title: TGFβ1 treatment of A2058 melanoma cells

first: Jillian

last: Howlin

address: Scheelevägen 2

department: Division of Oncology & Pathology

institute: Lund University Cancer Center/ Medicon Village

summary: 4 replicates were prepared from A2058 melanoma cells [transfected with 10ng of empty vector (pcDNA3.1+)] and treated with 5ng/ml TGFβ1 or vehicle control for 24hrs

overall_design: This is the control arm of a larger experiment where cells transfected with a particular expression plasmid were treated with TGFβ1 or control vehicle. The transfection with the expresion plasmid was unsucessful so this empty vector data has been used alone to simply examine the effect of TGFβ1 treatment on A2058 cells.


title: Altered expression of genes in WDR5 knockdown

status: Public on Feb 09 2015

city: Guangzhou

first: Xu

last: Chen

state: Guangdong

address: 107. W. Yanjiang Road

department: Department of Urology

country: China

institute: Sun Yat-sen Memorial Hospital

summary: WDR5 (WD repeat domain 5) plays an important role in the epigenetic regulation of gene transcription, involing in regulation of embryonic stem cell and cancer cell.Bladder cancer is one of the most common cancers that cause approximately 150,000 deaths per year worldwide.The goal of this study is to identify the target genes of WDR5 in bladder cancer.Our results inditcate that the genes regulated by WDR5 involved in a variety of biological functions, such as proliferation and anti-apoptosis.

overall_design: Bladder cancer cell line UM-UC-3 was transfected with the contol siRNA or two different WDR5 siRNA for 48h. The RNA of the transfected cells was extracted and hybridized on Affymetrix microarrays. We indentified the putative target genes of WDR5 in both WDR5 siRNA by comparing  the diferent expressed genes among control, si-WDR5-2 and si-WDR5-3. We futher validated the data of microarray in UM-UC-3 and T24 by RT-qPCR and Western bloting.

first: Weibin

last: Xie

first: Peng

last: Gu

first: Tianxin

last: Lin

first: Jian

last: Huang


title: Genome-wide analysis of gene expression in human macrophages in response to different stimuli

status: Public on Feb 18 2015

city: Helsinki

first: Maria

last: Anastasina

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 non-infected and treated with the saliphenylhalamide, obatoclax, expressing wild type NS1 protein or its mutant R38A, K41A. The hypothesis tested was that R38 and K41 residues within viral NS1 protein are essential for transctiptional control of cellluar gene expression.
Cells were infected with influenza  A/WSN/33 viruses expressing wild type NS1 protein (WT), its R38A, K41A mutant (RK/AA) or non-infected (Mock)

overall_design: Total RNA isolated from macrophages 8 hours post stimuation.

first: Denis

last: Kainov


title: Human induced pluripotent stem cells: diploid, chr7q deletion, spontaneous chr7 correction

status: Public on Feb 16 2015

city: New York

first: Eirini

last: Papapetrou

state: NY

address: 1470 Madison Avenue

department: Oncological Sciences

country: USA

institute: Icahn School of Medicine at Mount Sinai

summary: Gene expression analysis, a) comparing isogenic karyotypically normal iPSCs to del7q-iPSCs, b) comparing del7q-iPSCs to spontaneously corrected iPSCs. The chr7q deletion results in reduced expression levels of a large number of genes in the chr7q deleted region

overall_design: Two-condition experiment, del7q-iPSCs vs. isogenic normal iPSCs and del7q-iPSCs vs spontaneously corrected-iPSCs. Biological replicates: 3 control replicates, 3  del7q-iPSC replicates and 3 spontaneously corrected-iPSC replicates


title: Effect of extracellular S100A4 on melanoma cells of different phenotypes

status: Public on Feb 13 2015

city: Oslo

first: Lina

last: Prasmickaite

address: Ullernchausseen 70

department: Department of Tumor Biology

country: Norway

institute: Oslo University Hospital

summary: S100A4 is a known metastasis-promoting factor, rich in the tumor microenvironment. To clarify how extracellular S100A4 execute its pro-metastatic function, we analyzed gene expression in melanoma cells stimulated with recombinant protein rS100A4 and compared it to the expression in control non-stimulated cells. Two melanoma cell lines representing two distinct phenotypes – invasive (Melmet 1) and non-invasive/proliferative (Melmet 5) – were included in the study. The response at the gene expression level was much stronger in Melmet 5 than in Melmet 1. Melmet 5 down-regulated genes associated with melanocytic differentiation, indicating that Melmet 5 cells gained dedifferentiated, more invasive phenotype after stimulation with rS100A4. The observed changes in the expression of metabolism associated genes suggested the occurrence of metabolic reprogramming. We conclude that extracellular S100A4 stimulate the transition to the invasive phenotype in poorly-invasive melanoma cells, and that this transition is associated with metabolic reprogrammingve

overall_design: Total RNA was isolated from Melmet 1 and Melmet 5 cells stimulated with rS100A4 protein for 48hrs compared to non-stimulated cells.

first: Ingrid

middle: J

last: Bettum

first: Gunhild

middle: M

last: Mælandsmo

first: Vigdis

middle: V

last: Nygaard

first: Kotryna

last: Vasiliauskaite


title: The effect of SubAB treatment on Wnt-High and Wnt-Low sorted human colon cancer stem cells

status: Public on Feb 12 2015

city: Amsterdam

first: Mattheus

middle: Caroluc Benignus

last: Wielenga

state: Noord Holland

address: Meibergdreef 69-71

department: Gastroenterology

country: Netherlands

institute: Academic Medical Center

summary: The effect of ER-stress and subsequent activation of the unfolded protein response was investigated in colon cancer stem cells and more differentiated colon cancer cells

overall_design:
Human colon cancer derived spheroid cultures with a TCF/LEF driven GFP reporter for Wnt signaling activity were treated for 24 hours with SubAB or protease-dead SubABco (1µg/ml)
Treated spheroid cultures were sorted into colon-cancer stem cell fraction (highest 10% Wnt-GFP) and differentiated colon cancer fraction (10% Lowest(Wnt Low) for micro array

first: M

middle: C

first: S

last: Colak


title: Genome-wide hsa-miR-503, hsa-miR-103, and hsa-miR-494 target profiles [array]

status: Public on Feb 04 2015

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

summary: Gene expression profile following transfection with miR-503, miR-103, or miR-494 mature duplex

overall_design: Examination of mRNA levels in HeLa cells following transfection of miR-503, miR-103, or miR-494 mature duplex, control siRNA against GFP, or mock transfection (lipofectamine 2000 alone)

first: Damon

last: Polioudakis

first: Vishwanath


title: Expression profiling of MDA-MB-231 breast cancer cells treated with DOT1L inhibitors and siDOT1L

city: Houston

first: Yongcheng

last: Song

address: One baylor plaza, Baylor College of Medicine

department: PHARMACOLOGY

institute: BAYLOR COLLEGE OF MEDICINE

summary: MDA-MB-231 cell line with relatively high DOT1L levels was treated with two potent, selective inhibitors of the DOT1L histone methyl transferase. These compounds can inhibit cells migration and invasion and induce differentiation. Here we provide expression profiling data of cells treated with two DOT1L inhibitors [1] [2], DOT1L siRNA (siDOT1L) or control.

overall_design:
MDA-MB-231 cells were treated with 1uM compound [1], 5uM compound [1], 2uM compound [2], 10 uM compound [2] (DOT1L inhibitors) or control (0.1% DMSO) for 14 days, or siDOT1L for 7 days. For each unique condition, 2 biological replicates were generated for expression profiling.
Compound [1]: EPZ004777 (in Diagle et al., 2011)
Compound [2]: Compound 55 (in Anglin et al., 2012)

first: Li

last: Zhang

first: Fengju

last: Chen


title: Genome-wide analysis of gene expression in human macrophages in response to infection with recombinant A/WSN/33 influenza A viruses expressing wild type NS1 protein or its mutant R38A, K41A. [RPE]

status: Public on Feb 07 2015

first: Maria

summary:
Analysis of gene expression in human retinal pigment epithelium cell line (RPE) infected with influenza A viruses expressing wild type NS1 protein or its mutant R38A, K41A. The hypothesis tested was that R38 and K41 residues within viral NS1 protein are essential fro transctiptional control of cellluar gene expression.
Cells were infected with influenza  A/WSN/33 viruses expressing wild type NS1 protein (WT), its R38A, K41A mutant (RK/AA) or non-infected (Mock)

overall_design: Total RNA isolated from RPE cells after 10 hours of infection with wild type or mutant influenza A virus (multiplicity of infection = 1)


title: Genome-wide analysis of gene expression in human macrophages in response to infection with recombinant A/WSN/33 influenza A viruses expressing wild type NS1 protein or its mutant R38A, K41A. [macrophages]

summary:
Analysis of gene expression in human macrophages infected with influenza A viruses expressing wild type NS1 protein or its mutant R38A, K41A. The hypothesis tested was that R38 and K41 residues within viral NS1 protein are essential fro transctiptional control of cellluar gene expression.
Cells were infected with influenza  A/WSN/33 viruses expressing wild type NS1 protein (WT), its R38A, K41A mutant (RK/AA) or non-infected (Mock)

overall_design: Total RNA isolated from macrophages after 10 hours of infection with wild type or mutant influenza A virus (multiplicity of infection = 1)

first: Denis


title: Genome-wide analysis of gene expression in human macrophages in response to infection with recombinant A/WSN/33 influenza A viruses expressing wild type NS1 protein or its mutant R38A, K41A.

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

overall_design: Refer to individual Series


title: Global cellular biological processes governed by MET amplification

city: Shanghai

first: Meiyu

last: Geng

address: 555 Zuchongzhi Road

institute: Shanghai Institute of Material Medica

summary: We used microarrays to probe the global programme of gene expression under treatment with c-Met inhibitor and identified distinct classes of up- and down-regulated genes during this process

overall_design: We treated MET addicted EBC-1 and MKN-45 cells with selective c-Met kinase inhibitor SGX-523 at 1uM for 24 and 48 hours, using HCC827 cells with activated c-Met but lacking MET dependency as a negative control


title: Analyzing human neural stem cell ontogeny by consecutive isolation of Notch active neural progenitors

city: Munich

first: Michael

middle: Johannes

last: Ziller

address: Kraepelinstrasse 2-10

department: Translational Psychiatry

country: Germany

institute: Max Planck Institute of Psychiatry

summary: Decoding heterogeneity of pluripotent stem cell (PSC)-derived neural progeny is fundamental for revealing the origin of diverse progenitors, for defining their lineages, and for identifying fate determinants driving transition through distinct potencies. Here we prospectively isolated consecutively appearing PSC-derived primary progenitors based on their Notch activation state. We first isolate early neuroepithelial cells and show their broad Notch-dependent developmental and proliferative potential. Neuroepithelial cells further yield successive Notch-dependent functional primary progenitors, from early and mid neurogenic radial glia and their derived basal progenitors, to gliogenic radial glia and adult-like neural progenitors, together recapitulating hallmarks of neural stem cell (NSC) ontogeny. Gene expression profiling reveals dynamic stage specific transcriptional patterns that may link development of distinct progenitor identities through Notch activation. Our observations provide a platform for characterization and manipulation of distinct progenitor cell types amenable for developing streamlined neural lineage specification paradigms for modeling development in health and disease.

overall_design: Human embryonic stem cells (hESCs) H9 were differentiated into 5 distinct populations of neural precursor cells (NPCs) over a time course of 200 days. Each neural precursor populations was then sorted for HES5 expression based on a GFP-HES5 reporter. Both the HES5 positive and HES5 negative populations were then subjected to microarray profiling in singlicate, as well as the hESCs using GeneChipPrimeView Human Gene Expression Array

first: Yechiel

last: Elkabetz


title: Over-expression of YAP1 in NCI-H716 colorectal cancer cells

first: Sangbae

last: Kim

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

summary: YAP1 plays importance roles in development of colorectal cancer as evidenced by their overexpression in colorectal cancer and their expression promoted cell proliferation and survival of colorectal cancer cells. In order to understand potential roles of YAP1 in colorectal cancer, we over-expressed constitutively active YAP1 mutant in NCI-H716 colorectal cancer cells and identified and analyzed genes whose expression is activated by YAP1 activation in colorectal cancer.

overall_design: Pre-clinical study

first: Keun-Wook

last: Lee

first: Sung

middle: S

first: Ju-Seog


title: Comparative analysis of monocytes from healthy donors, patients with metastatic breast cancer, sepsis or tuberculosis.

status: Public on Feb 03 2015

city: Lund

first: Kristoffer

last: von Stedingk

country: Sweden

institute: Lund University

summary: Myeloid-derived suppressor cells (MDSCs) are highly immunosuppressive myeloid cells, which increase in cancer patients. The molecular mechanism behind their generation and function is unclear. Whereas granulocytic-MDSCs correlate with poor overall survival in breast cancer, the presence and relevance of monocytic-MDSCs (Mo-MDSCs) is unknown. Here we report for the first time an enrichment of functional blood Mo-MDSCs in breast cancer patients before they acquire a typical Mo-MDSC surface phenotype. A clear population of Mo-MDSCs with the typical cell surface phenotype (CD14+HLA-DRlow/-Co-receptorlow/-) increased significantly first during disease progression and correlated to metastasis to lymph nodes and visceral organs. Furthermore, monocytes, comprising the Mo-MDSC population, from patients with metastatic breast cancer resemble the reprogrammed immunosuppressive monocytes in patients with severe infections, both by their surface and functional phenotype but also at their molecular gene expression profile. Our data suggest that monitoring the Mo-MDSC levels in breast cancer patients may represent a novel and simple biomarker for assessing disease progression.

overall_design: Peripheral blood monocytes were isolated using magnetic cell sorting from 4 patients with metastatic breast cancer, 3 healthy controls, 3 patients with sepsis and 3 patients with active tuberculosis were immediately frozen at -80°C in TRIZOL.

first: Caroline

last: Bergenfelz

first: Sofia

last: Gruvberger-Saal

first: Karin

last: Leandersson


title: siRNA induced silencing of CITED1 in HT144 human melanoma cells

status: Public on Feb 20 2015

first: Jillian

last: Howlin

summary: To investigate the function of CITED1 in melanoma, its expression was transiently down regulated using CITED1-targeting siRNA. The HT144 melanoma cell line was chosen as it had a relatively high level of detectable CITED1 mRNA and protein expression.

overall_design: HT144 melanoma cells were transfected with 2 siRNAs targeting CITED1 (4 replicates each) and a negative control non-targeting siRNA (4 replicates). RNA was harvested at 48 h post-transfection.


title: Interleukin-1- and Type I Interferon-Dependent Enhanced Immunogenicity of an NYVAC-HIV-1 Env-Gag-Pol-Nef Vaccine Vector with Dual Deletions of Type I and Type II Interferon-Binding Proteins

status: Public on Jan 30 2015

city: Cleveland

first: Peter

middle: A

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

summary: NYVAC, a highly attenuated, replication-restricted poxvirus, is a safe and immunogenic vaccine vector. Deletion of immune evasion genes from the poxvirus genome is an attractive strategy for improving the immunogenic properties of poxviruses. Using systems biology approaches, we describe herein the enhanced immunological profile of NYVAC vectors expressing the HIV-1 clade C env, gag, pol, and nef genes (NYVAC-C) with single or double deletions of genes encoding type I (B19R) or type II (B8R) interferon (IFN)-binding proteins. Transcriptomic analyses of human monocytes infected with NYVAC-C, NYVAC-C with the B19R deletion (NYVAC-C- B19R), or NYVAC-C with B8R and B19R deletions (NYVAC-C- B8RB19R) revealed a concerted upregulation of innate immune pathways (IFN-stimulated genes [ISGs]) of increasing magnitude with NYVAC-C- B19R and NYVAC-C- B8RB19R than with NYVAC-C. Deletion of B8R and B19R resulted in an enhanced activation of IRF3, IRF7, and STAT1 and the robust production of type I IFNs and of ISGs, whose expression was inhibited by anti-type I IFN antibodies. Interestingly, NYVAC-C- B8RB19R induced the production of much higher levels of proinflammatory cytokines (tumor necrosis factor [TNF-], interleukin-6 [IL-6], and IL-8) than NYVAC-C or NYVAC-C- B19R as well as a strong inflammasome response (caspase-1 and IL-1 ) in infected monocytes. Top network analyses showed that this broad response mediated by the deletion of B8R and B19R was organized around two upregulated gene expression nodes (TNF and IRF7). Consistent with these findings, monocytes infected with NYVAC-C- B8RB19R induced a stronger type I IFN-dependent and IL-1-dependent allogeneic CD4  T cell response than monocytes infected with NYVAC-C or NYVAC-C- B19R. Dual deletion of type I and type II IFN immune evasion genes in NYVAC markedly enhanced its immunogenic properties via its induction of the increased expression of type I IFNs and IL-1  and make it an attractive candidate HIV vaccine vector.

overall_design: Primary Human monocytes from 5 donors were incubated with each following vectors  nyvacdb, nyvadb19r, nyvaccdb8rb19r_6h, untreated control and collected at 6h.

first: J

last: Delaloye

first: A

last: Filali-Mouhim

first: M

last: Cameron

first: E

last: Haddad

last: Harari

middle: P

last: Goulet

first: C

last: Gomez

first: B

last: Perdiguero

last: Esteban

first: G

last: Pantaleo

first: T

last: Roger

first: R

last: Sekaly

last: Calandra

last: Duque

first: P

last: Stafova


title: LN-308/U-138MG shVEGFR-2 knock-down analysis

status: Public on Jan 31 2015

city: Heidelberg

first: Tobias

last: Kessler

address: Im Neuenheimer Feld 280

institute: DKFZ

summary: The goal of this study was to evalute the genetic regulations upon knok-down of VEGFR-2 in two different glioma cell lines in partiular focussing on genes related to glioma migration and invasion as well as resistance to chemotherapy.

overall_design: Total RNA obtained from glioma cells harbouring shVEGFR-2 knock-down compared to controls


title: Genome wide analysis of Visceral adipose tissue CD14+ cells from obese subjects

status: Public on Feb 11 2015

city: Paris

first: Nicolas

last: VENTECLEF

address: Cordeliers Research Center

country: France

institute: INSERM

summary:
Identification of the inflammatory signature in visceral adipose tissue CD14+ cells (adipose tissue macrophage)
Total RNA obtained from CD14+ cells (Immunoselcted cells from stromal adipose tissue cells)

overall_design: Adipocytes and cells of the stroma vascular fraction (SVF) were obtained by collagenase digestion of adipose tissue. SVF cells were resuspended in endotoxin-free PBS supplemented with 2% FCS and 1 mM EDTA. Isolation of CD14+ using positive selection magnetic beads (Stemcell technologies) and CD4+ cells was performed using positive selection magnetic beads (Stemcell Technologies, Vancouver, Canada). An Illumina (San Diego, CA) RNA amplification kit (NuGEN, BiotinIL Module) was used according to the manufacturer's instructions to obtain biotinlabeled cDNA from 50 ng of total RNA extracted from adipose tissue CD14+ cells.

last: Venteclef

first: KARINE

last: Clement

first: PATRICIA

last: Ancel


title: Directed differentiation of oligodendrocytes from human embryonic stem cells

status: Public on Feb 01 2015

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: Here we compare the transcriptional profile of the undifferentiated hESC with the anterior oligodendroctes derived from the hESC using our new differentiation protocol.

overall_design: Total RNA was isolated from undifferentiated hES cells and from hES derived oligodendrocytes, 70 days old and FACS sorted for O4 marker. Samples for each group in triplicate were processed for Illumina bead arrays (Illumina HT-12) by the MSKCC genomics core facility according to the specifications of the manufacturer.

first: Tamara

last: Major

first: Viviane

last: Tabar


title: Epigenetic therapy for Friedreich ataxia.

status: Public on Jan 29 2015

city: La Jolla

first: Kristopher

middle: L.

last: Nazor

state: CA

address: 10550 North Torrey Pines Road

department: Regenerative Medicine

institute: The Scripps Research Institute

summary: We set out to investigate whether a histone deacetylase inhibitor (HDACi) would be effective in an in vitro model for the neurodegenerative disease Friedreich ataxia (FRDA) and to evaluate safety and surrogate markers of efficacy in a phase I clinical trial in patients. In the neuronal cell model, HDACi 109/RG2833 increases FXN mRNA levels and frataxin protein, with concomitant changes in the epigenetic state of the gene. Chromatin signatures indicate that histone H3 lysine 9 is a key residue for gene silencing through methylation and reactivation through acetylation, mediated by the HDACi. Drug treatment in FRDA patients demonstrated increased FXN mRNA and H3 lysine 9 acetylation in peripheral blood mononuclear cells. No safety issues were encountered.

overall_design: We used a human FRDA neuronal cell model, derived from patient induced pluripotent stem cells, to determine the efficacy of a 2-aminobenzamide HDACi (109) as a modulator of FXN gene expression and chromatin histone modifications. FRDA patients were dosed in 4 cohorts, ranging from 30mg/day to 240mg/day of the formulated drug product of HDACi 109, RG2833. Patients were monitored for adverse effects as well as for increases in FXN mRNA, frataxin protein, and chromatin modification in blood cells. Gene expression profiles were obtained using the Illumina HT12v4 Gene Expression BeadArray.

last: Soragni

first: W

last: Miao

last: Iudicello

first: D

last: Jacoby

first: S

last: De Mercanti

last: Clerico

first: F

last: Longo

last: Piga

last: Ku

last: Campau

first: J

last: Du

last: Penalver

last: Rai

last: Madara

first: K

last: O'Connor

last: Maximov

middle: F

last: Loring

last: Pandolfo

first: L

last: Durelli

last: Gottesfeld

middle: R

last: Rusche


title: Gene expression profiling of L-540 Hodgkin lymphoma cell line after in vitro and in vivo treatment with perifosine in combination with sorafenib

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: Three HL cell lines (HD-MyZ, L-540 and HDLM-2) were used to investigate the effects of perifosine and sorafenib using in vitro assays analyzing cell growth, cell cycle distribution, gene expression profiling (GEP), and apoptosis. Western blotting (WB) experiments were performed to determine whether the two-drug combination affected MAPK and PI3K/AKT pathways as well as apoptosis. Additionally, the antitumor efficacy and mechanism of action of perifosine/sorafenib combination were investigated in vivo in nonobese diabetic/severe combined immunodeficient (NOD/SCID) mice using tumor growth rates and survival as endpoints. RESULTS: While perifosine and sorafenib as single agents exerted a limited activity against HL cells, exposure of HD-MyZ and L-540 cell lines, but not HDLM-2 cells, to perifosine/sorafenib combination resulted in synergistic cell growth inhibition (40% to 80%) and cell cycle arrest. Upon perifosine/sorafenib exposure, L-540 cell line showed significant levels of apoptosis (up to 70%, P ≤.0001) associated with severe mitochondrial dysfunction (cytochrome c, apoptosis-inducing factor release and marked conformational change of Bax accompanied by membrane translocation). Apoptosis induced by perifosine/sorafenib combination did not result in processing of caspase-8, -9, -3, or cleavage of PARP, and was not reversed by the pan-caspase inhibitor Z-VADfmk, supporting a caspase-independent mechanism of cell death. In responsive cell lines, WB analysis showed that antiproliferative and pro-apototic events were associated with dephosphorylation of MAPK and PI3K/Akt pathways. GEP analysis of HD-MyZ and L-540 cell lines, but not HDLM-2 cells indicated that perifosine/sorafenib treatment induced upregulation of genes involved in amino acid metabolism and downregulation of genes regulating cell cycle, DNA replication and cell death. In addition, in responsive cell lines, perifosine/sorafenib combination strikingly induced the expression of tribbles homologues 3 (TRIB3) both in vitro and in vivo. Silencing of TRIB3 prevented cell growth reduction induced by perifosine/sorafenib treatment. In vivo, the combined perifosine/sorafenib treatment significantly increased the median survival of NOD/SCID mice xenografted with HD-MyZ cell line as compared to controls (81 vs 45 days, P ≤.0001) as well as mice receiving perifosine alone (49 days, P ≤.03) or sorafenib alone (54 days, P ≤.007). In mice bearing subcutaneous nodules generated by HD-MyZ and L-540 cell lines but not HDLM-2 cell line, perifosine/sorafenib treatment induced significantly increased levels of apoptosis (2- to 2.5-fold, P ≤.0001) and necrosis (2- to 8-fold, P ≤.0001), as compared to controls or treatment with single agents. In addition, perifosine/sorafenib treatment had no effect on HDLM-2 nodules, but significantly reduced L-540 nodules with 50% tumor growth inhibition, compared to controls. CONCLUSIONS: Perifosine/sorafenib combination resulted in strong anti-HL activity both in vitro and in vivo. These results warrant clinical evaluation of  perifosine/sorafenib combined-treatment in HL patients.

overall_design:
The Hodgkin lymphoma cell line L-540 was obtained from the DSMZ (Braunschweig, Germany, EU). Cells were routinely maintained in RPMI medium 1640 (Lonza, Basel, Switzerland) supplemented with 20% FBS (Lonza) and 2 mM glutamine (Lonza). Cells were maintained at 37°C in a water-saturated atmosphere of 5% CO2 in air. 10x10^6 L-540 cells were seeded in 75 cm2 flask and, after 24 hrs, cells were treated with 10 µM perifosine (Aeterna Zentaris, Frankfurt, Germany, EU) and/or 5 µM sorafenib (Bayer, Berlin,
Germany, EU) in culture medium for 24 hours. At the end of treatment, cells were collected and RNA extracted.

first: A

last: Anichini


title: Gene expression profiling of HD-MyZ Hodgkin lymphoma cell line after in vitro and in vivo treatment with perifosine in combination with sorafenib

overall_design:
The Hodgkin lymphoma cell line HD-MyZ was obtained from the DSMZ (Braunschweig, Germany, EU). Cells were routinely maintained in RPMI medium 1640 (Lonza, Basel, Switzerland) supplemented with 10% FBS (Lonza) and 2 mM glutamine (Lonza). Cells were maintained at 37°C in a water-saturated atmosphere of 5% CO2 in air. 10x10^6 HD-MyZ cells were seeded in 150 cm2 flask and, after 24 hrs, cells were treated with 10 µM perifosine (Aeterna Zentaris, Frankfurt, Germany, EU) and/or 5 µM sorafenib (Bayer, Berlin,
Germany, EU) in culture medium for 24 hours. At the end of treatment, cells were collected and RNA extracted.


title: Gene expression profiling of HDLM-2 Hodgkin lymphoma cell line after in vitro and in vivo treatment with perifosine in combination with sorafenib

summary: Three HL cell lines (HD-MyZ, L-540 and HDLM-2) were used to investigate the effects of perifosine and sorafenib using in vitro assays analyzing cell growth, cell cycle distribution, gene expression profiling (GEP), and apoptosis. Western blotting (WB) experiments were performed to determine whether the two-drug combination affected MAPK and PI3K/AKT pathways as well as apoptosis. Additionally, the antitumor efficacy and mechanism of action of perifosine/sorafenib combination were investigated in vivo in nonobese diabetic/severe combined immunodeficient (NOD/SCID) mice. While perifosine and sorafenib as single agents exerted a limited activity against HL cells, exposure of HD-MyZ and L-540 cell lines, but not HDLM-2 cells, to perifosine/sorafenib combination resulted in synergistic cell growth inhibition (40% to 80%) and cell cycle arrest. Upon perifosine/sorafenib exposure, L-540 cell line showed significant levels of apoptosis (up to 70%, P ≤.0001) associated with severe mitochondrial dysfunction (cytochrome c, apoptosis-inducing factor release and marked conformational change of Bax accompanied by membrane translocation). Apoptosis induced by perifosine/sorafenib combination did not result in processing of caspase-8, -9, -3, or cleavage of PARP, and was not reversed by the pan-caspase inhibitor Z-VADfmk, supporting a caspase-independent mechanism of cell death. In responsive cell lines, WB analysis showed that antiproliferative and pro-apototic events were associated with dephosphorylation of MAPK and PI3K/Akt pathways. GEP analysis of HD-MyZ and L-540 cell lines, but not HDLM-2 cells indicated that perifosine/sorafenib treatment induced upregulation of genes involved in amino acid metabolism and downregulation of genes regulating cell cycle, DNA replication and cell death. In addition, in responsive cell lines, perifosine/sorafenib combination strikingly induced the expression of tribbles homologues 3 (TRIB3) both in vitro and in vivo. Silencing of TRIB3 prevented cell growth reduction induced by perifosine/sorafenib treatment. In vivo, the combined perifosine/sorafenib treatment significantly increased the median survival of NOD/SCID mice xenografted with HD-MyZ cell line as compared to controls (81 vs 45 days, P ≤.0001) as well as mice receiving perifosine alone (49 days, P ≤.03) or sorafenib alone (54 days, P ≤.007). In mice bearing subcutaneous nodules generated by HD-MyZ and L-540 cell lines but not HDLM-2 cell line, perifosine/sorafenib treatment induced significantly increased levels of apoptosis (2- to 2.5-fold, P ≤.0001) and necrosis (2- to 8-fold, P ≤.0001), as compared to controls or treatment with single agents. Perifosine/sorafenib combination resulted in strong anti-HL activity both in vitro and in vivo. These results warrant clinical evaluation of  perifosine/sorafenib combined-treatment in HL patients.

overall_design:
The Hodgkin lymphoma cell line HDLM-2 was obtained from the DSMZ (Braunschweig, Germany, EU). Cells were routinely maintained in RPMI medium 1640 (Lonza, Basel, Switzerland) supplemented with 20% FBS (Lonza) and 2 mM glutamine (Lonza). Cells were maintained at 37°C in a water-saturated atmosphere of 5% CO2 in air. 10x10^6 HDLM-2 cells were seeded in 75 cm2 flask and, after 24 hrs, cells were treated with 10 µM perifosine (Aeterna Zentaris, Frankfurt, Germany, EU) and/or 5 µM sorafenib (Bayer, Berlin,
Germany, EU) in culture medium for 24 hours. At the end of treatment, cells were collected and RNA extracted.


title: Stromal contribution to expression signatures of colorectal cancer

status: Public on Jan 27 2015

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

institute: Candiolo Cancer Institute, University of Torino

sample_organism:
Homo sapiens
Mus musculus


title: Targeting EZH2 methyltransferase activity in ARID1A mutated cells as a synthetic lethal therapeutic strategy

status: Public on Jan 20 2015

city: Philadelphia

first: Louise

last: Showe

state: PA

address: 3601 Spruce St

institute: The Wistar Institute

summary: ARID1A, an epigentic modifier, is often mutated in ovarian clear cell carcinoma (OCCC). In addition, EZH2 is frequently upregulated in OCCC.  Inhibtion of EZH2 with an inhibitor (GSK126) selectively inhibits ARID1A-mutated cells.  This study was designed to understand changes in gene expression profiles following EZH2 inhibition or ARID1A restoration.

overall_design: Chromatin remodelers such as ARID1A are frequently mutated in a broad array of cancers. However, targeted cancer therapy based on ARID1A mutation status has not been described. Intriguingly, ARID1A mutated cancers typically lack genomic instability, suggesting significant involvement of epigenetic mechanisms. Here we show that inhibition of the EZH2 methyltransferase acts in a synthetic lethal manner in ARID1A mutated cells. Remarkably, ARID1A mutation status correlated with response to EZH2 inhibitor. Genome-wide profiling revealed antagonistic roles of ARID1A and EZH2 in gene regulation. Further, we identified PIK3IP1 as a direct ARID1A/EZH2 target gene whose upregulation contributes to the observed synthetic lethality in the EZH2 inhibitor treated ARID1A mutated cells. Significantly, EZH2 inhibitor caused the regression of established ARID1A mutated tumors in vivo. Together, this data demonstrate a synthetic lethality between ARID1A mutation and EZH2 inhibition. They indicate that pharmacological inhibition of EZH2 represents a novel treatment strategy for ARID1A mutated cancers.

first: Rugang

last: Zhang


title: The Role of Macrophages in the Development of Human Renal Allograft Fibrosis in the First Year after Transplantation

status: Public on Jan 28 2015

city: Westmead

first: Philip

middle: John

last: O'Connell

state: NSW

address: 176 Hawkesbury Rd

department: Centre for Transplant and Renal Research

country: Australia

institute: Westmead Millennium Institute

summary: The aim of this study was to investigate the role of infiltrating macrophages in renal allograft fibrosis. Forty-six protocol renal allograft biopsies obtained one-year after transplantation were stained with Sirius Red to quantify fibrosis and double stained with CD68 and CD206 to identify the proportion of alternately activated (M2) macrophages. 23 protocol biopsies obtained 12 months post transplant were analyzed for gene expression by microarray, which was correlated with macrophage infiltration and the severity of fibrosis. Phenotypic analysis showed 92% of infiltrating macrophages exhibited an M2 phenotype with CD68+CD206+  dual staining. Gene microarrays demonstrated a distinct alloimmune response despite the lack of rejection and inflammatory infiltrate with upregulation of interferon-γ-response genes.  This suggests that following initiation of Th1 driven macrophage proliferation or infiltration, M2 macrophages contribute to tubular injury and progression of fibrosis.

overall_design: 23 protocol renal biopsies were obtained from patients at 12 month post transplant. The study population was divided into two groups according to the number of infiltrating macrophages (CD68 positive cells) (Group I: Recipients with a low number of infiltrating macrophages, CD68 positive cells < 400/mm2; Group II: Recipients with a high number of infiltrating macrophages, CD68 positive cells ≥ 400/mm2). Additional analyses were undertaken by dividing the group into those with fibrosis (ci score >1) and those without. To correlate gene expression with kidney fibrosis, or intensity of CD68 infiltrate, Spearman correlations analysis of the gene expression data with 12 month IFTA was performed and the correlation co-efficiency and its p value calculated. Gene Ontology enrichment and IPA pathway and network analysis (Ingenuity System Inc.) were performed on the associated genes. All p-values were two-sided, and p < 0.05 was considered significant.

first: Daisuke

last: Toki

first: Weijia

first: Katie

last: Hor

first: Barbara

last: Murphy


title: ALTERED MONOCYTE GENE EXPRESSION AND EXPANSION OF  CD14+CD16+ SUBSET IN IgA NEPHROPATHY PATIENTS

status: Public on Mar 30 2015

city: Valenzano-Bari

first: Sharon

middle: Natasha

last: Cox

department: Renal Lab

institute: Schena Foundation

summary: The basic defect of IgA nephropathy (IgAN) lies within peripheral blood mononuclear cells rather than local kidney abnormalities. Previously we showed an altered gene expression in monocytes compared to B and T cells isolated from IgAN patients (Kidney Int, 2010), thus our aim here was to study this subset more closely at genome-wide level.

overall_design: total of 35 IgAN patients and 35  healthy blood donors (HBD) were included in this study. Illumina microarray technology was used to evaluate global differences in gene expression between monocytes isolated from IgAN patients and HBD. Bioinformatic analysis was performed with GenomeStudio and Genespring software. The connectivity between genes was evaluated using Ingenuity Pathway Analysis. Aberrantly expressed genes and  pathways were then validated on an independent set of patients with RT-PCR western blot and flow cytometric analysis.

middle: N

first: Grazia

last: Serino

first: Fabio

last: Sallustio

first: Francesco

last: Pesce

last: Schena


title: MIF-CXCR4 as a novel axis for Mesenchymal Stem Cells recruitment to tumours in vivo.

city: London

first: Vitor

middle: H

last: Teixeira

address: 5 University Street

department: Medicine

country: United Kingdom

institute: University College London

summary: MSCs are inherently tumor-homing and immunosuppressive and can be isolated, cultured, expanded, and transduced, making them viable candidates for cell therapy. MSCs can also be useful in allogeneic transplantation because of their immunocompatibility. MSCs have the capacity to home specifically to tumors including gliomas and breast, colon, ovarian, and lung carcinomas, among many other primary and metastatic tumors. Some discrepancies are however present regarding the mechanism and the involvement of molecules/receptors in MSC homing to tumours.  We have used in this study a combination of genome expression profiling and cytokine arrays to screen for candidates mediating MSC homing to two different cancer cell lines: A549 and MDAMB231. We found a variety of interleukines and cytokines already described as players in the process, such as IL6, IL8, CCL2. Additionally, from in vitro migration and invasion assays, we show that CXCR4 is a major player in this mechanism being the essential MSC receptor for the process to occur. For the first time, we have identified in this study a novel axis: MIF-CXCR4, showing a physical interaction between them and validating their essential role in vitro and in vivo. A better understanding of MSC homing players towards tumours will help the development of novel strategies in their use as vehicles in cancer cell therapy.

overall_design: Total RNA obtained from mesenchymal stem cells up to passage 5 stimulated or not with conditioned medium from MDAMB231 cell line or A549 cell line for 24h

first: Sofia

last: Lourenco


title: Genome-wide analysis of SIK2 regulated genes and pathways

status: Public on Jan 12 2015

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

summary: Identification of SIK2 regulated genes and pathways after SIK2 knock-down and overexpression of a wild-type and kinase-dead SIK2. The hypothesis is that SIK2 regulated gene expression via CREB1

overall_design: Total RNAs were obtained after SIK2 gene was knocked down with siRNA and after a wild-type SIK2 or a kinase-dead SIK2 construct were over-expressed in LNCaP cells. A control where the cells were treated with a CREB1 inducer (Forskolin) was also included.

first: Helene

last: Bon

first: Thomas

last: Carroll

first: Michelle

last: Osborne


title: EMT Alters Interstitial Fluid Flow-induced Signaling in ERBB2-positive Breast Cancer

status: Public on Jan 06 2015

city: Dallas

first: Alimatou

last: Tchafa

state: TEXAS

address: 5323 Harry Hines Blvd, Rm Y4.306

department: Biochemistry

institute: UT Southwestern Medical Center

summary: A variety of mechanotransduction forces are altered in the tumor microenvironment (TME) and these biophysical forces can influence cancer progression. One such force is interstitial fluid flow (IFF) - the movement of fluid through the tissue matrix. IFF was previously shown to induce invasion of cancer cells, but the activated signaling cascades remain poorly understood. Here, it is demonstrated that IFF induces invasion of ERBB2/HER2 expressing breast cancer cells via activation of phosphoinositide-3-kinase (PI3K). In constitutively activate ERBB2 expressing cells that have undergone epithelial-to-mesenchymal transition (EMT), IFF-mediated invasion requires the chemokine receptor CXCR4, a gradient of its ligand CXCL12, and activity of the PI3K catalytic subunits p110a and β. In wild-type ERBB2 expressing cells, IFF-mediated invasion is chemokine receptor-independent and requires only p110a activation. To test whether cells undergoing EMT alter their signaling response to IFF, TGFb1 was used to induce EMT in wild-type ERBB2-expressing cells resulting in IFF-induced invasion dependent on CXCR4 and p110β.

overall_design: 2 cell lines (NeuN, NeuT), 2 conditions (flow, static), 3 replicates each, 12 samples total


title: Stromal contribution to expression signatures of colorectal cancer (CRC tumor)

first: Enzo

last: Medico

summary: We noticed that a recently identified poor prognosis stem/serrated molecular subtype of colorectal cancer (CRC) is characterized by up-regulation of transcripts known to be also expressed by stromal cells. To better define the origin of such transcripts, we analyzed  RNAseq and microarray datasets from CRC mouse xenografts, where human cancer cells are supported by murine stroma. The analysis revealed that mRNA levels of stem/serrated subtype genes are mostly due to stromal expression, even when the stromal fraction is below 5%. Indeed, a classifier based on genes exclusively expressed by cancer-associated fibroblasts was significantly associated, in multiple datasets, to poor prognosis of CRC and to radioresistance of rectal cancer.

overall_design:
Tumor Matched with Corresponding PDX.
Samples were obtained and analysed under review board approval and after receiving informed consent from the patients.

first: Claudio

last: Isella

first: Andrea

last: Bertotti


title: Gene expression analysis of Hodgkin lymphoma cell lines treated with the AKT inhibitor perifosine and the multikinase inhibitor sorafenib

first: Loris

last: De Cecco

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

overall_design: Refer to individual Series

first: L

first: A

last: Anichini

first: G

last: Stirparo


title: Restricted Dendritic Cell and Monocyte Progenitors in Human Cord Blood  and Bone Marrow

status: Public on Jan 22 2015

first: Peter

last: Wilkinson

summary: In mice, two restricted DC progenitors, macrophage-dendritic progenitor (MDP) and common dendritic cell progenitor (CDP) demonstrate increasing commitment of DC lineage as they sequentially lose granulocyte and monocyte potential respectively. Identifying these progenitors has enabled understanding of the role of DCs and monocytes in immunity and tolerance in mice. In humans, however, restricted monocyte and DC progenitors remain unknown. Progress in studying human DC development has been hampered by lack of an in vitro culture system that recapitulates in vivo DC hematopoiesis. Here we report a culture system that supports development of CD34+ hematopoietic stem cell progenitors into the three major human DC subsets, monocytes, granulocytes, NK and B cells. Using this culture system we defined the pathway for human DC development, and revealed the sequential origin of human DCs from increasingly restricted progenitors: a granulocyte-monocyte-DC progenitor (hGMDP) that develops into a monocyte-DC progenitor (hMDP) that develops into monocytes and a common DC progenitor (hCDP) that is restricted to produce the three major DC subsets. The phenotype of the DC progenitors partially overlaps with granulocyte monocyte progenitors (GMPs). These progenitors reside in human cord blood and bone marrow but not in the blood or lymphoid tissues in the steady state.

overall_design: We performed whole transcriptome expression analysis on monocytes and subsets of dendritic cells i.e. CD1c+ DCs, CD141+ DCs and CD303+ pDCs isolated from blood or differentiated in culture from cord blood CD34+ cells in presence of MS5 stromal cells and Flt3l, GM-CSF and SCF cytokines.

first: T

last: Lee

last: Gaelle

last: Kikuchi Oliveira

last: Zhou

last: Aljoufi

first: S

last: Puhr

first: M

last: Cameron

first: R

last: Sekaly

last: Nussenzwieg

first: K

last: Liu

last: Smith

last: Richards

first: P


title: Human induced pluripotent stem cells generated from intervertebral disc cells improve  neurologic functions in spinal cord injury

status: Public on Jan 15 2015

city: Seongnam

first: Kangin

last: lee

address: 335 Pankyoro, Bundanggu

department: Biomedical Science

country: South Korea

institute: CHA University

summary: We generated iPSCs from human intervertebral disc cells which were obtained during spine fusion surgery of patients with spinal cord injury. The disc cell-derived iPSCs (diPSCs) showed similar characteristics to human embryonic stem cells (hESCs) and were efficiently differentiated into neural progenitor cells (NPCs) with the capability of differentiation into mature neurons in vitro.   To examine whether the transplantation of NPCs derived from the diPSCs showed therapeutic effects, the NPCs were transplanted into mice at 9 days post-spinal cord injury. We detected a significant amelioration of hind limb dysfunction during the follow up recovery periods.   Histological analysis at 5 weeks post-transplantation, we could identify undifferentiated human NPCs (Nestin+) as well as early (TUJ1+) and mature neurons (MAP2+) derived from the NPCs. Furthermore, the NPC transplantation demonstrated a preventive effect on the spinal cord degeneration resulting from the secondary injury.   This study revealed that the intervertebral disc, a “to-be-waste” tissue, removed from the surgical procedure, could provide a unique opportunity to study iPSCs derived from hardly accessible somatic cells in normal situation and also be a useful therapeutic resource to generate autologous neural cells to treat patients suffering from spinal cord injury.

overall_design: Total RNA was isolated using the NucleoSpin RNA II Kit (Macherey-Nagel, Duren, Germany, www.mn-net.com) according to the manufacturer’s suggestions and was utilized for a genome-wide gene expression profiling experiment using the Illumina array (Illumina, San Diego, CA, USA, www.illumina.com) at Macrogen (Macrogen, Seoul, Korea, www.macrogen.com).

first: D

middle: Y

last: Hwang


title: Regulatory T cells require the phosphatase PTEN to restrain type 1 and follicular helper T-cell responses

status: Public on Jan 05 2015

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary: The interplay between effector and regulatory T (Treg) cells is crucial for adaptive immunity, but how Treg control effector cell flexibility is elusive. We found that the phosphatase PTEN links Treg stability to the repression of TH1 and TFH (follicular helper) responses. Depletion of PTEN in Treg resulted in excessive TFH and germinal center responses and spontaneous inflammatory disease. These defects are considerably blocked by deletion of Interferon-γ, indicating coordinated control of TH1 and TFH responses. Mechanistically, PTEN maintains Treg stability and proper metabolic balance between glycolysis and mitochondrial fitness. Moreover, PTEN deficiency markedly upregulates mTORC2-Akt activity, and loss of this activity restores PTEN-deficient Treg function. Our studies establish a PTEN-mTORC2 axis that actively maintains Treg stability and coordinates Treg-mediated control of effector cell flexibility.

overall_design: We used microarrays to explore the gene expression profiles differentially expressed in CD4+CD25+Foxp3-YFP+ Treg cells from wild-type (WT; C57BL/6 crossed with Foxp3-Cre) and Ptenfl/flFoxp3-Cre  (Ptenfl/fl mice crossed with Foxp3-Cre) mice

first: Sharad

last: Shrestha

first: Kai

last: Yang

first: Cliff

last: Guy

last: Vogel

first: Hongbo

last: Chi


title: Comparison of gene expression profiles between the CD110+ tumor initiating cells from primary colorectal tumors and their liver metastases.

status: Public on Jan 01 2015

city: Shanghai

first: Li

last: Qingquan

address: No.138，Yixueyuan Rd.

institute: fudan university

summary:
We  established an in vivo model of organ-specific colorectal cancer metastasis and demonstrated that the CD110+ tumor initiating cells contribute for colorectal liver metastasis. To gain a deeper understanding of its metastatic capacity, we performed a genome-wide transcriptome analysis on the
CD110+ tumor cells derived from primary colon xenografts and their matched liver metastases. Results provide important information of the responses of the CD110+ cells during the process of liver colonization.

overall_design: Total RNA obtained from the CD110+ cells sorted from primary colorectal tumors (CRC102-PT and CRC108-PT) compared to those from the corresponding liver metastases (CRC102-LM and CRC108-LM).

first: WenChao

last: Gao

first: Zhengming

last: Wu


title: Hematopoietic differentiation of human embryonic stem cells - timecourse and d7 CD34 and CD41 fractions

status: Public on Jan 13 2015

city: Parkville

first: Andrew

last: Elefanty

state: Victoria

address: Flemington Road

institute: Murdoch Childrens Research Institute

summary: This study aimed to examine gene expression in human ES cells (the RUNX1C GFP reporter line) differentiated towrads hameatopoietic mesoderm in a defined serum free medium. At day 7 of differentiation, the cells were sorted into fractions based on CD34 and CD41 expression and the four fractions analysed by microarray.

overall_design: The total number of samples analysed was 13. Undifferentiated hESC (RUNX1C GFP/w, based on the HES3 cell line) plus samples from d1 to d8 of differentiation comprised one experiment (9 samples) and four flow sorted fractions from d7 differentiated cells (CD34-CD41-, CD34lo CD41-, CD34hi CD41- and CD34lo CD41lo) comprised the second experiment. The parent cell line was maintained on mouse feeder cells in KOSR containing medium supplemented with 10 ng/ml FGF2. Differentiation was performed as spin EBs in APEL medium (Ng et al Nature Protocols 2008). For the first 4 days, medium was supplemented with BMP4, VEGF, SCF and Activin. Medium was changed at d4 to fresh APEL medium supplemented with BMP4, VEGF, SCF, FGF2 and IGF2.

first: Elizabeth

last: Ng

first: Claire

last: Hirst

middle: G


title: mRNA expression data from adenoma, gene modified, and colorectal cancer organoid.

status: Public on Jan 18 2015

city: Tokyo

first: Mariko

last: Shimokawa

address: 35, Shinanomachi, Shinjuku-Ku

country: Japan

institute: Keio University

summary:
We established human colorectal tumor organoids from benign adenoma, primary colorectal cancer or metastasized colorectal cancer. The gene signature of tumor organoids associated with their tumor progression status. We also generated genome-edited organoids from human intestinal organoids recapitulating adenoma-carcinoma sequence. Gene expression signature of the genome engineered organoids were similar to that of adenoma organoids. This result indicated multiple (up to five) genetic mutations were insufficient for gene expression reprogramming of colorectal cancer.
We used microarrays to detail the global program of gene expression in human colorectal tumor organoids and artificially mutation introduced organoids.

overall_design:
To assess the expression profiling of genome-engineered organoids, we prepared total-RNA from cultured adenoma, carcinoma and genome-engineered organoids. We produced two types of genome-engineered organoids using the CRISPR/Cas9 or lentivirus vector system. Each engineered gene and engineered methods are described as a single alphabet and method name, respectively, in the sample characteristics field.   The abbreviations for the engineered genes are as follows.
1) Genome-engineered organoids with CRISPR/Cas9
A = APC deletion; K = KRAS G12V knock in;
S = Smad4 deletion; T = TP53 deletion;
P = PIK3CA E545K knock in.
2) Genome-engineered organoids with Lent virus vector
B = CTNNB1 S33Y overexpression; K = KRAS G12V overexpression;
S = Smad4 shRNA overexpression; T = TP53 shRNA overexpression;
P = PIK3CA E545K overexpression.

first: Shoichi

last: Date


title: Gene expression profiling of 18 hepatocellular carcinoma and adjacent non-tumorous liver tissue

city: Taipei

last: Kao

state: Taiwan

address: 125 Lih-Der Road, Peitou District

department: Research

country: Taiwan

institute: Koo Foundation SYS Cancer Center

summary:
These paired HCC and non-tumorous liver tissues were used to determine highly dfferentially expressed genes in HCC and non-tumorous liver tissue.
Hepatocellular carcinoma (HCC) is a malignancy with poor survival outcome. Genes showing extreme differential expression between paired human HCC and adjacent non-tumorous liver tissue were investigated. PLVAP was identified as a gene specifically expressed in vascular endothelial cells of HCC but not in non-tumorous liver tissues. This finding was confirmed by RT-PCR analysis of micro-dissected cells and immunohistochemical staining of tissue sections. A recombinant monoclonal anti-PLVAP Fab fragment co-expressing extracellular domain of human tissue factor (TF) was developed. The potential therapeutic effect and toxicity to treat HCC were studied using a Hep3B HCC xenograft model in SCID mice. Infusion of recombinant monoclonal anti-PLVAP Fab-TF into the tumor feeding artery induced tumor vascular thrombosis and extensive tumor necrosis at doses between 2.5 µg and 12 µg. Tumor growth was suppressed for 40 days after a single treatment. Systemic administration did not induce tumor necrosis. Little systemic toxicity was noted for this therapeutic agent. The results of this study suggest that anti-PLVAP Fab-TF may be used to treat HCC cases for which transcatheter arterial chemoembolization (TACE) is currently used, but without major drawbacks of TACE. Anti-PLVAP Fab-TF may improve therapeutic outcome and be a viable therapeutic agent in patients with more advanced disease and compromised liver function.

overall_design: Frozen hepatocellular carcinoma  and adjacent non-tumorous liver tissues were used for gnee expression profiling study. Affymetrix U133A genechips were used for gene expression profiling.

first: K

middle: J


title: Gene expression profile upon miR-10b overexpression or knockdown

city: indianapolis

first: Haoxu

last: Ouyang

state: in

address: 980 w walnut street

institute: IUPUI

summary: miR-10b precusor or miR-10b inhibitor was used to overexpress or knockdown miR-10b expression in PANC-1 cells. Microarray analysis was used to characterize the changes in gene expression profiles of PANC-1 upon miR-10b overexpression or knockdown

overall_design: PANC-1 cells were transfected with different microRNA oligos for 20 hr. Total RNA was extracted using Trizol method. Each expreimental condition had three biological triplicates.  Twelve samples were analyzed in total.

first: Murray

last: Korc


title: Genome-wide analysis of day 31 hESC-cardiomyocytes treated with DMSO (control) or retinoic acid (RA) during differentiation

city: Leiden

first: Harsha

middle: D

last: Devalla

address: Einthovenweg 20

department: Anatomy & Embryology

institute: Leiden University Medical Center

summary: Human embryonic stem cell-reporter line hESC-NKX2.5(eGFP/w) were differentiated to cardiomyocytes (CMs) by utilizing the spin embryoid body method. During differentiation the cells were treated with DMSO or retinoic acid (RA) from day 4-7. At day 31, cells were sorted based on GFP prior to RNA isolation. The results of this microarray demonstrate that CMs treated with RA during differentiation exhibit atrial-like gene expression profile, while DMSO-treated cells show ventricular-like gene profile.

overall_design: CMs treated with DMSO or RA during differentiation were sorted for GFP and analyzed for differential gene expression.

first: Robert

last: Passier


title: Deregulated Myc Requires MondoA for Metabolic Reprogramming and Tumorigenesis

city: Seattle

first: Lisa

last: McFerrin

state: WA

address: 1100 Fairview Ave

institute: FHCRC

summary: In order to investigate the effect of MondoA loss on the expression of Myc-dependent genes, we performed a microarray analysis from RNAs isolated from TET21N cells expressing either control (siControl) or MondoA (siMondoA) siRNAs either with (NT) or without (Doxy) induced N-Myc expression.

overall_design: TET21N cells were grown in medium with either Doxy (Myc-Off) or No Treatment (Myc-On), then transiently transfected with either non-specific siRNA or MondoA siRNA in replicates. Cells were then lysed and RNA isolated.

first: Patrick

last: Carroll

first: Daniel

last: Diolaiti

last: Eisenman


title: Characterization of novel ovarian tumor cell lines that retain the phenotype of primary tumors [Illumina]

status: Public on Jun 16 2015

city: Miami

first: Tan

last: Ince

state: FL

address: 1501 NW 10th Avenue, Rm 926

department: Sylvester Cancer Center

institute: University of Miami - Miller School of Medicine

summary: The inability to establish stable cell lines from the vast majority of human tumors has limited the use of in vitro models to study human cancer. Currently available tumor cell lines fail to represent the biological diversity of human tumors. We have developed a cell culture medium that enabled us to routinely establish cell lines from diverse subtypes of ovarian tumors. Importantly, the twenty-five ovarian tumor cell lines described here retain the genomic landscape, histopathology, and molecular features of the original tumors. Furthermore, the molecular profile and drug response of these cell lines correlated with distinct groups of primary tumors with different outcomes. Thus, tumor cell lines derived using this methodology represent a significantly improved new platform to study human tumor biology and treatment.

overall_design:
Total RNA was obtained from untreated ovarian cancer cell lines and clustering analysis was performed.

The 'Median-Cent_5147_probes.txt' is a list of the 5147 gene probes that has at least 2-fold difference relative to median value across cell lines in at least 4 samples. These are the probes that were used for hierarchial clustering analysis.

The 'Combined_and_GSE9891.txt' is a combination of gene probes from this study of ovarian cell lines and of human ovarian cancer cell lines (GSE9891[GPL570]: Expression profile of 285 ovarian tumour samples). Only the 3832 overlapping gene probes between the this study and the GSE9891[GPL570] study are listed. The 3832 gene probes listed have at least 2-fold difference relative to median value across samples in at least 4 samples.

first: Marit

last: Krohn

first: Wenbin

last: Liu

first: Aurea

last: Sousa


title: ATAXIN2 is crucial for megakaryocyte protein homeostasis and proper platelet functionality

status: Public on Dec 31 2014

city: Amsterdam

first: Daphne

middle: C.

last: Thijssen-Timmer

address: Plesmanlaan 125

department: Hematopoiesis

institute: Sanquin Blood Supply

summary: Expression of the RNA-binding protein is increased upon megakaryocyte commitment, and may coordinate with mRNA stability and translation during megakaryopoiesis. Reduced expression of ATXN2 in human megakaryocytic cells decreased protein synthesis and total protein content despite equal mRNA expression. Genome-wide comparision of subpolysomal versus polysomal mRNA showed that both protein synthesis and protein degradation are derailed in absence of ATXN2. Furthermore, ATXN2 was associated with PABP and DDX6, proteins that control mRNA stability through the polyA-tail. These findings indicate that ATXN2 is involved in protein metabolism in megakaryocytes and platelet function.

overall_design: The human megakaryoblastic cell line Meg01 was transduced with either a short hairpin against ATXN2 (sh95) or a short hairpin control (shc002). 48 hours after transduction, cells were sorted for successful transduction by GFP-expression, lysed and subsequently loaded on a sucrose gradient to separate mRNA based on the amount of ribosomes attached to it. The first eight fractions of the gradient containing subpolysomal, untranslated mRNA were pooled as were the remaining eight fractions containing polyribosomal, translated mRNA. Subpolysomal and polysomal mRNA from three independent experiments were then hybridized to an Illumina beadchip array.

first: Sabrina

last: Zeddies


title: Functional and pathological features of ALS in iPSC-derived motor neurons from patients with C9orf72 expansions

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


title: Gene expression profiles upon Meis1 knockout in Hoxa9/Meis1-induced AML

first: Takuro

last: Nakamura

address: 3-8-31 Ariake, Koto-ku

department: The Cancer Institute

institute: Japanese Foundation for Cancer Research

summary:
Meis1 is found cooperatively activated with Hoxa7/a9 in AML, and it indeed promotes leukemogenic activities of Hoxa9. It is important to identify downstream target genes of Meis1 to understand its cooperative activity with Hoxa9 in leukemogenesis.
We used microarrays to detail the global programme of gene expression upon Meis1 knockout.

overall_design: Murine primary bone marrow cells of the Rosa26-Cre-ERT2 knock-in mouse were transformed by retroviral transduction of Hoxa9 and floxed Meis1. The immortalized bone marrow cells were treated with 2 μM of 4-hydroxytamoxifen to delete Meis1 cDNA. Gene expression profiles were compared between the original Hoxa9/Meis1-expressing cells and Meis1 deleted (Hoxa9 only) cells.

first: Takashi

last: Yokoyama


title: Transcriptomic identification of genes for obesity and insulin resistance in human adipose tissue in a Mexican American population sample drawn from the Veterans Administration Genetic Epidemiology Study (VAGES)

city: San Antonio

first: Christopher

last: Jenkinson

state: Texas

address: 7703 Floyd Curl Drive

institute: University of Texas Health Sciences Center at San Antonio

summary: Total RNA obtained from human fasted subcutaneous abdominal adipose tissue (FAT) was used to measure genome-wide gene expression. Expression values which were significantly present were standardized by quantile normalization and correlated with clinical data.

overall_design: Gene expression was analyzed for correlation with multiple obesity and insulin resistance related traits.

first: Ravindranath

last: Duggirala

first: Harald

last: Goring


title: The zinc finger protein ZNF658 regulates the transcription of genes involved in zinc homeostasis and affects ribosome biogenesis through the zinc transcriptional regulatory element (ZTRE)

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

institute: Newcastle University

summary: We previously identified the ZTRE in genes involved in zinc homeostasis and showed that it mediates transcriptional repression in response to zinc. We now report that ZNF658 acts at the ZTRE.  ZNF658 was identified by MALDI-TOF mass spectrometry of a band excised after EMSA using a ZTRE probe.  The protein contains a KRAB domain and 21 zinc fingers.  It has similarity with ZAP1 from Saccharomyces cerevisiae, which regulates the response to zinc restriction, including a conserved DNA binding region we show to be functional also in ZNF658.  siRNA targeted to ZNF658 abrogated the zinc-induced, ZTRE-dependent reduction in SLC30A5 (ZnT5), SLC30A10 (ZnT10) and CBWD transcripts in human Caco-2 cells and the ability of zinc to repress reporter gene expression from corresponding promoter-reporter constructs. Microarray analysis of the effect of reducing ZNF658 expression by siRNA uncovered large changes in rRNA.  We find that ZTREs are clustered within the 45S rRNA precursor. We also saw effects on expression of multiple ribosomal proteins.  ZNF658 thus links zinc homeostasis with ribosome biogenesis, the most active transcriptional, and hence zinc-demanding, process in the cell.  ZNF658 is thus a novel transcriptional regulator that plays a fundamental role in the orchestrated cellular response to zinc availability.

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: Ogo

last: Ogo

first: John

last: Tyson

first: Ruth

last: Valentine

first: Dianne

last: Ford


title: Genome-wide analysis of responsive gene expression by eIF2α phosphatase inhibitors in multiple myeloma cells

city: Singapore

first: Wei

last: Zhou

address: 8 College Road

department: Signature Program in Cardiovascular and Metabolic Disorders

country: Singapore

institute: DUKE-NUS Graduate Medical School

summary: Analysis of mechano-regulation of eIF2α phosphatases in multiple myeloma cells at gene expression level. The hypothesis tested in the present study was Guanbenz (GBZ) and Sal003, 2 different eIF2α phosphatases induce different responses in multiple myeloma cells . Results provide important information of the responses of multiple myeloma cells, such as specific mechano-responsive genes, up- or down-regulated specific cellular functions

overall_design: Total RNA was isolated from control RPMI8226 cells and cells exposed to either 50 μM GBZ or 20 μM Sal003 for 24 hr in triplicate using RNeasy Kit (Qiagen). Quality and quantity of RNA was determined by Agilent Bioanalyzer.  Microarray hybridization was undertaken using Illumina® Whole-Genome Gene Expression Human HT-12 v4 expression and the data analysed by Partek Genome Suite 6.6 software.


title: Essential role of IRF4 and MYC signaling for survival of anaplastic large cell lymphoma survival

status: Public on Jan 03 2015

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

institute: University of Münster

summary: Three ALCL cell lines DEL, FEPD and K299 were induced with an IRF4-specific shRNA for up to 96 hours.

overall_design: The three ALCL cell lines DEL, FEPD and K299 were induced with an IRF4-specific shRNA for four durations and compared with the corresponding not-induced control.

first: Georg

last: Lenz


title: Transcriptional changes induced by KRAS mutants

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité

summary: The small GTPase KRAS transmits signals from cell surface receptors to various downstream signaling pathways, thereby regulating a multitude of cellular processes. Activating KRAS mutations occur in approximately 30% of human cancers and contribute to malignant transformation through constitutive activation of downstream signaling cascades. These mutations cluster in several hotspots, with codons 12 and 13 being most commonly. It has been suggested that the position and type of amino acid exchange influence the transforming capacity of mutant KRAS proteins. To address this hypothesis, we used MCF10A human mammary epithelial cells to establish isogenic cell lines that express eight different cancer-associated KRAS mutations (G12C, G12D, G12V, G13C, G13D, A18D, Q61H, K117N) at physiological levels, and investigated the biochemical and functional consequences of the different KRAS variants in vitro. In addition, selected effects were evaluated in comparison to cells that overexpress mutant KRAS. The overall effects of mutants expressed at normal levels were moderate compared to overexpressed variants, but allowed delineation of biological functions that were related to specific alleles rather than KRAS expression level. None of the mutations induced morphological changes or migratory abilities. KRAS-G12D, -G12V, -G13D, and -K117N were able to mediate EGF-independent proliferation, whereas anchorage-independent growth was primarily induced by the K117N and Q61H variants. Analysis of known RAS effectors showed that none of the mutations led to increased phosphorylation of ERK, PDK1, or AKT. Both codon 13 mutations were associated with increased EGFR expression, which was not seen with other variants. Finally, comparative gene expression analysis of MCF10A-G13D versus MCF10A-G12D revealed distinct transcriptional changes, such as enhanced cytokine and p53 signaling, upon G13D expression. Together, we describe a useful resource for investigating the function of multiple KRAS mutations and provide insights into the differential effects of these variants in MCF10A cells.

overall_design: Total RNA was isolated using the RNeasy Mini Kit (Qiagen), and 500 ng of quality-checked total RNA was labeled and hybridized to HumanHT-12 v4 Expression BeadChips using whole genome BeadChip® Sentrix assays (Illumina). Measurements were performed in biological triplicates and data normalization and filtering was performed as previously reported using BRB Array Tools software package (available at http://linus.nci.nih.gov/BRB-ArrayTools.html).

first: Britta

last: Stolze

first: Stefan

last: Fröhling

first: Claudia

last: Scholl


title: Gene expression data from human fibroblasts and induced Pluripotent Stem cells from amyotrophic lateral sclerosis patients

first: Sally

last: Cowley

summary:
We have generated human induced Pluripotent Stem cells (hiPSc) from amyotrophic lateral sclerosis (ALS, motor neuron disease) patients, using Sendai virus-mediated delivery of reprogramming factors. hiPSc lines have been screened using SNP array to assess chromosomal stability (alongside the fibroblast lines from which they derived), and validation of the pluripotency of the hiPSc lines is provided by Pluritest assessment of transcriptome datasets, prior to differentiation to motor neuron cultures and downstream functional assays.
Mutihac R., Scaber J., Lalic T., Ababneh N., Vowles, J., Fletcher-Jones A., Douglas A.G.L., Browne C., Nakanishi M., Turner M., Wade-Martins R., Cowley S.A. and Talbot K. Altered ER calcium homeostasis and stress granule formation in iPSC-derived motor neurons from ALS/FTD patients with C9orf72 expansions. Submitted

overall_design:
human iPSc lines were derived from human dermal fibroblasts from 3 ALS patients with C9orf72 mutations (2 lines per patient) and control donors. SNP datasets for control fibroblasts HDF OX1 and NHDF, and SNP and gene expression datasets from control lines iPS OX1-19 and iPS NHDF-1, have been published previously: Van Wilgenburg B., Browne C., Vowles J. & Cowley S. A. Efficient, long term production of monocyte-derived macrophages from human pluripotent stem cells under partly-defined and fully-defined conditions. PLoS One 8, e71098 (2013). GEO Superseries GSE45472 ;  Physiological characterisation of human iPS-derived dopaminergic neurons. Hartfield EM, Yamasaki-Mann M, Ribeiro Fernandes HJ, Vowles J, James WS, Cowley SA, Wade-Martins R.PLoS One. 2014 9(2):e87388 GEO superseries GSE43904. SNP dataset for control fibroblasts HDF AH017 is in press, and is available in GEO Superseries GSE69302.

Hartfield EM, Yamasaki-Mann M, Ribeiro Fernandes HJ, Vowles J, James WS, Cowley SA, Wade-Martins R.PLoS One. 2014 9(2):e87388 GEO superseries GSE43904. SNP dataset for control fibroblasts HDF AH017 is in press, and is available in GEO Superseries GSE69302.

first: J

last: Scaber

first: T

last: Lalic

first: N

last: Ababneh

last: Vowles

first: A

last: Fletcher-Jones

last: Douglas

first: C

last: Browne

first: M

last: Nakanishi

last: Turner

first: R

last: Wade-Martins

first: S

first: K

last: Talbot


title: Gene espression Profile by YAP1 and TAZ

city: Houston

first: Sangbae

last: Kim

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

summary: The Hippo signaling pathway is evolutionarily well conserved, and all core components have one or more mammalian orthologs, including MST1/2 (Hippo), SAV1 (Salvador), LATS1/2 (Warts), MOB1 (Mats), YAP1/TAZ (Yorkie), and TEAD1/2/3/4 (Scalloped) (Halder and Johnson, 2011; Pan, 2007; Dong et al., 2007; Saucedo and Edgar, 2007). When Hippo signaling is active, YAP1/TAZ is phosphorylated by LATS1/2 and sequestered by 14-3-3 proteins in cytoplasm. When Hippo signaling is absent, unphosphorylated YAP1/TAZ enters the nucleus and increases transcriptional activation of genes involved in cell proliferation and survival. The indispensability of the Hippo pathway in restricting cell growth and proliferation has prompted speculation that many members of the pathway might be involved in tumorigenesis. To see the effect of YAP1 and TAZ in HCC  cell, we generated gene expression profile.

overall_design: SK-Hep1 cell was transfected with siRNA targeting YAP1 and TAZ for three days.

first: Yun

last: Park

first: Ju

last: Lee

first: Sang

middle: B


title: Extracellular Superoxide Dismutase Regulates the Expression of GTPase Guanine Nucleotide Exchange Factors (GEFs), GTPase-activating proteins (GAPs), and Rho Guanine nucleotide disassociation inhibitors (GDI)

city: Naples

first: Mikko

last: Laukkanen

address: Via E. Gianturco 111-113

institute: SDN Foundation

summary: Extracellular superoxide dismutase (SOD3), which dismutases hydrogen peroxide to superoxide anion at cell membranes, mimics RAS oncogene action inducing primary cell immortalization at sustained low-level expression while high expression activates cancer barrier signaling through p53-p21 growth arrest pathway. We have previously demonstrated that the growth regulation of SOD3 occurs at the level of RAS and is mediated through non-transcriptional and transcriptional routes. Therefore, in the current work we assayed the growth suppressive mechanisms of SOD3 by characterizing the main signal transduction routes from the cell membrane into the nucleus. Based on our data robust over-expression of SOD3 in anaplastic thyroid cancer 8505c cells increased EGFR, RYK, ALK, FLT3, and EPHA10 tyrosine kinase receptor phosphorylation with consequent downstream SRC, FYN, YES, HCK, and LYN kinase activation. However, RAS pull-down experiment suggested lack of mitogen pathway stimulation that was confirmed by MEK1/2 and ERK1/2 Western blot. Interestingly, mRNA expression analysis indicated that SOD3 regulated in a dose dependent manner the expression of selected guanine nucleotide exchange factors (Rho GEF16, Ral GEF RGL1), GTPase activating proteins (ArfGAP ADAP2, Ras GAP RASAL1, RGS4), and Rho guanine nucleotide disassociation inhibitors (Rho GDI 2) therefore controlling the signal transduction through RAS GTPases to downstream signal transduction pathways. Our current data suggests a SOD3-induced activation of growth signal transduction is controlled in a dose dependent manner through GEF, GAP, and GDI.

overall_design: Four samples were analyzed: Control plasmid transfected stable 8505c cells, SOD3 transfected stable 8505c cells, Control plasmid transfected stable 8505c cells with long-term culture without medium change, SOD3 transfected stable 8505c cells without medium change

first: Maria

last: Castellone

first: Francesca

last: Cammarota

first: Tiziana

last: Esposito

first: Marco

last: Salvatore

middle: O


title: Genetic Variation, Not Cell Type of Origin, Underlies Regulatory Differences in iPSCs [Expression]

status: Public on Jan 16 2015

city: Chicago

first: Nicholas

middle: E

last: Banovich

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

summary: Analysis of contribution of cell type of origin and individual to gene expression differences in iPSCs. The hypothesis tested in the present study was that cell type of origin affects iPSC gene expression. Results show that individual has a much stronger effect than cell type of origin on differences between iPSCs derived from multiple individuals.

overall_design: Total RNA obtained from feeder-free iPSCs derived from multiple individuals and tissues and their corresponding cell type of origin

first: Courtney

middle: L

last: Kagan

first: Nick

first: Bryan

last: Pavlovic

first: Kristen

last: Patterson

first: Irene

last: Romero

first: Jonathan

middle: K

last: Pritchard

first: Yoav

last: Gilad


title: Genome-wide expression analysis of evolution of multi-drug resistance in Ramos cells

first: Andrew

last: Strand

address: 1100 Fairview Ave. N.

institute: Fred Hutchinson Cancer Research Center

summary: Examine gene expression in several variants of a human Burkitt's lymphoma cell line that had been selected to grow in media containing increaseing concentrations of doxorubicin.

overall_design:
The six cell lines were Ramos cells; Dox100, a derivative of the Ramos cells that grows in media plus 100nM doxorubicin; Dox250, a derivative of Dox100 that grows in 250nM doxorubicin; Dox500, a derivative of Dox250 cells that grows in 500nM doxorubicin; Dox750, a derivative of Dox500 cells that grows in 750nM doxorubicin; and Dox1000, a derivative of Dox750 cells that grows in 1000nM doxorubicin.
The six cell lines were grown in RPMI media plus 10% fetal bovine serum. Doxorubin was added to the media of the drug resistant lines to a final concentration equal to the line's stated resistance, i.e., Dox100 grown in media containing 100nM doxorubicin, etc. Four technical replicates of each cell line were made by splitting a single 25mL culture into four new 25mL cultures and allowing that to grow to a cell density of 10^6 cells/mL. Cells were centrifuged and total RNA was generated from all cultures in parallel.

first: Richard

last: Klinghofer


title: METRONOMIC TOPOTECAN CAUSES THERAPY-INDUCED TUMOR CELL SENESCENCE AND LOSS OF AGGRESSIVE PROPERTIES IN MYCN-AMPLIFIED CHILDHOOD CANCER [IN VIVO]

city: Vienna

first: Maximilian

last: Kauer

address: Zimmermannplatz 10

department: Molecular Biology

country: Austria

institute: CCRI, St.Anna Children Cancer Research Institute

summary:
Evidence is accumulating that senescence drives cure in various murine and human malignancies. We demonstrate that metronomic, repetitive low-dose topotecan treatment leads to tumor cell senescence in vitro and in vivo and long-term cure in a model for the aggressive childhood cancer neuroblastoma. By using the senescence-associated secretory phenotype (SASP) as a discriminator for beneficial versus adverse effects of senescence, we identified topotecan as inducer of a favorable SASP. Senescent tumor cells are growth arrested and act growth inhibitory on co-cultured non-senescent tumor cells. MYCN oncogene amplification and expression, hallmarks of aggressive neuroblastoma, are significantly reduced, supporting an initial transition to a more favorable phenotype. These new aspects of metronomic drug treatment are clinically relevant and might apply to other tumor entities.
Keywords: stress response, therapy induced senescence, cellular response, cancer treatment, neuroblastoma

overall_design: In total, 6 samples were analysed: The MYCN amplified neuroblastoma cell line STA-NB-10 was subcutaneously transplanted in T-cell deficient nude mice (Crl:CD1/Foxn1nu/nu), tumors were grown until a mean volume of 0.5 cm3 was reached and treated for 2 weeks with 0.1 mg/kg/d Topotecan i.p., daily. After sacrificing the mice, tumors were immediately prepared, snap frozen at liquid N2 and subsequently stored at -80°C.

first: Sabine

last: Taschner-Mandl

first: Magdalena

last: Schwarz

first: Johanna

last: Blaha

first: Martin

last: Hohenegger

first: Florian

last: Kromp

first: Neli

last: Frank

first: Fikret

last: Rifatbegovic

first: Inge

middle: M

last: Ambros

first: Peter


title: METRONOMIC TOPOTECAN CAUSES THERAPY-INDUCED TUMOR CELL SENESCENCE AND LOSS OF AGGRESSIVE PROPERTIES IN MYCN-AMPLIFIED CHILDHOOD CANCER [IN VITRO]

overall_design: In total, 17 samples were analysed: two different neuroblastoma cell lines, STA-NB-10 and CLB-Ma, control and drug-treated (hydroxyurea, captothecin, topotecan, Bromo-deoxy-uridine, All-trans-retinoic acid

middle: F


title: METRONOMIC TOPOTECAN CAUSES THERAPY-INDUCED TUMOR CELL SENESCENCE AND LOSS OF AGGRESSIVE PROPERTIES IN MYCN-AMPLIFIED CHILDHOOD CANCER

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Differentiation of Mesenchymal Glioblastoma Multiform by Bexarotene

city: Daejeon

first: Ji-Hwan

last: Park

address: 125 Gwahak-ro, Yuseong-gu

institute: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

summary: Glioblastoma multiforme (GBM) is the most aggressive malignant brain tumor. Differentiation can attenuate or block tumor growth; thus, phenotypic screenings were performed to search for drugs inducing differentiational morphological changes in mesenchymal recurrent GBM, a temozolomide (TMZ)-resistant brain cancer. Bexarotene, a selective retinoid X receptor agonist, showed strong inhibition of neurospheroidal colony formation and migration of cultured GBM stem cells. Bexarotene decreased nestin expression and significantly increased GFAP expression. Gene expression changes by bexarotene and all-trans retinoic acid (ATRA), a well-known differentiation inducer, were compared. Both drugs largely altered the gene expression pattern into a tumor-ameliorating direction. These drugs increased the gene expression levels of Krüppel-like factor 9 (KLF9), regulator of G-protein signaling 4 (RGS4), growth differentiation factor 15 (GDF15), angiopoietin-like protein 4 (ANGPTL4), and lowered the level of chemokine receptor type 4 (CXCR4). Both drugs also induced a potential oncogene, transglutaminase 2 (TG2), but the fold-change induced by bexarotene was considerably lesser than that by ATRA. Consistently, the TG2 activity in GBM was elevated several folds by ATRA. Because TG2 upregulation is correlated with tumor transformation and resistance, it is important to control its overexpression. Bexarotene does not upregulate TG2 as much as ATRA, and bexarotene showed in vivo tumoricidal effects in a GBM xenograft mouse model. Thus, these findings strongly suggest that bexarotene is more beneficial than ATRA and should be considered as a differentiation therapeutic agent for mesenchymal GBM.

overall_design: Mesenchymal GBM cell line (total 12 samples) : (a) Control (0.1% DMSO), (b) 10uM ATRA, (c) 10uM Bexarotene, and (d) 1uM Bexarotene. Each condition has 3 replicates, repectively.

first: Tae-Hoon

last: Jung

first: Jin-Chul

last: Heo

first: Sungjin

last: Lee

first: Hyun

last: Kim

first: Gildon

last: Choi

first: Myungeun

first: Daeyoung

first: Heung

first: Jung-Ok

first: Daehee

last: Hwang

first: Ho

last: Seol

first: Heeyeong

last: Cho


title: Effect of DHA enriched fish oil on human placental cells

city: Perth

first: Sam

last: Buckberry

address: 35 Stirling Highway, Crawley

institute: The University of Western Australia

summary: The omega-3 long chain poly-unsaturated fatty acid (n-3 LCPUFA) docosahexaenoic acid (DHA) plays a central role in fetal and neonatal development in humans, in particular the development of the brain and nervous system, and this has led to numerous studies focussed on determining the effect of exposure to an increased supply of DHA on pregnancy and neonatal outcomes. The aim of this study was to determine the impact of treatment with a DHA-enriched fish-oil emulsion on fatty acid composition, proliferation rate and gene expression in human placental HTR8/SVneo cells in vitro.

overall_design: This set contains 12 arrays culture experiments. 4 controls, 4 treated with DHA-enriched fish-oil emulsion, 4 treated with soy-oil emulsion.

first: Jing

last: Zhou

first: Tina

last: Bianco-Miotto

first: Beverly

last: Mühlhäusler


title: Transcriptome wide target profiling for miR-3118-3p and miR-4307-3p.

city: Herston

first: Nicole

last: Cloonan

state: Queensland

address: 300 Herston Road

institute: QIMR Berghofer Medical Research Institute

summary: Whole transcriptome Identification of  direct targets of miR-3118-3p and miR-4307-3p using biotinylated pull-downs found that both miRNAs have roles relevant to pancreatic cancer.

overall_design: HEK293T cells were transfected with biotinylated miRNAs (either miR-3118-3p or miR-4307-3p). The miRNAs and target mRNA were pulled down with streptavidin and compared to the input control.


title: Evaluation of poly (ADP) ribose polymerase (PARP) inhibitor, veliparib (ABT-888), in combination with platinum, etoposide and radiation in small cell lung cancer

city: Atlanta

first: Gregory

last: Doho

state: GA

address: 1365B Clifton Rd NE

institute: Emory University

summary: Veliparib showed limited single agent cytotoxicity but selectively potentiated (≥50% reduction in IC50) cisplatin, carboplatin and etoposide in vitro in 5 of 9 SCLC cell lines. Veliparib with cisplatin, etoposide or with both cisplatin and etoposide showed greater delay in tumor growth than chemotherapy alone in H146 but not H128. The potentiating effect of veliparib was associated with in vitro cell line sensitivity to cisplatin (CC=0.672; p=0.048) and DNA-PKcs protein modulation. Gene expression profiling identified differential expression of a 5-gene panel (GLS, UBEC2, HACL1, MSI2 and LOC100129585) in cell lines with relatively greater sensitivity to platinum and veliparib combination. Veliparib potentiates standard cytotoxic agents against SCLC in a cell specific manner. This potentiation correlates with platinum sensitivity, DNA-PKcs expression and a 5-gene expression profile.

overall_design: In vitro cytotoxicity of veliparib, cisplatin, carboplatin, and etoposide singly and combined was determined by MTS in 9 SCLC cell lines (H69, H128, H146, H526, H187, H209, DMS53, DMS153, and DMS114). Subcutaneous xenografts in athymic nu/nu mice of H146 and H128 with relatively high and low platinum sensitivity, respectively, were employed for in vivo testing. Mechanisms of differential sensitivity of SCLC cell lines to PARP inhibition were investigated by comparing protein and gene expression profiles of the platinum sensitive and the less sensitive cell lines.

first: Taofeek

last: Owonikoko

first: Guojing

last: Zhang

first: Xingming

last: Deng

first: Michael

middle: R

last: Rossi

first: Zhengjia

last: Chen

first: Jeffrey

last: Switchenko

first: Chunyang

last: Li

first: Ping

last: Yue

first: Gabriel

last: Sica

first: Suresh

middle: S

last: Ramalingam

first: Jeanne

last: Kowalski

first: Fadlo

last: Khuri

first: Shi-Yong

last: Sun


title: DNA METHYLATION DURING αβ T CELL DEVELOPMENT IN THE HUMAN THYMUS [expression]

status: Public on Dec 30 2014

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

summary: Thymocyte differentiation is a complex process which involves well-defined sequential developmental stages that finally result in the generation of mature αβ and γδ T cells. Here, we analyzed DNA methylation and gene expression profiles at successive human thymus developmental stages from early T-cell progenitors to single positive (SP) CD4+ and CD8+ subpopulations

overall_design: Expression data sets were generated from two technical replicates per cell type. Samples were obtained from a pool of  3 individuals each.


title: The Sweden Canceromics Analysis Network - Breast (SCAN-B) Initiative: a large-scale multicenter infrastructure towards implementation of breast cancer genomic analyses in the clinical routine [microarrays]

city: Lund

first: Lao

last: Saal

address: Scheelevägen 2, MV404B2

department: Department of Oncology and Pathology

institute: Lund University

summary: Breast cancer exhibits significant molecular, pathological, and clinical heterogeneity. Current clinicopathological evaluation is imperfect for predicting outcome, which results in overtreatment for many patients, and for others, leads to death from recurrent disease. Therefore, additional criteria are needed to better personalize care and maximize treatment effectiveness and survival. To address these challenges, the Sweden Cancerome Analysis Network - Breast (SCAN-B) consortium was initiated in 2010 as a multicenter prospective study with longsighted aims to 1) analyze breast cancers with next-generation genomic technologies for translational research in a population-based manner and integrated with healthcare; 2) decipher fundamental tumor biology from these analyses; 3) utilize genomic data to develop and validate new clinically-actionable biomarker assays; and 4) build the infrastructure for real-time clinical implementation of molecular diagnostic, prognostic, and predictive tests. In the first phase, we focus on molecular profiling by next-generation RNA-sequencing on the Illumina platform. In the three years from August 30, 2010 through August 31, 2013, we have consented and enrolled 3,979 patients with primary breast cancer at the seven hospital sites in South Sweden, representing approximately 85% of eligible patients in the catchment area. Pre-operative blood samples have been collected for 3,942 (99%) patients and primary tumor specimens collected for 2,929 (74%) patients. Herein we describe the study infrastructure and present initial proof of concept results from prospective RNA-sequencing including tumor molecular subtyping and detection of driver gene mutations. We demonstrate that large-scale population-based collection and RNA-sequencing analysis of breast cancer is feasible. The SCAN-B Initiative should significantly reduce the time to discovery, validation, and clinical implementation of novel molecular diagnostic and predictive tests. We welcome the participation of additional comprehensive cancer treatment centers.

overall_design: 55 RNA samples (49 tumors, 6 as technical replicates) were sequenced (Illumina paired-end) and in parallel analyzed on Human HT12 v4 BeadChip microarrays following the manufacturer’s standard protocol (Illumina). Intrinsic subtypes were determined for both platforms using the gene lists PAM50, Sorlie and Hu. Mutation calling was performed on the RNA-seq data.

first: Johan

last: Vallon-Christersson

first: Jari

last: Häkkinen

first: Cecilia

last: Hegardt

first: Dorthe

last: Grabau

first: Christof

last: Winter

first: Christian

last: Brueffer

first: Man-Hung

last: Tang

first: Christel

last: Reuterswärd

first: Ralph

last: Schulz

first: Anna

last: Karlsson

last: Ehinger

first: Janne

last: Malina

first: Jonas

last: Manjer

first: Martin

last: Malmberg

first: Christer

last: Larsson

first: Lisa

last: Rydén

first: Niklas

last: Loman

first: Åke

last: Borg


title: Reexpression of LSAMP inhibits tumor growth in a preclinical osteosarcoma model

city: Oslo

first: Leonardo

middle: A.

last: Meza-Zepeda

address: Ullernchausseen 70

department: Department of Tumor Biology

institute: Oslo University Hospital

summary: Osteosarcomas are the most common primary malignant tumors of bone, showing complex chromosomal rearrangements with multiple gains and losses. A frequent deletion within the chromosomal region 3q13.31 has been identified by us and others, and is mainly reported to be present in osteosarcomas. We have previously proposed the gene limbic-system associated membrane protein (LSAMP) as the target for the deletion. In the present study, we found reduced copy number of LSAMP in 45/76 osteosarcoma samples, reduced expression level in 26/42 samples and protein expression in 9/42 samples. The high observed frequency of the deletion and the specificity indicates that it is important for the development of osteosarcomas. By restoring the expression of LSAMP in a cell line with a homozygous deletion of the gene, the proliferation rate in vitro was significantly reduced and tumor growth in vivo was significantly delayed. In response to reexpression of LSAMP, mRNA expression profiling revealed consistent upregulation of the genes hairy and enhancer of split 1 (HES1), cancer/testis antigen 2 (CTAG2) and kruppel-like factor 10 (KLF10). Based on these findings, the tumor suppressor function of LSAMP is most likely exerted by reducing the proliferation rate of the tumor cells, possibly by indirectly upregulating one or more of the genes HES1, CTAG2 or KLF10. To our knowledge, this study describes novel functions of LSAMP, a first step to the understanding of its specific deletion in osteosarcomas.

overall_design: Comparison of gene expression of different clones reexpressing LSAMP

first: Tale

last: Barøy

first: Stine

last: Kresse

first: Magne

last: Skårn

first: Marianne

last: Stabell

first: Russell

last: Castro

first: Silje

last: Lauvrak

first: Antionio

last: Llombart-Bosch

first: Ola

last: Myklebost

middle: A


title: T cell responses to H1N1v and a longitudinal study of seasonal influenza vaccination - 2012

status: Public on Dec 25 2014

city: palo alto

first: weiqi

last: wang

state: ca

address: 1291 welch road

institute: stanford

summary: Systems biology approach to examine effects of seasonal flu vaccination in adults of different ages on gene expression, cytokine stimulation and serum cytokines with parameters such as immune senescence to uncover new markers and mechanisms behind failure of immune function in many older people.

overall_design: 1. Combinatorial tetramer analysis by FACS and/or CyTOF; Phosphoflow. 2. Luminex; Gene expression profiling (Affymetrix microarray). 3. Luminex; Gene expression profiling (Affymetrix microarry); Microneutralization assays. 4. Gene expression profiling (Affymetrix microarray); Immune phenotyping by CyTOF. 5. Gene expression profiling (Affymetrix microarray). 6. Immune phenotyping by CyTOF; Luminex. 7. ELISA.

first: Mark

last: Davis


title: TNF-alpha and IL-17 synergize to inhibit IL-13 bioactivity via IL-13Ra2 induction in human lung fibroblasts

city: Bethesda

first: Timothy

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

summary: IL-17 and TNF-alpha synergistically induce surface expression of IL-13Ra2 on primary lung fibroblasts, rendering them unresponsive to IL-13. Neutralizing antibodies to IL-13Ra2 restored IL-13-mediated signaling and transcriptome studies confirmed IL-13Ra2 is an IL-13 decoy receptor.

overall_design: Human fibroblasts were stimulated with IL-13, or stimulated with IL-13 after pre-treatment with TNF-alpha plus IL-17, or stimulated with IL-13 after pre-treatment with TNF-alpha plus IL-17 plus anti-IL13Ra2 antibody. Media and pre-treatment controls are included. 4 replicates per condition: 2 cell passages (biological replicates) each including 2 independent experiments.

first: Vahe

last: Badalyan

first: Kezia

last: Addo

first: Robert

middle: W

last: Thompson

first: Lee

last: Borthwick

first: Tatiana

last: Ort

first: Thomas

last: Wynn

first: Thirumalai

last: Ramalingam


title: Global analyses revealed age-related alterations in innate immune responses after stimulation of pathogen-recognition receptors

city: Cleveland

first: Peter

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

summary: Aging leads to dysregulation of multiple components of the immune system that result in increased susceptibility to infections and poor response to vaccines in the aging population. The dysfunctions of adaptive T- and B-cells are well documented but the effect of aging on innate immunity remains incompletely understood. Therefore, we first undertook transcriptional profiling of peripheral blood mononuclear cells (PBMCs) and found that PBMCs isolated from old individuals (≥65 yrs) exhibited a delayed and altered response to stimulation with TLR4, TLR7/8, and RIG-I agonists compared to cells obtained from adults (≤40 yrs). This delayed response to innate immune agonists resulted in the reduced production of pro-inflammatory and antiviral cytokines and chemokines including TNFα, IL-6, IL-1β, IFNα, IFNγ, CCL2 and CCL7. While the major monocyte and dendritic cell subsets did not change numerically with aging, activation of specific cell types was altered. We observed old PBMCs had a lower frequency of CD40+ monocytes, impaired up-regulation of PD-L1 on monocytes and T cells and increased expression of PD-L2 and B7-H4 on B cells. The defective innate immune response adversely affected adaptive immunity as TLR-stimulated PBMCs (minus CD3 T cells) from old subjects’ elicited significantly lower levels of adult T cell proliferation than those from adult subjects in an allogeneic mixed lymphocyte reaction (MLR). Collectively, these age-associated changes in cytokine, chemokine and interferon production, as well as co-stimulatory protein expression, could be responsible for the blunt memory B and T cell immune responses to vaccines and infections.

overall_design: PBMCs were treated with TLR and RIG-I agonists as follows: LPS-TLR4 (0.5 µg/ml) or CLO97-TLR7/8 (0.5 µg/ml) or poly I:C/Lyovec-RIGI/MDA5 (2 µg/ml) or 5’-pppRNA/Lyovec-RIG-I (400 ng/ml). PBMCs were cultured for 6 and 24 hrs at 37C in a 5% CO2-humidified environment.

first: T

last: Metcalf

first: R

last: Cubas

first: K

last: Ghneim

first: M

last: Cartwright

first: J

last: Van Grevenynghe

last: Richner

first: D

last: Olagnier

first: P

last: Cameron

last: Hiscott

last: Diamond

first: A

last: Wertheimer

last: Nikolich-Zugich

first: E

last: Haddad


title: Transcriptome wide target profiling for miR-23b and miR-27a.

first: Nicole

last: Cloonan

summary: Whole transcriptome Identification of  direct targets of miR-23b and miR-27a using biotinylated pull-downs found that both miRNAs have roles relevant to the mammalian cell cycle and cancer.

overall_design: HEK293T cells were transfected with biotinylated miRNAs (either miR-23b or miR-27a). The miRNAs and target mRNA were pulled down with streptavidin and compared to the input control.