title: PMP22 Regulates Self-Renewal and Chemoresistance of Gastric Cancer Cells

status: Public on Feb 10 2017

city: Xiamen

first: Wangyu

last: Cai

address: 201-209 South Hubin Rd

department: Department of Gastrointestinal Surgery

country: China

institute: Zhongshan Hospital of Xiamen University

summary: Cancer stem cells (CSCs) possess self-renewal and chemoresistance activities. However, the manner in which these features are maintained remains obscure. We sought to identify cell surface protein(s) that mark self-renewing and chemoresistant gastric cancer cells using the Explorer Antibody Microarray. We identified PMP22, a target gene of the Wnt/β-catenin pathway, as the most upregulated cell surface protein in gastric cancer xenografts exposed to cisplatin (DDP). PMP22 expression was markedly upregulated in tumorspheric cells and declined with differentiation. Infecting gastric cancer cells with lentivirus expressing PMP22 shRNAs reduced proliferation, tumorsphere formation, and chemoresistance to cisplatin in vitro and in NOD/SCID mice. When combined with bortezomib, a PMP22 inhibitor, the chemotherapeutic sensitivity to cisplatin treatment was dramatically increased by inducing cell apoptosis in cultured cells and xenograft mouse models. Finally, mRNA expression levels of PMP22 were detected in 38 tumor specimens from patients who received 6 cycles of perioperative chemotherapy. A strong correlation between PMP22 level and tumor recurrence was revealed, thus showing a pivotal role of PMP22 in the clinical chemoresistance of gastric cancer. Our study is the first to show the role of PMP22 in gastric cancer stemness and chemoresistance and reveals a potential new target for the diagnosis and treatment of recurrent gastric cancer.

overall_design: To determine PMP22 downstream regulated genes in gastric cancer cells,the MGC-803 cells stable expressed PMP22 shRNA2 (n=3) and Control shRNA (n=3) were screened by microarray systems.

first: Gang

last: Chen

first: Qicong

last: Luo


title: Impact of Visceral Fat Adiposity on Gene Expression Profile in Peripheral Blood Cells

status: Public on Feb 08 2017

city: Suita

first: Norikazu

last: Maeda

state: Osaka

department: Graduate School of Medicine

country: Japan

institute: Osaka University

summary: We profiled gene expression in peripheral blood cells from 17 obese patients by microarray analysis and revealed that visceral fat adiposity impact on gene expression profile in peripheral blood cells compared to subcutaneous fat accumulation.

overall_design: Obesity was defined as body mass index (BMI) greater than 25 kg/m2 according to the Japanese criteria. Visceral fat area (VFA) and subcutaneous fat area (SFA) were measured by computed tomography (CT) and determined in the cross-sectional slice at the umbilical level. Subjects with type 1 diabetes mellitus, malignant diseases, autoimmune diseases, and infectious diseases were excluded. Patients treated with anti-diabetic drugs were also excluded.

first: Yoshinari

last: Obata

first: Seiji

last: Nakamura

first: Tohru

last: Funahashi

first: Ken-ichi

last: Matsubara

first: Yuji

last: Matsuzawa

first: Iichiro

last: Shimomura


title: Comparison of gene expression response to neutron and x-ray irradiation using mouse blood

status: Public on Feb 01 2017

city: New York

first: Sally

last: Amundson

state: NY

department: Center for Radiological Research

country: USA

institute: Columbia University

summary:
Background: In the event of an improvised nuclear device detonation, the prompt radiation exposure would consist of γ rays plus a neutron component that would contribute to the total dose. As neutrons cause more complex and difficult to repair damage to cells that would result in more severe health burden to affected individuals, it is paramount to be able to estimate the contribution of neutrons to an estimated dose, to provide information for those making treatment decisions.
Results: Mice exposed to either 0.25 or 1 Gy of neutron or 1 or 4 Gy x-ray radiation were sacrificed at 1 or 7 days after exposure. Whole genome microarray analysis identified 7,285 and 5,045 differentially expressed genes in the blood of mice exposed to neutron or x-ray radiation, respectively. Neutron exposure resulted in mostly downregulated genes, whereas x-rays showed both down- and up-regulated genes. A total of 34 differentially expressed genes were regulated in response to all ≥1 Gy exposures at both times. Of these, 25 genes were consistently downregulated at days 1 and 7, whereas 9 genes, including the transcription factor E2f2, showed bi-directional regulation; being downregulated at day 1, while upregulated at day 7. Gene ontology analysis revealed that genes involved in nucleic acid metabolism processes were persistently downregulated in neutron irradiated mice, whereas genes involved in lipid metabolism were upregulated in x-ray irradiated animals. Most biological processes significantly enriched at both timepoints were consistently represented by either under- or over-expressed genes. In contrast, cell cycle processes were significant among down-regulated genes at day 1, but among up-regulated genes at day 7 after exposure to either neutron or x-rays. Cell cycle genes downregulated at day 1 were mostly distinct from the cell cycle genes upregulated at day 7. However, five cell cycle genes, Fzr1, Ube2c, Ccna2, Nusap1, and Cdc25b, were both downregulated at day 1 and upregulated at day 7.
Conclusions: We describe, for the first time, the gene expression profile of mouse blood cells following exposure to neutrons. We have found that neutron radiation results in both distinct and common gene expression patterns compared with x-ray radiation.

overall_design: Radiation induced gene expression in mouse blood was measured at 1, 3, and 7 days after 0.25 Gy and 1 Gy neutron exposure or after 1 Gy and 4 Gy of x-rays. Six independent experiments were performed at each dose and time point.

first: Constantinos

middle: G

last: Broustas

middle: A


title: Gene expression profile of Pafah2-deficient bone marrow derived mast cells (BMMCs) treated with w3 epoxides or GW9662

status: Public on Feb 07 2017

city: Hongo, Bunkyo-ku

first: Yuta

last: Shimanaka

state: Tokyo

department: Graduate School of Pharmaceutical Sciences

institute: University of Tokyo

overall_design: To investigate gene expression changes induced by w3 epoxides (a mixture of 17,18-EpETE and 19,20-EpDPE) or PPARg antagonist (GW9662) treatment in mast cells,  we performed microarray gene profiling of Pafah2-deficient BMMCs treated with them. Pafah2-deficient BMMCs were treated with a mixture of the synthetic w3 epoxides (17,18-EpETE/19,20-EpDPE = 2/3; 300 nM), whose compositions mimicked those detected in the conditioned medium of wild-type BMMCs, or GW9662 (0.5 μM) for 12h. DMSO was used as a vehicle.  We found that several hundreds of genes were up- or down-regulated by w3 epoxides or GW9662 treatment, and hundreds of genes down-regulated by  ω3 epoxides or GW9662 were intriguingly overlapped.

first: Nozomu

last: Kono

first: Hiroyuki

last: Arai

first: Yasumasa

last: Nishito

first: Yoshitaka

last: Taketomi

first: Makoto

last: Murakami


title: Rapid decay of engulfed extracellular miRNA by XRN1 exonuclease promotes transient epithelial-mesenchymal transition

status: Public on Jan 25 2017

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: To analyze the effect of miR-223-3p expression on the mRNA level we employed whole genome microarray expression profiling to identify genes with a potential seed region targeted by miR-223-3p.   A549 cells were transfected for 48h with either a mirVana miRNA mimic Control or miR-223-3p.

overall_design: Four independent experiments were performed for A549_miRCT. Three independent experiments were performed for A549_miR223.

first: P

last: Brest

first: K

first: N

last: Nottet

last: Barbry

first: J

last: Zangari

first: A

last: Popa


title: Interferon-g and Tumor Necrosis Factor-a Polarize Bone Marrow Stromal Cells Uniformly to a Th1 Phenotype

status: Public on Feb 09 2017

city: BETHESDA

first: PING

last: JIN

state: MD

address: 9000 ROCKVILLE PIKE

department: DTM

institute: CC/DTM/NIH

summary: Activated T cells polarize mesenchymal stromal cells (MSCs) to a proinflammatory Th1 phenotype which likely has an important role in amplifying the immune response in the tumor microenvironment. We investigated the role of interferon gamma (IFN-g) and tumor necrosis factor alpha (TNF-a), two factors produced by activated T cells, in MSC polarization. Gene expression and culture supernatant analysis showed that TNF-a and IFN-g stimulated MSCs expressed distinct sets of proinflammatory factors. The combination of IFN-g and TNF-a was synergistic and induced a transcriptome most similar to that found in MSCs stimulation with activated T cells and similar to that found in the inflamed tumor microenvironment; a Th1 phenotype with the expression of the immunosuppressive factors IL-4, IL-10, CD274/PD-L1 and indoleamine 2,3 dioxygenase (IDO). Single cell qRT-PCR analysis showed that the combination of IFN-g and TNF-a polarized uniformly to this phenotype.  The combination of IFN-g and TNF-a results in the synergist uniform polarization of MSCs toward a primarily Th1 phenotype. The stimulation of MSCs by IFN-g and TNF-a released from activated tumor infiltrating T cells is likely responsible for the  production of many factors that characterize the tumor microenvironment.

overall_design: BMSCs (passage 4) were stimulated with 6.5 or 65 ng/ml of IFN-g (R&D System Minneapolis, MN, USA), and with 1.5 or 15 ng/ml of TNF-a (R&D System Minneapolis, MN, USA), or the combination of IFN-g and TNF-a   (1.5 ng/ml of TNF-a + 6.5 ng/ml of IFN-g or 15 ng/ml of TNF-a + 65 ng/ml of IFN-g).  After the adherent BMSCs were incubated with the cytokines for 48 hours, the BMSCs were harvested using trypsin and they were then evaluated by gene expression profiling.

first: Ping

last: Jin

first: Yuanlong

last: Zhao

first: Hui

last: Liu

first: Jinguo

last: Chen

first: Jiaqiang

last: Ren

first: Jianjian

first: Davide

last: Bedognetti

first: Shutong

first: Ena

last: Wang

first: Francesco

last: Marincola

first: David

last: Stroncek


title: Metabolic alterations in aged human skin in vivo

status: Public on Jan 20 2017

city: Zürich

first: Nicola

last: Zamboni

state: Zurich

address: Auguste-Piccard-Hof 1

department: Institute for Molecular Systems Biology

country: Switzerland

institute: ETH Zurich

summary:
Aging human skin undergoes significant morphological and functional changes such as wrinkle formation, reduced wound healing capacity, and altered epidermal barrier function. Besides known age-related alterations like DNA-methylation changes, metabolic adaptations have been more recently linked to impaired skin function in old humans. Understanding of these metabolic adaptations in aged skin are of special interest, because topical treatments  could reverse age-dependent metabolic changes of human skin in vivo to affect age associated skin disorders.
Results: We investigated the global metabolic adaptions in human skin during aging with a combined transcriptomic and metabolomic approach applied to epidermal tissue samples of young and old human volunteers. Our analysis confirmed known age-dependent metabolic alterations, e.g. reduction of coenzyme Q10 levels, and also revealed novel age effects that are seemingly important for skin maintenance. Integration of donor-matched transcriptome and metabolome data highlighted transcriptionally-driven alterations of metabolism during aging such as altered activity in upper glycolysis and glycerolipid biosynthesis or decreased protein and polyamine biosynthesis. Together, we identified several age-dependent metabolic alterations that might affect cellular signaling, epidermal barrier function, and skin structure and morphology.
Conclusion: Our study provides a global resource on the metabolic adaptations and its transcriptional regulation  during aging of human skin. Thus, it represents a first step towards an understanding of the impact of metabolism on impaired skin function in aged humans and therefore will potentially lead to improved treatments of age related skin disorders

overall_design: Gene expression in epidermal skin samples from the inner forearms 24 young (20 to 25 years) and 24 old (55 to 66 years) human volunteers were analysed using Agilent Whole Human Genome Oligo Microarrays 8x60K V2.

first: Andreas

last: Kuehne

first: Janosch

last: Hildebrand

first: Joern

last: Soehle

first: Horst

last: Wenck

first: Lara

last: Terstegen

first: Stefan

last: Gallinat

first: Anja

last: Knott

first: Marc

last: Winnefeld


title: Essential roles of Lamtor1 in CD4+ T cell-mediated autoimmunity

status: Public on Jan 16 2017

first: Daisuke

last: Okuzaki

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Lamtor1 is a protein that is required for amino acid sensing and activation of mechanistic target of rapamycin complex 1 (mTORC1) at lysosomes. The critical role of Lamtor1 in macrophage polarization has been clarified recently. However, the role of Lamtor1 in adaptive immune system has not been investigated. Here we show that Lamtor1-deficient T cells showed markedly reduced IL-2 production, decreased mTORC1 activity, and decreased expression of purine-synthesis and lipid-synthesis enzymes.

overall_design: The labeled cRNAs were hybridized on 4X44K ver.2 Agilent Whole Mouse Genome dual colour Microarrays (G4846A) in a dye swap experiment.

first: Takashi

last: Hosokawa

first: Tetsuya

last: Kimura

first: Atsushi

last: Kumanogoh


title: lung metastasis 100% vs 0%

city: YOKOHAMA

first: Hiroshi

last: Hyakusoku

state: KANAGAWA

department: ENT

institute: Yokohama City University

summary: Lung metastatic potential of the 29 HNSCC was examined with tail vein metastatic assay as described previously. 1 ×10E6 HNSCC cells in a volume of 200 µL were injected into the lateral tail vein using a 30 gauge needle. Eight to 10 mice were prepared for each cell line. Mice were euthanized using carbon dioxide asphyxiation when they lost more than 15% of their pre-injection body weight or at 90 days after cell injection. Necropsy was performed, and lung was harvested. The lungs were then evaluated for the presence of lung metastases and also weighed.

overall_design: Lung metastatic potential of HNSCC was examined using experimental lung metastatic mouse models to study the detail of mechanism of distant metastasis of HNSCC.

last: Sano


title: Candidate ERalpha targets for DNA methylation-mediated gene silencing

status: Public on Feb 05 2017

city: Philadelphia

first: Eric

middle: A.

last: Ariazi

state: PA

address: 333 Cottman Avenue

institute: Fox Chase Cancer Center

summary:
DNA methylation of specific CpG sites associates with estrogen receptor α (ERα)-positive status in human breast cancer. Therefore, ERα may regulate gene expression in part via DNA methylation. This hypothesis was tested in a panel of antihormone-resistant T47D and MCF-7 cells with varying levels of ERα expression/activity that were derived by long-term fulvestrant treatment and by estrogen deprivation. Using Agilent’s Whole Human Genome 4x44K v2 gene expression microarrays, the intersection of ERα inversely-related genes and genes induced by the DNA methyltransferase-inhibitor decitabine were identified and revealed 39 candidate ERα DNA methylation targets. Enrichment analysis indicated over-representation of ERα-binding sites, basal-up/luminal-down markers, cancer stem cell genes, epithelial-mesenchymal transition (EMT) genes, inflammatory genes and tumor suppressors.
Kaplan-Meier survival curve and Cox proportional hazard regression analyses indicated these candidate targets predicted poor distant metastasis-free survival among 2,116 breast cancer patients. The basal and EMT genes LCN2 and IFI27 showed the greatest inverse relationship with ERα expression/activity and contain ERα-binding sites, therefore they were selected for validation. LCN2 and IFI27 CpG methylation levels, quantitated by pyrosequencing, were inversely related to ERα expression/activity in wild-type and antihormone-resistant ERα-negative T47D cells, in ERα-negative T47D cells infected with lentiviral ERα, and in a panel of 11 breast cancer cell lines.
Implications: ERα directs DNA methylation-mediated silencing of specific genes, such as basal markers, and thereby may in part program breast cancers as the prognostically more favorable luminal subtype. Thus, genes that can be methylated in an ERα-dependent manner may serve as predictive biomarkers in breast cancer.

overall_design: The intersection of ERα inversely-related genes and decitabine (DAC)-induced genes was determined. This intersection represented the set of genes that fulfilled the following criteria: i) genes induced by DAC versus CON-treated wild-type T47D cells, ii) genes up-regulated in each of the ERα-low/negative cell lines, i.e., T47D/FUL, T47D/ED1, and T47D/ED2 cells, versus wild-type T47D cells, iii) genes down-regulated by 17β-estradiol (E2) in T47D/ED2/E2 versus T47D/ED2 cells, iv) genes up-regulated in ERα-low MCF7/FUL week 8 versus wild-type MCF-7 cells, and v) genes down-regulated in ERα-positive MCF-7/FUL week 21 versus ERα-low MCF-7/FUL week 8 cells. These selection criteria pinpointed 39 high-value candidates for ERα-mediated silencing via DNA methylation.

first: John

middle: C

last: Taylor

first: Michael

last: Black

first: Emmanuelle

last: Nicolas

middle: J

last: Slifker

first: Jeff

last: Boyd


title: Microarray of SIRT6 KO in hepatocellular carcinoma

city: Toronto

first: Dae-Kyum

last: Kim

state: ON

address: 88 Wellesley Street East

department: Donnelly centre

country: Canada

institute: University of Toronto

summary: We identified the specific role of Sirtuin 6 (SIRT6) in the progression of hepatocellular carcinoma (HCC) and evaluated its therapeutic and prognostic potential. SIRT6 knockdown by shRNA inhibited the proliferation of HCC cells; moreover, depletion of SIRT6 suppressed HCC tumor growth in vivo. SIRT6 silencing significantly down regulated the growth of HCC cell lines via induction of cellular senescence, which was attributed by DNA damage in p16/Rb and p53/p21-independent manners. We also showed that SIRT6 knockdown increased the number of G2/M phase arrested cells by increasing cyclin B1 and 14-3-3-∂. Moreover, SIRT6 levels were significantly higher in HCC cell lines than a normal hepatic cell line, and were higher in HCC than non-tumor tissues. Aberrant SIRT6 expression correlated with poor prognostic features of HCC. Taken together, our findings suggest SIRT6 may act as a tumor promoter by preventing cellular senescence attributed by DNA damage and suggests that targeting SIRT6 could be a promising therapeutic approach for cancer treatment.

overall_design: Two-condition experiment, Control vs. SIRT6 KO. Biological replicates: 2 control replicates, 2 KO replicates.

first: Namgyu

last: Lee

first: Kwang

middle: Y

last: Choi


title: Fas- and DR3-dependent transcriptome changes in naïve T-cells from EBV carrier during and after acute mononucleosis

status: Public on Feb 22 2017

city: Nizhny Novgorod

first: Dmitry

last: Knyazev

address: Malaya Yamskaya, 71

country: Russia

institute: I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology

summary: EBV-encoded proteins interfere with extrinsic and intrinsic apoptotic pathways so that homeostasis of infected cells shifts to survival and proliferation favoring to evasion of virus from immune surveillance.The aim of investigation is to reveal the key factors regulating Fas- и DR3-triggered cascades influenced by EBV in naïve T-cells. We developed the splicing-sensitive microarray covering 221 genes encoding apoptosis-associated factors, adaptor proteins, kinases, RNA-binding proteins (including spliceosome elements) etc. Naïve CD4+ and CD8+ T-cells isolated from the same EBV-infected patient during acute mononucleosis and after therapy were analyzed.

overall_design:
Each microarray encompassed 4 identical probe-containing areas. Each area contains 1042 target probes in PM- and MM-version (2084 total) and 140 negative control probes. MM-probes were excluded from processed data. Freshly isolated naïve T-cells were either subjected to immediate NA extraction or were cultivated for 24 hours in 1) empty media [control]; 2) Fas-agonist containing media [Fas]; 3) DR3-agonist containing media [DR3]. The following comparisons were made: [control]/[Freshly isolated]; [Fas]/[control]; [DR3]/[control]. Experiments were performed for CD4+ and CD8+ T-cells isolated before and after therapy. Additional comparisons [Freshly isolated after]/[Freshly isolated before] were made for each subpopulation.

Please note that the data was normalized only within COMPARED samples (like 'Cd4_control_before*' samples vs.'cd4_fas_before*' samples), *not* across ALL the samples.

first: Nikolay

last: Sakharnov

first: Leonid

last: Solntsev

first: Oleg

last: Utkin


title: Gene expression of liver sinusoidal endothelial cells from an 8-week-old WT and ob/ob mouse

status: Public on Feb 15 2017

city: Bunko-ku

first: Yasutaka

last: Miyachi

address: 1-5-45 Yushima

department: Molecular Endocrinology and Metabolism

institute: Tokyo Medical and Dental University

summary: Obesity may promote myeloid cell accumulation in liver.  Intravital liver tissue imaging revealed that the number of myeloid cells attached to sinusoidal wall significantly increased in ob/ob mice. To assess the pathophysiological roll of liver sinusoidal endothelial cells (LSEC) in obese livers, we performed microarray analysis  in LSEC isolated from an 8-week-old wild-type and ob/ob mouse. Pathway analysis in microarray data shows genes related to cell adhesion, chemokine signaling and leukocyte transendothelial migration are upregulated in LSEC from ob/ob.

overall_design: Liver sinusoidal endothelial cells were isolated by collagenage digestion of livers from an 8-week-old male wild-type and ob/ob mouse. Cells were cultured overnight in DMEM containing 10% FBS.

first: Y

first: S

last: Yamaguchi

first: K

last: Tsuchiya

last: Ogawa


title: Gene expression profiling of cancer cells with genetic disruption of DNA methyltransferases [Agilent-026652]

status: Public on Jan 13 2017

city: Baltimore

first: Stephen

middle: B

last: Baylin

address: 1650 Orleans St. Suite 541

institute: Johns Hopkins University

summary: Maximizing DNA methyltransferase (DNMT’s) inhibition for cancer therapy requires defining the roles and interactions between these enzymes for maintaining the widespread DNA methylation abnormalities in cancer.  Combining genetic  and shRNA depletion  in colon and other cancer cells reveals that DNMT1 is extremely dominant in this maintenance, with DNMT’s 3A and 3B playing minor roles,  at all genomic loci including promoters and enhancers.  Reducing DNMT1 below a deep threshold level, especially at promoters, is required for reversing abnormal DNA methylation and re-expressing key tumor suppressor genes.  Current DNMT inhibitors (DNMTis) are challenged, at tolerable patient doses, for achieving such reductions.  We introduce a new approach in which reducing levels of the DNMT targeting protein, UHRF1, complements low DNMTi doses to DNA demethylate and reactivate expression of such genes.

overall_design: To understand precisely how the three DNMT’s, 1, 3A, and 3B, interact for maintaining DNA methylation abnormalities in cancer. We perfomed genome-wide DNA methylation and gene expression anaylses in colon cancer and other cancer cell lines following  a series of genetic and shRNA depletions of each enzyme. Our data revealed that DNMT1 overwhelmingly plays the essential maintenance role.  Even with combined deletions of the proteins, lowering DNMT1 below a threshold level is required for maximal loss of  DNA methylation at all genomic regions and is required for maximally reversing promoter DNA promoter DNA hypermethylation with associated re-expression of key tumor suppressor genes.

first: Hsing-Chen

last: Tsai

first: Yi

last: Cai


title: Modular Transcriptional Repertoire and microRNA-target Analyses in Thymic Tissue of Down Syndrome Infants

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

country: Brazil

institute: Faculdade de Medicina da Universidade de Sao Paulo

summary: Trisomy 21- driven transcriptional alterations in human thymus were characterized through gene coexpression network (GCN) and microRNA-target analyses. We used whole thymic tissue (corticomedullar sections) - obtained at heart surgery from Down syndrome (DS) and karyotipically normal individuals (CT) - and a network-based approach for GCN analysis that allows the identification of modular transcriptional repertoires and the interactions between all the system’s constituents through community detection. Changes in the degree of connections observed for hierarchically important hubs/genes in CT and DS gene networks corresponded to sub-network changes, i.e. module (communities) changes. Distinct communities of highly interconnected gene sets were topologically identified for DS and CT networks. The role of microRNAs in modulating the expression of highly connected genes in CT and DS was revealed through microRNA-target analysis. Trisomy 21 gene dysregulation in thymus may well be depicted as the breakdown and altered reorganization of functional modules.

overall_design: Thymus transcriptomic profiles of patients with and without Down Syndrome were compared in order to identify differentially expressed transcripts.

first: Silvia

last: Bando

first: Fernanda

last: Bertonha

first: Filipi

middle: N

last: Silva

first: Luciano

middle: F

last: Costa

first: Leandro

middle: R

last: Ferreira

first: Madga

last: Carneiro-Sampaio


title: KG1a cells, irradiated at 8Gy, incubated for 48hr

status: Public on Dec 31 2016

city: Delhi

first: Gangenahalli

middle: Ugraiah

last: Gurudutta

state: Delhi

address: Lucknow Road, Timarpur

department: Division of Stem Cell & Gene Therapy

country: India

institute: Institute of Nuclear Medicine and Allied Sciences (INMAS)

summary: To compare the irradiated KG1a data with other irradiated cells/cell lines for finding out the similarity and differences with respect to various gene ontologies

overall_design: KG1a cells with and without 8Gy of radiation in triplicate

middle: U

first: Yogesh

middle: K

last: Verma


title: Targeting metastasis stem cells through the fatty acid receptor CD36 (DID+, DID- and CD44DIM).

status: Public on Dec 16 2016

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

summary: Metastasis is the leading cause of cancer-related deaths. For most human cancers, the identity of the cells that initiate and promote metastasis is still unknown, hampering our ability to develop therapies to prevent or inhibit the spread of tumour cells to distant sites. Using an orthotopic model of human oral squamous cell carcinoma (OSCC), we have now identified a subpopulation of CD44bright cells within the primary lesion with the highest potential to develop lymph node and lung metastasis. This population is slow-cycling, expresses high levels of the receptor CD36 at the cell membrane and relies on fatty acid metabolism to thrive in lymph nodes and bronchoalveolar environments. Importantly, inhibition of CD36 by either shRNA or neutralizing monoclonal antibodies severely impairs metastatic spread of primary OSCC patient samples and established cell lines. Further underscoring its importance, CD36 overexpression in poorly disseminating tumours confers an aggressive metastatic behaviour. Analyses of public gene expression data indicate that the presence of the signature-defining CD36+ cells also strongly correlates with a poor prognosis in patients with lung SCC, ovarian cancer, bladder cancer, or luminal breast cancer. By identifying metastasis-promoting cells and then targeting them with CD36 inhibition, novel anti-metastatic therapies could be developed for patients with these types of tumours.

overall_design: 5 biological replicates Detroit (#1,#2,#3,#4,#6) were included. From each biological replicate, 3 independent populations were sorted (DID+, DID- and CD44DIM).

first: Salvador

last: Aznar-Benitah

first: Camille

last: Stephan-Otto Attolini


title: Targeting metastasis stem cells through the fatty acid receptor CD36

overall_design: 3 (LN2 #1#2#3)+4(PT1 #2#3#4#5) biological replicates were included. From each biological replicate, 2 independent populations were sorted (CD36+ and CD36-).


title: Downregulation of WDR20 due to loss of 14q is involved in the malignant transformation of clear cell renal cell carcinoma (WDR20 overexpression in RCC cell line)

status: Public on Dec 07 2016

city: Yufu

first: Mika

last: Takahashi

address: Idaigaoka 1-1

institute: Oita University

summary: Previously, we have reported that genomic loss of 14q occurs more frequently in high grade clear cell renal cell carcinomas (ccRCCs) than low grade ones and shows a significant impact on the expression levels of genes located on this region, suggesting that the genes located on the region and downregulated by the loss may be involved in the malignant transformation of ccRCCs. Here, among the genes located on the minimal common region of 14q loss, we found that 6 were significantly downregulated in high grade ccRCCs due to copy number loss. Using the data set from The Cancer Genome Atlas (TCGA) Research Network, downregulation of one out of the 6 genes, WDR20, was significantly associated with poorer prognosis for the patients with ccRCC, suggesting that downregulation of WDR20 may be involved in the malignant transformation of ccRCC. In this array study, we aimed to investigate the effect of WDR20 overexpression on the gene expression profile of an RCC cell line, 786_O. For this aim, we established 3 cell clones stably transfected with the WDR20 expressing vector (786O_WDR20cl1, 786O_WDR20cl2 and 786O_WDR20cl3) and one cell clone stably transfected with the corresponding empty vector (786O_vector) and performed expression microarray analysis using RNAs from these cell lines.

overall_design: In this array study, we aimed to investigate the effect of WDR20 overexpression on the gene expression profile of an RCC cell line, 786_O. For this aim, we established 3 cell clones stably transfected with the WDR20 expressing vector (786O_WDR20cl1, 786O_WDR20cl2 and 786O_WDR20cl3) and one cell clone stably transfected with the corresponding empty vector (786O_vector). RNA samples from these clonal cells were subjected to expression microarray and differentially expressed genes between control and WDR20 overexpressing cells were analyzed by GeneSpring. Average expression levels of genes in three kinds of WDR20 expressing clones (786O_WDR20cl1, 786O_WDR20cl2 and 786O_WDR20cl3) were compared with those in two replicates of the control clone (786O_vector).

first: Yoshiyuki

last: Tsukamoto

first: Tomoki

last: Kai

first: Akinori

last: Tokunaga

first: Chisato

last: Nakada

first: Naoki

last: Hijiya

first: Tomohisa

last: Uchida

first: Tsutomu

last: Daa

first: Takeo

last: Nomura

first: Fuminori

last: Sato

first: Hiromitsu

last: Mimata

first: Keiko

last: Matsuura

first: Masatsugu

last: Moriyama


title: Role of MSX1 in Osteogenic Differentiation of Dental Pulp Cells

city: Hiroshima

first: katsumi

last: Fujimoto

address: 1-2-3 Kasumi, Minami-ku

institute: Hiroshima University

summary:
Msh homeobox 1 (MSX1) is a transcriptional factor regulating embryonic development of limbs and craniofacial tissues including bone and teeth. The purpose of this study was to investigate contribution of MSX1 to the osteogenic potential and calcification-related phenotypic expression of dental pulp stromal/mesenchymal cells  isolated from human teeth. Immunohistochemisitry of a 3 week-old mouse molar showed that MSX1 protein was localized to odontoblasts and pulpal mesenchymal cells at different levels and in different manners depending upon the position of the cells in pulp tissue.
When dental pulp stromal/mesenchymal cells were exposed to osteogenesis-induction medium, runt-related transcription factor-2 (RUNX2), bone morphogenetic protein-2 (BMP2), alkaline phosphatase (ALPL) and osteocalcin (OCN) mRNA levels, as well as alkaline phosphatase activity, increased on days 4-12, and, thereafter, the matrix was calcified on day 14. However, knockdown of MSX1 with small interfering RNA abolished this induction of the osteoblast-related gene expression, alkaline phosphatase activity and calcification. Interestingly, DNA microarray and quantative PCR analyses revealed that the MSX1 knockdown induced the sterol regulatory element-binding protein 2 (SREBP2) transcriptional factor and its downstream target genes in cholesterol-synthesis pathway. Inhibition of cholesterol synthesis enhances osteoblast differentiation of various mesenchymal cells. Thus, MSX1 may down-regulate the cholesterol synthesis-related genes to ensure osteoblast differentiation of dental pulp stromal/mesenchymal cells.

overall_design: Extracted healthy deciduous teeth were collected from children with informed consent under the ethics codes of Hiroshima University. The pulp tissue specimens from deciduous teeth were minced, and digested with collagenase and dispase to isolate dental pulp stromal/mesenchymal cells (DPSCs). Small interfering RNA oligonucleotides were used to knockdown MSX1 expression in DPSCs. DPSCs were incubated with growth medium or osteogenesis-induction medium. Four days after the onset of differentiation, total RNA was extracted. DNA microarray analysis was performed using the Agilent SurePrint G3 Human GE v2 8x60K Microarray. Raw data were standardized by the global median normalization method using GeneSpring.

first: Noriko

last: Goto

first: Katsumi

first: Yukio

last: Kato


title: Human Oral cancer cells KB: Control vs. CD133 Overexpression

status: Public on Dec 20 2016

city: GWANGJU

first: Wonbong

last: Lim

address: 309 PILMUN-DAERO, DONG GU

department: Department of Premedical Science

country: South Korea

institute: School of Medicine, Chosun University

summary: Transcriptional profiling of human oral cancer cells KB comparing control blank vector with KB cells transfected with a pcDNA-CD133

overall_design: One-Condition experimnet, KB vs. KBCD133+

first: YoungJong

last: Ko


title: EZH2 inhibition in multiple myeloma downregulates myeloma associated oncogenes and upregulates microRNAs with potential tumor suppressor functions

status: Public on Jan 10 2017

city: Uppsala

first: Prasoon

last: Agarwal

state: Sweden

address: Dag Hammarshkojlds vag 20

department: IGP

country: Sweden

institute: Rudbeck Laboratory, Uppsala University

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

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

overall_design: Refer to individual Series


title: Effects of rapamycin exposure on zebrafish ZF4 cells

city: Ankara

first: Ozlen

last: Konu

address: Bilkent University

department: Molecular Biology and Genetics

country: Turkey

institute: Bilkent University

summary:
mTOR inhibitor rapamycin is a well-known anticancer and immunosuppressant agent. Effects of rapamycin on zebrafish cells have not been previously studied using transcriptome analyses.
Our microarray analysis on ZF4 cells showed that rapamycin treatment modulated a large set of genes with varying functions including protein synthesis, assembly of mitochondrial and proteosomal machinery, cell cycle, metabolism, and oxidative phosphorylation.

overall_design: Zebrafish ZF4 cells exposed to 100nM rapamycin was profiled using Zebrafish Affymetrix Gene Chips. Normalization by RMA and class comparison analyses were performed using BRB Array Tools.

first: Ceren

last: Sucularli


title: Assessing the mechanism and therapeutic potential of modulators of the human Mediator complex-associated protein kinases

status: Public on Dec 01 2016

city: Sutton

first: Robert

middle: te

last: Poele

state: Surrey

address: 15 Cotswold Road

department: Cancer Reserach UK Unit for Cancer Therapeutics

country: United Kingdom

institute: The Institute of Cancer Research

summary: Mediator-associated kinases CDK8/19 are context-dependent drivers or suppressors of tumorigenesis.  Their inhibition is predicted to have pleiotropic effects, but it is unclear whether this will limit the clinical utility of CDK8/19 inhibitors.  We discovered two series of potent chemical probes with high selectivity for CDK8/19.  Despite pharmacodynamic evidence for robust on-target activity, the compounds exhibited only modest efficacy against human tumor cell line or patient-derived xenografts.  Expression profiling detected altered gene expression consistent with CDK8/19 inhibition, including profiles associated with superenhancer–regulated gene expression.  In a mouse model expressing oncogenic beta-catenin, treatment shifted cells within hyperplastic intestinal crypts from a stem cell to a transit amplifying phenotype.  Finally, in two species, neither test compound was tolerated at therapeutically-relevant exposures.  The complex nature of the toxicity observed with two structurally-differentiated chemical series is consistent with on-target effects posing significant challenges to the further clinical development of CDK8/19 inhibitors.

overall_design: Colo205 colon cancer cells were grown as xenografts in female NCr athymic mice and once established, treated twice daily  with 70 mg/kg of Compound 1, 20 mg/kg of Compound 3 or vehicle. Two and six hours after the final dose tumours were snap frozen. Tumour sample RNA was hybridised against human reference. Compound 1 and 3 are from a series of close analogues of a 3,4,5-trisubstituted pyridine series identified from a high-throughput cell-based reporter assay of WNT signalling. They were shown to be potent and selective inhibitors of the Mediator complex-associated protein kinases CDK8 and CDK19. They are ATP competitive inhibitors with >100-fold selectivity over 291 other kinases. X-ray crystallography demonstrates Type 1 binding involving insertion of the CDK8 C-terminus into the ligand-binding site.

first: Paul

last: Clarke

first: Maria-Jesus

last: Ortiz-Ruiz

middle: H

last: te Poele

first: Olajumoke

last: Adeniji-Popoola

first: Gary

last: Box

first: Will

last: Court

first: Samer

last: El Bawab

first: Christina

last: Esdar

first: Ken

last: Ewan

first: Sharon

last: Gowan

first: Alexis

last: de Haven Brandon

first: Philip

last: Hewitt

first: Stephen

middle: M

last: Hobbs

first: Wolfgang

last: Kaufmann

first: Aurelie

last: Mallinger

first: Florence

last: Raynaud

first: Roe

last: Toby

first: Felix

last: Rohdich

first: Kai

last: Schiemann

first: Stephanie

last: Simon

first: Richard

last: Schneider

first: Melanie

last: Valenti

first: Julian

last: Blagg

first: Andree

last: Blaukat

first: Trevor

last: Dale

first: Suzanne

last: Eccles

first: Stefan

last: Hecht

first: Klaus

last: Urbahns

last: Workman

first: Dirk

last: Wienke


title: Transcriptomic analysis of pro-invasive fibroblasts activation short and long term response

status: Public on Dec 04 2016

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS


title: Transcriptome profiling of Ccng1-/-Ccng2-/- double knockout (DKO) deficient mouse embryonic fibroblasts

status: Public on Dec 19 2016

city: Suita

first: Daisuke

last: Okuzaki

institute: Osaka univ.

summary: To examine if lack of CycG1 and/or CycG2 causes genome-wide alterations of gene expression, we performed DNA microarray analysis on G1KO, G2KO and DKO MEFs at their logarithmic growth phase. Notably, the fold change values are much larger in DKO MEFs compared with those of G1KO or G2KO MEFs, which suggested that loss of both CycG1 and CycG2 caused uncontrolled expression of these genes because they are mutually regulated by CycG1 and CycG2. Moreover, the fold change of up- or down-regulated genes in DKO MEF are much larger than those of G1KO or G2KO MEFs, suggesting that functions of CycG1 and CycG2 somehow overlap and complement each other in G1KO and G2KO MEFs.

overall_design: Microarray analyses were performed as single-color experiments regarding among WT, G2KO and DKO MEFs.


title: EZH2 inhibition in multiple myeloma downregulates myeloma associated oncogenes and upregulates microRNAs with potential tumor suppressor functions [miRNA expression]

first: Prasoon

last: Agarwal

summary: Multiple Myeloma (MM) is a plasma cell tumor localized to the bone marrow (BM). Despite current progress in improving patient outcome, MM remains largely incurable. Disease clonal and interpatient heterogeneity has hampered identification of a common underlying mechanism for disease establishment and have slowed the development of novel targeted therapies. Epigenetic aberrations are now emerging as increasingly important in tumorigenesis, thus selective targeting of crucial epigenetic enzymes may provide new therapeutic potential in cancer including MM. Recently, we and others suggested the histone methyltransferase enhancer of zeste homolog 2 (EZH2), to be a potential therapeutic target in MM. Now we show that pharmacological inhibition of EZH2 suppresses the MM cell growth through downregulation of MM-associated oncogenes; IRF-4, XBP-1, PRDM1/BLIMP-1and c-MYC. We also show that downregulation of these genes is mediated via reactivated expression of microRNAs with tumor suppressor functions; primarily miR125a-3p and miR320c. Using chromatin immunoprecipitation (ChIP) we demonstrate that miR125a-3p and miR320c are targets of EZH2 and H3K27me3 in MM cell lines and primary MM cells. Our results further highlight the importance of polycomb-mediated silencing in MM to include microRNAs with tumor suppressor activity. This novel role further strengthens the oncogenic features of EZH2 and its potential as a therapeutic target in MM.

overall_design: 4 biological replicates with 8 samples were used in the study. The controls were treated with DMSO while the treatment was done using EZH2 inhibitor UNC1999. The anti-myeloma effects exerted by EZH2 inhibition was investigated using UNC1999, small specific inhibitor of EZH2, at 120 hours post-treament by analyzing global changes in mRNA and miRNA expression

first: Mohammad

last: Alzrigat


title: HeLa cells: control vs IFN-gamma-treated

status: Public on Jan 01 2017

city: Nagasaki

first: Yoshinao

last: Kubo

address: 1-12-4 Sakamoto

institute: Nagasaki University

summary:
Transcriptional profiling of HeLa cells comparing control untreated HeLa cells with IFN-gamma-treated HeLa cells
To infect host cells, many viruses use small cellular compartments, called endosomes, for entry, and the thiol/disulfide interchange in viral envelope glycoproteins (Envs) is crucial for infection. By screening cysteine-reacting chemicals, we found a compound, 4,4’-dithiopyridine, which is active at acidic pH, efficiently restricts retrovirus vector infection. We thus hypothesized that some products of endosome-localized, interferon-stimulated genes (ISGs) exhibit anti-viral activity by inhibiting thiol/disulfide interchange in viral Envs. Among the hundreds of ISGs, gamma-interferon (IFN)-inducible lysosomal thiolreductase (GILT) is the only molecule that resides in the endosomes/lysosomes and digests the S-S bonds of proteins under acidic conditions. We now report that GILT significantly inhibits the replication of retroviruses, including HIV-1 and MLV, by restricting both the early and late phases of their life cycles. Using the VSV-G pseudotyped HIV-1 model, we found that GILT digests the S-S bonds of viral Env proteins. GILT also inhibits HIV-1 viral release by digesting the S-S bond of CD63, an endosome-localized molecule reportedly involved in HIV-1 particle release. The effect of -IFN on HIV-1 is limited, although GILT induced by gamma-IFN is supposed to have anti-HIV-1 activity. We found that while gamma-IFN effectively inhibits MLV replication through GILT, the gamma-IFN signaling is remarkably inhibited by the HIV-1 Env protein, but not the MLV Env protein. These findings suggest that GILT functions as an anti-viral host factor induced by gamma-IFN, however, HIV-1 may have evolved to inhibit gamma-IFN signaling by the Env protein.

overall_design:
Two-condition experiment, control HeLa cells vs IFN-gamma-treated HeLa cells. Biological replicates: 1 control replicate, 1 treated replicate.

Please note that sample data tables contain raw data. The raw values of beta actin and GAPDH (that are commonly used as controls) showed that expression levels of beta actin and GAPDH were elevated 1.3 and 0.8 times by gamma-IFN, respectively, suggesting the raw values of these control genes were not significantly affected by gamma-IFN. However, when the raw values are normalized by GAPDH in gamma-IFN-treated cells, beta-actin expression is activated 1.6-time by gamma-IFN. Therefore, the raw data was used for the further analysis.


title: Analysis of Notch-regulated lncRNA in human glioma stem cell

status: Public on Nov 23 2016

city: Nagoya

first: Keisuke

last: Katsushima

address: 1 Kawasumi, Mizuho-cho, Mizuho-ku

department: Department of Epigenomics

institute: Nagoya City University Graduate School of Medical Sciences

summary: Glioblastomas show heterogeneous histological features. These distinct phenotypic states are thought to be associated with the presence of glioma stem cells (GSCs), which are highly tumorigenic and self-renewing sub-population of tumor cells that have different functional characteristics. To investigate Glioblastomas (GBMs) show heterogeneous histological features. These distinct phenotypic states are thought to be originated by the glioma stem cells (GSCs), which are highly tumorigenic and self-renewing sub-population of tumor cells. Notch signaling has been shown to be important for maintenance of GSC population both in vitro and in vivo. A recent study showed that NOTCH -triggered oncogenic activity can be due to not only its ability to regulate coding genes but also long non-coding RNAs (lncRNAs). Here, we investigated the molecular effects of lncRNA in GSC, whose expression is induced by Notch signaling. We searched for downregulated lncRNAs in GSCs by treatment of small interfering RNA (siRNA) targeting Notch1 and JAG1 (si-Notch1 and si-JAG1) and γ-secretase inhibitors (N-S-phenyl-glycine-t-butyl ester (DAPT) and RO4929097) using SurePrint G3 Human GE 8×60K array slides (G4851B, Agilent Technologies).gene expression profiling in GSC, we have performed microarray experiment using Agilent Whole Human Genome Oligo Microarrays (G4112F).

overall_design: Microarray experiment was performed as single-color hybridization on SurePrint G3 Human GE 8×60K array.

first: Atsushi

last: Natsume

first: Fumiharu

last: Ohka

first: Keiko

last: Shinjo

first: Akira

last: Hatanaka

first: Norihisa

last: Ichimura

first: Yutaka

last: Kondo


title: Creb overexpression induces leukemia in zebrafish by blocking myeloid differentiation process

status: Public on Dec 06 2016

city: Padova

first: Chiara

last: Borga

address: Corso Stati Uniti,4

country: Italy

institute: University of Padua

summary: To examine the role of CREB overexpression in hematopoiesis, we created a model of leukemia in zebrafish by overexpressing the human CREB in the myeloid hematopoietic lineage. Whole transcriptome analysis of kidney-marrow revealed 171 genes differently expressed between CREB- and control-zebrafish (five per group). Interestingly, the integration of this signature with human deposited data revealed that this tumor resembled a human AML at transcriptome level.

overall_design: Gene expression analysis of kidney marrow from CREB-zebrafish and zebrafish controls (five animals per group).

first: Claudia

last: Tregnago

first: Martina

last: Pigazzi

first: Giuseppe

last: Basso


title: Identification of signaling pathways modulated by kiaa0101 in HepG2 cells

city: Wuhan

first: Fan

state: HUbei

address: #169, East Lake Road, Wuchang District, Wuhan

institute: Second clinical hospital of Wuhan University

summary: Kiaa0101 (p15PAF) was previously observed overexpressed in hepatocelluler carcinoma tissues and promoted tumorigenesis. In order to identify potential biological pathways modulated by Kiaa0101, a lentivirus vector with Kiaa0101 was  constructed and transfected into an HepG2 cell  line to obtain a stable cell line with high expression of Kiaa0101. Interestingly, all the protein levels of P21, phosphorylated P21, Akt and phosphorylated Akt were induced. Further, gene expression profiles of Kiaa0101 overexpressed hepatocelluler cancer cells were analyzed using the DNA microarray technique. Differentially expressed genes (DEGs) were screened and followed by Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. 1361 genes and 942 genes were upregulated and downregulated, respectively. The most represented enriched GO biological process, cellular component and molecular function categories included DNA-dependent regulation of transcripton, plasma membrane and DNA binding, respectively. KEGG pathway analysis showed that the most significantly expressed genes were linked to pathways in cancer, MAPK signaling pathway and Wnt signaling pathway. Our study provides a comparative transcriptome analysis and revealed the downstream genes and signaling pathways that are possibly involved in Kiaa0101-induced hepatocelluler carcinoma.

overall_design: Three kiaa0101-overexpressing stable cells and three control cells were chosen for microarray analysis. Subsequently, the RNAs were analyzed using microarray chips (Agilent Technologies) according to the manufacturer's protocol.Gene Ontology (GO) and KEGG pathways were performed to investigate the involved pathways

last: Fan

first: Mei

last: Liao

first: Han

last: Zhang

first: Jie

last: Chen

first: Dong

last: Zhu


title: Transcriptomic analysis of pro-invasive fibroblasts activation long term response

first: Kevin

last: Lebrigand

summary: The effect at long term (15 days) of leukemia inhibitory factor (LIF), TGFβ or TGFβ + anti-Lif stimulation on the human primary dermal fibroblast (hDF) transcriptome was analyzed by whole genome microarray expression profiling.

overall_design: Total RNA of human primary dermal fibroblasts (hDFs) stimulated by LIF, TGFβ or TGFβ + anti-Lif have been performed in DMEM supplemented with 0.5% FCS containing 2ng/ml final concentration of human recombinant proteins for 7 days. Next, hDFs were cultured for 7 days in 0.5% FCS media prior to experiments. One-color experiment with 2 biological replicates (marked 1 or 2) of the 4 experimental conditions. Total of 8 samples.

first: C

last: Gaggioli

first: K

first: N

last: Nottet

first: P

last: Barbry

first: B

last: Mari


title: Profile of microRNAs potentially regulated by Bmi1 in Sca1+ Cardiac Protenitor Cells (CPC)

city: Madrid

first: Fatima

last: Sanchez-Cabo

address: Melchor Fernandez Almagro

institute: CNIC

summary: We compared miRNA expression profiles of B+ and sh-Bmi1 CPCs, looking for miRNAs that show a significant upregulation in B+ CPCs and reduction in sh-Bmi1 CPCs.

overall_design: To assess the potential involvement of BMI1 in control of miRNA expression in Sca1-CPCs, we transduced freshly isolated CPCs with lentiviral vectors overexpressing or silencing Bmi1. Different replicates of infection were used.

first: Francisco

last: Cruz

first: María

last: Tomé

first: Juan

last: Bernal

first: Antonio

last: Bernad


title: Comparative gene expression profiling of primary and metastatic renal cell carcinoma stem cell-like cancer cells

status: Public on Nov 04 2016

city: Warsaw

first: Mohammed

middle: Imran

last: Khan

address: ul. Szaserów 128

department: Department of Oncology

country: Poland

institute: Military Institute of Medicine

summary: Recent advancement in cancer research has shown that tumours are highly heterogeneous and multiple phenotypically different cell populations are found in single nodule. Cancer development and tumour growth is driven by specific type of cells - cancer stem cells or tumour initiating cells (CSCs/TICs), which are to be responsible for tumour growth, metastatic spread and drug resistance. This research was designed to verify the presence of tumour initiating cells in renal cancer cell lines. Subsequently, we aimed to characterize phenotype and cell biology of CD105+ cells, defined previously as renal cell carcinoma tumour initiating cells. Main goal of the project was to describe gene expression profile of tumour initiating cells originating from primary tumour and of metastatic origin. Metastatic RCC cell lines (ACHN and Caki-1) demonstrated higher colony forming ability comparing to primary RCC cell lines. We investigated presence of CD105+ cells in RCC cell lines. Furthermore, metastatic RCC cell lines have higher CD105+ cell population and higher expression for stemness genes (Oct-4 and Nanog). CD105+ cells adopt 3D grapes like structure under handing drop condition. Sorted CD105+ cells were found positive for human MSC makers such as CD90, CD73, CD44, CD146 and alkaline phosphatase activity. In addition, CD105+ cells were unable to expressed maker for CD24, CD34, CD11b, CD19, CD45 and HLA-DR. 1411 genes were commonly differentially expressed in CD105+ cells (both from primary (Caki-2) and metastatic RCC (ACHN)) cells in comparison to healthy kidney epithelial cell line (ASE-5063). TGF-β, Wnt/β-catenine, Epithelial-Mesenchymal Transition (EMT), Rap1 signaling, PI3K-Akt signaling and Hippo signaling pathway were altered in CD105+ cells after IPA and KEGG pathway analysis. TGFB1, ERBB2, and TNF are most significant transcriptional regulators activated in these cells. Altogether, our results indicate that RCC-CD105+ cells may represents a novel target for CSCs/TICs phenotype and their gene expression profile could be used as initial data for new functional studies and drug design.

overall_design: Compatative gene expression profiling of CD105+ cells isolated from primary (Caki-2) and metastatic (ACHN) renal cell carcinoma cell lines compared with healthy kidney epithelial (ASE) cells.

middle: I

first: Anna

last: Czarnecka

first: Cezary

last: Szczylik


first: Robert

last: Poele

overall_design: SW620 colon cancer cells were grown as xenografts in female NCr athymic mice and once established, treated twice daily  with 70 mg/kg of Compound 1 or vehicle. Two and six hours after the final dose tumours were snap frozen. Tumour sample RNA was hybridised against human reference. Compound 1 is from a series of close analogues of a 3,4,5-trisubstituted pyridine series identified from a high-throughput cell-based reporter assay of WNT signalling. It was shown to be a potent and selective inhibitor of the Mediator complex-associated protein kinases CDK8 and CDK19. It is an ATP competitive inhibitor with >100-fold selectivity over 291 other kinases. X-ray crystallography demonstrates Type 1 binding involving insertion of the CDK8 C-terminus into the ligand-binding site.

first: Paul

middle: A

last: Clarke

first: Maria-Jesus

last: Ortiz-Ruiz

last: te Poele

first: Olajumoke

last: Adeniji-Popoola

first: Gary

last: Box

first: Will

last: Court

first: Samer

last: El Bawab

first: Christina

last: Esdar

first: Ken

last: Ewan

first: Sharon

last: Gowan

first: Alexis

last: de Haven Brandon

first: Philip

last: Hewitt

first: Stephen

last: Hobbs

first: Wolfgang

last: Kaufmann

first: Aurelie

last: Mallinger

first: Florence

last: Raynaud

first: Roe

last: Toby

first: Felix

last: Rohdich

first: Kai

last: Schiemann

first: Stephanie

last: Simon

first: Richard

last: Schneider

first: Melanie

last: Valenti

first: Julian

last: Blagg

first: Andree

last: Blaukat

first: Trevor

last: Dale

first: Suzanne

last: Eccles

first: Stefan

last: Hecht

first: Klaus

last: Urbahns

last: Workman

first: Dirk

last: Wienke


title: Assessing the mechanism and therapeutic potential of modulators of the human mediator complex-associated protein kinases

first: Robert

last: Poele


title: PNPLA1 has a crucial role in skin barrier function by directing acylceramide biosynthesis

status: Public on Dec 23 2016

city: Tokyo

first: Tetsuya

last: Hirabayashi

address: 2-1-6 Kamikitazawa, Setagaya-ku

institute: Tokyo Metropolitan Institute of Medical Science

summary: Mutations in PNPLA1 (patatin-like phospholipase domain containing 1) cause autosomal recessive congenital ichthyosis, but the mechanism involved remains unclear. Here we show that PNPLA1, an enzyme expressed in highly differentiated keratinocytes, plays a crucial role in the biosynthesis of acylceramide, a lipid component essential for skin barrier function. Pnpla1-deficient mice showed neonatal lethality due to epidermal permeability barrier defects with severe transepidermal water loss, decreased intercellular lipid lamellae in the stratum corneum, and impaired terminal differentiation of keratinocytes. In Pnpla1–/– epidermis, three unique linoleate-containing lipids, including acylceramides, acylglucosylceramides and (O-acyl)-ω-hydroxy fatty acids, were almost absent with reciprocal increases in their precursors ω-hydroxy (glucosyl)ceramides and ω-hydroxy fatty acids, indicating that PNPLA1 catalyzes the ω-O-esterification step with linoleic acid to form acylceramides. Our results suggest that PNPLA1 represents the missing piece in the process of acylceramide biosynthesis required for establishment of a permeability barrier.

overall_design: We compared gene expression in Pnpla1-/- (knockout) epidermis at P0 with Pnpla1+/+ (wild type) controls. Individual array samples were generated by pooling equal amounts of total RNA derived from skins of 6 animals.

first: Tatsuki

last: Anjo

first: Yasumasa

last: Nishito

first: Makoto

last: Murakami


title: HUVEC gene profile after Sox7/Sox17 siRNA silencing

city: DALLAS

first: KANGSAN

last: KIM

state: TX

address: 5323 Harry Hines Blvd

department: Pathology

institute: UT Southwestern Medical Center

summary: To find out the target of transcription factor Sox7 and Sox17, DNA microarray analysis was performed with RNA from Sox7 and Sox17 knockdown HUVECs.

overall_design: Control / Sox7 knockdown / Sox17 knckdown / Sox7,Sox17 double knockdown. 2 independent experiments.

first: Kangsan

last: Kim

first: Injune


title: Gene expression in porcine induced pluripotent stell (iPS) cell lines and mouse embryonic stem (ES) cells

city: Tsukuba

first: Hirohide

last: Uenishi

state: Ibaraki

address: 2-1-2 Kannondai

institute: National Institute of Agrobiological Sciences

summary:
Transcriptional profiling of porcine induced pluripotent cell lines and comparison with fibroblasts.
Transcriptional profiling of mouse ES cell lines and comparison with fibroblasts as a control for an experiment of porcine induced pluripotent stem cells.

sample_organism:
Sus scrofa
Mus musculus

platform_organism:
Sus scrofa
Mus musculus

overall_design:
[Ss] Gene expression of two newly established porcine iPS clones was compared with a parental embryonic fibroblast cell line of the iPS clones.
[Mm] Gene expression of mouse ES cells was compared with embryonic fibroblasts.

first: Toshimi

last: Matsumoto

first: Tomokazu

last: Fukuda


title: miRNA expression profiling in human glioma stem cell upon TUG1 inhibition

first: Keisuke

last: Katsushima

summary: Glioblastomas show heterogeneous histological features. These distinct phenotypic states are thought to be associated with the presence of glioma stem cells (GSCs), which are highly tumorigenic and self-renewing sub-population of tumor cells that have different functional characteristics. We found that TUG1, a long non-coding RNA (lncRNA), plays pivotal roles in maintaining the self-renewal properties of GSC. Some lncRNAs are known to act as a miRNA sponge in the cytoplasm, where lncRNAs bind to miRNAs and quench their activity. To investigate miRNA expression profiling in GSC upon TUG1 inhibition, we have performed microarray experiment using SurePrint G3 Human miRNA 8x60K Microarray (G4872A, Agilent Technologies).

overall_design: Microarray experiment was performed as single-color hybridization on Agilent human miRNA catalog 8x60k array.

first: Atsushi

last: Natsume

first: Fumiharu

last: Ohka

first: Keiko

last: Shinjo

first: Akira

last: Hatanaka

first: Norihisa

last: Ichimura

first: Yutaka

last: Kondo


title: Transcriptomic analysis of pro-invasive fibroblasts activation short term response

first: Kevin

last: Lebrigand

summary: The effect at short term (48 hours) of leukemia inhibitory factor (LIF), TGFβ or TGFβ + anti-Lif stimulation on the human primary dermal fibroblast (hDF) transcriptome was analyzed by whole genome microarray expression profiling.

overall_design: Total RNA of human primary dermal fibroblasts (hDFs) stimulated by LIF, TGFβ or TGFβ + anti-Lif have been performed in DMEM supplemented with 0.5% FCS containing 2ng/ml final concentration of human recombinant proteins for 48 hours. One-color experiment with 2 biological replicates (marked 1 or 2) of the 4 experimental conditions. Total of 8 samples.

first: C

last: Gaggioli

first: K

first: N

last: Nottet

first: P

last: Barbry

first: B

last: Mari


title: The impact of SpiB overexpression on gene expression profile in A549 cells

status: Public on Nov 30 2016

city: Tianjin

first: Zhe

last: Liu

address: Heping District Qixiangtai Road No. 22

institute: Tianjin Medical University

summary: SpiB, an Ets family transcription factor, is expressed exclusively in mature B cells, T-cell progenitors, and plasmacytoid dendritic cells. To understand the genes regulated by SpiB in epithelial cells, we overexpressed SpiB in lung cancer cell line A549 and examined the change of transcription profile using Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarray (Agilent Technologies).

overall_design: Two-condition experiment, A549-empty vs. A549-SpiB cells. Biological replicates: 3 control, 3 transfected, independently grown and harvested. One replicate per array.

first: Wei

last: Du

first: Xing

last: Xu

first: Qing

last: Niu

first: Xuexi

last: Zhang

first: Yiliang

last: Wei

first: Ziqiao

last: Wang

first: Jun

last: Yan

first: Zheng

last: Fu

first: Xiaobo

last: Li

first: Xichuan

first: Yuan

last: Jiang

first: Zhenfa

first: Zhi

last: Yao

first: Zhenyi

last: Ma


title: Palmitate-induced inhibition of C2C12 insulin pathway modifies the release of exosomes and their biological actions on muscle cells

status: Public on Nov 03 2016

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

summary: Exosomes are cell-released bioactive nanovesicles now considered as new partners in the inter-organ cross-talks. The possibility that skeletal muscle (SkM)-derived exosomes act as a mode of systemic communication has hitherto never been described. Thus, in this study we have tested the hypothesis that through the exosomal route, muscle cells might transmit specific signals during insulin-resistance.

overall_design: C2C12 myoblasts were differentiated into myotubes and then treated with 0.5mM palmitate in order to alter insulin signaling pathway or BSA as control. Exosomes released from palmitate-treated cells (EXO-palm)  and from BSA-treated cells (EXO-BSA) were collected by ultracentrifugation. Then C2C12 were treated with either EXO-palm or EXO-BSA. RNA was extracted and global transcriptomic analysis was performed.

first: Sophie

last: Rome

first: Emmanuelle

last: Meugnier


title: Initial Gene Epxression Responses to Bleomycin Treatment

city: Houston

first: Tao

last: Lu

state: Texas

address: 2101 E NASA Pkwy

department: Radiation Research

institute: NASA Johnson Space Center

summary: To understand initial gene expression responses in confluent human fibroblasts to different bleomycin drug doses and their potential effects on later cellular events.

overall_design: Confluent human fibroblasts AG01522 were treated with 0.1, 1.0 and 10 microgram/ml of bleomycin for 3 hours. Duplicate treatments were done.

first: Ye

first: Honglu

last: Wu


title: Gene expression profile in tumor tissue in murine human lung cancer model between p-T-miR-7 and p-Cont injection group

status: Public on Dec 13 2016

city: Zunyi

first: Lin

state: Guizhou

address: 201 Dalian Road

department: Immunology

institute: Zunyi Medical College

summary: Human lung cancer cell line 95D cells were injected subcutaneously into right flank of Balb/c nude mice (n=8). 7 days later, the plasmid of p-T-miR-7 (100mg) or p-Cont (100mg) was remote given by subcutaneous injection into the left flank of nude mice five times every three days. 3 days after last injection, tumor mass were collected. We sent the tumor tissue to Shanghai Kang Cheng company to detecte the cDNA chip in order to detect the gene expression in p-T-miR-7 injection group.

overall_design: Human lung cancer cell line 95D cells were injected subcutaneously into right flank of Balb/c nude mice (n=8). 7 days later, the plasmid of p-T-miR-7 (100mg) or p-Cont (100mg) was remote given by subcutaneous injection into the left flank of nude mice five times every three days. 3 days after last injection, all mice were killed and we got the tumor tissues.We sent the tumor tissue to Shanghai Kang Cheng company to detecte the cDNA chip. In this study,the total RNA was extracted from in tumor tissue between p-T-miR-7 and p-Cont injection group.Then the expression profiles of gene on these tumors was detected by microarray.

first: L

last: xu

last: Lei


title: Gene expression profile Colorectal Tumor and Normal tissue samples

city: Guangzhou

first: Shineng

state: Guangdong

address: No.107 Yanjiang West Road

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

summary: Analysis of 4 pairs of colorectal cancer tissue and paraneoplastic tissue. The fresh frozen samples were obtained during surgical procedures. Results provide insight into molecular mechanisms underlying malignancy.

overall_design: Differential lncRNA and gene expression in human colorectal cancer was measured between tumor tissues and paraneoplastic tissues. Four independent experiments were performed using four donors for each experiment.

first: Fengting

last: Huang


title: Antigen specific human conventional T cells (CD154+) or regulatory T cells (CD137+) directed agains A. fumigatus or Birch pollen lysate isolated from Birch pollen allergic patients or healthy controls.

status: Public on Oct 25 2016

city: Bergisch Gladbach

first: Jutta

last: Kollet

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

country: Germany

institute: Miltenyibiotec GmbH

summary: Foxp3+ regulatory T cells (Treg) play a central role for tolerance against self and innocuous environmental antigens. However, the role of antigen-specificity for Treg-mediated tolerance is only incompletely understood. Here we show by direct ex vivo characterization of human CD4+ T cells, that the response against innocuous airborne antigens, such as plant pollen or fungal spores, is dominated by memory-like antigen-specific Treg. Surprisingly, breakdown of tolerance in atopic donors was not accompanied by a quantitatively or qualitatively altered Treg response, but instead correlated with a striking dichotomy of Treg versus Th2 target specificity. Allergenic proteins, are selectively targeted by Th2 cells, but not Treg. Thus human Treg specific for airborne antigens maintain tolerance at mucosal sites and the failure to generate specific Treg against a subgroup of antigens provides a window of opportunity for allergy development.

overall_design: PBMCs from sex and age matched birch pollen allergic patients and healthy controls, were stimulated (7h) with airborne fungal (A. fumigatus) or birch pollen antigen (birch) and sorted into antigen specific conventional and regulatory T cells according to their expression of CD154+ and CD137+ on CD4+ T cells, respectively. Number of samples per group in parentheses: Healthy controls stimulated with A. fumigatus (n=5), allergic patients stimulated with A. fumigatus (n=6), healthy controls stimulated with birch (n=6), allergic patients stimulated with birch (n=4).

first: Petra

last: Bacher

first: Bernhard

last: Gerstmayer

first: Silvia

last: Rüberg

first: Michail

last: Knauel

first: Alexander

last: Scheffold

first: Frederik

last: Heinrich


title: Gene expression analysis of papillary and reticular dermis microdissected from the same skin sample

status: Public on Oct 04 2016

city: Showa-ku, Nagoya

first: Yasushi

last: Date

address: 65 Tsurumai-cho

department: Graduate School of Medicine

institute: Nagoya University

summary: The dermis is divided into two distinct layers. The upper, papillary dermis is characterized by thin and sparse fibers. The lower, reticular dermis is composed of solid tissue made up of thicker highly dense fibers. It has been reported that cultured fibroblasts isolated from the papillary and the reticular dermis exhibit different properties. In this study, we analyzed gene expression profiles of human papillary dermis and reticular dermis obtained using laser capture microdissection.

overall_design: Gene expression was compared between papillary dermis and reticular dermis microdissected from a normal skin biopsy sample.


title: Study of transcriptional effects of drugs on SNU-423 hepatocellular carcinoma cell lines

status: Public on Nov 15 2016

city: Rennes

first: Cedric

last: Coulouarn

address: CLCC Eugène Marquis, Rue de la Bataille Flandres Dunkerque, Bat D, 1er étage

institute: INSERM

summary: Hepatocellular carcinoma (HCC) is the second most common cause of cancer-related death worldwide. Like in many cancers, tumor heterogeneity in HCC hampers the development of personalized therapies. Integrative genomics contributed to characterize HCC subtypes by identifying specific genetic alterations and molecular signatures, leading to targeted drug candidates. However, no consensus was achieved for genes and pathways recurrently altered in HCC. Here, a meta-analysis of 15 independent HCC datasets identifies a comprehensive signature consisting of 935 genes commonly deregulated in HCC as compared to the surrounding non-tumor tissue (P<0.01). The 935-gene HCC signature covers well-established cancer hallmarks (e.g. proliferation, metabolic reprogramming, microenvironment remodeling) together with specific hallmarks associated with protein turnover and epigenetics. Accordingly, the 935-gene HCC signature highlights relevant drugs for systemic therapies, including including two histone deacetylase (HDAC) inhibitors (trichostatin A and vorinostat), PI3K inhibitor LY294002, mTOR inhibitor sirolimus (also known as rapamycin), alpha-estradiol and resveratrol. The impact of these drugs as compared to sorafenib that is currently used for the treatment of advanced HCC was evaluated on the viability of 6 HCC-derived cell lines. We concluded that combined therapies targeting common and subtype-specific cancer networks may represent a relevant strategy to efficiently treat liver cancer.

overall_design: SNU-423 cells (ATCC® CRL-2238™, grade III/IV) were grown in a RPMI-1640 medium supplemented with 100U/ml penicillin, 100μg/ml streptomycin and 10% fetal bovine serum. Cultures were performed at 37°C in a 5% CO2 atmosphere. Alpha-estradiol, LY294002, rapamycin, resveratrol, sorafenib and vorinostat were purchased from Santa Cruz Biotechnology (Heidelberg, Germany). Trichostatin A was purchased from Sigma-Aldrich (St. Louis, MO, USA). All molecules were solubilized in a dimethyl sulfoxide (DMSO) solution. For the microarray experiments the concentrations were optimized to induce 50% cell mortality after a 72h drug exposure, in order to allow the extraction of nucleic acids from the remaining viable cells. Experiments were performed in monoplicates.


title: DNA methylation is required for chromatin binding by Mbd2 and Mbd3 in ES cells (mRNA)

city: Pittsburgh

first: Sarah

last: Hainer

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

institute: University of Pittsburgh

summary: Cytosine methylation on DNA is an important epigenetic and regulatory mark. Chromatin remodeling complexes containing methyl-CpG binding domain (MBD) proteins modulate chromatin structure and transcription at methylated loci. Two MBD proteins, Mbd2 and Mbd3, are mutually exclusive members of the NuRD chromatin remodeling complex, and have been shown to bind methylated or hydroxymethylated DNA, respectively. However, a recent study called both results into question, showing that chromatin binding by these proteins is partially (Mbd2) or completely (Mbd3) independent of DNA methylation/hydroxymethylation. Here we re-analyze these data and observe discrepancies with both conclusions. Furthermore, we describe multiple new datasets that demonstrate the dependence of endogenous Mbd2 and Mbd3 on DNA methylation. Interestingly, we find that Mbd2 and Mbd3 are also dependent on one another for binding, likely due to the fact that both are required for normal levels of DNA methylation/hydroxymethylation. These findings describe a regulatory loop controlling the DNA methylation machinery and its readers.

overall_design: knockdowns

first: Kurtis

last: McCannell

first: Jun

last: Yu

first: Ly-Sha

last: Ee

first: Lihua

last: Zhu

first: Oliver

last: Rando

first: Thomas

middle: G

last: Fazzio


title: MicroRNA expression profiling of prefrontal cortex samples from C57 mice treated with saline or morphine

status: Public on Nov 01 2016

city: Washington

first: Bi-Dar

last: Wang

state: DC

address: 2300 I street, NW

department: Pharmacology and Physiology

institute: The George Washington University Medical Center

summary: Our previous study showed that Dicer1 expression is positively correlated with the development of analgesic tolerance. To further understand the miRNA regulation by Dicer in the development of tolerance, we performed microRNA profiling using Agilent mouse miRNA arrays to identify the miRNA profiles in the prefrontal cortex from C57BL/6J (C57) mice under saline or morphine treatment.

overall_design: 8 prefrontal cortex samples derived from C57 mice treated with saline or morphine. 8 RNA samples, purified from the collected prefrontal cortex samples using Qiagen miRNeasy kit, were processed and applied to Agilent-019119 mouse miRNA arrays. Array data was normalized and analyzed using Agilent GeneSpring program.

first: Bi

middle: D

first: Norman

last: Lee


title: Comparison of gene expression between Human umbilical vein endothelial cells and Human liver sinusoidal endothelial cells

status: Public on Oct 24 2016

city: Birmingham

first: Shishir

last: Shetty

address: Wolfson Drive

department: Institute of Immunology and Immunotherapy

institute: University of Birmingham

summary: To identify leukocyte adhesion receptors which differentially regulate recruitment in human liver sinusoidal endothelial cells compared to a protoptypic venular endothelium

overall_design: Gene expression was measured in four groups Group 1: cultured human liver sinusoidal endothelial cells (HSEC) Group 2: cultured human umbilical vein endothelial cells (HUVEC) Group3: Interferon gamma and tumour necrosisfactor alpha treated HSEC and Group 4: Interferon gamma and tumour necrosisfactor alpha treated HUVEC. Two replicates were used for each group.

first: Dalan

last: Bailey


title: Effect of NR4A3 siRNA treatment on gene expression of islet derived hybrid cell of 1.1B4

status: Public on Sep 15 2016

city: Minato-ku

first: Yuzuru

last: Otsuka

state: Tokyo

department: Department of Nutrition

institute: Toita Women's College

summary:
Gene regulation associated with antioxidant defense system in pancreatic beta cells still needs to be elucidated, we found NR4A3 gene expression was up-regulated with 100mM H2O2, therefore, we analyzed the genes expression with Agilent micro-array after NR4A3 siRNA4 treatment by one color method, and found 1044 genes were up-regulated and 859 genes were down regulated in NR4A3 knocked down cell. Changes of some genes expressions were confirmed by real time PCR.
The genes of 1044 in NR4A3 siRNA treated cell were up-regulated over 2 folds and 859 genes were down-regulated under 0.67 folds compared with control sample.

overall_design: We analyzed the comprehensive gene expression changes treated by NR4A3 siRNA in pancreatic beta-cell derived 1.1B4 cells using Agilent microarray.

first: Motoko

last: Yamada

first: Etsuko

last: Ueta


title: Study of transcriptional effects of Vorinostat, Sorafenib and Resveratrol on SNU-387 and HepG2/C3A hepatocellular carcinoma cell lines

overall_design: SNU-387 (ATCC® CRL-2237™, grade IV/V) and HepG2/C3A (ATCC® CRL-10741™) were grown in a RPMI-1640 medium supplemented with 100U/ml penicillin, 100μg/ml streptomycin and 10% fetal bovine serum. Cultures were performed at 37°C in a 5% CO2 atmosphere. Resveratrol, sorafenib and vorinostat were purchased from Santa Cruz Biotechnology (Heidelberg, Germany). All molecules were solubilized in a dimethyl sulfoxide (DMSO) solution. For the microarray experiments the concentrations were optimized to induce 50% cell mortality after a 72h drug exposure, in order to allow the extraction of nucleic acids from the remaining viable cells. Experiments were performed in monoplicates.


title: Long Term Culture of the A549 Cell Line Promotes Differentiation Towards an Alveolar Type II (ATII) Phenotype; A549 Time course.

status: Public on Oct 19 2016

city: Salisbury

first: James

middle: Ross

last: Cooper

state: Wiltshire

address: PHE Porton, Manor Farm Road

department: ECACC

institute: Public Health England

summary: Pulmonary research requires models that represent the physiology of alveolar epithelium but concerns with reproducibility, consistency and the technical and ethical challenges of using primary or stem cells has resulted in widespread use of continuous cancer or other immortalized cell lines.  The A549 ‘alveolar’ cell line has been available for over four decades but there is an inconsistent view as to its suitability as an appropriate model for primary alveolar type II (ATII) cells.  Since most work with A549 cells involves short term culture of proliferating cells, we postulated that culture conditions that reduced proliferation of the cancer cells would promote a more differentiated ATII cell phenotype.  We examined A549 cell growth in different media over long term culture and then used microarray analysis to investigate temporal regulation of pathways involved in cell cycle and ATII differentiation; we also made comparisons with gene expression in freshly isolated human ATII cells.  Analyses indicated that long term culture in Ham’s F12 resulted in substantial modulation of cell cycle genes to result in a quiescent population of cells with significant up-regulation of autophagic, differentiation and lipidogenic pathways.  There were also increased numbers of up- and down-regulated genes shared with primary cells suggesting adoption of ATII characteristics and multilamellar body (MLB) development.  Subsequent Oil Red-O staining and Transmission Electron Microscopy confirmed MLB expression in the differentiated A549 cells.  This work defines a set of conditions for promoting ATII differentiation characteristics in A549 cells that may be advantageous for studies with this cell line.

overall_design: The A549 Cell Line was maintained in long term culture in Ham's F12 medium with 10% Foetal Bovine Serum for 25 days in triplicate in order to drive differentation towards an alveolar type II differentated state. Cells were harvested at T0 (log phase), day 7, 11, 18 and 25 to evaluate their gene expression over the differentation period.


title: Long Term Culture of the A549 Cell Line Promotes Differentiation Towards an Alveolar Type II (ATII) Phenotype;  Comparison of A549 cells with Primary ATII Cells

overall_design: The A549 Cell Line was harvested in log phase growth. The gene expression profile of the triplicate cultures of A549 cells in this state was compared to cells from replicate primary alveolar type cultures obtained from macroscopically normal areas of lung tissue from a single donor with lung cancer undergoing lung resection surgery.


title: Gene Signature of High White Blood Cell Count in B-precursor Acute Lymphoblastic Leukemia

status: Public on Oct 13 2016

city: Detroit

first: Yubin

last: Ge

state: MI

address: 110 East Warren Ave.

institute: Karmanos Cancer Institute

summary: Microarray gene expression profiling of ETV6-RUNX1-positive BP-ALL patient samples to identify differentially expressed genes based on the presenting white blood cell count (<50,000/cumm vs >50,000/cumm).

overall_design: Ten samples from patients with low white blood cell counts ( <50,000/cumm) were compared with five samples from patient with high white blood cell counts (>50,000/cumm).

first: Alan

last: Dombkowski

first: Jeffrey

last: Taub

first: Holly

last: Edwards

first: Mara

last: Rubenstein


title: Long Term Culture of the A549 Cell Line Promotes Differentiation Towards an Alveolar Type II (ATII) Phenotype

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

overall_design: Refer to individual Series


title: The cellular response of immortalized TRF2dB fibroblast cells by 4-hydroxytamoxifen drug treatments

status: Public on Sep 01 2016

city: Nankang

first: Liuh-Yow

last: Chen

state: Taipei

address: 128, Section 2, Academia Rd,

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

summary: In our study, we have successfully generated a cell line that stably expresses a mutant TRF2 with a truncated N-terminal basic domain from BJ normal human fibroblasts. This mutant named, TRF2∆B, can artificially loop out telomeric DNA as ECTR in circular forms, mediated by XRCC3 holiday junction resolution protein and SLX4 associated recombination endonucleases. To avoid the deleterious effect on cell growth resulting from constant TRF2∆B expression, we fused TRF2ΔB with an estrogen receptor ligand-binding domain variant ERT2 to keep TRF2∆B inactive in the BJTL cells, and in the presence of 4-hydroxytamoxifen (4-OHT),which binds to ERT2, TRF2∆B becomes active. With this system, we aim to investigate the cellular response of immortalized BJ fibroblast cells to 4-OHT drug treatments.

overall_design:
Cellular response in immortalized human fibroblast transduced with ERT2-TRF2dB gene was measured at 0, 12, 24, 36, 48 and 60 hours of 1 µM  4-hydroxytamoxifen (4-OHT).  IFNb gene expression in immortalized human fibroblast transduced with vector was measured at 0 and 48 hrs of 1 µM  4-hydroxytamoxifen (4-OHT) as controls. Cellular expression of treated ERT2-TRF2dB cells are normalized to untreated ERT2-TRF2dB cells and compared to the expressions of 4-OHT treated vector fibroblast cells that are normalized to untreated vector fibroblast cells. Three independent experiments were performed at each time for each experiment.
Liuh-Yow, Chen

first: Yi-An

first: Yee-Peng

last: Tiang


title: miR-449 regulated mitotic genes

status: Public on Sep 30 2016

city: Wien

first: Daniel

middle: W

last: Gerlich

state: Select State/Province

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA

summary: Progression trough cell cycle depends on the cycling of a significant fraction of the transcriptome and the proteome. This involves transcription and translation of large groups of cycling mRNAs in a given cell cycle stage, and their subsequent rapid degradation and/or translation inhibition in another. miRNAs are strong candidates as regulators of these important fluctuations during cell cycle progression, since they mediate both degradation of target mRNAs with fully complementary sequences, and down-regulation of the translation of mRNAs with non-perfect complementarity. A growing body of evidence suggests that miRNAs play an important role in the control of cell cycle, cell division, and proliferation. In this project we address mitotic gene regulation by miRNA-449 using a gene expression approach.

overall_design: miR-449 and negative control mimic induced gene expression was measured 48 hours after transfection of the mimic molecules.

first: Juan

middle: P

last: Fededa


title: Gene Expression Profiling of Resting and Activated CD4+ T Cells in Patients with Multiple Sclerosis

status: Public on Sep 13 2016

city: Linkoping

last: Eklund

address: Universitetssjukhuset

institute: Linkoping University

summary: Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system with varying disease course as well as response to treatment. Thus, biomarkers for personalized treatment are highly needed. We tested the hypothesis that in vitro activation of CD4+ T cells from MS patients could reveal pathways containing potential biomarkers and found a dysregulated dynamic gene response upon activation. By integrating our findings with data from genome-wide association studies and using a network-based approach, we constructed a highly connected MS gene module disclosing cell activation and chemotaxis as central components.

overall_design: Gene expression in isolated CD4+ T cells from MS patients and controls was measured after 24 hours of anti-CD3/-CD28 stimulation (0.03 µg/ml) or in unstimulated cells. Cells from each of the 14 patients and 14 control subjects, were both stimulated and nonstimulated i.e. samples are paired.

first: Mika

last: Gustavsson


title: Expression data from fetal sheep lung tissue (right lower lobe)

status: Public on Sep 22 2016

city: Darlinghurst

first: Tim

last: Molloy

state: NSW

address: Level 8, 405 Liverpool St

department: Haematology

country: Australia

institute: St Vincent's Centre for Applied Medical Research

summary:
Study investigating responses of lung to sub-clinical antenatal steroid (betamethasone phosphate) exposure
Microarray was used to determine the inflammatory transcriptome in homogenised lung tissue samples

overall_design: Fetal sheep at 115d GA were catheterised prior to 2 maternal IV infusions of betametahasone phosphate

first: M

last: Kemp

first: T

middle: J


title: Gene expression profiling for intravascular large B-cell lymphoma (IVLBCL)

status: Public on Aug 13 2016

city: NAGOYA

first: KAZUYUKI

last: SHIMADA

address: 65, Tsurumai-cho, Showa-ku

department: HEMATOLOGY AND ONCOLOGY

country: Japan

institute: NAGOYA UNIVERSITY

summary: IVLBCL is a rare distinct disease entity of extranodal large B-cell lymphoma. The disease is characterized by selective growth of tumor cells in the lumina of small vessels and by the absence of remarkable lymphoadenopathy. We have developed patient derived xenograft IVLBCL mouse models from primary bone marrow samples. This dataset includes the gene expression profiling of IVLBCL tumor cells from the mouse xenograft models.

overall_design: To evaluate the gene expression profiling of IVLBCL, tumor cells in tumor formed spleen in 4 mouse models (IVLBCL#1, #2, #3, and #4) and peripheral blood mononuclear cells from 4 normal healthy volunteer donors (PB#1, #2, #3, and #4) were purified by CD19 positive magnetic beads selection. Total RNA was extracted from these CD19 positive cells.Total eight RNA samples were then analyzed to evaluate the gene expression profiling for IVLBCL.

first: Kazuyuki

last: Shimada

first: Masahiro

last: Nakatochi

first: Akihiro

last: Hirakawa

first: Yusuke

last: Takagi


title: Gene expression profiling and array CGH analysis for intravascular large B-cell lymphoma (IVLBCL)

type: Genome variation profiling by genome tiling array


title: Proteasome inhibition and oxidative biochemistry are synergistic triggers of metabolic heme toxicity (part 2)

status: Public on Aug 21 2016

city: Zurich

first: Christian

middle: Andreas

last: Schaer

address: Raemistrasse 100

country: Switzerland

institute: University Hospital Zurich

summary:
Control of intracellular heme levels by extracellular scavenger proteins and intracellular heme oxygenases are essential functions during disease states with enhanced extracellular heme release. During severe hemolysis or rhabdomyolysis uncontrolled heme exposure can cause acute kidney injury and endothelial damage. The cytotoxic activity of heme has been primarily attributed to its pro-oxidative potential. However, the mechanisms of heme toxicity have never been systematically explored. Besides its redox reactivity, heme could also adversely alter cellular functions through its broad binding affinity to multiple non-hemoproteins. Such interactions may impair protein functions and support heme toxicity.
In this study we mapped the gene expression profile of Hb triggered acute kidney injury in old blood transfused guinea pigs by serial analysis of gene expression (SAGE). Additionally, the toxic heme response of mouse embryo fibroblasts was systematically characterized on the gene and protein expression levels by gene array experiments and quantitative mass-spectrometry of stable isotope labeled cells. In all these studies, in addition to oxidative stress signals, the most significant signals were reproducibly found for biologic networks related to altered protein degradation, which ultimately triggers the response to unfolded proteins and apoptosis. These screening data could be mechanistically explained by heme-proteasome interactions and a proteasome inhibitor activity of heme. Proteasome inhibition drastically reduced the threshold of cellular toxicity during heme exposure. We therefore propose a novel model of heme toxicity whereby proteasome inhibition by the porphyrin fuels a vicious cycle of oxidative protein modification, accumulation of damaged proteins, cell damage and apoptosis.

overall_design: A two color common reference design was chosen with 2-8 independent biological replicates of each condition. Each experimental sample (Cy5 labeled) was hybridized against a non-treated reference sample (Cy3 labeled). To compensate for dye bias control arrays with competitively hybridized Cy3- and Cy5-labeled non-treated reference samples were used. The latter allowed for a very robust statistical analysis with pair-wise comparison of treatment array replicates versus the corresponding control array replicates.

first: Dominik


title: Human bone marrow-derived mesenchymal stem cells (Human BM-MSCs): Control (recombinant human LIGHT, rhLIGHT 0 ng/ml) vs rhLIGHT 200 ng/ml

status: Public on Aug 23 2016

city: Ulsan

first: Sook-Kyoung

last: Heo

address: 877 Bangeojinsunhwan-doro

department: Biomedical Research Center

institute: University of Ulsan College of Medicine

summary: Transcriptional profiling of Human BM-MSCs comparing between control (BSA-treated) and rhLIGHT treated human BM-MSCs at 72hr

overall_design: one-condition experiment, Control (rhLIGHT 0 ng/ml) vs  rhLIGHT 200 ng/ml. Biological replicates: 1.

first: Sook

first: Eui

last: Noh


title: Proteasome inhibition and oxidative biochemistry are synergistic triggers of metabolic heme toxicity (part 1)

overall_design: A two color common reference design was chosen with 2-4 independent biological replicates of each condition. Each experimental sample (Cy5 labeled) was hybridized against a non-treated reference sample (Cy3 labeled). To compensate for dye bias control arrays with competitively hybridized Cy3- and Cy5-labeled non-treated reference samples were used. The latter allowed for a very robust statistical analysis with pair-wise comparison of treatment array replicates versus the corresponding control array replicates.


title: Cathelicidin insufficiency in patients with fatal leptospirosis

status: Public on Sep 23 2016

city: New Haven

first: Albert

last: Ko

state: CT

address: 60 College St, PO Box 208034

department: Epidemiology of Microbial Diseases

country: USA

institute: Yale University

summary: Whole blood transcriptional profiling of Brazilian patients with acute leptospirosis to identify mechanisms associated with case fatality

overall_design: Independent whole blood was collected during early acute illness, convalescence, or from healthy volunteers directly into PAXgene solution and stored at -70C until RNA was extracted. RNA was isolated using Qiagen PAXgene Blood Kit, and Cy3-labeled cRNA was generated using the Low Input QuickAmp Labeling Kit One-Color and RNA Spike-In Kit, One-Color. 600ng of Cy3-labeled cRNA was fragmented and hybridized to Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarrays

first: Janet

middle: C

last: Lindow

first: Patty

last: Lee


title: Gene Expression Analysis in Different Macrophage Phenotypes

status: Public on Aug 10 2016

city: Chui-ku,Kobe

first: Kyoko

last: Yamashiro

address: 6-4-3, inatojima-Minamimachi,

institute: Asubio pharma co.,LTD.

summary: Macrophage activation is the main immunological process occurring during the development of several diseases, and the heterogeneity of macrophage activation or differentiation has been suggested to be involved in disease progression. In the present study, we attempted to identify molecules specifically expressed on human classically activated macrophages (M1) to investigate the significance of the M1-like phenotype in human diseases. Human monocyte-derived macrophages were differentiated into M1, M2a, M2b, and M2c phenotypes, and gene expression profiles were analyzed by cDNA microarray analysis and were used for bioinformatics examination. The gene expression profiles of murine macrophages were additionally evaluated. We identified guanylate-binding protein 5 (GBP5), which is associated with leucine-rich repeat protein 3-mediated inflammasome assembly in the M1 macrophages of both humans and mice. Notably, GBP5 protein expression was detected in cultured M1 macrophages by Western blot analysis. GBP5 is a useful candidate marker of the M1 phenotype.

overall_design: CD14+ monocytes from human PBMC were cultured with GM-CSF(10 ng mL−1) or M-CSF (50 ng mL−1) for seven days to differentiate into macrophages.To induce macrophage subtypes [M1, M1(-), M2a, M2b, and M2c], the macrophages were further stimulated for 24 h with LPS (10 ng mL−1) + IFN-γ (50 ng mL−1), IFN-γ (50 ng mL−1), IL-4 (10 ng mL−1), IL-1β (10 ng mL−1), and IL-10 (10 ng mL−1). Control macrophages (M0) were prepared by incubating for 24 h without additional factors.Two independent experiments were performed using different donors.

first: Yukio

last: Fujiwara

first: Yoshiyuki

last: Hizukuri

first: Naoyuki

last: Makita

first: Koji

last: Ohnishi

first: Motohiro

last: Takeya

first: Yoshihiro

last: Komohara

first: Yasuhiro

last: Hayashi


title: Comparation the mRNA Expression Profile of the MV4-11 Sorafenib Resistant Cells and the Parental Cells

status: Public on Aug 01 2016

city: Guangzhou

first: Amin

last: Huang

address: 651 Dongfengdong East Rd

country: China

institute: Sun Yat-sen University Cancer Center

summary: Our gene set analysis of MV4-11-R versus MV4-11 indicated decreased depolarization of mitochondria and mitochondrial membrane, mitochondrial dysfunction and anti-apoptosis as other top ranked molecular or cellular functions of differential gene sets. expression of most genes encoding glycolytic enzymes was up-regulated in MV4-11-R cells we revealed a metabolic alteration in sorafenib-resistant cell lines with mitochondrial respiration deficiency, leading to substantial decrease of mitochondria-derived ATP generation and a significant increase in glycolytic activity to maintain sufficient ATP production. Our study revealed a metabolic signature of sorafenib resistance and indicated that increase of glycolytic activity including upregulation of major glycolytic enzymes may be viewed as a marker for early detection of sorafenib resistance in AML patients with FLT3/ITD mutation and glycolytic inhibitors warrant further investigation as alternative therapeutic agents for sorafenib-resistant cells

overall_design: Sorafenib resistant cells MV411-R VS. parental MV4-11 cells. Biological replicates: 3 control replicates,  3 treated replicates.

first: Yumin

last: Hu


title: Mouse iNKT cell: Wild type Vs Bcl11b deficient

city: Albany

first: Dorina

last: Avram

state: NY

address: 43 New Scotland Avenue

department: Center for Immunology and Microbial Disease

institute: Albany Medical Center

summary: Transcriptional profiling of mouse iNKT cells comparing wild type and Bcl11b deficient cell. The mice were treated with 4 μg of α-galactosylceramide. Goal was to determine the effects of transcription  factor Bcl11b removal in iNKT cells.

overall_design: Intraperitoneal treatment with 4 μg of  α-Galactosylceramide. Two pair of wild type (BCL11b F/F  Vα14 transgenic) and  Knock out (BCL11b F/F PLZF-Cre Vα14 transgenic)) mice were treated. Lymphocytes from spleen and liver were enriched and stain with PBS-57 Loaded CD1d tetramer. Pure iNKT cells were collected  through cell sorter.

first: Mohammad

middle: N

last: Uddin


title: Transcriptome response to ODC downregulation and reduced polyamine titres in tobacco

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

summary: Although a lot is known about polyamines (PAs) and their functions, scientists have not yet been able to completely understand and elucidate their mode of action and interactive molecular partners. An attempt has been made in this direction by RNAi-mediated down-regulation of a key biosynthetic gene in PA metabolic pathway, ornithine decarboxylase (ODC), under a constitutive promoter and to correlate various morphological and physiological abnormalities observed in response to reduced PA titres with a genome wide transcriptome analysis of ODC-knockdown tobacco RNAi line. The analysis has not only thrown up a number of candidate genes whose expression could be directly or indirectly affected by cellular PA levels but has also been very informative with regards to the regulation of PA pathway.

overall_design:
Tobacco wild-type and transgenic lines were grown under the culture room conditions of 16 h light at 25°C
Agilent  Tobacco Gene Expression 4x44k K (AMADID: 021113) , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Ami

last: Choubey

first: M

middle: V

last: Rajam