cells were maintained at 37°C in a water-saturated atmosphere of 5% CO2 in air. 6x106 cells were seeded in 75 cm2 flasks; after 72h Me 4405 and Me26635  were untreated or  treated with fotemustine at 300 μmol/L for 6 hours. Each treatment or combination was performed in triplicate. The cells were collected and RNA extracted.

first: L

first: A

last: Anichini


title: Gene expression analysis of human induced pluripotent stem cell-derived (hiPSC) cardiomyocytes in 2D versus 3D (Engineered heart tissue) format

status: Public on Apr 20 2016

city: Hamburg

first: Ingra

last: Mannhardt

address: Martinistr. 26

country: Germany

institute: University Medical Center Hamburg-Eppendorf

summary: Analysis of cardiomyocytes cultivated in 2D or age-matched 3D (Engineered heart tissue, EHT) format.

overall_design: Total RNA obtained from hiPSC-CM cultivated in 2D versus 3D format. Array data  (Illumina Human HT-12 v2) were processed on the Illumina GenomeStudio V2011.1 Platform (Gene Expression Module 1.9.0), two slides, five conditions with four to five biological replicates each:  cardiomyocytes (N=4), cardiomyocytes 2D (N=5), cardiomyocytes EHT (N=6; table 1). The array data have been quantile normalized on probe level (47,310 probes) without background correction. Data have been log2 transformed after an offset addition (16).

first: Arne

last: Hansen

first: Herbert

last: Schulz

first: Norbert

last: Huebner


title: Gene profiling of human HOS cell line over-expressed with miR-23a and differentiated by beta-glycerophosphate (BGP) treatment

status: Public on Apr 07 2016

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

country: USA

institute: NCI

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

overall_design: Refer to individual Series


title: Effects of ERG knockdown on HeLa cells mRNA stability

status: Public on Apr 19 2016

city: Liège

first: Franck

last: Dequiedt

address: 1 Avenue de l'hôpital

department: GIGA-Research

country: Belgium

institute: University of Liège

summary: Control of mRNA levels is a fundamental aspect in the regulation of gene expression and is achieved through a balance between mRNA synthesis and decay. E-twenty-six-related gene (Erg) proteins are canonical transcription factors whose described functions are confined to the control of mRNA synthesis. Here, we report that ERG also regulates gene expression by affecting mRNA stability and identify the molecular mechanisms underlying this function. ERG is recruited to mRNAs via its interaction with the RNA-binding protein RBPMS and promotes mRNA decay by binding to CNOT2, a component of the CCR4 deadenylation complex. Transcriptome-wide mRNA stability analysis revealed that ERG controls the degradation of a subset of mRNAs highly connected to Aurora signaling, and whose decay during S-phase is necessary for mitotic progression. Our data indicate that control of gene expression by mammalian transcription factors may follow a more complex scheme than previously anticipated, integrating mRNA synthesis and degradation.

overall_design: HeLa cells treated with a control (siCTL) or anti-ERG (siERG) siRNA were transcriptionally arrested with actinomycin D for 0, 0.5, 1, 2 and 4h. Total RNA was extracted at each time point (T0, T0.5, T1, T2 and T4) and were anaysed using HumanHT-12 v4 BeadChip . Analysis were performed on four biological replicates.

first: Xavier

last: Rambout


title: Gene expression profiling of human HOS cell line differentiated by beta-glycerophosphate (BGP) treatment

summary: Human HOS cell line was differentiated by beta-glycerophosphate (BGP) treatment and gene expression profiling was studied with Illumina expression microarray (HumanHT12_V4).

overall_design: Three negative control replicates vs. three BGP 3-day treatment replicates

first: Princy

last: Francis

first: Bob

last: Walker

first: Paul

last: Meltzer


title: Microarray analysis of lymphocytes isolated from healthy donors ex-vivo exposed to alpha particle radiation

status: Public on Apr 22 2016

city: Ottawa

first: Vinita

last: Chauhan

state: Ontario

address: 775 Brookfield Rd

country: Canada

institute: Health Canada

summary:
The purpose of this study was to  identify genes that are modulated by alpha particle radiation
Cell types were independently exposed to alpha particle radiation using Americium-241 discs (0.9Gy/hr) at a dose range from 0-1.5 Gy. Twenty-four hours post-exposure cells were harvested and RNA was extracted and subjected to microarray analysis.

overall_design: Expression profiling by array analysis-Sample set, 0, 0.5, 1.0, 1.5 Gy (n=12), analysed 24h post exposure

first: Matthew

last: Howland


title: Methylome and transcriptome of EAC (expression)

status: Public on May 01 2016

city: Brisbane

first: Katia

last: Nones

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer MEdical Research Institute

summary: genome-wide methylation profile of 250 samples including 125 EAC, 19 Barrett’s, 64 normal adjacent squamous and 21 normal stomach. Transcriptome data was performed for 70 samples with methylation profile (48 EAC, 4 Barrett’s and 18 normal adjacent squamous). This is the first study to use methylome, transcriptome and ENCODE data to characterize the regulatory role of methylation in EAC.

first: Lutz

last: Krause

first: Kelly

middle: A

last: Loffler

first: Derek

last: Nancarrow

first: Yue

middle: H

last: Tang

first: Harald

last: Oey

first: Nicci

last: Wayte

first: Ann

middle: M

last: Patch

first: Sandra

last: Brosda

first: Suzanne

last: Manning

first: Guy

last: Lampe

first: Andrew

last: Clouston

first: Janine

last: Thomas

first: Jens

last: Stoye

first: Damian

middle: J

last: Hussey

first: David

middle: I

last: Watson

first: Reginald

middle: V

last: Lord

first: Wayne

last: Phillips

last: Gotley

first: B

last: Smithers

middle: C

last: Whiteman

first: Nicholas

middle: K

last: Hayward

first: Sean

last: Grimmond

first: Nicola

last: Waddell

middle: P

last: Barbour


title: Gene expression profiling of human HOS cell line overexpressed with miR23a

first: Yuelin

last: Zhu

summary: Human HOS cell line was overexpressed with  miR23a and gene expression profiling was studied with Illumina expression microarray (HumanHT12_V4).

overall_design: Three negative control replicates vs. three miR23a over-expression replicates

first: Princy

last: Francis

first: Bob

last: Walker

first: Paul

last: Meltzer


title: Tipping Point Biomarkers in Human Airway Cells

status: Public on Apr 28 2016

city: RTP, NC

first: Jenna

last: Currier

address: 109 TW Alexander Dr.

institute: ORISE at USEPA

summary: Determining mechanism-based biomarkers that distinguish adaptive and adverse cellular processes is critical to understanding the health effects of environmental exposures. Shifting from in vivo, low-throughput toxicity studies to high-throughput screening (HTS) paradigms and risk assessment based on in vitro and in silico testing requires utilizing toxicity pathway information to distinguish adverse outcomes from recoverable adaptive events. Little work has focused on oxidative stresses in human airway for the purposes of predicting adverse responses. We hypothesize that early gene expression-mediated molecular changes could be used to delineate adaptive and adverse responses to environmentally-based perturbations. Here, we examined cellular responses of the tracheobronchial airway to zinc (Zn) exposure, a model oxidant. Airway derived BEAS-2B cells exposed to 2–10 µM Zn2+ elicited concentration- and time-dependent cytotoxicity. Normal, adaptive, and cytotoxic Zn2+ exposure conditions were determined with traditional apical endpoints, and differences in global gene expression around the tipping point of the responses were used to delineate underlying molecular mechanisms. Bioinformatic analyses of differentially expressed genes indicate early enrichment of stress signaling pathways, including those mediated by the transcription factors p53 and NRF2. After 4 h, 154 genes were differentially expressed (p <0.01) between the adaptive and cytotoxic Zn2+ concentrations. Nearly 40% of the biomarker genes were related to the p53 signaling pathway with 30 genes identified as likely direct targets using a database of p53 ChIP-seq studies. Despite similar p53 activation profiles, these data revealed widespread dampening of p53 and NRF2-related genes as early as 4 h after exposure at higher, unrecoverable Zn2+ exposures. Thus, in our model early increased activation of stress response pathways indicated a recoverable adaptive event. Overall, this study highlights the importance of characterizing molecular mechanisms around the tipping point of adverse responses to better inform HTS paradigms.

overall_design: Total RNA obtained from BEAS-2B cells exposed to zinc sulfate in the presence of pyrithione compared to unexposed control cells.

first: Wan-Yun

last: Cheng

first: Daniel

last: Menendez

first: Rory

last: Conolly

first: Brian

middle: N

last: Chorley


title: Genome-wide analysis of SNB19 and SHSY5Y cells with single or double knockdown of SDHD and CDKN1C or SLC22A18

city: Leiden

first: attje

middle: sietske

last: hoekstra

address: Einthovenweg 2

department: Human Genetics

country: Netherlands

institute: Leiden University Medical Center

summary:
Analysis of knockdown of SDHD with or without knockdown of CDKN1C or SLC22A18 at gene expression level.
The hypothesis tested in this study was to determine whether the gene expression signature following SDHD knockdown together with SLC22A18 or CDKN1C more closely resembles the signature found in tumors than the signature resulting from SDHD knockdown alone.

overall_design: Total RNA obtained from SNB19 and SHSY5Y cells with single or double knockdown of SDHD and CDKN1C or SLC22A18 compared to scrambled control

first: A

middle: S

last: Hoekstra


title: Structural design of engineered costimulation determines tumor rejection kinetics and persistence of CAR T cells

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: The choice of costimulatory domain in CAR design dictates the kinetics of in vivo anti-tumor responses, affecting potency, quality and durability. We show that 1928z results in more vigorous effector functions, whereas 19BBz design compensates for their lesser cytotoxic potency by steadily building up their numbers. Therapeutic function can be further improved by combining CD28 and 4-1BB costimulation. 1928z-41BBL was revealed to provide optimal combined costimulation, exhibiting highly therapeutic efficiency with balanced T cell effector function and accumulation. Endogenous IFN-β/IRF7 pathway activation was found in 1928z-41BBL T cell and is required for effector function acquisition. The role of the IFN-β/IRF7 pathway provides a novel mechanism through which engineering T cells improve therapeutic effect by self-providing ‘signal 3’.

overall_design: In order to understand the molecular mechanisms underlying the improved anti-tumor function induced by 1928z-41BBL, we performed genome wide gene expression profile of CD4 and CD8 1928z-41BBL CAR T cells and compared it to 19z1, 19z1-41BBL and 1928z, which represent the individual signaling modalities within the design.

first: Zeguo

first: Maud

last: Condomines

first: Sjoukje

last: van der Stegen

first: Fabiana

last: Perna

first: Christopher

last: Kloss

first: Gertrude

last: Gunset

first: Jason

last: Plotkin

first: Michel

last: Sadelain


title: Proteasome machinery is instrumental in a common gain-of-function program of the p53 missense mutants in cancer.

status: Public on Apr 27 2016

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

institute: ICGEB

summary: Mutant p53 proteins, resulting from the missense mutations of the TP53 tumor suppressor gene, possess gain-of-function activities and are among the most robust oncoproteins in human tumors. They are potentially important therapeutic targets. No studies to date have distinguished common, therapeutically relevant mutant p53 gain-of-function effects from effects specific to different mutant variants and cell backgrounds. here we perform the analysis of transcriptomes,rRegardless of the cell background, of different mutant p53s.

overall_design: Four different cell lines were transfected with control or p53 siRNA.So The study comprises four experimental cell lines, each in triplicate.

first: Dawid

last: Walerych

first: Kamil

last: Lisek

first: Giannino

last: Del Sal


title: Down-regulation of linc00598 affects cell cycle related genes in HEK293t cells

city: Seoul

first: Oh-Seok

last: Jeong

address: Chungang Univ., Heukseok-dong, Dongjak-gu, Seoul, Republic of Korea

department: Department of Life Science

country: South Korea

institute: Chung-Ang university

summary: linc00598 is a nuclear localized long noncoding RNA which transcribed in downstream of FoxO1. Previous studies showed that several nuclear retained lncRNAs function as transcriptional regulators. To find out the function of linc00598 as a transcriptional regulator, we performed microarray analysis using linc00598 knock down stable HEK293t cells. The results showed that positive cell cycle regulation related genes including cyclin D2 were regulated transcriptionally by linc00598. It was also observed that knock down of linc00598 induces G0/G1 cell cycle arrest and inhibit proliferation. Therefore linc00598 represents a novel cell cycle regulatory lncRNA and may be involved in promoting transformation of human cells.

overall_design: We used lentiviral based shRNAs to knockdown linc00598 in human HEK293t cells. We harvested total RNA from linc00598 knockdown and control knockdown samples and subjected the total RNA to microarray analysis (two replicates for each condition)

first: Yun-Cheol

last: Chae


title: Endothelial to Mesenchymal Transition

status: Public on Apr 05 2016

first: Gaurav

last: Pandey

state: New York

address: 1 Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Driving HUVECs toward mesenchymal fate

overall_design: Comparison of untreated HUVECs, HUVECs treated with TGF-B, HUVECS treated with TGF-B and oxidative stress, and comparator human dermal fibroblasts

last: Kovacic


title: Expression data of Human Decidual NK cells, Peripheral blood, CD56Bright NK cells and CD56Dim NK cells on HGU133B arrays

status: Public on Apr 06 2016

summary: Fragmented RNA cocktails from FACS sorted Human  decidual NK cell, and peripheral blood CD56Bright and CD56Dim NK cells,  previously  hybridization to  HGU95AV2 chips (Koopman et al J Exp Med. 2003 Oct 20;198(8):1201-1), were stored long term at -80C, thawed and hybridized to HG-U133B arrays.

overall_design: Transcriptome analysis of Human decidual NK cells and NK cells from peripheral blood using Affymetrix UGU133B arrays.

first: Hernan

last: Kopcow

first: Jack

last: Strominger


title: TGF-beta and TLR4-induced transcriptional response

status: Public on Apr 23 2016

city: Chicago

first: Swati

last: Bhattacharyya

state: IL

address: 240 E Huron st McGAE M230

department: Medicine

institute: Northwestern University

summary: To assess the pattern of TGF-beta and TLR4-induced gene expression changes at the genome-wide level, confluent healthy skin fibroblasts were incubated with the classic TLR4 ligand, LPS, TGF-beta or transfected with CD4TLR4. At the end of incubation, total RNA was harvested and processed for hybridizations to Illumina Human HT-12V4 microarray chips.

overall_design: Part 1: Seed three FS fibroblasts (passage 4) in DMEM (10% FBS) in 12-well or 100mm dishes at confluence, change to fresh serum-free DMEM medium with 0.1% BSA for 24 hours.  Triplicate treatment: Control---no treatment, LPS (1ug/ml) for 24h, TGF-beta (10 ng/ml) for 24h, and LPS and TGF-beta for 24h.  Part 2.  Foreskin fibroblasts transfected and after five hrs media changed to 0.1% BSA for 48h. Then empty vector transfected (8ug/100mm dish), CD4TLR4 transfected (8ug/100mm dish), or LPS (1ug/ml) for 6h.


title: Expression data of Human Decidual NK cells and Peripheral bood NK cells analyzed with two Affymetrix array platforms


title: Dermal papilla signature gene expression in immortalized human dermal papilla cells from balding and non-balding scalp

city: Cologne

first: Axel

last: HILLMER

address: Kerpener Str. 62

department: Institute of Pathology

institute: University of Cologne

summary: Transcriptome analysis of DP signature gene expression in hTERT-immortalized balding (BAB) and non-balding (BAN) dermal papilla cells derived from frontal and occipital scalp of male patients with androgenetic alopecia Hamilton grade IV.

overall_design: RNA obtained from BAB and BAN, 3 replicates for each cell line

last: Hillmer


title: Genome-wide analysis of gene expression in influenza A infected human macrophages treated with VX-787

status: Public on Apr 03 2016

city: Helsinki

first: Yu

last: Fu

address: Tukholmankatu 8

department: Institute for Molecular Medicine, Finland

country: Finland

institute: University of Helsinki

summary: Analysis of gene expression in macrophages infected with influenza A virus or Mock and treated with the VX-787 to investigate the effects VX-787 have on transcriptional response in human macrophages.

overall_design: Human macrophages were infected with influenza A/WSN/1933(H1N1) or A/Udorn/307/72(H3N2) viruses, or non-infected (Mock). 10nM VX-787 was treated to WSN, Udorn or Mock infected cells, repectively.

first: Denis

last: Kainov


title: Gene expression profiles of erythroid progenitors treated with vehicle or the HDAC1/2-selective inhibitor ACY-957

status: Public on Apr 11 2016

city: Boston

first: Jeff

last: Shearstone

state: MA

address: 70 Fargo Street

department: Biology

institute: Acetylon Pharmaceuticals

summary: Determine the effects of HDAC1/2-selective chemical inhibtion on the gene expression profiles of erythroid progenitors derived from human CD34+ bone marrow cells.

overall_design: CD34+ cells isolated from human bone marrow of healthy normal donors were cultured in a 2-phase system. This system has been described previously (Sankaran, Menne et al. 2008).  Cells were expanded for 7 days in expansion media, followed by an additional 5 days culture in erythroid differentiation media in the presence of vehicle or ACY-957 (an HDAC1/2-selective inhibitor). Experiments were conducted in triplicate for each condition.  Each replicate experiment utilized cells from different donors.

first: Jeffrey

middle: R

first: Olga

last: Golonzhka

first: Apurva

last: Chonkar

first: David

last: Tamang

first: John

last: van Duzer

first: Simon

last: Jones

first: Matthew

middle: B

last: Jarpe


title: Expression data of Human Decidual NK cells, Peripheral blood, CD56Bright NK cells and CD56Dim NK cells on HGU133A arrays

summary: Fragmented RNA cocktails from FACS sorted Human  decidual NK cell, and peripheral blood CD56Bright and CD56Dim NK cells,  previously  hybridization to  HGU95AV2 chips (Koopman et al J Exp Med. 2003 Oct 20;198(8):1201-1), were stored long term at -80C, thawed and hybridized to HG-U133A arrays.

overall_design: Transcriptome analysis of Human decidual NK cells and NK cells from peripheral blood using Affymetrix UGU133A arrays.


title: Rapid Inflammasome Activation Following Mucosal SIV infection of Rhesus Monkeys

city: Cleveland

first: Rafick

last: Pierre-Sekaly

state: OH

address: 2103 Cornell Avenue

department: Pathology

institute: Case Western Reserve University

summary: The purpose of this study was to evaluated the kinetics of virus dissemination to distal tissues and the initial innate and adaptive host immune responses following intravaginal SIV infection of rhesus monkeys.

overall_design:
We performed comprehensive serial necropsies in rhesus monkeys (M. mulatta) on day 0, day 1, day 3, day 7 and day 10 following intravaginal inoculation of 5x104 TCID50 SIVmac251, measured viral RNA, and performed transcriptomic analysis to measure gene expression changes that correlate with virus spread.
note: Grouped different sections of a tissue based on similar transcriptomic profiles; example: FRT = vagina+uterus+cervix

first: Dan

last: Barouch

first: Khader

last: Ghneim

first: William

last: Bosche

first: Yuan

last: Li

first: Brian

last: Berkemeier

first: Michael

last: Hull

first: Sanghamitra

first: Mark

last: Cameron

first: Jinyan

last: Liu

first: Kaitlin

last: Smith

first: Erica

last: Borducchi

first: Crystal

last: Cabral

first: Lauren

last: Peter

first: Amanda

last: Brinkman

first: Mayuri

last: Shetty

first: Hualin

first: Courtney

last: Gittens

first: Chantelle

last: Baker

first: Wendeline

last: Wagner

middle: G

last: Lewis

first: Arnaud

last: Colantonio

first: Hyung-Joo

last: Kang

first: Wenjun

middle: D

last: Lifson

first: Rafick-Pierre

last: Sekaly

last: Piatak Jr


title: Extracellular matrix-dependent generation of integration- and xeno-free iPS cells using a modified mRNA transfection method

status: Public on Apr 21 2016

city: Bundanggu

first: Kangin

last: lee

state: Seongnam

address: 335 Pankyoro

department: Biomedical Science

institute: CHA University

summary:
In this study, we sought to examine whether an extracellular matrix (ECM)-based xeno-free culture system that we recently established could be used together with a microRNA-enhanced mRNA reprogramming method for the generation of clinically safe iPS cells. The notable features of this method are (1) the use of a xeno-free/feeder-free culture system for the generation and expansion of iPS cells rather than the conventional labor-intensive culture systems using human feeder cells or human feeder-conditioned medium and (2) the enhancement of mRNA-mediated reprogramming via the delivery of microRNAs.
Strikingly, we observed the early appearance of iPS cell colonies (~11 days), substantial reprogramming efficiency (~0.2-0.3%), and a high percentage of ESC-like colonies among the total colonies (~87.5%), indicating enhanced kinetics and reprogramming efficiency.
Therefore, the combined method established in this study provides a valuable platform for the generation and expansion of clinically safe (i.e., integration- and xeno-free) iPS cells, facilitating immune-matched cell therapy in the near future.

overall_design: Test (iPS generated by ECM-based xeno-free culture system with a microRNA-enhanced mRNA reprogramming method) vs. Control (hESC and fibroblast)

first: Kang

last: Lee

first: S

middle: Y

first: Dong

last: Hwang


title: Expression data from human placental derived mesenchymal stem cells (PDMSCs)

status: Public on Mar 30 2016

city: Hangzhou

first: Chenxia

last: Hu

state: Zhejiang

address: School of Medicine; First Affiliated Hospital; Zhejiang University

country: China

institute: Zhejiang University

summary:
When PDMSCs were induced to heptocytes in vitro, cells mophology, stem cell markers, mitochondrial metabolism will change according to the differentiated status.But dedifferentiation reverses differentiated cells to a more primitive phenotype and PDMSCs will retain the multilineage potency. Furthermore, it will leads to the alteration of gene expression pattern.
We used microarrays to detail the global programme of gene expression underlying dedifferentiation and hepatogenic differentiation prcocesses, we intend to identify distinct classes of differentiated genes during these processes.

overall_design: Human PDMSCs at passage 5 were induced to hepatocytes for 11 days, then the inductive medium was replaced by general culture medium for 1 day. Then human PDMSCs, hepatogenic PDMSCs at 11 days, dedifferentiated PDMSCs were selected for RNA extraction and hybridization on Affymetrix microarrays. To that end, we hand-selected cells at three time-points: before hepatogenic induction (P), hepatogenic PDMSCs at 11 days (H) and dedifferentiated PDMSCs for 1 day (DH) .

first: Yuchao

last: Yu


title: Transcriptome analysis reveals differences in vasculature signalling between human dermal papilla cells from balding and non-balding scalp

first: Axel

last: HILLMER

summary: Transcriptome analysis of hTERT-immortalized balding (BAB) and non-balding (BAN) dermal papilla cells derived from frontal and occipital scalp of male patients with androgenetic alopecia Hamilton grade IV. Interrogation of transcriptome differences between BAB and BAN after dihydrotestosterone (DHT, active metabolite of androgen) treatment revealed significant enrichment of vasculature-related genes among down-regulated genes in BAB compared to BAN.

overall_design: RNA obtained from BAB and BAN after treatment with 1nM or 10nM of DHT, 2-3 replicates for each condition

last: Hillmer


title: Genome-wide analysis of basal gene expression in pediatric acute lymphoblastic leukemia xenograft cells

status: Public on Apr 01 2016

city: Randwick

first: Duohui

last: Jing

state: NSW

address: Lowy Cancer Research Centre, UNSW

department: Leukaemia Biology

institute: Children’s Cancer Institute Australia

summary: Analysis of basal gene expression in patient-derived xenograft cells. A panel of pediatric ALL xenografts was utilized to further understand the biology of leukemia.

sample_organism:
Homo sapiens
Mus musculus

overall_design: Total RNA was isolated from patient-derived xenograft cells. Array analysis was carried out on Illumina beadchip HT12.

first: Santi

last: Suryani

first: Richard

last: Lock


title: Heterogeneity in global gene expression profiles between biopsy specimens taken peri-surgically from primary ER-positive breast carcinomas (diagnostic/surgical samples)

status: Public on Mar 29 2016

city: London

first: Alice

last: Gao

state: London

address: 237 Fulham Road

department: Breast Cancer Now

country: United Kingdom

institute: The Institute of Cancer Research

summary: Gene expression is widely used for the characterization of breast cancers. Variability due to tissue heterogeneity or measurement error or systematic change due to peri-surgical procedures can affect measurements but is poorly documented. We studied the variability of global gene expression between core-cuts of primary ER+ breast cancers and the impact of delays to tissue stabilization due to sample x-ray and of diagnostic core-cutting. Twenty-three and 56 sample pairs, respectively, were suitable for analysis. In general, there is a good correlation in gene expression between pairs of core-cuts except where genes have a narrow dynamic range. Increases in the expression of several stress/early-response genes (e.g., FOS, FOSB, JUN) were found in both studies. Substantial changes in expression of early response genes occur within an hour after surgery and in IL6, IGFB2 and MYC as a result of diagnostic core-cut biopsy. Similar correlation coefficients to the average gene expression profiles of intrinsic subtype, particularly LumA and LumB, can lead to discordances between assigned subtypes.

overall_design: Fifty-six paired core-cuts were taken at diagnosis and 2 weeks later at surgical excision. Whole genome expression analysis was conducted on extracted RNA. Correlations and differences were assessed between the expression of individual genes, gene-sets/signatures and intrinsic subtypes.

first: Qiong


title: Generation of Stem Cell-Derived β Cells from Type 1 Diabetic Patients

city: Cambridge

first: Jeffrey

middle: Robert

last: Millman

state: Massachusetts

address: 7 Divinity Ave

department: HSCRB

institute: Harvard University

summary: We recently reported the scalable in vitro production of functional stem cell-derived β cells.  Here we extend this approach to generate SC-β cells from Type 1 diabetic patients (T1D), a cell type that is destroyed during disease progression and has not been possible to extensively study.  These cells express β cell markers, respond to glucose both in vitro and in vivo, prevent alloxan-induced diabetes in mice, and respond to anti-diabetic drugs.  Furthermore, we use an in vitro disease model to demonstrate the cells respond to different forms of β cell stress. Using these assays, we find no major differences in T1D SC-β cells compared to SC-β cells derived from non-diabetic patients (ND).  These results show that T1D SC-β cells can be used for the treatment of diabetes, drug screening, and the study of β cell biology.

overall_design: Differentiated cells were sorted and processed for RNA isolation using the MARIS protocol published previously (PMID: 24516164.)  Human induced pluripotent stem cell (hiPSC) line were differentiated into SC-beta cells or dysfunctional, polyhormonal cells (PH). Four biological replicates were assessed with differentiation to both SC-beta and PH cells.  Those data were normalized together with and compared to existing, previously published data from Hrvatin et al. (PMID: 24516164) and Pagliuca et al. (PMID: 25303535) from human islet-derived insulin+ cells, undifferentiated HUES8 hES cells, SC-beta cells derived from HUES8 and PH cells derived from HUES8 according to previously published protocols.

first: Chunhui

last: Xie

first: Alana

last: VanDervort

first: Mads

last: Gürtler

first: Felicia

middle: W

last: Pagliuca

first: Douglas

middle: A

last: Melton


title: Human induced pluripotent stem cell derived neurons as a model for Williams-Beuren syndrome

city: Toronto

first: James

last: Ellis

address: 686 Bay Street

department: Developmental and Stem Cell Biology

institute: Hospital for Sick Children

summary: Williams-Beuren Syndrome (WBS) is caused by the microdeletion of approximately 25 genes on chromosome 7q11.23, and is characterized by a spectrum of cognitive and behavioural features. We generated cortical neurons from a WBS individual and unaffected (WT) control by directed differentiation of induced pluripotent stem cells (iPSCs). Single cell mRNA analyses and immunostaining demonstrated very efficient production of differentiated cells expressing markers of mature neurons of mixed subtypes and from multiple cortical layers. We found that passive membrane properties were comparable in these WBS and WT neurons, but there was a profound alteration in action potentials, with significantly prolonged WBS repolarization times and a WBS deficit in voltage-activated K+ currents. Miniature excitatory synaptic currents were normal, indicating that unitary excitatory synaptic transmission was not altered. Gene expression profiling identified 136 negatively enriched gene sets in WBS compared to WT neurons. These genes are involved in synaptic transmission and assembly, cation transport, axon guidance and elastic fibre pathways, and some encode ion channels. Our findings provide insight into gene dysregulation and electrophysiological defects in WBS patient neurons.

overall_design: 6 week-old neurons were generated from one control WT iPSC lines and three WBS iPSC lines (A100, B100, I100). Three independent replicates were pooled together and spotted on one array each

first: Shahryar

last: Khattak

first: Elise

last: Brimble

first: Wenbo

last: Zhang

first: Kirill

last: Zaslavsky

first: Jason

last: Hendry

first: P

middle: J

last: Ross

first: Seema

last: Mital

first: Michael

last: Salter

first: Lucy

last: Osborne


title: Expression data from Huh-7 cells

status: Public on Mar 23 2016

city: shanghai

first: Chu

last: Liang

state: shanghai

address: 320 Yue-Yang Road

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary:
Small nucleolar RNAs (snoRNAs) dysfunction have been associated with cancer development. We investigated the function of an orphan C/D box class snoRNA, SNORD126, in hepatocellular carcinoma (HCC) and colorectal cancer (CRC) cells
We used microarrays to identify targets with roles in SNORD126’s activity in Huh-7 cells

overall_design: SNORD126- or EGFP-overexpressed Huh-7 cells were collected and followed by RNA extraction, then hybridized with Affymetrix microarrays. We sought to obtain the differentially expressed genes between the two groups.

first: Xian-Long

last: Fang

first: Liang

last: Chu


title: ER alpha rapid signaling is required for estrogen induced proliferation and migration of vascular endothelial cells

status: Public on Mar 22 2016

first: Gavin

middle: R.

last: Schnitzler

address: 800 Washington St. Box 80

department: Molecular Cardiology Research Institute

institute: Tufts Medical Center

summary: Estrogen receptor alpha (ERa) is required for the protective effects of 17-beta-estradiol (E2, the active, endogenous form of estrogen) after vascular injury or in atherosclerosis. E2-bound ERa can function as a transcription factor which binds directly to chromatin (the genomic pathway). Some ERa is also associated with the plasma membrane and, when bound by E2, activates cellular kinases, including PI3K, Akt and ERK (the rapid signaling pathway). Rapid signaling is mediated by interaction between ERa and the adaptor molecule striatin. Here we identify a triple point mutation (AA 231,233 & 234 KRR->AAA) of full length ERa that blocks its association with striatin and eliminates its ability to perform rapid signaling (without affecting its ability to perform genomic signaling). We have created stably-transfected human vascular endothelial cell lines expressing either WT ERa (WT ECs) or KRR mutant ERa (KRR ECs), and use these cells to show that rapid signaling through ERa is required for the proper regulation of most E2-regulated genes (the data presented in this record), and also for the ability of E2 to stimulate EC migration and proliferation and to inhibit inflammatory monocyte adhesion to ECs.

overall_design: Human Eahy 926 stable cell lines carrying a full length wild-type human estrogen receptor alpha (ERa) expression vector (WT ECs) or a full length KRR mutant ERa expression vector (KRR ECs, where the KRR mutant ERa is deficient in rapid signaling) were treated with or without 17-b-estradiol (E2) for 16 hrs. RNA from 3 bioligical replicates per condition was harvested and used to probe Illumina bead arrays.

first: Qing

last: Lu

first: Kazutaka

last: Ueda

first: Lakshmanan

last: Iyer

first: Olga

middle: I

last: Diomede

first: Andrade

last: Tiffany

first: Richard

middle: H

last: Karas


title: Transportome profiling identifies profound alterations in Crohn’s disease partially restored by commensal bacteria

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: In the present study, the transcriptional analysis of CD biopsies reveals profound alterations in the ileum transportome profile. More than 60 SLC transporters showed different expression pattern compared with the healthy donors, being mostly decreased. Changes were confirmed in almost all the eighteen altered SLCs analyzed by RT-PCR. The results obtained display alterations in amino acid transporters, purinome members, Zn transporters and metallothioneins. All together, these alterations which mainly involve transporters localized at the apical membrane of the enterocyte anticipate impaired amino acid uptake and purinergic responses. Remarkably, incubation of explants with specific commensal bacteria restored almost all CD transportome alterations.

overall_design: Genome wide transcriptomic profile of Ileal mucosa from five healthy and six Chron's disease samples .

first: S

last: Pérez-Torras

first: I

last: Iglesias

first: M

last: Llopis

first: J

last: Antolin

first: F

last: Guarner

last: Pastor-Anglada


title: Low dose irradiation enhances gene targeting in human pluripotent stem cells

city: Los Angeles

first: Jie

last: Tang

address: 8700 Beverly Blvd

institute: Cedars Sinai Medical Center

summary: Human pluripotent stem cells (hPSCs) are now being used for both disease modeling and cell  therapy. However, efficient homologous recombination (HR) is often crucial to develop  isogenic control or reporter lines. Here we show that limited low dose irradiation (LDI) using  either γ-ray or X-ray exposure (0.4 Gy) significantly enhances HR frequency, possibly through  induction of DNA repair/recombination machinery including ataxia-telangiectasia mutated,  Histone H2A.X and RAD51 proteins. LDI could also increase HR efficiency by over 30- fold  when combined with the targeting tools zinc finger nucleases (ZFNs), transcription activator–like  effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats  (CRISPRs). Whole exome sequencing confirmed that the LDI to hPSCs did not induce gross  genomic alterations, or affect cellular viability. Irradiated and targeted lines were karyotypically  normal and made all differentiated lineages that continued to express green fluorescent protein  targeted at the AAVS1 locus. This simple method allows higher throughput of new targeted  hPSC lines that are crucial for the research community as this growing field develops.

overall_design: 4 samples

first: Seigo

last: Hatada

first: Vicent

last: Funari

first: Dhruv

last: Sareen

first: Clive

last: Svendsen


title: Gene expression analysis of MCF-10a breast epithelail cells upon enforced expression of G alpha 13 (GNA13)

status: Public on Mar 18 2016

city: SIngapore

first: Suhail Ahmed Kabeer

last: Rasheed

address: 8 College Road

department: Programme in Cancer and Stem Cell Biology

country: Singapore

institute: Duke-NUS Medical School

summary: G alpha 13 is known to be upregulated in multiple cancer types including breast, prostate, head and neck etc. This analysis was carried out ot identify the down stream effectors of G alpha 13 signaling in breast cancer cells.

overall_design: MCF-10a cells were transfected with pMSCV-vector ( a retroviral vector) or pMSCV-GNA13. Cells were kept under selection in Blasticidine. MCF-10a cells  stably expressing either pMSCV-Vector or pMSCV-GNA13 are seeded in a 10 cm dish.

first: Teo

middle: C

last: Rong

first: Suhail

first: Patrick

last: Casey


title: Reduced Proteolytic Shedding of Receptor Tyrosine Kinases is a Post-Translational Mechanism of Kinase Inhibitor Resistance.

status: Public on Mar 21 2016

first: Miles

last: Miller

address: 185 Cambridge St

institute: Massachusetts General Hospital

summary:
Expression data from MDA-MB231 human breast cancer cells treated with metalloproteinase inhibitor (10uM BB94), MEK inhibitor (3uM PD325901), or DMSO control shows substantial overlap in the transcriptional responses arising from MEK and protease inhibition, suggesting a shared mechanism of action.
Kinase inhibitor resistance often involves upregulation of poorly understood “bypass” signaling pathways.  Here, we show that extracellular proteomic adaptation is one path to bypass signaling and drug resistance. Proteolytic shedding of surface receptors, which can provide negative feedback on signaling activity, is blocked by kinase inhibitor treatment and enhances bypass signaling.
In particular, MEK inhibition broadly decreases shedding of multiple receptor tyrosine kinases (RTKs) including HER4, MET, and most prominently AXL, an ADAM10 and ADAM17 substrate, thus increasing surface RTK levels and mitogenic signaling. Progression-free survival of melanoma patients treated with clinical BRAF/MEK inhibitors inversely correlates with RTK shedding reduction following treatment, as measured non-invasively in blood plasma.  Disrupting protease inhibition by neutralizing TIMP1 improves MAPK inhibitor efficacy, and combined MAPK/AXL inhibition synergistically reduces tumor growth and metastasis in xenograft models.  Altogether, extracellular proteomic rewiring through reduced RTK shedding represents a surprising mechanism for bypass signaling in cancer drug resistance.

overall_design: Human breast cancer MDA-MB231 cells were plated in 10cm plates at 70% confluency, treated the following day with either 0.1% DMSO vehicle control, 10uM BB94, or 3uM PD325901, and lysed 24h later.  RNA was prepared using the Qiagen RNeasy Mini kit, and samples were analyzed using Affymetrix Primeview arrays processed by Massachusetts Institute of Technology BioMicroCenter.  Treatments were performed with n=4 (control), n=3 (PD325901), and n=2 (BB94) successful biological replicates.  Data were preprocessed using the R/Bioconductor package “affy” and the RMA normalization routine.

first: Douglas

last: Lauffenburger


title: Disulfiram when combined with copper enhances the therapeutic effects of temozolomide for the treatment of Glioblastoma

city: calgary

first: Xueqing

last: Lun

state: Alberta

address: 3330 hospital drive nw

department: oncology

institute: University of calgary

summary:
Dilsulfiram together with Copper shows efficacy against patient derived Brain Tumor Initiating Cells (BTICs) in vitro and sensitizes BTICs to the DNA damaging agent TMZ. In addition, preclinical assessment found that DSF/Cu potentiaties the efficicacy of TMZ in vivo and  prolongs survival.
We used microarrays to detail the global profile of gene expression underlying DSF/Cu treatment in vitro and in vivo in BTICs.

overall_design: BTICs grown in brain tumor stem cels media containing EGF and FGF were treated with DSF (50nM) and Cu (1uM) together for 12 hrs. Cells were then collected and prepared for gene expression analysis.  For the in vivo study, 4 wks after BT147 was implanted into the brain of CB17 SCID mice, animals were treated with control vehicle (oral-plus) or DSF (100mg/kg) daily via oral administration for two weeks (5 days on, two days off) and Copper (2mg/kg) daily via oral administartion for two weeks. Animals were then sacrificed and the brain tumor tissue was collected and prepared for gene expression analysis.

first: Donna

last: Senger

first: Stephen

last: Robbins

first: Connor

last: Wells


title: Pretreatment microRNA expression impacting on epithelial to mesenchymal transition predicts intrinsic radiosensitivity in head and neck cancer cell lines and patients [UTSCC43A]

status: Public on Mar 19 2016

city: Amsterdam

first: Monique

middle: C.

last: de Jong

address: Plesmanlaan 121

department: Dept of Biological Stress Response and Dept. of Radiation Oncology

institute: Netherlands Cancer Institute

summary:
Purpose: Predominant causes of head and neck cancer recurrence after radiotherapy are rapid repopulation, hypoxia, fraction of cancer stem cells and intrinsic radioresistance. Currently, intrinsic radioresistance can only be assessed by ex-vivo colony assays. Besides being time-consuming, colony assays do not identify causes of intrinsic resistance. We aimed to identify a biomarker for intrinsic radioresistance to be used before start of treatment and to reveal biological processes that could be targeted to overcome intrinsic resistance.
Experimental design: We analyzed both micro- and messenger RNA expression in a large panel of HNSCC cell lines. Expression was measured on both irradiated and unirradiated samples. Results were validated using modified cell lines and a series of laryngeal cancer patients.
Results: MiRs, mRNAs and gene sets that correlated with resistance could be identified from expression data of unirradiated cells. The presence of epithelial to mesenchymal transition (EMT) and low expression of miRs involved in the inhibition of EMT were important radioresistance determinants. This finding was validated in two independent cell line pairs, in which the induction of EMT reduced radiosensitivity. Moreover, low expression of the most important miR (miR-203) was shown to correlate with local disease recurrence after radiotherapy in a series of laryngeal cancer patients.
Conclusions: These findings indicate that EMT and low expression of EMT-inhibiting miRs, especially miR-203, measured in pre-treatment material, causes intrinsic radioresistance of HNSCC, which could enable identification and treatment modification of radioresistant tumors.

overall_design: To test if the induction of epithelial to mesenchymal transition increases radioresistance, these cell lines were obtained from M. Takkunen (University of Helsinki) and tested. Detailed information about development of the cell lines can be read from the original publication (PMID:16899764).

first: Jelle

last: tenHoeve

first: Reidar

last: Grénman

first: Lodewyk

middle: F

last: Wessels

first: Ron

last: Kerkhoven

first: Hein

last: te Riele

first: Michiel

last: van den Brekel

first: Marcel

last: Verheij

first: Adrian

last: Begg


title: Comparison of spheroid-based 3-dimensional culture to monolayer of larynx carcinoma cell line HLaC78.

status: Public on Mar 11 2016

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

institute: University Hospital Würzburg

summary:
In vitro proliferation and/or invasion tests (such as MTT assay, Boyden Chamber Assay, Scratch assay) using established and well-characterized cell lines can provide easy and reproducible tools to investigate anti-tumour or anti-invasion agents ex vivo. However, in vivo cells in a tissue context interact with neighbouring cells and extracellular matrix components. In 2-dimensional monolayer cultures cells tend to loose tissue-specific properties.
2-D culture models therefore seem unsuitable to mimic the behaviour of cells in a natural, 3-dimensional microenvironment, especially for testing of growth or invasion inhibiting substances. Spheroids on the other hand resemble in many aspects solid, non-vascularized tumour tissue.

overall_design: Within this study the larynx carcinoma cell line HLaC78 was used as a model for comparing overall gene expression in 2D monolayer culture with 72 hrs old HLaC78 multicellular spheroids, providing evidence for extensive restructuring of gene expression in the 3-dimensional context.

first: Marianne

last: Schmidt


title: Analysis of gene expression in hypoxic and normoxic HeLa cells.

city: Lund

first: Mattias

last: Belting

address: Barngatan 2B

department: Department of Oncology

country: Sweden

institute: Lund Univercity

summary: The purpose of experiment is to compare the mRNA expression differences between HeLa cells conditioned with normoxia 21% oxygen and hypoxia 1% oxygen at 6h and 20h.

overall_design: Total RNA was obtained from HeLa cells for 4 different conditions, 3 biological replicate experiments were performed, resulting in a total of 12 samples.

first: E

last: Bourseau-Guilmain

first: J

last: Lidfeldt


title: fibroblasts and iPS cells from patients with insulin receptor mutations

status: Public on Mar 04 2016

first: Grace

last: Daher

address: 1 Joslin Place

institute: Joslin Diabetes Center

summary:
Insulin resistance is central to diabetes and metabolic syndrome. To define the consequences of genetic insulin resistance distinct from those secondary to cellular differentiation or in vivo regulation, we generated induced pluripotent stem cells (iPSCs) from individuals with insulin receptor mutations and age-appropriate control subjects and studied insulin signaling and gene expression compared with the fibroblasts from which they were derived. iPSCs from patients with genetic insulin resistance exhibited altered insulin signaling, paralleling that seen in the original fibroblasts. Insulin-stimulated expression of immediate early genes and proliferation were also potently reduced in insulin resistant iPSCs. Global gene expression analysis revealed marked differences in both insulin-resistant iPSCs and corresponding fibroblasts compared with control iPSCs and fibroblasts. Patterns of gene expression in patients with genetic insulin resistance were particularly distinct in the two cell types, indicating dependence on not only receptor activity but also the cellular context of the mutant insulin receptor. Thus, iPSCs provide a novel approach to define effects of genetically determined insulin resistance. This study demonstrates that effects of insulin resistance on gene expression are modified by cellular context and differentiation state. Moreover, altered insulin receptor signaling and insulin resistance can modify proliferation and function of pluripotent stem cell populations.
To investigate the impact of genetic insulin resistance on transcriptional regulation in iPSCs, we analyzed global gene expression using microarrays in both fibroblasts and iPSCs.

overall_design: Human skin fibroblasts were obtained from six subjects with insulin receptor mutations and five healthy controls. iPS cells were then generated from these fibroblasts. RNA was extracted and hybridized on Affymetrix microarrays to determine differences in gene expression as a result of cell type and genotype

first: Salvatore

last: Iovino

first: Alison

middle: M

last: Burkart

first: Kristina

last: Kriauciunas

first: Laura

last: Warren

first: Katelyn

last: Hughes

first: Michael

last: Molla

first: Youn-Kyoung

last: Lee

first: Mary-Elizabeth

last: Patti

first: C

last: Kahn


title: SRT2014 and the whole blood leukocyte transcriptional response during human endotoxemia

status: Public on Mar 07 2016

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

summary: Healthy subjects injected with 4ng/kg e.coli LPS treated with placebo or SRT2014

overall_design: Double-blind clinical trial

middle: P

first: Tom

last: van der Poll


title: DHT-dependent AR activity in LNCaP cells

status: Public on Mar 15 2016

city: Houston

first: Leif

middle: E

last: Peterson

state: TX

address: 6565 Fannin, Suite MGJ6-031

department: Center for Biostatistics

institute: HMRI

summary: AR transcriptional activity is regulated by DHT

overall_design: DNA microarrays we employed to determine changes in gene expression caused by DHT treatment

first: William

middle: T

last: Schrader

last: Ittmann

first: Nancy

middle: L

last: Weigel

first: Irina

middle: U

last: Agoulnik


title: TNF dependent induction of inhibitory pathways in CD4+ T cells in HIV and LCMV [TNF stimulation]

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary:
Chronic viral infections caused by HIV in humans or LCMV in mice are characterized by immunodeficiency and chronic inflammation. During chronification, T cells progressively lose effector functions, a process associated with immunoregulatory pathways and known as T-cell exhaustion. A link between ‘exhaustive’ T-cell reprogramming and chronic inflammation has not been established. Using a systems biology approach we demonstrate in HIV and LCMV infection that TNF, a prototypical mediator of chronic inflammation, functions upstream of major immunoregulatory pathways in T cells during chronic viral infection. In vivo blockade of TNFR-signaling interferes with the exhaustive T-cell program during chronic infection and reduces viral loads by several log. Continuous TNFR-signaling during disease progression towards chronic infection seems to be causative for T-cell exhaustion and an important link between immunodeficiency and chronic inflammation. TNF blockade might represent a novel therapeutic option during late stage infections caused by HIV and other virus causing chronic infections.
TNF stimulation of CD4+ T cells to generate a CD4+ T-cell specific RNA-fingerprint

overall_design: 4 experimental conditions with 3 biological replicates for each condition

first: Marc

last: Beyer

first: Jens

last: Chemnitz


title: Genome-wide gene expression in Marfan Syndrome smooth muscle cells (MFS-SMCs) in comparison to that in mutation corrected (mcMFS-SMCs)

status: Public on Mar 03 2016

city: Taipa

first: Jung

middle: Woo

last: Park

state: Macau

department: Faculty of Health Sciences

institute: University of Macau

summary: Analysis of gene expression comparison between MFS- and mcMFS-SMCs

overall_design: Total RNA was isolated from MFS- and mcMFS-SMCs, differentiated from equivalent induced pluripotent cells (iPSCs)

first: Ren-He

last: Xu


title: A metabolic co-regulator bioinformatics screen reveals that PGC1α suppresses prostate cancer metastasis

status: Public on Mar 16 2016

city: Derio

first: Verónica

last: Torrano Moya

address: 801 Building. Technology Park of Vizcaya

institute: CICbioGUNE

summary: The current view of cellular transformation and cancer progression supports the notion that cancer cells must reprogram their metabolism in order to survive and progress in different microenvironments. Master co-regulators of metabolism orchestrate the modulation of multiple metabolic pathways through transcriptional programs, and hence constitute a probabilistically parsimonious mechanism for general metabolic rewiring. Here we show that the transcriptional co-activator PGC1α suppresses prostate cancer progression and metastasis. A metabolic co-regulator data mining analysis unveiled that PGC1α is consistently  down-regulated in multiple prostate cancer patient datasets and its alteration is associated with reduced disease-free survival and metastasis. Genetically engineered mouse model studies revealed that compound prostate epithelium-specific deletion of Pgc1a and Pten promotes prostate cancer progression and metastasis, whereas, conversely, PGC1α expression in cell lines inhibits the pre-existing metastatic capacity. Through the application of integrative metabolomics and transcriptomics we demonstrate that PGC1α expression in prostate cancer is sufficient to elicit a global metabolic rewiring that opposes cell growth, consisting of sustained oxidative metabolism at the expense of anabolism. This metabolic program is regulated downstream the Oestrogen-related receptor alpha (ERRα), and PGC1α mutants lacking ERRα activation capacity lack metabolic rewiring capacity and metastasissuppressive function. Importantly, an ERRα signature in prostate cancer recapitulates the prognostic features of PGC1A. Our findings uncover an unprecedented causal contribution of PGC1α to the metabolic switch in prostate cancer and to the suppression of metastatic dissemination.

overall_design: Total RNA was isolated from prostate cancer cell line PC3 expressing or not PGC1a (for induction, cells were treated with doxycycline for 2 passages)

first: V

last: Torrano


title: Regulatory consequences of SOX4 knock-down in MDA-LM2 cell line

first: Myriam

last: Heiman

address: 43 Vassar St

institute: Massachusetts Institute of Technology

summary: Transcriptomic profiling of SOX4 knock-down MDA-LM2 cell line resulted in down-regulation of its transcriptional target gene, TMEM2.

overall_design: Two independent siRNAs were used to knock down SOX4 in metastatic MDA-LM2 cells. The cells were then subjected to transcripome profiling in comparison to control siRNA-transfected cells.

first: H

last: Lee

last: Goodarzi

last: Alarcón

first: S

last: Tavazoie


title: Whole genome expression analysis of SaOS2 cells expressing anti-sense APC RNA

city: Delhi

first: Gurudutta

last: Gangenahalli

state: Delhi

address: Brig. S. K. Mazumdar Marg, Timarpur

department: Stem Cell Research Division

country: India

institute: Institute of Nuclear Medicine & Allied Sciences

summary: Osteoblasts represent an important cell type playing a role in not only bone formation but also regulate hematopoiesis by secreting factor as well as via contact with hematopoietic stem cells in the bone marrow. Since Wnt signalling plays an important role in osteoblast differentiation, we were interested in looking at how canonical Wnt signalling activation in osteoblastic cells is likely to affect hematopoietic cell adhesion and regulate their fate. Endogenous Wnt signaling activation in osteoblastic SaOS2 cells was achieved by generating doxycycline (DOX) inducible antisense-APC expressing SaOS2 cells. Gene expression profiling was performed on SaOS2 cells induced with DOX (1μg/ml) for 3 days and further on DOX treated cells allowed to recover for 3 days. The results reveal changes in expression of a number of cell adhesion and extracellular matrix protein genes as well as genes involved in osteoblast differentiation.

overall_design:
Doxycycline inducible antisense APC expressing SaOS2 cells were treated with DOX for  3 days and compared with control (untreated) cells. In addition, a set of DOX induced cells was further cultured for 3 days in absence of Dox to allow for the cells to recover and see the change in gene expression compared to Dox treated and control cells. All experiments were done in triplicates (in total 9 samples).

This study has not been published

first: Neeraj

last: Satija


title: PNAs-A15 effects on non-small cell lung cancer cell line

status: Public on Mar 17 2016

city: Bangkok

first: Preeyaporn

middle: Plaimee

last: Phiboonchaiyanan

address: 254  Phyathai Rd. Wangmai Patumwan Bangkok

department: Department of Pharmacology and Physiology

country: Thailand

institute: Faculty of Pharmaceutical Sciences, Chulalongkorn University

summary: Expression profile of parental wild type non-small cell lung cancer, NCI-H460, and cancer stem cell-rich (CSC-rich) populations treated with PNAs-A15 for 6 h. Results provide the information that PNAs-A15, a peptide nucleic acid of A-repeats length 15 bp, suppressed up-regulated A-repeats containing genes in both parental wild type and CSC-rich cells.

overall_design: In this study, we isolate cancer stem cell-rich (CSC-rich) population from a non-small cell lung cancer (NSCLC) cell line, NCI-H460, by selectively propagating the cells in a spheroid culture condition. The parental wild type H460 and CSC-rich cells were maintained at 37°C in 5% CO2 under sterile conditions in Roswell Park Memorial Institute (RPMI) 1640 medium. Cells were treated with PNAs-A15 in 6-well microplates for 6 h. Total RNA was isolated and hybridized on the HumanHT-12 v4 Expression BeadChip. The RNA expressions were evaluated.


title: Deciphering targets of CD271-dependent signaling mediating chemo-resistance in MeWo cells

status: Public on Mar 05 2016

city: Berlin

first: Christian

last: Regenbrecht

address: Chariteplatz 1

department: Tumor stem cells

institute: Charité University Medicine Berlin, Germany

summary: Parental MeWo cells sensitive to chemotherapeutic drugs Etoposide, Fotemustine, Vindesine and Cisplatin, as well as their resistant derivatives, were analyzed for expression of potential mediators of resistance using genome-wide expression profiling.

overall_design: 11 samples of MeWo cells either sensitive or resistant to chemotherapeutic drugs were analysed.

first: Torben

last: Redmer

first: Reinhold

last: Schaefer


title: Analysis of gene expression in hTERT/cdk4 immortalized human myoblasts compared to their primary populations in both undifferentiatied (myoblast) and differentiated (myotube) states

city: Londonderry

first: William

middle: John

last: Duddy

address: C-TRIC building, Altnagelvin Hospital Campus

department: Northern Ireland Centre for Stratified Medicine

institute: Ulster University

summary: hTERT/cdk4 immortalized myogenic human cell lines represent an important tool for skeletal muscle research, being used as therapeutically-pertinent models of various neuromuscular disorders and in numerous fundamental studies of muscle cell function. However, the cell cycle is linked to other cellular processes such as integrin regulation, the PI3K/Akt pathway, and microtubule stability, raising the question as to whether transgenic modification of the cell cycle results in secondary effects that could undermine the validity of these cell models. Here we subjected healthy and disease lines to intensive transcriptomic analysis, comparing immortalized lines with their parent primary populations in both differentiated and undifferentiated states, and testing their myogenic character by comparison with non-myogenic (CD56-negative) cells. We found that immortalization has no measurable effect on the myogenic cascade or on any other cellular processes, and that it was protective against the systems level effects of senescence that are observed at higher division counts of primary cells.

overall_design: This dataset includes gene expression profiles for 94 samples comprising primary myoblasts and their corresponding immortalized clones in both differentiated and undifferentiated states (average of 4 cell culture replicates each) from 5 human subjects (2 healthy and 3 Duchenne muscular dystropy - DMD), together with primary populations of non-myogenic (CD56-ve) cells from the muscles of 8 other human subjects. Total RNA was extracted from, myoblasts, myotubes (after 9 days of differentiation), or CD56-ve cells by dissolving cell pellets in TRIzol then using PureLink RNA Mini Kit.


title: Myc-dependent purine biosynthesis regulates the expression of oncogenes and tumour suppressors in prostate cancer cells

city: Oslo

first: Ian

last: Mills

address: Gaustadalleen 21

department: Centre for Molecular Medicine Norway

country: Norway

institute: University of Oslo

summary: Prostate cancer is the commonest male cancer in Europe and the USA. The androgen receptor is a key transcription factor contributing to the development of all stages of the disease. In addition, other transcription factors have been associated with poor prognosis in prostate cancer, amongst which c-Myc is a well-established oncogene in many other cancers.  We have previously reported that a role for the androgen receptor in prostate cancer is to promote glycolysis and anabolic metabolism.  Many of these metabolic pathways are also c-Myc-regulated in other cancers. In this study we report that  de novo purine biosynthesis is a c-Myc-dependent pathway in prostate cancer cells as determined by commensurate changes in the levels of enzymes in the pathway in response to siRNA knockdown of c-Myc and inducible overexpression of c-Myc.  In addition c-Myc is recruited to the promoters of genes in the pathway as determined by chromatin immunoprecipitation. Using immunohistochemistry and real-time transcript detection we show that two enzymes (PAICS and IMPDH2) within the pathway are overexpressed in prostate cancers.  An inhibitor of IMPDH2 reduces cell proliferation and significantly reduces the levels of guanosine triphosphate within treated cells.  This imposes nucleolar stress on cells as determined by significant reductions in the levels of guanine nucleotide binding protein-like 3 (GNL3).  In addition the levels of c-Myc, p53 and the androgen receptor are affected and the expression of tumour suppressive microRNA-34b is increased.  Combining the IMPDH2 inhibitor with anti-androgens results in a combinatorial inhibition of cell proliferation.  In conclusion we propose using enzymes within the de novo purine biosynthesis as cancer biomarkers and applying drugs to alter the flux through this pathway may represent an effective means of stratifying patients for therapy and sensitising some to AR-targeted therapies.

overall_design: Total RNA of three biological replicates for each condition was extracted using the RNeasy kit (Qiagen), conditions are: 5 h vehicle, 5 h Doxycycline, 12 h vehicle, 12 h Doxycyline

first: Stefan

middle: J

last: Barfeld

middle: G


title: Analysis of gene expression in human malignant rhabdoid cells following prolonged treatment with the histone deacetylase inhibitor, Panobinostat

status: Public on Mar 01 2016

city: Clayton

first: Jason

last: Cain

address: 27-31 Wright St

institute: Hudson Institute of Medical Research

summary: We hypothesized that prolonged treatment of malignant rhabdoid tumor cells with low-dose HDACi will drive cellular differentiation. We assessed changes in gene expression following 21 days treatment with the HDACi, Panobinostat, versus a DMSO vehcile control in three human MRT cell lines.

overall_design: Total RNA obtained from three human malignant rhabdoid tumor cell lines (G401, SJSC, STM91-01) cultured for 21 days in the presence of low-dose Panobinostat was compared to 21-day treated DMSO control cells. All treatments and cell lines were performed in triplicate.

first: Andrea

last: Muscat

first: Dean

last: Popovski

first: Samantha

middle: N

last: Jayasekara

first: Fernando

last: Rosello

first: Melissa

last: Ferguson

first: Kieren

middle: D

last: Marini

first: Muhammed

last: Alamgeer

first: Elizabeth

last: Algar

first: Peter

last: Downie

first: D

last: Watkins

first: David

last: Ashley


title: A Molecular Portrait of the replication stress response defects via Genome-wide Transcriptome Profiling

status: Public on Feb 29 2016

first: Chun-Jen

middle: Curtis

last: Lin

state: Texas

address: 7345 Fannin Street

department: Systems Biology

institute: University of Texas MD Anderson Cancer Center

summary: Defects in replication stress response (RSR) allow the survival and proliferation of genomically unstable cells, ultimately leading to tumorigenesis. Therefore, the RSR status can potentially serve as a powerful indicator to predict the possibility of early tumorigenesis. Here, we identified an RSR defects (RSRD) gene signature that robustly predicted RSR status. For the clinical benefit, our identification of RSRD gene signature gives the possibility to assess the risk of early tumorigenesis in the precancerous patients.

overall_design: Various shRNAs that target genes involved in replication stress response were transfected in MCF-10A non-transformed breast cell lines after oncogenic cyclin E overexpressed. All MCF-10A variants were seeded 200000 at 10 cm plate. Cells were harvested after 48 hours culturing and used for gene expression profiling.

first: Curtis

middle: C

first: Hui

last: Dai

first: Shiaw-Yih


title: Generation of Mature Megakaryocytes from Pluripotent Stem Cells by a Chemically-Defined Transcription Factor-Based Forward Programming Approach

city: Hinxton

first: Louella

last: Vasquez

address: Genome Campus

institute: Wellcome Trust Sanger Institute

summary: Microarray gene expression data is used to compare the transcriptomics of hiPSC, hiPSC derived forward programmed-, hiPSC derived directed differentiated- megakaryoctes AND cord- blood derived megakaryocytes

overall_design: Total RNA obtained from human induced plutipotent stem cells (hiPSC), megakaryocytes differentiated in vitro from haematopoetic stem cells obtained from cord blood and megakaryocytes differentiated from hiPSC

first: Thomas

last: Moreau


title: Contribution of WDR77 and p53 to androgen response in prostate cancer cells

city: Buffalo

first: Qiang

last: Hu

state: NY

address: Elm & Carlton Streets

institute: Roswell Park Cancer Institute

summary: To decipher the contribution of WDR77 and p53 to androgen-responsive gene expression, effect of siRNA-mediated silencing of WDR77 and p53 on expression of androgen-dependent genes was studied.

overall_design: Human LNCaP prostate cancer cells were transfected with individual siRNA SmartPools targeting WDR77 or p53 or a non-targeting siRNA SmartPool.  Forty-two hours after transfection, cells were treated with synthetic androgen R1881 (5nM) or vehicle.  Three biological replicates were generated per treatment group.  Forty-eight hours later, total RNA was isolated and processed for Illumina oligoarray analysis.

first: Hannelore

last: Heemers

first: Xiwei

last: Chen

first: Dan

last: Wang

first: Song

last: Liu


title: Gene expression analysis in NB adherent primary cell lines after endothelin-1 treatment

status: Public on Feb 25 2016

city: Seville

first: Ricardo

last: Pardal

address: Avda. Manuel Siurot, s/n.

department: Medical Physiology and Biophysics

institute: University of Seville

summary:
We cultured adherent primary cell lines from NB tumor samples.
Adherent primary cell lines from NB tumor samples have a subpopulation of neural crest progenitors that grow as spheres when cultured in low-binding conditions.

overall_design: We tested the changes in gene expression induced by endothelin-1 (ET1), a cytokine that regulates proliferation, migration, differentiation and survival of NC cells .

first: Pedro

last: Linares-Clemente


title: Selective CDK8 inhibitor SEL120-34A alters expression of interferon-related DNA damage resistance signature genes in colorectal cancer

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

summary: CDK8 (cyclin-dependent kinase 8) is a kinase component of a multi - protein Mediator complex, involved in transcription control. Several studies indicated that high overexpression and activity of CDK8 could be a driver of malignant progression in colorectal cancer (CRC). Herewith we present molecular insights into mechanism of action of SEL120-34A - a selective small molecule inhibitor of CDK8 kinase. Biochemical and binding studies indicated that SEL120-34A selectively binds and inhibits enzymatic activity of CDK8 in the low nM range. Recently CDK8 has been described as a regulator of STAT1 activity in NK cells where by phosphorylating STAT1 serine 727 (Ser727) influences a possible immunoescape mechanism in various cancers. Consistently, SEL120-34A and other recently reported selective CDK8 inhibitors could repress phosphorylation of STAT1 at a Ser727 at low nM concentrations in cancer cells without any significant changes on tyrosine sites directly regulated by JAK kinases. SEL120-34A inhibited expression of several STAT1 dependent genes in CRC cell lines, stimulated by various cytokines and growth factors. These results were further corroborated with specific CDK8 siRNA knockdown experiments and chromatin immunoprecipitation studies showing CDK8 occupancy on promoters of SEL120-34A regulated genes. In order to better characterize in vivo mechanism of action, mice bearing HCT116 and Colo205 xenograft tumors were treated with SEL120-34A and gene expression changes were measured with microarrays in excised tumors. In animals treated with the CDK8 inhibitor a dose dependent repression of STAT1 Ser727 was observed. The functional analyses of significantly (adj. p. value < 0.05) altered genes with Gene Ontology revealed that those with reduced expression belong to interferon I pathway and type I interferon-mediated signaling pathway terms. This subset of STAT regulated genes was further characterized as an interferon-related DNA damage resistance signature (IRDS) - a prosurvival pathway which correlated strongly with resistance to radiation and chemotherapy in various tumors. Consistently, SEL120-34A has shown very potent cytotoxic synergy with standard of care drugs in CRC, particularly in cells stimulated with interferons. Taken together, for the first time we have shown that selective CDK8 inhibitors are potent regulators of STAT related - IRDS signaling pathway in vitro and in vivo. In addition to previously reported stand-alone efficacy of CDK8 inhibitors in vivo, we provide also a combination treatment rationale for CRC.

overall_design:
Female mice, SCID beige , 7-8 weeks old, were maintained according to the standards of the specific pathogen free conditions. Colo205 or HCT116 cells were centrifuged at 1000 rpm for 5 min and counted using Trypan blue method. A 5M cells were suspended in PBS and Matrigel® (BD Biosciences) (3:1, v:v) and were injected subcutaneously (SC), on the right hind limb. As the tumor was maintained until it reached ~100-150 mm3. Mice were randomized into uniform groups and subjected to the compound administrations. Prior to use, compound was dissolved freshly in water and administered 30mg/kg BIDx3 per os using cannula in a volume of 10 ul per 1 g of body weight. Tumor samples were collected 4 and 16 hours after last compound dose and preserved in RNAlater.
Three Colo205 cell culture (control) samples were also analyzed.

first: Tomasz

last: Rzymski

first: Michał

last: Mikula

first: Małgorzata

last: Szajewska-Skuta

first: Eliza

last: Zyłkiewicz

first: Łukasz

last: Sapała

first: Izabela

last: Dolata

first: Agata

last: Kitlińska

first: Aleksandra

last: Grochowska

last: Cabaj

first: Agnieszka

last: Dreas

first: Katarzyna

last: Kucwaj

first: Artur

last: Białas

first: Adam

last: Radzimierski

first: Aniela

last: Gołas

first: Renata

last: Windak

first: Jerzy

last: Ostrowski

last: Brzózka


title: Zinc sensing by metal-responsive transcription factor 1 (MTF1) controls metallothionein and ZnT1 expression to buffer the sensitivity of the transcriptome response to zinc

status: Public on Feb 24 2016

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

institute: Newcastle University

summary: Only a small number of genes are known direct targets of the zinc-responsive transcription factor MTF1; therefore, the aim of this study was to gain a more complete understanding of the MTF-1 regulated zinc-responsive component of the transcriptome.  A targeted siRNA was used to deplete MTF1 expression in the human intestinal cell line Caco-2. We predicted that the response to zinc of direct MTF1 target genes would be abrogated by MTF1 knockdown. Surprisingly, a greater number of genes were regulated by zinc following MFT1 knockdown, and most genes that responded to zinc under both control and MTF1-depleted conditions had an augmented response in the latter condition. Exceptions were the zinc effluxer ZnT1 and a suite of metallothionein genes, suggesting that responses of other genes to zinc are usually buffered by increases in these proteins. We propose that MTF1 heads a hierarchy of zinc sensors, and through controlling the expression of a raft of metallothioneins and other key proteins involved in controlling intracellular zinc levels (e.g. ZnT1) alters zinc buffering capacity and total cellular zinc content.  We tested and validated this model by overexpressing metallothionein and observing the predicted curtailment in response of the zinc-repressed SLC30A5 (ZnT5) promoter. The model provides the framework for an integrated understanding of cellular zinc homeostasis. Because MTs can bind metals other than zinc, this framework links with overall cellular metal homeostasis.

overall_design: Gene expression profiling by Illumina BeadArray of the effects of ZNF658 gene knockdown by siRNA. 2 different siRNAs were used, with appropriate non-targetting controls. All experiments were carried out in triplicate.

first: Joy

last: Hardyman

first: John

last: Tyson

first: Kelly

middle: A

last: Jackson

first: Christine

last: Aldridge

first: Ruth

last: Valentine

first: Dianne

last: Ford


title: Deciphering targets of CD271-dependent signaling processes

status: Public on Feb 23 2016

first: Christian

last: Regenbrecht

country: Germany

summary: Genome-wide expression profiling of stably NGFR transfected melanoma cells was used to identify genes driven by expression of the nerve growth factor receptor CD271 (NGFR).

overall_design:
Stable overexpression of NGFR (CD271):
Generation of cell lines stably overexpressing CD271 (NGFR), melanoma cells were transfected with 2 µg of a plasmid expressing GFP-tagged human NGFR (RG207966, OriGene) and selected with G418 (100-300 µg/ml, PAA) over a period of two weeks followed by sub-cloning or FACS.
Gene expression profiling:
Whole genome expression profiling of T20/02 and A375 cells (NGFR) and control cells (Mock or GFP) was performed with three biological replicates. Illumina raw data of BeadChip HumanHT-12V4 platform were summarized via the BeadStudio without normalization and background correction. Follow-up processing was done via the R/Bioconductor environment employing packages lumi, limma and q-value. Data were normalized with quantile normalization. Genes were termed significantly differentially expressed when the average detection p-value of at least one case was < 0.05  the ratio was outside the interval [0.75,1.33], one of the p-values from limma test, Student's t-test, Welch test and Wilcoxon test was < 0.05. At least one of the q-values corresponding to one of these tests < 0.05.

first: Torben

last: Redmer

first: Reinhold

last: Schaefer


title: Acquired Resistance to the Second-Generation Androgen Receptor Antagonist Enzalutamide in Castration-Resistant Prostate Cancer

city: Chicago

first: Donald

last: Vander Griend

address: 909 S. Wolcott Ave, COMRB Room 5051

department: Pathology

country: USA

institute: The University of Illinois at Chicago

summary: Illumina gene array analyses of prostate cancer cell lines that had acquired resistance to Enzalutamide (MDV3100).

overall_design: mRNA analyses of four cell lines (CWR-R1, LAPC-4, LNCaP, and VCAP) cells that were either untreated, treated for 48hrs with Enz (short-term), or continuously grown in Enzalutamide for >6 months.

first: Steven

last: Kregel


title: Silcening YWHAE gene expression suppresses the proliferation of colon cancer cells by inducing gene differentially expressed.

status: Public on Feb 20 2016

city: Haikou

first: Yousheng

last: Huang

state: Hainan

address: The 3rd Xueyuan Road

department: Department of pathology

institute: Hainan Medical university

summary: In this study,YWHAE expression was silenced by RNA interference in colon cancer cell lines, and investigate the correlation between YWHAE expression and colon cancer proliferation,and differential expressed genes were analized by gene assay and qPCR technologe.The proliferation and colony formation ability of colon cancer cells were significantly reduced after YWHAE knockdown. More 1200 known genes were found to be involved in the YWHAE functions related tumorigenesis by genechip analysis, these genes related to cell proliferation/apoptosis and cell cycle process. qRT-PCR results showed an expression pattern consistent with that of the genechip analysis.

overall_design: Lentivirus-mediated RNA interference was used to knockdown YWHAE expression in colon cancer cell lines. And cell proliferation assays . GeneChip analysis were carried out for mRNA expression profiling, followed, the expressed levels of mRNA and protein were measured by Quantitative real-time polymerase chain reaction (qRT-PCR) and western blot , respectively.

first: You

middle: S

last: Xie


title: Whole genome transcriptional analysis of leukemic CLL cells purified from bone marrow of xeno-transplanted mice

status: Public on Feb 16 2016

city: Milano

first: Michela

last: Riba

address: via Olgettina 60

department: COSR, Center for Omics Sciences

country: Italy

institute: IRCCS, Ospdale San Raffaele

summary: The development and progression of CLL are dependent upon a complex microenvironmental network of cellular and molecular signals. As an example the in vitro survival of CLL cells is supported by nurse-like cells, which have been identified as a CLL-specific tumor-associated macrophage (TAM) population. However little is known regarding the role of TAMs in CLL development and progression. In the CLL xenograft model based on the engraftment of MEC1 human CLL cell line into Rag2-/-γc-/-, we analyzed the whole-genome transcriptome of leukemic B cells, exposed in vivo to TAMs, isolated from the bone marrow. We found an enrichment of genes involved in inflammation and interaction between TAMs and leukemic cells.

overall_design: Rag2-/-γc-/- were injected intravenously with MEC1 cells and sacrificed at early stage of leukemia (n=3). RNA was isolated from: i) in vitro pre-injected human CD19+ MEC1 cells and ii) human CD19+ MEC1 cells purified from murine bone marrow by magnetic separation and processed for illumina whole-genome gene expression direct-hybridization assay

first: Maria

last: Bertilaccio

first: Giovanni

last: Galletti

first: Cristina

last: Scielzo

first: Tania

middle: V

last: Rodriguez

first: Federica

last: Barbaglio

first: Dejan

last: Lazarevic

first: Davide

last: Cittaro

first: Giorgia

last: Simonetti

first: Michele

last: De Palma

first: Paolo

last: Ghia

first: Federico

last: Caligaris-Cappio


title: Sorted leukocyte populations from acute HIV-1 patients.

status: Public on Feb 15 2016

city: Dallas

first: Damien

last: Chaussabel

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

summary: The aim of this study was to identify cell-type specific contributions to the acute HIV transcriptional signature identified in the CHAVI 001 acute 32 prospective cohort.

overall_design: Four AHI patients and four healthy individuals were apheresed and different leukocyte populations were sorted by flowcytometry. Genome wide transcriptional profiling was done for AHI B cells (n=4), Healthy B cells (n=2) , AHI CD4 T cells (n=3), Healthy CD4 T cells (n=4), AHI CD8 T cells (n=4), Healthy CD8 T cells (n=2), AHI polymorphonuclear cells (n=2), Healthy polymorphonuclear cells (n=3), AHI monocytes (n=3), Healthy monocytes (n=4), AHI NK cells (n=3), Healthy NK cells (n=3) making a total of 37 samples.


title: Effects of ONC201 on mantle cell lymphoma cell lines

city: Houston

first: Wencai

last: Ma

address: 7455 Fannin st

institute: MD Anderson Cancer Center

summary: The small molecule ONC201 is toxic in vitro to multiple cell lines and primary tumor samples of mantle cell lymphoma (MCL) and acute myeloid leukemia, even ones with unfavorable genetic features (notably including TP53 inactivation) or acquired resistance to other agents. Because the mechanism of action in these malignant hematologic cells appeared to differ from that in solid tumors, we performed gene expression profiling (GEP) studies on MCL lines treated with ONC201 and other agents with known mechanisms of action. Treatment of JeKo-1 cells with 5 uM ONC201 showed consistent and progressive increases or decreases over time in two sets of genes: upregulated genes, which implicated an ER stress response and mTOR pathway inhibition, and downregulated genes, which implicated reduced proliferation. These implicated effects of ONC201 were validated by confirmatory experiments. Similar GEP changes were observed in ONC201-naive Z138 cells after 24 hr of ONC201 treatment, but were not seen in Z138 cells made ONC201-resistant by chronic exposure. Finally, the GEP effects of ONC201 in JeKo-1 cells were mimicked by the ER stress inducer tunicamycin, but not by the direct MTOR inhibition rapamycin, further confirming an ER stress response and suggesting that inhibition of the mTOR pathway was by an indirect mechanism.

overall_design: For each experiment, cells from a single stock culture of each cell line used were aliquoted into individual culture plate wells, establishing individual replicates, and drugs were added to start the experiment. Treated replicates were harvested after the times of treatment indicated, by pelleting cells, lysing pellets in TriZOL, and freezing TriZOL until RNA isolation. Untreated replicates, serving as controls, were either harvested at the beginning of the experiment or at later times, as specified below.

first: Jo

last: Ishizawa

first: Kensuke

last: Kojima

first: Zhiqiang

last: Wang

first: Michael

last: Andreeff

first: R

last: Davis


title: Vitamin A-deficient mice experience increased viral antigens and enhanced cytokine/chemokine production in nasal tissues following respiratory virus infection despite the presence of FoxP3+ T cells

status: Public on Feb 11 2016

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary: Vitamin A deficiencies and insufficiencies affect hundreds of millions of people in both developing and developed countries. These individuals experience higher rates of mortality and increased morbidity during enteric and respiratory infections compared to those who are vitamin A sufficient. Previously, our laboratory has demonstrated that vitamin A-deficient (VAD) mice have significantly impaired virus-specific IgA and CD8+ T cell responses in the airways. Here we demonstrate that VAD mice experience enhanced cytokine/chemokine gene expression and release in the respiratory tract 10 days following virus infection compared to control vitamin A-sufficient animals. Cytokines/chemokines that are reproducibly upregulated at the gene expression and protein levels include IFNγ and IL-6. Despite previous indications that cytokine dysregulation in VAD animals might reflect low forkhead box (Fox)P3+ T cell frequencies, we found no reduction in FoxP3+ T cells in VAD respiratory tissues. As an alternative explanation for the high cytokine levels, we found that virus infection and viral antigen persistence were enhanced on day 10 post-infection in VAD animals compared to controls, and that respiratory tract tissues had an increased potential to activate virus-specific T cells. Results encourage cautious management of virus infections in patients with VAD; efforts to enhance FoxP3+ T cell frequencies and quell immune effectors might in some cases exacerbate disease if virus has not been cleared.

overall_design: We used microarrays to explore the gene expression profiles differentially expressed in nasal-associated lymph tissue (NALT) lymphocytes from vitamin A-sufficient and vitamin A-deficient mice following infection with Sendai virus.

first: Rhiannon

last: Penkert

first: Sherri

last: Surman

first: Julia

last: Hurwitz


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

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

overall_design: Microrrays were used to identify gene expression profiles and pathways that are differentially activated after enforced expression of PROX1 in the PROX1-negative human pancreatic ductal adenocarcinoma (PDAC) cell line Capan1. MSCV retroviral transduction was used to generate Capan1 cells that ectopically express PROX1 and selected for puromycin resistance. Three independent transductions with control virus (MSCV_puro) and 3 independent transductions with Prox1-cDNA virus (MSCV_PROX1_puro) were conducted for these experiments.

first: Yiannis

last: Drosos

first: Beatriz

last: Sosa-Pineda


title: m1A marks translation initiation sites in human and mouse messenger RNA [microarray]

status: Public on Feb 12 2016

city: Tel-Hashomer

first: Sharon

last: Moshitch-Moshkovitz

address: Laboratory wing

department: Cancer Research Center

country: Israel

institute: Sheba Medical Center

summary: We developed a novel approach, m1A-seq, for high-resolution mapping of the transcriptome-wide m1A landscape, based on antibody-mediated capture followed by massively parallel sequencing. Using this method we performed immunodepletion of methylated transcipts to assess the average methylation level

overall_design: Immunodepletion of m1A modified transcripts in human compared to the input, allows for estimation of the fraction of methylated transcripts. We compared the expression levels of sup (immunodepleted) and input methylated transcripts to deduce the fraction of m1A methylation.

first: Dan

last: Dominissini

first: Chuan

last: He

first: Gideon

last: Rechavi


title: Gene expression and SNP genotype data from induced Pluripotent Stem cells from Parkinson's Disease patients harbouring G2019S mutations in the LRRK2 gene

status: Public on Feb 09 2016

city: Oxford

first: Sally

last: Cowley

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

type:
SNP genotyping by SNP array
Expression profiling by array

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

overall_design: Refer to individual Series


title: Systematic Evaluation Of Genes And Genetic Variants Associated With Type 1 Diabetes Susceptibility

status: Public on Feb 27 2016

city: Nedlands

first: Ramesh

last: Ram

state: WA

address: 6 Verdun Street

department: Centre for Diabetes Research

country: Australia

institute: University of Western Australia

summary: Application of Systems Genetics analysis for systematic evaluation of candidate causal genes associated with risk of Type 1 Diabetes along with follow-up bioinformatics pathway analysis.

overall_design: Total RNA obtained from whole blood (for EBV-B cells) and Peripheral blood mononuclear cells (PBMCs) (for T-cells)

first: Munish

last: Mehta

first: Quang

last: Nguyen

first: Irma

last: Larma

first: Bernhard

middle: O

last: Boehm

first: Flemming

last: Pociot

first: Patrick

last: Concannon

first: Grant

last: Morahan


title: Analysis of differentially expressed genes between Huntington’s disease and control iPSCs derived GABA MS-like neurons

status: Public on Feb 04 2016

city: Moscow

first: Evgeny

last: Nekrasov

address: gubkina, 3

country: Russia

institute: Vavilov Institute of General Genetics

summary: Huntington’s disease (HD) is an incurable hereditary neurodegenerative disorder, which manifests itself as a loss of GABAergic medium spiny (GABA MS) neurons in the striatum and caused by an expansion of the CAG repeat in exon 1 of the huntingtin gene. There is no cure for HD, existing pharmaceutical can only relieve its symptoms. Here, induced pluripotent stem cells were established from patients with low CAG repeat expansion in the huntingtin gene, and were then efficiently differentiated into GABA MS-like neurons under defined culture conditions. Analysis of differentially expressed genes between Huntington’s disease and wild type iPSCs derived GABA MS-like neurons has been performed.

overall_design: Total RNA obtained from three pairs of WT and HD neurons differentiated in parrallel from human pluripotent stem cells.

first: Tatiana

last: Semashko


title: microRNA-7-5p inhibits melanoma cell proliferation and metastasis by suppressing RelA

status: Public on Feb 10 2016

middle: Aaron

last: Candy

state: Western Australia

address: 6 Verdun St

department: Cancer Medicine

institute: Perkins Institute

summary: microRNA-7-5p (miR-7-5p) is an established tumor suppressor in multiple cancer types and inhibits growth and invasion by suppressing expression and activity of the epidermal growth factor receptor (EGFR) signaling pathway. While melanoma is not typically driven by EGFR signaling, expression of miR-7-5p is reduced in metastatic tumors compared to primary melanoma. Here, we investigated the biological and clinical significance of miR-7-5p in melanoma. Our results showed that augmenting miR-7-5p expression in vitro markedly reduced tumor cell viability, colony formation and induced cell cycle arrest. Furthermore, ectopic expression of miR-7-5p reduced migration and invasion of melanoma cells in vitro and reduced melanoma lung colonizationmetastasis in vivo. To investigate the mechanism underlying this effect, we used cDNA microarray analysis to identify a subset of putative miR-7-5p target genes associated with melanoma and metastasis. Of these, we confirmed nuclear factor kappa B (NF-κB) subunit RelA, as a novel direct target of miR-7-5p in melanoma cells, such that miR-7-5p suppresses NF-κB activity to decrease expression of canonical NF-κB target genes, including IL-1a, IL-6 and IL-8. Importantly, the effects of miR-7-5p on melanoma cell growth, cell cycle, migration and invasion were recapitulated by RelA knockdown. Finally, analysis of gene array datasets from multiple melanoma patient cohorts revealed an association between elevated RelA expression and poor survival, further emphasizing the clinical significance of RelA and its downstream signaling effectors.. Taken together, our data suggest that miR-7-5p replacement therapy might have clinical utility in melanoma to inhibit the metastatic process, in part through its inactivation of RelA/NF-kB signaling.

overall_design: Total RNA was extracted from WM266-4 cells transfected with miR-NC or miR-7-5p precursor molecules (30 nM) for 24 h, using Qiazol reagent (Qiagen).


title: Effect of RUNX1 depletion in MCF7 breast cancer cells in the presence or absence of Estradiol

status: Public on Feb 02 2016

city: Los Angeles

first: Nyam-Osor

last: Chimge

state: CA

address: 2250 Alcazar street

department: IGM

institute: USC

summary: Effect of RUNX1 depletion in the presence or absence of Estradiol

overall_design: MCF7 cells constitutively expressing shRNA targeting RUNX1 and non-specific shRNA was kept in charcoal stripped serum for 48h prior prior to treatment with Estradiol


title: MiR-23b/-27b Targets in Prostate Cancer Cell Lines

city: Miami

first: Kerry

last: Burnstein

state: Fl

department: Molecular and Cellular Pharmacology

institute: University of Miami

summary: Analysis of genes regulated by miR-23b/-27b overexpression in aggressive PC3-ML cells, confirmed by antagomiR inhibition of miR-23b and miR-27b in the relatively indolent cell line LNCaP. Genes that were downregulated in PC3-ML overexpression and upregulated with LNCaP inhibition were further explored as downstream targets of miR-23b/-27b.

overall_design: PC3-Ml cells were transduced with miR-23b/-27b or a scrambled miRNA control, and only cells expressing greater than 95% transduction efficiency were used for array. LNCaP cells were transfected with antagomiRs to miR-23b and miR-27b, or a non-coding control.

first: Meghan

last: Rice

first: Reema

last: Ishteiwy


title: Role of the histone demethylase KDM2B in hematopoietic homeostasis and malignancies [human cell line gene expression]

status: Public on Feb 22 2016

city: Washington

first: Alexandros

last: Tzatsos

state: DC

address: 800 22nd St NW SEH 8850

department: GW Cancer Center

institute: George Washington University

summary: Development of the hematopoietic system is dynamically controlled by the interplay of transcriptional and epigenetic networks to determine cellular identity. Those networks are critical for homeostasis and frequently dysregulated in leukemias. We identified histone demethylase Kdm2b as a critical regulator of definitive hematopoiesis and lineage specification of hematopoietic stem and progenitor cells (HSPCs). RNA sequencing in murine HSPCs and genome-wide chromatin immunoprecipitation studies in human leukemias revealed that Kdm2b regulates differentiation, lineage choice, cytokine signaling, and quiescence.

overall_design: Identify the KDM2B dependent transcriptome in human leukemia cell lines by using the GeneChip® PrimeView™ Human Gene Expression Array

first: Yan

last: Kai


title: Gene expression profiling of Wilms tumors

city: Lund

first: Jenny

last: Karlsson

address: BMC C13

department: Clinical genetics

institute: Lund University

summary: The global gene expression pattern of  Wilms tumors in comparison with clear cell sarcoma of the kidney (CCSK) and non-neoplastic fetal and adult kidneys.

overall_design: Total RNA extracted from 32 fresh frozen Wilms tumors, 2 CCSKs, 2 non-neoplastic adult kidneys and comercially obtained RNA from 4 fetal kidneys, were hybridized to Illumina humanHT-12 v4.0 Expression BeadChip at the SCIBLU Lund University, Sweden (http://www.lth.se/sciblu).

first: Linda

middle: H

last: Mengelbier

first: David

last: Gisselsson


title: Expression Quantitative Trait Locus Mapping Studies in Mid-Secretory Phase Endometrial Cells Identifies HLA-F and TAP2 as Fecundability-Associated Genes

first: Courtney

middle: K

last: Burrows

state: Illinois

address: 920 E. 58th St. CLSC

department: Human Genetics

institute: University of Chicago

summary: We performed an unbiased genome-wide expression quantitative trait locus (eQTL) mapping study to identify common regulatory (expression) single nucleotide polymorphisms (eSNPs) in mid-secretory endometrium.

overall_design: 53 women underwent endometrial biopsies as part of their clinical evaluation for recurrent pregnancy loss, after obtaining informed consent. These women were between the ages of 26 and 43 years and had at least two previous pregnancy losses before10 weeks gestation.

first: Gülüm

last: Kosova

first: Catherine

last: Herman

first: Kristen

last: Patterson

first: Katherine

middle: E

last: Hartmann

first: Digna

middle: R

last: Velez Edwards

first: Mary

last: Stephenson

first: Vincent

last: Lynch

first: Carole

last: Ober