title: A novel Lysyl oxidase like 2 alternative splicing LOXL2 △e13 in esophageal squamous carcinoma cells

city: Shantou

first: Guo-Qing

last: Lv

state: Guangdong

address: Xinling road

institute: Department of Biochemistry and Molecular Biology

summary: A novel alternative splicing isoform of LOXL2 △e13 was expressed ubiquitously in all cell lines and ESCC tissues. In contrast to the impaired deamination enzymatic activity compared with full length LOXL2, LOXL2 △e13 showed an enhanced ability to promote cell mobility and invasiveness in ESCC cells than full length LOXL2 through a different mechanism.

overall_design: We used cDNA microarrays to identify genes that were differentially expressed upon LOXL2 △ e13 overexpressed. For this purpose, we selected LOXL2 △ e13, WT and empty vector control transfeced ESCC KYSE150 cell lines. Total RNA was extracted,compare the gene expression patterns between LOXL2 △e13, LOXL2 WT and empty vector control transfected cells through the Genechip Primeview Human Gene Expression Array.


title: Maternal-diabetes induced gene expression changes in the umbilical cord

status: Public on Jan 01 2016

city: Turku

first: Anna

last: Koskinen

address: Kiinamllynkatu 10

department: Research centre of Applied and Preventive Cardiovascular Medicine (CAPC)

country: Finland

institute: University of Turku

summary: Analysis of umbilical cord tissue in newborns of type 1 diabetic mothers at gene expression level. The hypothesis tested in the present study was that intrauterine diabetic milieu may effect of fetal umbilical cord gene expression, and via umbilical cord, the alterations may be produced in other fetal tissues as well. Results provide an information of the differentially expressed genes and enriched pathways, such as the dowregulated genes on the pathway on blood vessel development in umbilical cords from diabetic pregnancies.

overall_design: Umbilical cord  tissue was collected after elective ceasarean section and was immediately flash frozen in liquid nitrogen and stored at -80C until total RNA extraction from the whole tissue sample. Six cords exposed to maternal diabetes (DM) and six control cords (C) from healthy pregnancies were analyzed.

first: Hanna

last: Soukka

first: Asta

last: Laiho


title: Pioneer factor FOXA1 defines GATA2- and AR-mediated transcriptional program in prostate cancer [gene expression]

status: Public on Jan 11 2016

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

country: USA

institute: Emory University

summary: AR is tightly regulated by many transcriptional cofactors, including key pioneer factor such as FOXA1 and GATA2.  While FOXA1 was recently shown to be able to redistribute AR across the genome, how GATA2 regulates AR cistrome has not been carefully investigated.  Here, we report that, unlike FOXA1, GATA2 is unable to reprogram AR, but instead it enhances AR program by inducing AR expression and augmenting AR co-occupancy, thereby acting as a pure AR coactivator, rather than a pioneer factor.  On the other hand, AR co-occupancy enhances both GATA2 and FOXA1 binding on the chromatin, forming a positive feedback loop.  Importantly, we found that FOXA1 is also capable of reprogramming GATA2 by recruiting GATA2 from GATA motif to FKHD-containing regions, being analogous to its pioneering effect on AR signaling.  By contrast, GATA2 simply acts as a co-activator of FOXA1 with a lack of pioneering ability.

first: Jonathan

last: Zhao


title: Hormetic shifting of redox environment by the ROS-producing polyphenol resveratrol protects cells from oxidative stress

status: Public on Dec 31 2015

city: Berlin

first: Annabell

last: Plauth

state: Berlin

address: Ihnestrasse 63-73

department: OWL

country: Germany

institute: MPI Molgen

summary: Resveratrol is a natural product that has gained tremendous interest due to multiple reported health-beneficial effects. However, the underlying mechanisms of action of this compound remained largely controversial. Here, we demonstrate that major biological effects of resveratrol might be attributed to its bicarbonate-induced production of phenolic radicals and reactive oxygen species (ROS) such as superoxide and hydrogen peroxide under physiologically relevant conditions. These products derived from low hormetic micromolar concentrations of resveratrol led to gene expression reprogramming, which was mainly controlled by the redox-sensitive transcription factor nuclear factor (erythroid-derived 2) like 2 (Nrf2), whereas too high concentrations of resveratrol became detrimental for cells. Gentle but significant activation of Nrf2-controlled gene expression resulted in a metabolic switch and reduced cellular redox environment. Thereby cells could be preconditioned against stress, for example to protect primary keratinocytes of the human epidermis from oxidative stress that was induced by metabolization of ethanol. Hormetic shifting of cells by chemical triggers such as resveratrol towards a more reductive state might represent a powerful conceptual framework to improve cellular fitness at low nontoxic concentrations.

overall_design: Total RNA obtained from cultured primary neonatal normal human epidermal keratinocytes (NHEK) subjected to 16 hours treatment with 50 µM resveratrol (trans-3,5,4’-trihydroxystilbene, RSV) compared to vehicle-treated control NHEKs.


title: Microarray analysis of epithelial and fibroblast cells in chronic rhinosinusitis

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

country: United Kingdom

institute: Newcastle University

summary: Chronic rhinosinusitis without polyps (CRSsNP) is typified by inflammation of the sinonasal epithelium and the development of fibrosis.  The precise pathophysiology of this common condition remains elusive.  Here we aim to investigate the transcriptome (RNA transcripts in the cell) of the component nasal epithelial and fibroblast cells in CRSsNP and health to identify if there are clusters of differentially expressed genes as possible novel CRS therapeutic targets.

overall_design: Gene expression profiling by Illumina BeadArray of primary nasal epithelial and fibroblast cells in heatlh and chronic sinusitis.  Samples from consenting human donors (Epithelial Case, n=13, Epithelial Control, n=11, Fibroblast Case, n=12, Fibroblast Control, n=12).

first: Stephen

middle: L

last: Ball

middle: J

first: Derek

middle: A

last: Mann

first: Andrew

last: Fisher

first: Janet

last: Wilson


title: Similarities and Distinctions in Actions of Surface-Directed and Classic Androgen Receptor Antagonists

city: Houston

first: Paul

last: Webb

address: 6670 Bertner Ave

department: Genomic Medicine

institute: Houston Methodist Research Institute

summary: This study was undertaken to compare efficacy of MJC13 and the classic AR antagonist flutamide. Both compounds modulate endogenous AR target gene expression in Prostate cancer cells in a similar fashion despite different mechanisms of action.

overall_design: LNCaP cells were seeded within 6-well dishes at density of 1 × 100,000 within RPMI 1640 media supplemented with L-glutamine and 10% fetal bovine serum (FBS), day 2 the media replaced with RPMI 1640 media supplemented with L-glutamine and 10% charcoal-stripped FBS, day 3 the cells were treated with DMSO (control), 10nM DHT, 1μM Flutamide, 1μM Flutamide + 10nM DHT, 30μM MJC13, or 30μM MJC13 + 10nM DHT for 24 hours, after which total RNA was isolated.

first: Douglas

middle: H

last: Sieglaff


title: Metabolic reprogramming of triple-negative breast cancer and melanoma cell lines by the Let-7a microRNA

city: Oslo

first: Leonardo

middle: A.

last: Meza-Zepeda

address: Ullernchausseen 70

department: Department of Tumor Biology

country: Norway

institute: Oslo University Hospital

summary: Let-7 microRNAs (miRNAs) are a family of highly conserved well-established promoters of terminal differentiation that are expressed in all healthy adult tissues and frequently repressed in cancer cells. The tumour suppressive role of let-7 in a variety of cancers in vitro and in vivo has been widely documented and prompted these miRNAs to be candidate genes for miRNA replacement therapy. Reprogrammed metabolism, recently identified as a new hallmark of cancer, contributes to cancer cell growth, proliferation, invasiveness and drug resistance. In this study we identified a new metabolic role of let-7a in triple-negative breast cancer and metastatic melanoma cell lines. We show that let-7a down-regulates key anabolic enzymes, promotes oxidative phosphorylation and mitochondrial ROS formation accompanied by the up-regulation of the oxidative stress responsive genes. To assess if we could exploit these increased ROS levels for therapeutic purposes, we combined let-7a transfection with the antitumor drug doxorubicin. In both cancer types we observed a stronger response to the doxorubicin treatment in let-7a transfected cells. Pre-treatment with an antioxidant N-acetyl cysteine totally abolished this difference, indicating that the increased doxorubicin sensitivity of let-7a cells depends on the redox pathway. We demonstrated that let-7a plays a prominent role in regulating energy metabolism in cancer cells. We propose that a benefit from let-7 miRNA replacement therapy could come not only from the repression of oncogenic pathways targeted directly by let-7, but also by increased sensitivity to chemotherapeutic agents through indirect metabolic changes caused by let-7.

overall_design: Investigation of let-7a metabolic role in breast cancer and melanoma cells.

first: Anastassia

last: Serguienko

first: Iwona

last: Grad

middle: B

last: Wennerström

first: Bernd

last: Thiede

first: Eva

middle: W

last: Stratford

first: Ola

last: Myklebost

first: Else

last: Munthe


title: Oncogenic CARMA1 couples NF-κB and β-Catenin signaling in diffuse large B cell lymphomas

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

institute: University of Münster

summary: Constitutive activation of the anti-apoptotic NF-κB signaling pathway is a hallmark of the activated B-cell-like (ABC) subtype of diffuse large B-cell lymphomas (DLBCL) that is characterized by adverse survival. Recurrent oncogenic mutations are found in the scaffold protein CARMA1 (CARD11) that connects B-cell receptor (BCR) signaling to the canonical NF-κB pathway. We asked how far additional downstream processes are activated and contribute to the oncogenic potential of DLBCL-derived CARMA1 mutants. To this end, we expressed oncogenic CARMA1 mutants in the NF-κB negative DLBCL lymphoma cell line BJAB. By a proteomic approach we identified recruitment of β-Catenin and its destruction complex consisting of APC, AXIN1, CK1α and GSK3β to oncogenic CARMA1. Recruitment of the β-Catenin destruction complex was independent of CARMA1-BCL10-MALT1 (CBM) complex formation or constitutive NF-κB activation and promoted the stabilization of β-Catenin. Elevated β-Catenin expression was detected in cell lines and biopsies from ABC DLBCL that rely on chronic BCR signaling. Increased β-Catenin amounts alone were not sufficient to induce classical WNT target gene signatures, but could augment TCF/LEF dependent transcriptional activation in response to WNT signaling. In conjunction with NF-κB, β-Catenin enhanced expression of immune suppressive IL-10 and repressed anti-tumoral CCL3, indicating that β-Catenin may induce a favorable tumor microenvironment. Thus, parallel activation of NF-κB and β-Catenin signaling by gain-of-function mutations in CARMA1 can augment WNT stimulation and is required for maintaining high expression of distinct NF-κB target genes and can thereby trigger cell intrinsic and extrinsic processes that promote DLBCL lymphomagenesis.

overall_design: CARMA1 mutants were expressed in BJAB, an NF-κB negative GCB DLBCL lymphoma cell line. Gene expression induced by GCB DLBCL derived CARMA1 L225LI mutant was compared with the empty vector (mock) control, CARMA1 WT, CARMA1 point mutant R35A and with CARMA1 double mutant R35A/L225LI.

first: Georg

last: Lenz

first: Daniel

last: Krappmann


title: Curcumin Effectively Depletes Hepatic Cancer Stem-Like Cells

city: Mainz

first: Jens

middle: U.

last: Marquardt

address: Langenbeckstrasse 1

department: Department of Medicine I

institute: University of Mainz

summary: The cancer stem cells (CSCs) have important therapeutic implications for multi-resistant cancers including hepatocellular carcinoma (HCC). Among the key pathways frequently activated in liver CSCs is NF-kB signaling.  Here we evaluated the CSCs-depleting potential of NF-kB inhibition in liver cancer achieved by IKK inhibitor curcumin and specific peptide SN50 . The effects on CSCs were assessed by analysis of Side Population (SP) and expression levels of CSC-related genes as determined by RT-qPCR, gene expression microarray, EMSA, and Western blotting.  Curcumin caused anti-proliferative and pro-apoptotic responses directly related to the extent of NF-kB inhibition. In curcumin-sensitive tumor cells, the treatment led to a selective CSC depletion as evidenced by a reduced SP size, decreased sphere formation, down-regulation of CSC markers and suppressed tumorigenicity. Similarly, NF-kB inhibition by SN50 caused a general suppression of cell growth accompanied by a reduced SP fraction. In contrast, curcumin-resistant cells exhibited a paradoxical increase in proliferation and expression of CSC markers.  Mechanistically, CSC-depleting activity of curcumin was exerted by the NF-kB-mediated HDAC inhibition causing down-regulation of c-MYC and other key oncogenic targets. Co-administration of the class I/II HDAC inhibitor trichostatine sensitized resistant cells to curcumin. Further, integration of a predictive signature of curcumin sensitity with our HCC database indicated that HCC patients with poor prognosis and progenitor features are most likely to benefit from NF-kB inhibition. These results demonstrate that NF-kB inhibition can specifically target CSC populations and suggest a potential for combined inhibition of NF-kB and HDAC signaling for treatment of liver cancer patients with poor prognosis.

overall_design: Five human hepatoma cell lines with and without curcumin

middle: U


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

city: Warsaw

first: Michal

last: Swierniak

address: Banacha 2C

department: Centre of New Technologies

country: Poland

institute: University of Warsaw

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

overall_design: The human microarray data were obtained for: 27 papillary thyroid carcinomas including 18 BRAF(+), 8 RET(+), 1 RAS(+); 18 apparently healthy thyroids. In order to find BRAFV600E-specific gene signature data obtained from our transgenic mouse model of PTC were compared to human material. The analyses were performed taking into account not only the BRAF mutation but also other PTC initiating events including RET rearrangements and RAS poin mutations. Morover the microarray data were validated with the QPCR reaction.

first: Dagmara

last: Rusinek

first: Barbara

last: Jarzab


title: Long non-coding Satellite III RNAs link the heat shock response and cell proliferation

first: Lea

last: Sistonen

address: Tykistökatu 6 B

department: Department of Biosciences

institute: Åbo Akademi

summary: Genomes of complex organisms encode a wide variety of long non-coding RNAs (lncRNAs) that regulate gene expression. In human cells exposed to heat stress, transcription of lncRNAs is highly induced from Satellite III sequences located primarily within locus 9q12. Expression of Sat III transcripts is dependent on heat shock factor 1, the master regulator of the heat shock response. Sat III transcripts serve as the backbone of specific subnuclear structures called nuclear Stress Bodies, nSBs. Despite being known for two decades, the function of nSBs and Sat III transcripts is unknown, which prompted us to conduct RNA profiling in human cells where Sat III transcripts were either intact or downregulated. Comparison of these cells revealed that under stress conditions, Sat III transcripts are involved in regulating a plethora of genes, including such associated with cell growth and protein homeostasis. Our results show that the presence of Sat III transcripts has a repressive effect on cell proliferation. We propose a model in which the inducible expression of Sat III transcripts restrains cell proliferation, allowing the cell to assess whether to grow or undergo apoptosis, and thereby suggesting a function for these lncRNAs in cell fate decisions and in restoring protein homeostasis.

overall_design: Total RNA from HEK293T cells transfected with siRNA against Satellite III transcripts or scrambled siRNA and heat shocked 1 h at 42°C , or heat shocked 1 h at 42 °C followed by recovery for 6 h, or left untreated was compared.

first: Anton

last: Sandqvist


title: Transcriptome profiling of nasal polyp derived human IL17RB positive and negative T-helper cells

status: Public on Dec 22 2015

city: Leicester

first: David

middle: John

last: Cousins

address: NIHR BRC Respiratory, Glenfield Hospital

department: Respiratory Sciences

institute: University of Leicester

summary:
Background: Chronic rhinosinusitis with nasal polyposis (CRSwNP) in western countries is characterized by eosinophilia, IgE production and Th2 cytokine expression. Type 2 innate lymphoid cells (ILC2) from polyps produce IL-5 and IL-13 in response to IL-25 and IL-33 although the relevance of this axis to local mucosal T cell responses is unknown.
Objective: To investigate the role of the IL-25/IL-33 axis in local mucosal T cell responses in CRSwNP.
Methods: Polyp tissue and blood were obtained from patients undergoing nasal polypectomy. Control nasal biopsies and blood were obtained from healthy volunteers. Tissue was cultured in a short-term explant model. T cell surface phenotype/intracellular cytokines were assessed by flow cytometry. TCR Vβ analysis was performed with the immunoSEQ assay. Microarrays were performed for gene expression analysis.
Results: Using nasal polyp tissue, numerous IL-25 receptor (IL-17RB) positive polarized Th2 cells were identified which were absent in the healthy nasal mucosa and periphery. IL-17RB+CD4+ polyp Th2 cells co-expressed ST2 (IL-33 receptor) and responded to IL-25 and IL-33 with enhanced IL-5 and IL-13 production. Within IL-17RB+CD4+ T cells several identical TCR Vβ CDR3 sequences were identified in different subjects suggesting clonal expansion driven by a common antigen. Abundant IL-17 producing T cells were observed in healthy nasal mucosal and polyp populations with Th17-related genes the most overexpressed compared to peripheral blood T cells.
Conclusion: IL-25 and IL-33 may interact locally with IL-17RB+ST2+ polyp T cells to augment Th2 responses in CRSwNP.  A local Th17 response may be the default signature in healthy nasal mucosal immune homeostasis.

overall_design: Three biological replicates. T-helper cells were isolated nasal polyps by explant culture from patients with chronic rhinosinusitis. Cells were then sorted based upon expression of IL17RB by flow cytometric sorting. Resting and activated IL-17RB+ve cells were compared with resting and activated IL-17RB-ve cells.

first: Emily

last: Lam


title: Transcriptome profiling of  T-helper cells from normal nassal mucosa and matched peripheral blood

overall_design: Three biological replicates. T-helper cells were isolated from nasal mucosa by explant culture and from peripheral blood from healthy control subjects. CD4+ve cells were then sorted by flow cytometric sorting. Resting and activated nasal T-helper cells were compared with resting and activated blood T-helper cells.


title: Effect of nutritive conditions, adhesion and EMT on transcriptional profile of HMECs transduced by an oncogene RAS and SNAI1, SNAI2 or SNAI3

city: Lyon

first: Anne

last: Wierinckx

state: select a state

address: 8, av Rockefeller

country: France

institute: University Lyon1

summary: Oncogenic stress induces a global disturbance of cellular homeostasis and subsequently triggers the activation of tumour suppressor pathways. Energy capacity loss, redox state imbalance, and biosynthetic deficiency constitute the primary signals activating safeguard mechanisms, culminating in levels of stress that should not be compatible with infinite proliferative capacities of tumour initiating cells (TIC)s or cancer stem cells (CSC)s. Here, we show that the control of the glucocorticoid response by embryonic factors involved in mammary stemness5, 6 enables basal breast CSCs to not be faced with this oncogenic stress. The glucocorticoid response is thus correlated with stemness properties in basal breast cancers and is required for neoplastic transformation of mammary progenitors. This effect does not rely on hijacking  tumour suppressor pathways, but on homeostatic buffering capacity. Through extensive analysis of homeostatic parameters and metabolic profiling, we show that the glucocorticoid response in mammary CSCs limits the “Warburg effect”, the ability of an oncogene to drive glucose fermentation in the presence of oxygen. The glucocorticoid response dampens glycolytic flow and maintains respiratory capacity resulting in reduction of mitochondria energisation. This enables CSCs to sustain carbon and nitrogen flows generated via glycolysis and the tricarboxylic acid cycle (TCA), required for homeostasis and anabolism maintenance. Overall, our results reveal the role of hormonal control of metabolic reprogramming in a CSC in rendering the cell permissive to oncogenic activity.

overall_design: Immortalized human mammary epithelial cells (HMEC-hTERT cells) were infected with SNAIL retroviral expression constructs and an inducible form of RAS G12V. The gene expression profiles of the resulting cell lines, cultured in standard conditions, in limited nutrient supply  or after plating them 16h in low-adherent (LA) conditions, were performed.

first: Fabienne

last: Barbet

first: Marjorie

last: Carrere

first: Ebticem

last: Nouri

first: Alain

last: Puisieux

first: Arnaud

last: Vigneron


title: Linker histone H1.2 establishes chromatin comapction and gene silencing through recognition of H3K27me3

status: Public on Dec 21 2015

city: Los Angeles

first: Vasu

last: Punj

state: CA

address: Biggy Street

institute: USC

summary: Linker  histone H1 is a protein component of chromatin and has been linked to chromatin compaction and global gene silencing.It has been sugegsted that H1 plays a significant role, regulating a relatively small number of genes. Here we show that H1.2- a variant of H1 subtype is recruited to chromatin region and is dependent on EZH2-mediated H3K27me3. Therefore a Gene expression array analysis was carried out with H1.2 as well as EZH2 knockout MCF7 cells to confirm the interlationship of H1.2 and EZH2 activity.

overall_design: Total RNA was isolated from MCF7 cells in which EZH2 and H1.2 genes  have been depleted along with the wild type cells to study the differential regulation of various genes in each case.

first: Jin-Man

last: Kim

first: Kyunghwan

first: Wange

last: Lu

first: Woojin

last: An


title: Treatment of primary effusion lymphoma cell lines with lenalidomide

status: Public on Dec 28 2015

first: Timothy

middle: J.

last: Triche

address: 1450 Biggy St., Harlyne Norris Research Tower 3509

department: Norris Comprehensive Cancer Center

institute: University of Southern California, Keck School of Medicine

summary:
Technical replicates from BC3 and BCBL1 cell lines were treated with DMSO or 5 micromoles of lenalidomide for 24 hours.
NOTE: Detection p-values were neither computed nor used in this experiment.  All data was processed directly from IDATs and the proportion of present probes estimated from the negative and positive controls.

overall_design: 8 samples, two technical replicates per cell line per condition.

first: Ramakrishnan

last: Gopalakrishnan

first: Preet

middle: M

last: Chaudhary


title: LZTFL1 inhibits lung tumorigenesis by maintaining the differentiated state of lung epithelial cells and suppressing MAPK and SHH signaling pathways

city: Dallas

first: Zhi-Ping

last: Liu

state: TX

address: 5323 Harry Hines Boulevard

department: Internal Medicine

institute: University of Texas Southwestern Medical Center at Dallas

summary: Previously, we found that LZTFL1 is down-regulated in epithelial tumors including lung cancer and functions as a tumor suppressor in gastric cancers. However, the functional role of LZTFL1 in lung oncogenesis is undefined. We show here that downregulation of LZTFL1 expression in non-small cell lung cancer is associated with recurrence and poor survival, while re-expression of LZTFL1 in lung tumor cells inhibited extravasation/colonization of circulating tumor cells to the lung and inhibited tumor growth in vivo. Mechanistically, we found that LZTFL1 is expressed in ciliated human bronchial epithelial cells (HBECs) and its expression correlates with HBEC differentiation. LZTFL1 inhibits TGFβ-activated MAPK and hedgehog signaling. Alteration of intracellular levels of LZTFL1 resulted in changes of expression of genes associated with epithelial-to mesenchymal transition (EMT).  We conclude that LZTFL1 inhibit lung tumorigenesis, possibly by maintaining epithelial cell differentiation and/or inhibition of signalings that lead to EMT, and suggest that reactivation of LZTFL1 expression in tumor cells may be a novel lung cancer therapeutic approach.

overall_design: Examination of the whole genome expression profiles of HCC95-GFP, HCC95GFP+TGFβ,HCC95-LZTFL1-GFP,HCC95-LZTFL1-GFP+TGFβ, H460-GFP, and H460-LZTFL1-GFP cells

first: Qun

last: Wei


title: Gene expression changes during development of sunitinib resistance in renal cell carcinoma patient derived xenografts

status: Public on Dec 17 2015

city: Cleveland

first: John

last: Barnard

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic Foundation

summary: Transcriptome analysis was used to identify gene expression changes during development of sunitinib resistance in a renal cell carcinoma patient-derived xenograft (PDX) model.  During the response phase, tumors exhibited a 91% reduction in volume, characterized by induction of TNFRSF1A, TNFAIP3, NFKB2, CCL2, CCL20, BIRC3, and MOAP1. Ingenuity Pathway Analysis indicated decreased expression of cell survival genes during tumor response to sunitinib.  In this model, after 4 weeks of treatment, tumors developed resistance despite continued administration of the tyrosine kinase inhibitor (TKI) sunitinib (40 mg/kg/d p.o.). Resistance was associated with increased expression of VEGFA, EPO, IL-8, ANGPT2, TNFRSF12, MAPK3/7, MAPKBP1, and increased cell survival genes, suggesting activation of angiogenesis and MAPK/ERK pathways. Tumor lysate mRNA evaluated for murine gene expression to examine the contribution of host effects, indicated that tumor response was associated with downregulation of immune cell trafficking, cellular movement, and inflammatory response genes. During tumor escape, genes associated with cellular movement, inflammatory response, and immune cell trafficking were strongly induced, along with intratumoral accumulation of myeloid derived suppressor cells (MDSC), indicating a role for host factors during emergence of sunitinib resistance. The same PDX model was used to assess anti-tumor efficacy of sunitinib combined with MEK inhibitor (MEKi) PD-0325901 (4 mg/kg/d p.o.) using different schedules.  The most effective treatment regimen was either continuous treatment with both drugs or switching from sunitinib to PD-0325901 monotherapy at d30, which reduced tumor volume by 78.6% (p=0.0241) and 88.5% (p=0.0068), respectively. The combination of MEKi with TKI (sunitinib, axitinib, or pazopanib) suppressed levels of phospho-MEK1/2 and phospho-ERK1/2, and decreased intratumoral MDSC. Thus, continuous treatment with sunitinib alone did not maintain tumor response, and addition of a MEKi abrogated resistance leading to prolonged survival.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Study was comprised of three experimental groups (pre-treatment, response, escape). All tumors came from the same PDX model. There were four biological replicates in each group. Four mice were used, with each of the 3 groups per mouse. There were no control or reference samples.

first: C

last: Diaz-Montero

first: Frances

last: Mao

first: Yvonne

last: Parker

first: Maryam

last: Zamanian-Daryoush

last: Pink

first: James

last: Finke

first: Brian

middle: I

last: Rini

first: Daniel

last: Lindner


title: Gene expression analysis of skin fibroblast cells from patients with Bipolar Disorder

city: Athens

first: Marianthi

last: Logotheti

address: 48 Vassileos Constantinou Avenue

country: Greece

institute: National Hellenic Research Foundation

summary: Bipolar disorder is a severe, lifelong psychiatric disease. The main underlying pathophysiology of the disease is still incomprehensible. Many studies have suggested that many genes of small impact in combination with environmental factors contribute to the expression of the disease. In this study comparative transcriptomic profiling to characterize skin fibroblasts gene expression of bipolar disorder patients compared to healthy controls  has been performed.

overall_design: Total RNA obtained from skin fibroblast cells of 5 healthy control samples that were pooled into 2 samples and from 10 bipolar disorder patients, in order to compare their gene expression profiles.

first: Olga

last: Papadodima

first: Nikolaos

last: Venizelos

first: Aristotelis

last: Chatziioannou

first: Fragiskos

last: Kolisis


title: Metabolic re-programming of pancreatic cancer mediated by CDK4/6 inhibition elicits unique vulnerabilities

first: Erik

last: Knudsen

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Gene expression levels were determined with control or PD-0332991 treatment

overall_design: CAPAN2 Cells were subject to DMSO/ PD-0332991 treatment.   RNA was harvested at 72 hours post treatment and analyzed on Illumina microarrays

middle: S


title: PNAs-A15 effects on cervical cancer cells line

status: Public on Dec 23 2015

city: Bangkok

first: jirattha

last: siriluksana

address: Rama 4

country: Thailand

institute: Chulalongkorn university

summary: Expression profile of HeLa and C33A cervical cancer cells line treated with PNAs-A15 for 6 hours. PNAs-A15 is peptide nucleic acid of A-repeats length 15 bp that can suppress up-regulated A-repeats containing genes in cervical cancer cells line.

overall_design: The cervical cancer cell line HeLa and C33A  was maintained at 37C in 5% CO2  under sterile conditions in Dulbecco's modified Eagle medium, supplemented with 10% fetal bovine serum. Cells were treated with PNAs-A15 in 6-well microplates for 6 h. Total RNA was isolated and hybridized on the HumanHT-12 v4 Expression BeadChip. The RNA expressions were evaluated and compared with 2 repeats of controlled experiments.

first: Jirattha

last: Siriluksana


title: Combinatorial Control of RBP-jk and EBF1 Chromosome Occupancy induced by viral co-activator EBNA2 [expression array]

status: Public on Dec 16 2015

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Gene expression programs depend on sequence-specific DNA binding transcription factors, but the mechanisms that control the selective binding of these factors in a chromosomal and genomic context remain enigmatic.   Here, we show that two master regulators of B-cell fate, namely EBF1 and RBP-jk, show variable genome-wide chromosome distribution in two related B-lymphocyte lines carrying different forms of Epstein-Barr Virus (EBV) latency.  The latency-type specific EBV-encoded EBNA2 colocalized with RBP-jk and EBF1 at induced binding sites.  Colocalization of EBF1, RBP-jk, and EBNA2 correlated with transcriptional activation.  Conditional expression or repression of EBNA2 lead to a rapid alteration in RBP-jk and EBF1 binding.  Biochemical and shRNA depletion studies provide evidence for cooperative assembly at co-occupied sites.  These findings reveal that non-DNA binding cofactors can facilitate combinatorial interactions to induce new patterns of transcription factor occupancy and gene programming

overall_design: Examination of EBNA2/EBF1/EBP-jk binding and gene expression differences in MutuI and LCL cell lines

first: Paul

last: Lieberman

first: Fang

last: Lu


title: Endothelin-1 supports clonal derivation and expansion of cardiovascular progenitors derived from human embryonic stem cells

status: Public on Dec 15 2015

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

summary: Coronary arteriogenesis is a central step in cardiogenesis, requiring coordinated generation and integration of endothelial (EC) and vascular smooth muscle cells (SM). At present, it is unclear whether the cell fate program of cardiac progenitors to generate complex muscular or vascular structures is entirely cell autonomous. Here we demonstrate the intrinsic ability of vascular progenitors to develop and self-organize into cardiac tissues by clonally isolating and expanding second heart field (SHF) cardiovascular progenitors (CVPs) using WNT3A and Endothelin-1 (EDN1) human recombinant proteins. Progenitor clones undergo long-term expansion and differentiate primarily into endothelial and smooth muscle cell lineages in vitro, and contribute extensively to coronary-like vessels in vivo, forming a functional human-mouse chimeric circulatory system. Our study identifies EDN1 as a key factor towards the generation and clonal derivation of ISL1+ vascular intermediates, and demonstrates for the first time, the intrinsic cell-autonomous nature of these progenitors to differentiate and self-organize into functional vasculatures in vivo.

overall_design: The HumanHT-12 v4 BeadChip (Illumina) was used to analyse paracrine factors produced by sub-regions of the fetal heart, followed by pairing the paracrine factors present in these specific regions with corresponding receptors that are highly expressed in uncommitted cardiovascular progenitor cells.

first: Boon-Seng

last: Soh

first: Shi-Yan

last: Ng

first: Hao

last: Wu

first: Kristina

last: Buac

first: Christine

last: Park

first: Xiaojun

last: Lian

first: Jiejia

last: Xu

first: Kylie

last: Foo

first: Ulrika

last: Felldin

first: Xiaobing

last: He

first: Massimo

last: Nichane

first: Bu

last: Lei

first: Ronald

last: Li

first: Bing

last: Lim

first: Kenneth

middle: R

last: Chien


title: Active FOXO1 is a Key Determinant of Isoform-Specific Progesterone Receptor Transactivation and Senescence Programming

city: Minneapolis

first: Todd

middle: P

last: Knutson

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

summary:
The progesterone receptor specific gene targets were investigated in ovarian and breast cancer cell lines where FOXO1 was found to be a primary factor that cooperates with PR to activate cellular senescence genes (including p21) specifically in ovarian cells.

ABSTRACT:
Progesterone promotes differentiation coupled to proliferation and pro-survival in the breast, but inhibits estrogen-driven growth in the reproductive tract and ovaries. Herein, it is demonstrated, using progesterone receptor (PR) isoform-specific ovarian cancer model systems, that PR-A and PR-B promote distinct gene expression profiles that differ from PR-driven genes in breast cancer cells. In ovarian cancer models, PR-A primarily regulates genes independently of progestin, while PR-B is the dominant ligand-dependent isoform. Notably, FOXO1 and the PR/FOXO1 target-gene p21 (CDKN1A) are repressed by PR-A, but induced by PR-B. In the presence of progestin, PR-B, but not PR-A, robustly induced cellular senescence via FOXO1-dependent induction of p21 and p15 (CDKN2B). Chromatin immunoprecipitation (ChIP) assays performed on PR-isoform specific cells demonstrated that while each isoform is recruited to the same PRE-containing region of the p21 promoter in response to progestin, only PR-B elicits active chromatin marks. Overexpression of constitutively active FOXO1 in PR-A-expressing cells conferred robust ligand-dependent upregulation of the PR-B target genes GZMA, IGFBP1, and p21, and induced cellular senescence. In the presence of endogenous active FOXO1, PR-A was phosphorylated on Ser294 and transactivated PR-B at PR-B target genes; these events were blocked by the FOXO1 inhibitor (AS1842856). PR isoform-specific regulation of the FOXO1/p21 axis recapitulated in human primary ovarian tumor explants treated with progestin; loss of progestin sensitivity correlated with high AKT activity.
IMPLICATIONS:
This study indicates FOXO1 as a critical component for progesterone signaling to promote cellular senescence and reveals a novel mechanism for transcription factor control of hormone sensitivity.

overall_design: The study contains 6 different sample groups measured in triplicate, for a total of 18 individual samples (18 arrays). From parental ES-2 human ovarian cancer cell lines, we created three stable clones expressing either (1) an empty vector pIRES-neo3, or (2) the wild type progesterone receptor isoform A (pIRES-neo3-PR-A), or (3) the wild type progesterone receptor isoform B (pIRES-neo3-PR-B). These three cell lines were treated with either (1) vehicle control (ethanol) or (2) R5020 10e-8 M for 24 hours before total RNA harvest. Thus, the experiment contains three cell lines and two treatments (6 sample groups), treated and analyzed in triplicate (18 microarrays). Standard Illumina HumanHT-12 V4.0 chip controls were used during hybridization.

first: Caroline

last: Diep

first: Carol

last: Lange


title: Isolation and characterization of Renal Cancer Stem Cells (RCSCs) obtained from clear cell renal cell carcinoma (cc-RCC)

city: Bari

first: Fabio

last: Sallustio

state: Bari

address: Piazza G. Cesare N°11

country: Italy

institute: University of Bari

summary:
Purpose: The aim of the present study was to identify and characterize in tissue samples of clear cell-renal cell carcinoma (ccRCC) a population of CD133+/CD24+ cancer cells (RCC-derived cells-RDCs) and to study the differences with their nonneoplastic counterpart, tubular Adult Renal Progenitor Cells (ARPCs).

Materials and methods: CD133+/CD24+ RDCs were isolated from 40 patients. The mesenchymal phenotype and stemness proteomic profile of these RDCs were characterized. The colony-forming efficiency and self-renewal ability were tested with limiting dilution. The tumorigenic properties were evaluated in vitro with Soft Agar Assay. The angiogenic response was evaluated in vivo with the chorioallantoic membrane angiogenic assay. Microarray analysis was performed on 6 tARPCs and 6 RDCs clones. Expression of membrane proteins was evaluated with flowcytometry and immunofluorescence staining.

Results: CD133+/CD24+ cells were isolated from normal and tumoral kidney tissue. FACS analysis showed that RDCs did not express the mesenchymal stem cell markers. We showed that CD133+/CD24+ tumor cells were more undifferentiated than tARPCs. RDCs were clonigenic and able to differentiate into adipocytes,  epithelial and osteogenic cells. RDCs were able to regenerate tumor cells in vitro and to induce angiogenesis in vivo. The gene expression profile identified CTR2 as a membrane marker for this neoplastic population.

Conclusions: Our results indicate the presence, in ccRCC, of a CD133+/CD24+/CTR2+ cancer cells population. These cells possess some stem cell-like features, including in vitro self-maintenance and differentiating capabilities, and are able to induce an angiogenic response in vivo.

overall_design: Study of gene expression profiling  of Renal Cancer Cells (RCSCs), tubular Adult Renal Progenitor Cells (tARPCs), Renal Proximal Tubular Cells (RPTEC) and Mesenchymal Stem Cells (MSC). To highlight the similarities and the differences with known renal stem populations and with terminally differentiated renal cells, for each patient, 6 subcultures of tubular ARPCs (tARPCs), 3 subcultures of the MSC and 3 subcultures of the RPTEC were included in the analysis.

first: Vanessa

last: Galleggiante

first: Monica

last: Rutigliano


title: Genome-wide analysis of miR-552-3p- and miR-608-mediated gene silencing in A549 lung cancer cells

city: Yongin

first: Young-Chul

last: Choi

state: Gyeonggi-do

address: 1 Seocheon-dong Giheung-gu

country: South Korea

institute: Kyung Hee University

summary: Analysis of changes in gene expression after transfection with miR-552-3p or miR-608 mimic in A549 cells

overall_design: Total RNA was obtained from  A549 cells transfected with miR-552-3p or miR-608 or negative control mimic, and gene expression  was compared using microarrays.

first: Kwanghee

last: Baek

first: Sena

last: Yoon


title: Transcriptomics and proteomics show selenium affects inflammation, cytoskeleton and cancer pathways in human rectal biopsies

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

institute: Newcastle University

summary: Transcriptomics and proteomics analyses were carried out on rectal mucosal biopsies from 22 healthy adults with either optimal (n=11, mean plasma Se =1.43μmol/l, s.e.m ±0.06) or sub-optimal (n=11, mean plasma Se = 0.86umol/l, s.e.m ± 0.01) plasma Se status. Plasma Se status was associated with altered expression of 254 genes implicated in cancer, immune function and inflammatory response, cell growth and proliferation, cellular movement and cell death; 69 out of 254 genes had their expression significantly correlated with Se status, including two selenoprotein genes (SEPW1 and SELK). Proteomics identified 26 proteins differentially expressed between the two Se groups, including cytoskeletal proteins and factors involved in immune and inflammatory response and cancer pathways. Results from proteomics and transcriptomics support each other and integration of the two datasets was consistent with a reduced inflammatory and immune responses and a cytoskeleton remodelling in the rectal mucosa of individuals with sub-optimal Se status.

overall_design: Gene expression profiling by Illumina BeadArray of rectal mucosal biopsies to show the effects of serum selenium concentration on gene expression. Comparison of samples from healthy adults with differing Selenium levels (optimal or sub-optimal, n=11)

first: Catherine

last: Meplan

first: Iam

middle: T

last: Johnson

first: Abigael

middle: C

last: Polley

first: David

last: Bradburn

first: Daniel

last: Commane

first: Ramesh

last: Arasaradnam

first: Francis

last: Mulholland

first: Anze

last: Zupanic

first: John

last: Mathers

last: Hesketh


first: Todd

last: Knutson

summary:
Progesterone promotes differentiation coupled to proliferation and pro-survival in the breast, but inhibits estrogen-driven growth in the reproductive tract and ovaries. Herein, it is demonstrated, using progesterone receptor (PR) isoform-specific ovarian cancer model systems, that PR-A and PR-B promote distinct gene expression profiles that differ from PR-driven genes in breast cancer cells. In ovarian cancer models, PR-A primarily regulates genes independently of progestin, while PR-B is the dominant ligand-dependent isoform. Notably, FOXO1 and the PR/FOXO1 target-gene p21 (CDKN1A) are repressed by PR-A, but induced by PR-B. In the presence of progestin, PR-B, but not PR-A, robustly induced cellular senescence via FOXO1-dependent induction of p21 and p15 (CDKN2B). Chromatin immunoprecipitation (ChIP) assays performed on PR-isoform specific cells demonstrated that while each isoform is recruited to the same PRE-containing region of the p21 promoter in response to progestin, only PR-B elicits active chromatin marks. Overexpression of constitutively active FOXO1 in PR-A-expressing cells conferred robust ligand-dependent upregulation of the PR-B target genes GZMA, IGFBP1, and p21, and induced cellular senescence. In the presence of endogenous active FOXO1, PR-A was phosphorylated on Ser294 and transactivated PR-B at PR-B target genes; these events were blocked by the FOXO1 inhibitor (AS1842856). PR isoform-specific regulation of the FOXO1/p21 axis recapitulated in human primary ovarian tumor explants treated with progestin; loss of progestin sensitivity correlated with high AKT activity.
IMPLICATIONS:
This study indicates FOXO1 as a critical component for progesterone signaling to promote cellular senescence and reveals a novel mechanism for transcription factor control of hormone sensitivity.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Identification of a mitochondrial defect gene signature reveals NUPR1 as a key regulator of liver cancer progression

city: Suwon

first: Hyun Goo

last: Woo

address: 164 Worldcup-ro Yeongtong-gu

institute: Ajou University School of Medicine

summary: Many cancer cells require more glycolytic adenosine triphosphate production due to a mitochondrial respiratory defect. However, the roles of mitochondrial defects in cancer development and progression remain unclear. To address the role of transcriptomic regulation by mitochondrial defects in liver cancer cells, we performed gene expression profiling for three different cell models of mitochondrial defects: cells with chemical respiratory inhibition (rotenone, thenoyltrifluoroacetone, antimycin A, and oligomycin), cells with mitochondrial DNA depletion (Rho0), and liver cancer cells harboring mitochondrial defects (SNU354 and SNU423). By comparing gene expression in the three models, we identified 10 common mitochondrial defect–related genes that may be responsible for retrograde signaling from cancer cell mitochondria to the intracellular transcriptome. The concomitant expression of the 10 common mitochondrial defect genes is significantly associated with poor prognostic outcomes in liver cancers, suggesting their functional and clinical relevance. Among the common mitochondrial defect genes, we found that nuclear protein 1 (NUPR1) is one of the key transcription regulators. Knockdown of NUPR1 suppressed liver cancer cell invasion, which was mediated in a Ca2+ signaling–dependent manner. In addition, by performing an NUPR1-centric network analysis and promoter binding assay, granulin was identified as a key downstream effector of NUPR1. We also report association of the NUPR1–granulin pathway with mitochondrial defect–derived glycolytic activation in human liver cancer. Conclusion: Mitochondrial respiratory defects and subsequent retrograde signaling, particularly the NUPR1–granulin pathway, play pivotal roles in liver cancer progression.

overall_design: 15 samples

first: H

middle: G

last: WOO


title: Effect of high glucose on gene expression in ASCs

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

institute: University of Oslo

summary: The object of this study was to investigate the effect of elevated glucose concentrations (15 and 25 mM glucose) on gene expression in undifferentiated and adipogenic differentiated ASCs.

overall_design:
Undifferentiated (proliferating) ASCs were cultured in medium containing 5, 15 or 25 mM  glucose, and were passaged regularly. RNA was collected at day 21.
Adipogenic differentiated cells were seeded confluent at D-2, added DMEM/F12 with 5, 15 or 25 mM glucose at day -1 and induced to differentiate with IBMX, Dexamethasone, Indomethacin and insulin at day 0. Cell culture media was changed every 3 days. RNA was collected at day 21.

first: Torunn

last: Rønningen

first: Jan

last: Moskaug


title: Regulation of gene expression by WAC/RNF20/RNF40 in HEK293A cells

city: London

first: Sharon

last: Tooze

state: London

address: 44 Lincoln's Inn Fields

institute: Francis Crick Institute / London Research Institute

summary: WAC is a known positive regulator of (macro)autophagy. WAC also forms a complex with RNF20/RNF40 to promote H2B monoubiquitination and hence to affect transcriptional regulation. This study addresses whether the WAC/RNF20/RNF40 complex regulates autophagy through effects on gene expression.

overall_design: WAC, RNF20 and RNF40 were knocked-down using pools of siRNAs in HEK293A cells. Each knockdown was in triplicate and the control was RISCfree siRNA. mRNA expression profiles were investigated using an Illumina HT12v4 Bead Array.

first: Justin

last: Joachim

first: Probir

last: Chakravarty


title: Non-classical CD4+CD49b+ regulatory T cells as a better alternative to conventional CD4+CD25+ T cells to dampen arthritis severity

status: Public on Dec 10 2015

city: MONTPELLIER

first: Paul

last: CHUCHANA

address: 80 rue Augustin Fliche

institute: CNRS

summary: Regulatory T (Treg) cells actively control pathological immune responses and immunotherapeutic strategies triggering an increase in the number and/or the function of endogenous Treg cells emerge as a promising therapeutic strategy in autoimmune diseases to restore tolerance. A remarkable heterogeneity in peripheral Treg cells has been evidenced and underscored the need to better characterize them and compare their suppressive function to determine which Treg subset will be optimally suitable for a given clinical situation.   We demonstrated that repetitive injections of immature dendritic cells (DC) expand FoxP3-negative CD49b+ Treg cells that display an effector memory phenotype. Transcriptome analysis of ex-vivo isolated Treg-expanded by DC injections contains multiple transcripts of the canonical Treg signature shared mainly by CD25+ but also by other Treg subphenotypes. We provided an in-depth characterization of the CD49b+ Treg cells phenotype underscoring their similarities with CD25+ Treg cells and highlighting some specific expression pattern for several markers including LAG3, KLRG1, CD103, ICOS, CTLA-4 and GZB. Comparison of their suppressive mechanism in vitro and in vivo with that of FoxP3-positive Treg cells provide evidence of their potent suppressive activity in vivo, partly dependent on IL-10 secretion. Altogether our results underscore the therapeutic potential of IL-10 secreting CD49b+ Treg cells in arthritis and strongly suggest that expression of several canonical markers and suppressive function could be FoxP3-independent

overall_design: All gene expression profiles were obtained from highly purified T cell populations sorted by flow cytometry. To reduce variability, cells from multiple mice were pooled for sorting, and two to three replicates were generated for all groups. RNA from 2.5-10 x 105 cells was amplified, labeled, and hybridized to Affymetrix M430v2 microarrays.

first: Rita

last: Vicente

first: Julie

last: Quentin

first: Anne-Laure

last: Mausset-Bonnefont

last: Chuchana

first: Delphine

last: Martire

first: Maïlys

last: Cren

first: Christian

last: Jorgensen

first: Pascale

last: Louis-Plence


title: Double-stranded microRNA mimics can induce length- and passenger strand-dependent effects in a cell type-specific manner (RNA 2015), Exp 1

status: Public on Dec 09 2015

city: Cambridge

first: Anna

last: Git

state: Cambs

address: Robinson Way

department: CRUK Cambridge Institute

institute: University of Cambridge

summary:
Experiment 1 - miR-155 and miR-199 Phenotype
miR-155 and miR-199 as 23mer miRNA mimics induced a double-stranded RNA response

overall_design: Cells were transfected with miR-155, miR-199 23 mers, negative control or nothing (empty); samples collected in triplicate

first: M

middle: A

last: Goldgraben

first: A


title: Double-stranded microRNA mimics can induce length- and passenger strand-dependent effects in a cell type-specific manner (RNA 2015), Exp 2

summary:
Experiment 2 - MiRNA mimics have a length and passenger strand specific effect
Wildtype and mutant variants of miR-155 and negative control miRNA mimics were transfected to address the phenotype

overall_design: Cells were transfected with mimics and samples were collected in duplicate (except 23mer miR-155 wild type mimic and 23mer negative control mimic)


title: Double-stranded microRNA mimics can induce length- and passenger strand-dependent effects in a cell type-specific manner (RNA 2015)

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


title: Expression data on human MO-to-DC and MO-to-MAC differentiation

status: Public on Dec 12 2015

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

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

country: Spain

institute: Josep Carreras Research Institute (IJC)

summary:
Comparison of the RNA expression profiles of CD14+ monocytes from human peripheral blood with derived dendritic cells (DCs) and macrophages (MACs) obtained by exposure with GM-CSF/IL-4 and GM-CSF, respectively, and with mature DCs and MACs after lipopolysaccharide (LPS) exposure
The expression profiles of RNA of human CD14+ monocytes were compared with derived immature dendritic cells (iDCs) and macrophages (iMACs) following GM-CSF/IL-4  and GM-CSF incubation, and then activation/maturation with lypopolysaccharyde (LPS) using the Affymetrix PrimeView Human Gene Expression array (Affymetrix, Santa Clara, CA). This platform allows the interrogation of >36,000 transcrits and variants per sample. The samples were hybridized in the array following the manufacturer’s instructions.

overall_design: Total RNA isolated by standard procedures from CD14+ cells (total monocytes, MOs) corresponding to three sets of samples of monocytes (MOs), derived immature DCs and MACs (iDCS and iMACS) and activated/mature DCs and MACs following incubation with LPS (mDCS and mMACs)

first: Roser

last: Vento-Tormo

first: Carlos

last: Company

first: Javier

last: Rodríguez-Ubreva

first: Lorenzo

last: de la Rica

first: Jose

last: Urquiza

first: Biola

last: Javierre

first: Radhakrishnan

last: Sabarinathan

first: Ana

last: Luque

first: Manel

last: Esteller

first: Josep

last: Aran

first: Damiana

last: Álvarez-Errico


title: Molecular patterns of diffuse and nodular parathyroid hyperplasia in long-term hemodialysis

city: Praha 4

first: Petra

last: Hruba

address: Videnska 1958

department: Transplant Laboratory

country: Czech Republic

institute: Institute for Clinical and Experimental Medicine

summary: Secondary hyperparathyroidism is well known complication manifested in end-stage renal disease (ESRD). Both nodular and diffuse parathyreoid hyperplasia occur in ESRD patients. Distinct molecular mechanisms involved in parathyreoid hyperplasia remain poorly understood. Microarray screening proved homogeneity of gene transcripts in hemodialysis patients as compared to transplant cohort and primary hyperparathyreoidism, therefore further studies were performed in hemodialysis patints only. Enrichment analysis conducted on 485 differentially expressed genes between nodular and diffuse parathyreoid hyperplasia revealed highly significant differences in GO terms and KEGG database in ribosome structure (p=3.70-18). Next, RT-qPCR validation of microarray analysis proved higher expression of RAN guanine nucleotide release factor (RANGRF, p<0.001), calcyclin binding protein (CACYBP, p<0.05) and exocyst complex component 8 (EXOC8, p<0.05) and lower expression of peptidylprolyl cis/trans isomerase, NIMA-interacting 1 (PIN1, p<0.01) mRNA in nodular hyperplasia. Multivariate analysis revealed RANGRF and PIN1 expression along with parathyroid weight to be associated with nodular hyperplasia. Higher expression of genes associated with ribosomal structure and function underline extended translation mechanisms involved in parathyreoid nodular formation in long-term hemodialysis treated patients.

overall_design: Parathyroid tissue obtained from ESRD hyperparathyroidism patients who had undergone parathyroidectomy were used for transcriptome screening (Illumina HumanHT-12 v4.0 Expression BeadChips) and subsequently for discriminatory gene analysis, pathway mapping and gene-annotation enrichment analyses. Results were verified on enlarged group of hemodialysis patients with nodular (n=20) and diffuse (n=20) hyperplasia using RT-qPCR method.

first: Irena

last: Týcová

first: Sylvie

last: Dusilová Sulková

first: Zdeněk

last: Krejčík

first: Viktor

last: Stránecký

first: Eva

last: Girmanová

last: Hrubá

first: Marek

last: Černoch

first: Květoslav

last: Lipár

first: Tomáš

last: Marada

first: Jitka

last: Štěpánková

first: Ctibor

last: Povýšil

first: Ondřej

last: Viklický


title: Gene expression analysis of subcutaneous and omental adipose tissue from obese, insulin-resistant women

status: Public on Dec 07 2015

city: Roseworthy

first: Ruijie

last: Liu

state: South Australia

address: Mudla Wirra Rd

country: Australia

institute: the university of Adelaide

summary: The association between central obesity and insulin resistance reflects the properties of visceral adipose tissue. Our aim was to gain further insight into this association by analysing the lipid composition of subcutaneous and omental adipose tissue in obese women with and without insulin resistance. Subcutaneous and omental adipose tissue and serum were obtained from 29 obese nondiabetic women, 13 of whom were hyperinsulinemic. Histology, and lipid and gene profiling were performed. In omental adipose tissue of obese, insulin-resistant women, adipocyte hypertrophy and macrophage infiltration were accompanied by an increase in GM3 ganglioside and its synthesis enzyme ST3GAL5; in addition, phosphatidylethanolamine (PE) lipids were increased and their degradation enzyme, PEMT, decreased. ST3GAL5 was expressed predominantly in adipose stromovascular cells and PEMT in adipocytes. Insulin resistance was also associated with an increase in PE lipids in serum.

overall_design: Total RNA was isolated and up to 400 ng of total RNA per sample was labelled and hybridized to Illumina HumanHT-12_V4 expression BeadChip platform. Paired subcutaneous and omental samples from 6 women were analysed.


first: Todd

last: Knutson

overall_design: The study contains 6 different sample groups measured in triplicate, for a total of 18 individual samples (18 arrays). From parental T47D-Y human breast cancer cell lines (that is a naturally occurring PR-null variant of T47D cells), we created two stable clones expressing either (1) the wild type progesterone receptor isoform A (pSG5-PR-A), or (2) the wild type progesterone receptor isoform B (pSG5-PR-B). These three cell lines were treated with either (1) vehicle control (ethanol) or (2) R5020 10e-8 M for 24 hours before total RNA harvest. Thus, the experiment contains three cell lines and two treatments (6 sample groups), treated and analyzed in triplicate (18 microarrays). Standard Illumina HumanHT-12 V4.0 chip controls were used during hybridization.

first: Caroline

middle: H

last: Diep

first: Carol

last: Lange


title: Impact of Glucocorticoids and PI3K Inhibition on Gene Expression in Myeloma

city: Chicago

first: Nancy

last: Krett

state: IL

address: 840 South Wood Street, 740 CSB

department: Medicine

institute: University of Illinois Chicago

summary: We previously noted that combination glucocorticoids and PI3K inhibition induces synergistic cell death.  To identify genes involved in myeloma cell death we examined mRNA expression in each individual treatment and in the combination.  The glucocoriticoid resistant cells (MM.1RL) are used as a negative control.  Gene expression is assessed using Illumina Human HT-12v4 bead chips

overall_design:
For this experiment, the lab is using human multiple myeloma cell lines that were isolated from a patient.  MM.1S cells display sensitivity to glucocorticoids.  MM.1RL cells display resistance to glucocorticoid treatment due to spontaneous mutations that render the glucocorticoid receptor inoperable.
In this experiment, there will be 4 conditions for the MM.1S cells, and 2 conditions for the MM.1RL cells.  We will be treating the MM.1S cells with a glucocorticoid alone (Dexamethasone - 1 uM), a PI3K inhibitor alone (LY249002 - 25 uM), a combination of the two drugs, and a vehicle control.  The MM.1RL cells will be treated with a PI3K inhibitor alone, and with a vehicle control.  Since the PI3K inhibitor is diluted in DMSO, as a control an equal volume of DMSO will be added to all conditions not containing the PI3K inhibitor.  Conditions within the MM.1S cell line will be compared with each other.  Specifically, we hope to identify genes that are similarly affected by all three experimental conditions. The MM.1RL conditions will not be analyzed at this time.
There will be 4 biological replicates of each condition.

first: Steven

last: Rosen

first: Alexandra

last: Thomas

first: Cristian

last: Coarfa

first: Preethi

last: Gunaratne

first: Kimal

last: Rajapakshe


title: Expression profiling of NM1 KO and WT mice

status: Public on Dec 05 2015

city: Prague

first: Tomas

last: Venit

address: Videnska 1084

department: Depertment of Biology of the cell Nucleus

institute: Institute of Molecular Genetics

summary: Plasma membrane tension is an important feature that determines the cell shape and influences processes such as cell motility, spreading, endocytosis and exocytosis. Unconventional class 1 myosins are potent regulators of plasma membrane tension because they physically link the plasma membrane with the adjacent cytoskeleton. We identified nuclear myosin 1 (NM1) - a putative nuclear isoform of myosin 1c (Myo1c) - as a new player in the field. Although having specific nuclear function, we show that NM1 localizes preferentially to the plasma membrane. Deletion of NM1 causes more than 50% increase in the elasticity of the plasma membrane around the actin cytoskeleton as measured by atomic force microscopy. This higher elasticity of NM1 knock-out cells leads to 25% higher resistance to short-term hypotonic environment and rapid cell swelling. In contrary, overexpression of NM1 in WT cells leads to additional 30% reduction of their survival. We have brought evidence that NM1 has a direct functional role in the cytoplasm as a dynamic linker between the cell membrane and the underlying cytoskeleton, regulating the degree of effective plasma membrane tension.

overall_design: We used tissues from NM1 WT and KO mice with highest expression of NM1, lungs and heart (3 replicates each) and skin fibroblast derived from each mice (2 replicates each)


title: Gene microarray of sorted Vg9Vd2 subsets

status: Public on Dec 01 2015

first: Paul

middle: Leo

last: Ryan

address: 4 Newark Street

department: Centre for Immunobiology

institute: Queen MAry University of London

summary: Analysis of gene expression at RNA level by 4 different cell sorted Vg9Vd2 subsets (Subset 1=CD28+CD27+, Subset2=CD28-CD27+, Subset 3=CD28-CD7-CD16-, Subset 4 = CD28-CD27-CD16+). Results highlight differences in RNA expression characterising these four cell populations into distinct phenotypic subsets with distinct functional potential

overall_design: RNA was extracted from cell sorted fresh peripheral blood Vg9Vd2 T cell subsets (Subset 1=CD28+CD27+, Subset 2=CD28-CD27+, Subset 3=CD28-CD7-CD16-, Subset 4 = CD28-CD27-CD16+). Subsequently cDNA was made from RNA and finally converted to cRNA prior to array hybrdisation

middle: L

first: Christopher

middle: J

last: Holland

first: Nital

last: Sumaria

first: Natalia

last: Izotova

first: Capucine

last: Grandjean

first: Lesley

last: Bergmeier

first: Daniel

last: Pennington


title: Integrated analysis of genome-wide DNA methylation and gene expression profiles identifies potential novel biomarkers of rectal cancer [expression]

status: Public on Dec 02 2015

city: Harbin

first: Jiufeng

last: Wei

address: Yiyuan street

country: China

institute: the Fourth Affiliated Hospital of Harbin Medical University

summary: DNA methylation was suggested as the promising biomarker for rectal cancer diagnosis. However, it remains a great challenge to search for the optimal methylation biomarkers to obtain ideal diagnostic performance. We aimed to identify new molecular markers for rectal cancer by evaluating their epigenomic and transcriptomic profiles. Genome-wide methylation analysis revealed 18568 probes with significant methylation differences between the six rectal cancer and paired normal samples. Transcriptome profiling presented 773 low-expressed and 1,161 over-expressed genes. After merging the DNA methylation with gene expression data, we identified a panel of 36 genes with an inverse correlation between methylation and gene expression levels. A genome-wide DNA methylation approach merged with array-based gene expression profiles allowed identifying a number of novel, epigenetically regulated candidate tumor-related genes in rectal carcinogenesis, which can be a good strategy to discover optimal DNA methylation diagnostic panels.

overall_design:
Genome wide gene expression profiling of paired rectal cancers and adjacent normal tissues. The Illumina HumanHT-12 V4.0 expression beadchip was used to obtain gene expression profiles  in all samples. Samples included six pairs of rectal cancers and adjacent normal tissues.
Total RNA obtained from rectal cancers and paired adjacent normal tissues.

first: Ming

last: Liu


title: Effect of polymeric formula on inflammation in intestinal epithelial cells

status: Public on Dec 04 2015

city: Sydney

first: Susan

last: Corley

state: NSW

address: D26, Kensignton Campus

department: Biotechnology & Biomolecular Sciences

institute: UNSW

summary: Microarray analysis of HT-29 cells co-cultured with tumor necrosis factor (TNF-a) in the presence or absence of polymeric formula as used for Exclusive Enteral Nutrition (EEN) therapy. Results provide insights into the molecular mechanisms underlying the anti-inflammatory effect of polymeric formula on intestinal epithelium.

overall_design: Total RNA obtained from 9 samples of HT-29 cells. Six samples were treated with TNF-a in the presence (3 samples) or absence (3 samples) of Polymeric Formula. Three samples were untreated and used as a control.

last: Leach

first: Lily

last: Nahidi

first: Alhagamhmad

last: Moftah

first: Marc

last: Wilkins


title: Host transcriptomic analysis of THP-1 infected with Mtb and MtbΔwhiB3

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

summary: To study the role of WhiB3 in regulating host transcriptome, THP-1 were activated with PMA and infected with Mtb and MtbΔwhiB3, host transcriptome was studied.

overall_design: Total RNA was isolated from THP-1 infected with Mtb and MtbΔwhiB3 and total RNA wa isolated at 0 h, 12 h, 24 h and 48 h.

first: Mansi

last: Mehta

first: Amit

last: Singh


title: Gene Expression Changes in Definitive Endoderm in response to FGF Signaling

city: Milwaukee

first: Kirk

last: Twaroski

state: WI

address: 8701 W Watertown Plank Rd

department: CBNA

institute: Medical College of Wisconsin

summary:
FGF Signaling is required for hepatic progenitor cell formation from endoderm.  The mechanism of this process is poorly understood
We used microarrays to identify genes directly regulated by FGF signaling in definitive endoderm that may be involved in hepatic specification.

overall_design: Definitive endoderm cells were treated with BMP4 and FGF2 to induce hepatic progenitor cell formation.  We identified genes changed after 2 hours of BMP/FGF compared to endoderm.  Using FGFR inhibitors, we identified which of these genes are regulated by FGF signaling after 2 hours.  Finally we used the translation inhibitor cycloheximide to identify genes directly regulated by FGF signaling in definitive endoderm

first: Stephen

last: Duncan


title: Establishment of Afatinib-Resistant Non-Small Cell Lung Cancer Cells Derived from Tumor Xenograft Model [No treatment]

city: Zhunan Miaoli County

first: Cheng Ta

last: Chung

address: 35, Keyan Rd.

department: Institute of Biotechnology and Pharmaceutical Research

country: Taiwan

institute: National Health Research Institutes

summary: This experiment aimed to indentify signifcant expression genes in afatinib-resistant HCC827 cell lines. The nude mice bearing subcutaneous tumors were administerd with afatinib at different intensities and dosages (5–100 mg/kg). Finally, well-growing tumors were harvested and dissocciated by 450 units/ml collagenase IV and maintained in culture dishs. All the gene expression profiles of resistant cell lines were comapared to parental HCC827 cell.

overall_design: When cell lines isolated from xenograft tumors grew at 70% confluence, total RNA was isolated by using Qiagen RNEasy mini kit. The RNA integrity and QC reports were carried out based on manufacturer's manual. Labeled cRNA was hybridized to Illumina Human HT-12 Beadchips v4. Data were analysed by GeneSpring GX software (Agilent Techologies).

first: Cheng-Ta

first: Chiung-Tong

last: Chen

first: Chia-Huei

last: Lee


title: Establishment of Afatinib-Resistant Non-Small Cell Lung Cancer Cells Derived from Tumor Xenograft Model [Afatinib treatment]

summary: This experiment aimed to indentify signifcant expression genes in afatinib-resistant HCC827 cell lines under different treatment conditions. All the expression profiles of BR16-1 and BR16-2 cells were comapared to parental HCC827 cells.

overall_design: When cell lines isolated from tumors grew at 70% confluence, these cells were treated with afatinib at 0, 10 ,100, and 1000 nM. After 48hr, total RNA was isolated by using Qiagen RNEasy mini kit. The RNA integrity and QC reports were carried based on manufacturer's manual. Labeled cRNA was hybridized to Illumina Human HT-12 Beadchips v4. Data were analysed by GeneSpring GX software (Agilent Techologies).


title: Establishment of Afatinib-Resistant Non-Small Cell Lung Cancer Cells Derived from Tumor Xenograft Model

overall_design: Refer to individual Series


title: Gene expression analysis of uveal melanoma Class 1 tumors with and without metastasis

status: Public on Nov 30 2015

city: Miami

first: Matthew

middle: G.

last: Field

state: FL

address: 1501 NW 10th Avenue

country: USA

institute: University of Miami

summary:
Uveal melanoma can be classified by gene expression profiling (GEP) into Class 1 (low metastatic risk) and Class 2 (high metastatic risk), the latter being strongly associated with mutational inactivation of the tumor suppressor BAP1.
Nevertheless, a small percentage of Class 1 tumors give rise to metastatic disease, and the purpose of this study was to identify biomarkers of metastasis in Class 1 tumors.

overall_design: Total RNA was obtained from tumor samples that were collected at the time of enucleation


title: Impact of pre-analytical handling on neuroblastoma cells mRNA gene expression

city: Vienna

first: Maximilian

last: Kauer

address: Zimmermannplatz 10

department: Molecular Biology

country: Austria

institute: CCRI, St.Anna Children Cancer Research Institute

summary: Gene expression analyses of disseminated tumor cells can provide indispensable biological and clinical information at diagnosis, during therapy and at relapse. So far, however, disseminated tumor cells expression analyses have been hampered by insufficient infiltration rates and/or unclear consequences of transport duration, temperature and other pre-handling procedures. This study, using neuroblastoma as a model, focuses on the influences of pre-analytical procedures like tumor cell enrichment, transport time and temperature on the disseminated tumor cells expression profile.

overall_design:
Gene expression of one neuroblastoma cell line (LAN-1) was analyzed for three different conditions in triplicate  (=9 samples)
Analysis of the impact of freezing/thawing on the gene expression of neuroblastoma cells

first: Fikret

last: Rifatbegovic

first: Reza

last: Abbasi

first: Andreas

last: Weinhäusel

first: Sabine

last: Taschner-Mandl

first: Peter

middle: F

last: Ambros


title: Gene expression signature after γklotho knockdown in HCC1395 triple negative breast cancer cells

city: Ljubljana

first: Nusa

last: Trost

address: Vrazov trg 2

country: Slovenia

institute: Institute of Biochemistry

summary:
γKlotho is critical for the survival of triple negative breast cancer (TNBC) cells HCC1395, since its depletion leads to decreased cell viability, cell cycle arrest and apoptosis.
Here, we compare γKlotho knockdown cells with control HCC1395 cells at gene expression level in order to get insight into the possible cellular mechanisms contributing to the sensitivity of TNBC cells to γKlotho depletion.

overall_design: HCC1395 cells were transfected with control siRNA (siRevL1) or a pool of siRNAs targeting γKlotho and 48 h later RNA was extracted for microarray expression analysis.  Two biolgical replicates  for each siRNA-transfection were used.

first: Elisabeth

middle: D

last: Martinez

first: Klementina

last: Fon Tacer

first: Nuša

last: Trošt


title: The gene expression changes by CID 70698683

status: Public on Nov 25 2015

city: Louisville

first: Donghoon

state: Kentucky

address: 505 Hancock Street S

department: Microbiology and Immunology

institute: UNIVERSITY OF LOUSIVILLE

summary: CID 70698683 is a novel broad-spectrum antiviral compound. To understand the broad-spectrum antiviral mechanism, the cellular gene expression changes by the treatment of CID70698683 was measured.

overall_design: HEp-2 cells grown in 6-well plates were treated with 5 microM of CID 70698683 for overnight and the cellular RNA was extracted (Treatment group). For control, DMSO was used instead of CID 70698683 (final concentration of 0.25%). Three replicates per group used.

first: Jennifer

last: Golden


title: Gene exrpression profiling of childhood adrenocortical tumors

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary: Pediatric adrenocortical tumors (ACT) are rare and often fatal malignancies; little is known regarding their etiology and biology. To provide additional insight into the nature of ACT, we determined the gene expression profiles of 24 pediatric tumors (five adenomas, 18 carcinomas, and one undetermined) and seven normal adrenal glands. Distinct patterns of gene expression, validated by quantitative real-time PCR and Western blot analysis, were identified that distinguish normal adrenal cortex from tumor. Differences in gene expression were also identified between adrenocortical adenomas and carcinomas. In addition, pediatric adrenocortical carcinomas were found to share similar patterns of gene expression when compared with those published for adult ACT. This study represents the first microarray analysis of childhood ACT. Our findings lay the groundwork for establishing gene expression profiles that may aid in the diagnosis and prognosis of pediatric ACT, and in the identification of signaling pathways that contribute to this disease.

overall_design: We used microarrays to explore the expression profiles differentially expressed in childhood adrenocortical tumors and in normal adrenal gland tissues. Pediatric adrenocortical adenoma and carcinoma patients were enrolled on the International Pediatric Adrenocortical Tumor Registry (IPACTR) and Bank protocol. Tumor specimens were harvested during surgery and snap frozen in liquid nitrogen to preserve tissue integrity. Data have been compiled for eight males and 15 females between 0 and 16 years of age. Table 1 (West et al, Cancer Research 67:601-608, 2007) summarizes the primary clinical information for each subject (excluding sample Unk1 with ACT of undetermined histology), including stage of the disease, tumor class, sex, age, relapse-free survival, and overall survival.

first: Alina

middle: N

last: West

first: Bonald

last: Figueredo

first: Raul

last: Ribeiro

first: Gerard

last: Zambetti


title: Gene expression in glioblastoma (GBM) tissues, glioblastoma stem-like cell (GSC) cultures and neural foetal cell line (NFC)

status: Public on Nov 26 2015

city: Oslo

first: Biljana

last: Stangeland

address: Sognsvannsveien 20

department: Institute of Surgical Research

country: Norway

institute: Oslo University Hospital

summary: This microarray contains expression data for two GBM tissue samples, four GSC cultures grown as spheres and one NFC culture grown as spheres

overall_design: Total RNA was isolated from GSC cultures and GBM tissues


title: Genome-wide analysis of fatty acid synthase (FASN) gene silenced retinoblastoma cancer cells (WERI RB1) using cDNA microarray analysis

first: madavan

last: vasudevan

summary: Fatty acid synthase is a major enzyme involved in de novo lipogenesis and associated with tumor invasion and poor prognosis. The effect of fatty acid synthase knockdown in retinoblastoma cancer cells (WERI RB1) using siRNA mediated gene silencing were accessed for global gene deregulations. The analysis resulted in RB cancer cell death through deregulations of various cell signalling, metabolic, immunity, angiogenesis, apoptosis and cell cycle pathway related genes. Further validations were done using qRT-PCR and western analysis. Our results provide evidence that blockade in lipid metabolism inturn lead to RB cancer cell death through impaired cell signalling pathway.

overall_design: Total RNA was extracted from the WERI RB1 cells transfected with FASN siRNA at 48h, along with its untransfected control cells. cDNA converted samples were run on microarray platform- Illumina’s HumanHT-12_V4_0_R2 BeadChips

first: M

last: Sangeetha

first: P

last: Deepa

first: S

last: Krishnakumar


title: Discovery of immediate YAP target genes with inducible form of YAP

status: Public on Nov 23 2015

city: Cambridge

first: Tackhoon

last: Kim

state: Massachusetts

address: 500 Technology Square, NE47-221

institute: MIT

summary: Microarray analyses with cells/tissues overexpressing YAP have revealed many transcription targets of YAP (Dong et al, 2007; Zhao et al, 2008). However, as YAP induces transformation of non-cancerous cells, we thought many of known targets of YAP may be indirect consequence of transforming property of YAP. To identify the immediate transcription targets for YAP, we utilized immortalized mammary epithelial MCF-10A cells expressing a tamoxifen inducible, hyperactive (S127/381A) YAP mutant (MCF-10A ERT2-YAP 2SA).

overall_design: MCF-10A ERT2 and MCF-10A ERT2-YAP 2SA are generated. Each cell line was treated with 0.1% of ethanol (solvent) or 1uM of 4-hydroxytamoxifen for 2 or 6 hours. This makes 6 samples per set. The experiments were done in duplicate. The expression data from MCF-10A ERT2 and MCF-10A ERT2-YAP 2SA before tamoxifen treatment can serve as control.

first: Sukjin

last: Yang

first: Minchul

first: Jaebum

last: Ahn

first: Seon-Young

first: Dae-Sik

last: Lim


title: Knockdown of NAT12/NAA30 decreases glioblastoma stem cell growth and tumorigenicity by regulating hypoxia response, p-MTOR (Ser2448) and p53 pathway

summary: Gene knockdown of NAT12/NAA30 led to decreased proliferation, sphere forming ability and mitochondrial hypoxia tolerance in the GSC T65 culture. Intracranial transplantation of these cells into SCID mice showed that the decreased NAT12/NAA30 expression correlated with the prolonged animal survival and reduced tumor size

overall_design: Total RNA isolated from GSC cultures featuring NAT12/NAA30 gene knock-down (shRNA) was compared to total RNA from non-silencing control GSC cultures (NS-shRNA).


title: Expression data of Ell3 overexpressing MCF7 cell line

city: Seongnam-si

first: Kwang-Soo

address: 335, Pangyo-ro, Bundang-gu

institute: CHA Univ.

summary:
Ell3 is a RNA polymerase II transcription elongation factor that is enriched in testis. The C-terminal domain of Ell3 shows strong similarities to that of Ell (eleven-nineteen lysine-rich leukemia gene), which acts as a negative regulator of p53 and regulates cell proliferation and survival. Recent studies in our laboratory showed that Ell3 induces the differentiation of mouse embryonic stem cells by protecting differentiating cells from apoptosis via the promotion of p53 degradation. In this study, we evaluated the function of Ell3 in breast cancer cell lines. MCF7 cell lines overexpressing Ell3 were used to examine cell proliferation and cancer stem cell properties. Ectopic expression of Ell3 in breast cancer cell lines induces proliferation and 5-FU resistance. In addition, Ell3 expression increases the cancer stem cell population, which is characterized by CD44 (+) or ALDH1 (+) cells. Mammosphere-forming potential and migration ability were also increased upon Ell3 expression in breast cancer cell lines. Through biochemical and molecular biological analyses, we showed that Ell3 regulates proliferation, cancer stem cell properties and drug resistance in breast cancer cell lines partly through the MEK-extracellular signal-regulated kinase signaling pathway. Murine xenograft experiments showed that Ell3 expression promotes tumorigenesis in vivo.
The transcription elongation factor Ell3 induces chemosensitization of MCF7 cells to the chemotherapeutic agent cis-diamminedichloroplatinum (II) (CDDP) by stabilizing p53. Interestingly, Ell3 induced p53 stabilization in response to CDDP by promoting binding of p53 to NADH quinoneoxidoreductase 1 (NQO1), which is linked to an ubiquitin-independent degradation pathway, as well as by suppressing a MDM2 mediated ubiquitin-dependent degradation pathway. Furthermore, Ell3 enhanced interleukin-20 (IL-20) expression leading to the activation of the ERK1/2 signaling pathway. By analyzing the suppressive effects of IL-20 and ERK signaling in the Ell3 expressing MCF7 cells, we confirmed that the IL-20 mediated ERK1/2 signaling pathway is the main cause of p53 stabilization after CDDP exposure in MCF7 cells.

overall_design: Ell3-overexpressing breast cancer cell lines were established using the chromosomal integration of an Ell3 expression plasmid, which was constructed by cloning PCR-amplified Ell3 cDNA into pcDNA3.1 vectors (Invitrogen, Carlsbad, CA; https://www.lifetechnologies.com). Three independent Ell3 overexpressing cell lines were generated. The gene expression profiles of wild type MCF7 and Ell3 overexpressing cell line were compared using Affymetrix PrimeView arrays.

first: Kyung-Soon

last: Park


title: Knockout PTTG1 HCT116 cells

city: Los Angeles

first: Yunguang

last: Tong

state: CA

address: 8700 Beverly BLVD

institute: Cedars-Sinai Medical Center

summary: To identify potential PTTG1-targeted genes, total RNA from PTTG1+/+ and PTTG1-/- HCT 116 cells was isolated using the RNeasy Kit (Qiagen) and analyzed using Illumina microarrays (HumanHT-12_V4).  Raw data were processed according to the manufacturer’s standard procedure and further analyzed using Partek 6.5.

overall_design: PTTG1-/-  and parent HCT116 cells.  Experiment is performed in triplicate

first: H

last: Koeffler


title: Gene expression profiling of human colon cancer cell lines stimulated with dsDNA90

status: Public on Nov 21 2015

first: Tianli

last: Xia

address: 1550 NW 10th Ave

department: Sylvester Comprehensive Cancer Center

summary: Gene expression analysis of dsDNA90 stimulated human colon cancer cell lines. Genes whose expression that are affected by cytosolic DNA will be identified and compared between normal vs cancer colon epithelial cells.

overall_design: Human normal or colon cancer cells were transfected with dsDNA90 for 3 hours. Total RNA was extracted for array analysis.

first: Glen

last: Barber


title: GE/miRNA expression profile of Human Epicardial Adipose Tissue (EAT) and Subcutaneous Adipose Tissue (SAT) in Patients with Coronary Artery Disease (CAD) vs. Controls (CTRL) - PART 1 - Genes

status: Public on Nov 22 2015

city: Bari

first: Antonio

last: Moschetta

address: Via Orazio Flacco, 65

institute: IRCCS Ospedale Oncologico di Bari

summary: Gene expression profiles of Human EAT vs. SAT (CTRL & CAD). The aim of the present study was to assess a gene expression chart characterizing EAT vs. SAT, and CAD vs. CTRL. Results provide the information that EAT is characterized by a differential expression of different genes when compared to its reference tissue (SAT), and that EAT is characterized by specific gene expression changes in patients with CAD.

overall_design: RNA obtained from EAT & SAT of the same patients (paired samples). Comparisons: EAT vs. SAT (paired samples) & CAD vs. CTRL

first: Michele

last: Vacca

first: Andria

last: D'Orazio


title: Trascriptional profile of BRAF inhibitor-resistant SKMEL28 and WM3248 melanoma cells and changes upon YAP/TAZ siRNA knockdown

status: Public on Nov 18 2015

city: Daejeon

first: Min Hwan

address: KAIST 291 Daehak-ro, Yuseong-gu

department: Graduate School of Medical Science and Engineering

institute: KAIST

summary: The activation of transcriptional coactivators YAP and its paralog TAZ has been shown to promote resistance to anti-cancer therapies. YAP/TAZ activity is tightly coupled to actin cytoskeleton architecture. However, the influence of actin remodeling on cancer drug resistance remains largely unexplored. Here, we report a pivotal role of actin remodeling in YAP/TAZ-dependent BRAF inhibitor resistance in BRAF V600E mutant melanoma cells. Melanoma cells resistant to BRAF inhibitor PLX4032 exhibit an increase in actin stress fiber formation, which appears to promote the nuclear accumulation of YAP/TAZ. Knockdown of YAP/TAZ overcomes PLX4032 resistance, whereas overexpression of constitutively active YAP induces resistance. Moreover, inhibition of actin polymerization and cytoskeletal tension in melanoma cells suppresses both YAP/TAZ activation and PLX4032 resistance. Our siRNA library screening identifies actin dynamics regulator TESK1 as a novel vulnerable point of the YAP/TAZ-dependent resistance pathway. These results suggest that inhibition of actin remodeling is a promising synthetic lethal strategy to suppress resistance in BRAF inhibitor therapies.

overall_design: We compared expression profile of PLX4032 resistant SKMEL28 and WM3248 melanoma cells to parental cells (two biologic replicates each). We also compared expression profile changes from two biologic replicates of PLX4032-resistant SKMEL28 and WM3248 cells transfected with either control siRNA or YAP/TAZ siRNAs for 72 hrs

first: Min-Hwan

first: Jongshin

first: Hyowon

last: Hong

first: Si-Hyung

last: Lee

first: June-Koo

first: Eunji

last: Jung

first: Joon


title: Expression and function of NAT12/NAA30 in glioblastoma

first: Biljana

last: Stangeland

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


title: CC-122, a pleiotropic pathway modifier, mimics an interferon response and has antitumor activity in DLBCL

city: Summit

first: Anita

last: Gandhi

state: New Jersey

address: 86 Morris Avenue

department: Translational Development Ops

institute: Celgene Corporation

summary: Cereblon (CRBN), a substrate receptor of the E3 ubiquitin ligase complex CRL4CRBN, is the target of the immunomodulatory drugs lenalidomide and pomalidomide. Recently, it was demonstrated that binding of these drugs to CRBN promotes the ubiquitination and subsequent degradation of two common substrates, transcription factors Aiolos and Ikaros. Here we report that the pleiotropic pathway modifier CC-122, a new chemical entity termed pleiotropic pathway modifier binds CRBN and promotes degradation of Aiolos and Ikaros in diffuse large B-cell lymphoma (DLBCL) and T cells in vitro, in vivo and in patients, resulting in both cell autonomous as well as immunostimulatory effects. In DLBCL cell lines, CC-122-induced degradation or shRNA mediated knockdown of Aiolos and Ikaros correlates with increased transcription of interferon stimulated genes (ISGs) independent of interferon α, β, γ production and/or secretion and results in apoptosis in both ABC and GCB-DLBCL cell lines. Our results provide mechanistic insight into the cell of origin independent anti-lymphoma activity of CC-122, in contrast to the ABC subtype selective activity of lenalidomide.

overall_design: Microarray analysis of the OCI-LY10 activated B-cell diffuse large B-cell lymphoma (ABC-DLBCL) cell line treated with the compound CC-122 for 18 hours

first: Patrick

last: Hagner

first: Courtney

last: Havens

first: Celia

last: Fontanillo

first: Matthew

last: Trotter


title: Analysis of SOX2 overexpression in hESCs undergoing cardiac differentiation.

status: Public on Nov 13 2015

city: Münster

first: Boris

last: Greber

address: Von-Esmarch-Str. 54

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

summary: SOX2 downregulation is a pre-requisite for proper cardiac differentiation. This study was performed to reveal the neagtive effects of SOX2 on cardiac differentiation.

overall_design: Total RNA was isolated  in a time course manner, from differentiating in-vitro samples: (i) no doxycycline treated cells differentiated under standard cardiac differentiation conditions (II) 0.2ug/ml doxycycline treated cells differentiated under standard cardiac differentiation conditions

first: Rao

last: Jyoti

first: Greber

last: Boris


title: Genome-wide analysis of muscle gene expression in response to an intense cycling exercise. Effect of two protein-leucine enriched diets

city: Lausanne

first: Frederic

last: Raymond

address: Campus EPFL - Quartier de l'Innovation

department: Functional Genomics

country: Switzerland

institute: Nestle Institute of Health Sciences

summary: Protein-leucine supplement ingestion following strenuous endurance exercise accentuates skeletal-muscle protein synthesis and adaptive molecular responses, but the underlying transcriptome is uncharacterized. In a randomized single-blind triple-crossover design, 12 trained men completed 100 min of high-intensity cycling then ingested either 70/15/180/30g protein/leucine/carbohydrate/fat (15LEU), 23/5/180/30g (5LEU) or 0/0/274/30g (CON) beverages during the first 90 min of a 240-min recovery period. Vastus lateralis muscle samples (30 and 240-min post-exercise) underwent transcriptome analysis by microarray followed by bioinformatic analysis. Gene expression was regulated by Protein-leucine in a dose-dependent manner impacting the inflammatory response, muscle growth and development. At 30 min, 15LEU and 5LEU vs. CON activated transcriptome networks with geneset functions involving cell-cycle arrest (Z-score 2.0-2.7; P<0.01), leukocyte maturation (1.7; P=0.007), cell viability (2.4; P=0.005), promyogenic networks encompassing myocyte differentiation and myogenin (MYOD1, MYOG), and a proteinaceous extracellular matrix, adhesion, and development programme correlated with plasma lysine, arginine, tyrosine, taurine, glutamic acid, and asparagine concentrations. High protein-leucine dose (15LEU-5LEU) activated an IL1b-centered proinflammatory network and leukocyte migration, differentiation, and survival functions (2.0-2.6; <0.001). By 240 min, the protein-leucine transcriptome was anti-inflammatory and promyogenic (IL-6, NF-kβ, SMAD, STAT3 network inhibition), with overrepresented functions including decreased leukocyte migration and connective tissue development (-1.8-2.4; P<0.01), increased apoptosis of myeloid and muscle cells (2.2-3.0; P<0.002) and cell metabolism (2.0-2.4; P<0.01). The analysis suggests protein-leucine ingestion modulates inflammatory-myogenic regenerative processes during skeletal muscle recovery from endurance exercise. Further cellular and translational research is warranted to validate amino acid-mediated myeloid and myocellular mechanisms within skeletal-muscle functional plasticity.

overall_design: Total RNA obtained from isolated skeletal muscles

first: David

last: Rowlands

first: Andre

last: Nelson

first: Sylviane

last: Metairon

first: Robert

last: Mansourian

first: Jim

last: Clarke

first: Trent

last: Stellingwerff

first: Stuart

middle: M

last: Phillips


title: caArray_landi-00077: EAGLE Project

status: Public on Nov 24 2015

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

summary: The EAGLE (Environmental and Genetic Lung Cancer Etiology) gene expression study is case-control study of lung cancer conducted in Milan, Italy, designed to identify molecular alteration, particularly gene expression variation induced by smoking in lung carcinoma in this data set. The study is initiated by the Division of Cancer Epidemiology and Genetics (DCEG).

overall_design:
landi-00077
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HG-U133A
Organism: Homo sapiens (ncbitax)
Material Types: synthetic_DNA, synthetic_RNA, total_RNA

first: Wei

last: Lin

first: Maria

last: Landi


title: Analysis of SOX2 downregulation under self-renewal conditions.

summary: SXO2 is one of the factors involved in maintaining self-renewal and pluripotency in hESCs. This study was performed to reveal the effects of reduced SOX2 levels in self-renewing pluripotent hESCs.

overall_design: Total RNA was isolated from undifferentiated wildtype hESCs and SOX2 siRNA transfected hESCs after 48 hours of plating.


title: Analysis of early differentiation fates in human ES cells using diverse dosages of BMP and WNT signaling for the initial induction of differentiation

summary: Human ES cells were induced to differentiate by applying differenent concentrations of BMP4 and WNT (CHIR00921) for 24 hours. The resulting differences in global gene expression were then analyzed at 36 hours

overall_design: Total RNA isolated from differentiated in-vitro samples after two weeks of differentiation


title: Analysis of differentiation fates in human ES cells using diverse dosages of BMP and WNT signaling for the initial induction of differentiation

summary: Human ES cells were induced to differentiate using a directed cardiac induction protcol but varying the concentrations of BMP4 and WNT (CHIR00921) applied during the first 24 hours. The resulting differences in cell fate were then analyzed two weeks later.


title: Cardiac differentiation time-courses of human ES cells investigating the requirement for intermediate WNT inhibition

summary: Efficient directed cardiac induction of human embryonic stem cells requires an intermediate inhibition of WNT signaling, shortly after the initial induction of mesoderm. To reveal the significance of the WNT inhibition step during differentiation, two differential time-course analyses were performed - both comparing WNT-inhibited and non-WNT-inhibited samples: In the first time-course, the WNT inhibitor IWP-2 was either added or omitted on days 2 and 3, and in the second time-course, IWP-2 was either added or omitted on days 1 and 2.

overall_design: Total RNA isolated from differentiating in-vitro samples at the indicated time-points and of undifferentiated human ES cells before the induction of differentiation


title: Analysis of downstream effects of endogenous WNT signaling during cardiac differentiation of human ES cells

summary: WNT signaling inhibition at an intermediate stage of differentiation is a key requirement for cardiac induction of human ES cells, suggesting that endogenous WNT activity interferes with cardiomyocyte formation. Two downstream genes of endogenous WNT signaling, MSX1 and CDX2, were induced during cardiac differentiation to reveal whether they may account for the global negative effects played by endogenous WNT signaling in this process.

overall_design: Total RNA isolated from day 5 differentiating in-vitro samples: (i) Cells treated with a WNT inhibitor during differentiation to promote cardiac induction, (ii) cells not treated with the WNT inhibitor, (iii) cells treated with a WNT inhibitor and overexpressing MSX1 at the same time, and (iv) cells treated with a WNT inhibitor and overexpressing CDX2 at the same time


title: Near-whole-genome transcriptome analysis of gene expression in human skeletal muscle tissue at baseline in obese individuals with Type 2 Diabetes

status: Public on Nov 10 2015

city: Orlando

first: Lauren

middle: M.

last: Sparks

address: 301 E. Princeton St

department: Translational Research Institute for Metabolism and Diabetes

institute: FLORIDA HOSPITAL

summary: Analysis of gene expression associated with exercise response. The hypothesis tested was that individuals with Type 2 Diabetes that failed to demonstrate exercise-induced metabolic improvements would also reflect this lack of response in their skeletal muscle transcriptional profile at baseline. Of 186 genes identified by microarray analysis, 70% were upregulated in Responders and downregulated in Non-responders. Several genes involved in substrate metabolism and mitochondrial biogenesis differed significantly between the groups at baseline. This differential baseline gene expression indicated that Non-responders had blunted oxidative capacity.

overall_design: Total RNA extracted from baseline samples of skeletal muscle of obese individuals with Type 2 Diabetes who were characterized as either Responders or Non-responders was examined for differential expression of exercise response-assocated genes.

first: Natalie

last: Stephens

first: Hui

last: Xie

first: Neil

last: Johannsen

first: Timothy

last: Church

first: Steven

last: Smith