title: UNCOVERING VULVAR CARCINOMA: AN INTEGRATIVE APPROACH

city: Sao Paulo

first: Fabio

middle: Albuquerque

last: Marchi

address: Av Dr Arnaldo

department: CTO

country: Brazil

institute: ICESP

type:
Expression profiling by array
Genome variation profiling by array


title: Identification of a novel risk factor for intracranial aneurysms in ADPKD using iPSC models [Agilent]

status: Public on Aug 04 2016

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

summary: Cardiovascular complications are the leading cause of death in autosomal dominant polycystic kidney disease (ADPKD), and intracranial aneurysm (ICA) causing subarachnoid hemorrhage is among the most serious complications. The diagnostic and therapeutic strategies for ICAs in ADPKD have not been fully established. We here generated induced pluripotent stem cells (iPSCs) from seven ADPKD patients, including four with ICAs. The vascular cells differentiated from ADPKD-iPSCs showed altered Ca2+ entry and gene expression profiles compared with those from control-iPSCs. We found that the expression level of a metalloenzyme gene, matrix metalloproteinase (MMP) 1, was specifically elevated in the iPSC-derived endothelia from ADPKD patients with ICAs. Furthermore, we confirmed a statistically significant correlation between the serum MMP1 levels and the development of ICAs in 354 ADPKD patients, indicating that the serum MMP1 levels may be a novel risk factor and become more beneficial when combined with other risk factors. These results suggest that cellular disease models with ADPKD-specific iPSCs can be used to study the disease mechanisms and to identify novel disease-related molecules or risk factors.

overall_design: The gene expression profiles of vascular endothelia and smooth muscle cells derived from control- and ADPKD-iPSCs were analyzed. Seven control-iPSC derived endothelial cells (ECs), seven ADPKD-iPSC derived ECs, ten control-iPSC derived vascular smooth muscle cells (SMCs), and seven ADPKD-iPSC derived SMCs were analyzed.

first: Tomonaga

last: Ameku

first: Fumihiko

last: Shiota

first: Fumiyo

last: Kitaoka

first: Naoki

last: Amano

first: Masahiro

last: Nakamura

first: Kenji

last: Osafune


title: Increased expression of long non-coding RNAs in T cells from patients with rheumatoid arthritis facilitates the inflammatory responses

status: Public on Aug 01 2016

city: Chia-Yi

first: Hui

middle: Chun

last: Yu

address: No. 2, Min-Sheng Rd, Dalin Town

department: Medical research

country: Taiwan

institute: Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation

summary: The expression levels of LOC100652951 and LOC100506036 were increased in RA T cells. Treatment with biologic agents could lower the expression of LOC100652951 in RA T cells. LOC100506036 could regulate the expression of SMPD1 and NFAT1 and could contribute to the inflammatory responses in RA

overall_design: The aberrantly expressed lncRNAs were measured in Jurkat cells co-cultured with or without ionomycin and phorbol 12-myristate 13-acetate.

first: Ming-Chi

last: Lu


title: Identification of novel potential biomarkers and signaling pathways related to otitis media induced by diesel exhaust particle in in vivo system via transcriptomic analysis

status: Public on Sep 13 2016

city: Goyang

first: Hyo-Jeong

last: Kim

address: 32, Dongguk-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do 10326, Republic of Korea

country: South Korea

institute: Dongguk University

summary: Association between air pollutants and inflammatory diseases such as Otitis Media (OM) has been shown in recent studies. Indeed, significantly higher rates of OM incidence in air polluted area have been evident by epidemiological researchers. Diesel exhaust particle (DEP), one of major components among diverse air pollutants, is characterized by a carbonic mixture composed of polycyclic aromatic hydrocarbons (PAHs), nitro-PAHs, small amounts of sulfate, nitrate, metals, and other trace elements. The exposure to DEP as a risk factor for inflammatory diseases has been reported in several recent investigations. In line with these, our previous study identified potential biomarkers in in vitro system through gene expression microarray and pathway analysis. Although investigations in in vitro system have been conducted to elucidate plausible biomarkers and molecular mechanisms related with DEP, it is necessary to carry out in vivo study to identify exact biological relevance regarding incidence of OM caused by DEP exposure.   In this study, we discovered potential molecular biomarkers and pathways triggered by DEP exposure in rodent model.   Here, we conducted transcriptomic analysis to identify novel potential biomarkers in middle ears of DEP-exposed mice.   A total of 697 genes were differentially expressed in the DEP-exposed mice; 424 genes and 273 genes were up-and down-regulated, respectively. In addition, signaling pathways among differentially expressed genes mediated by DEP exposure were predicted from different two point of view. Subsequently, we identified several key molecular biomarkers, CHRM1, EPO, SOS1, ESR1, CD4, and IFNA1.   In conclusion, our results might ascertain related cell process and signaling interacted genes underlying DEP exposure and its effects. Moreover, the discovered biomarkers can be recognized as potential candidates for developing early diagnosis and effective treatment strategies of DEP-mediated disorders.

overall_design: One-condition experiment, DEP treated mouse ear. Biological replicates: 4 replicates.

first: Young-Rok

last: Seo

first: Jee-Young

last: Kwon

first: Moo-Kyun

last: Park


title: UNCOVERING VULVAR CARCINOMA: AN INTEGRATIVE APPROACH [GE]

status: Public on Sep 15 2016

summary: Array-based genomewide expression (GWE) analyses was used to analyze 17 VSCC samples from untreated patients. The data were validated using relative quantitative PCR.

overall_design: Experiment condition, 17 VSCC cDNA samples obtained from untreated patients were labeled with Cy3 and a pool of 11 adjacent normal tissue samples were labled with Cy5. Samples Cy3 and Cy5 were mixed and hybridized at slide glasses Agilent 8x60 platform.

middle: A

first: Andre

last: Laborato


title: Differentiation of DLBCL induced by HDAC inhibitors is associated with sensitization to proteasome inhibition

city: Montreal

first: Koren

last: Mann

state: Quebec

address: 3755 Cote Ste Catherine

country: Canada

institute: Lady Davis Institute

summary: Epigenetic modifying enzymes are commonly mutated in diffuse large B cell lymphoma (DLBCL), suggesting that epigenetic regulation is an important factor in DLBCL pathogenesis and a potential target for therapy.  We developed resistant cell lines to histone deacetylase inhibitors (HDACi), one such epigenetic therapy, in order to define mechanisms of response and resistance. Strikingly, using gene expression and metabolic profiling, we found that development of HDACi resistance was associated with differentiation toward a plasmablast-like phenotype. Differentiation correlated with decreased B cell receptor signaling, increased ER stress and activation of the unfolded protein response, and increased sensitivity to proteasome inhibitors.  Importantly, we found evidence of differentiation in lymphoma biopsies from patients treated with HDACi.  Together, these data show, for the first time, that HDACi are differentiating agents in lymphoma and may be used to prime DLBCL for targeted therapy including proteasome inhibitors.

overall_design: Gene expression in DLBCL cells from tumor biopsies after 15 days panobinostat therapy

middle: K

first: Wilson

middle: H

last: Miller


title: Whole genome RNA micro array analysis of Plasmodium berghei sporozoites infected host cells

status: Public on Sep 01 2016

city: Hyderabad

first: Mulaka

last: Maruthi

state: Telangana

address: Gachibowli

department: Animal Biology

country: India

institute: University of Hyderabad

summary: mRNA Transcripts expression profile of Plasmodium berghei infected host HepG2 cells with and without SUMO1 over expression. To check the changes in the transcript profiles upon SUMO1 over expression which is responsible for Plasmodium berghei parasite's growth arrest in host HepG2 cells.

overall_design: Agilent one-color experiment, Organism: Homo sapiens, Custom Agilent 8x60k Human Whole Genome Microarray Gene expression (AMADID: 039494), Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442).

first: Kota

last: Arun Kumar


title: Comparative gene profiling study: Pak1 deficient human breast cancer cells vs Pak1 wt breast cancer cells

status: Public on Jul 23 2016

city: Tlalnepantla

first: Luis

middle: E.

last: Arias-Romero

address: Avenida de los Barrios #1

country: Mexico

institute: UBIMED

summary: To identify differentially regulated genes between wild-type and Pak1 deficient human breast cancer cells, we performed a comparative gene profiling study by using human whole genome arrays.

overall_design: We compared the gene expression profiles of MCF10A.B2 cells (MCF10A cells expressing a chemically activatable form of Her2) stably expressing a Tet inducible shRNA directed against Pak1 gene. All the experiments were performed in duplicate using tumor derived cells from two different tumors per group.

middle: E

first: Jonathan

last: Chernoff


title: Human intestinal epithelial cells: Control vs. MIC-1 Transfected

city: Yangsan

first: YUSEOK

last: MOON

state: (Select)

address: Rm 704 PNU Med School

institute: PUSAN NATIONAL UNIV. med school

summary: Transcriptional profiling of human intestinal epithelial cells comparing control untreated HCT-8 cells with HCT-8 cells transfected with a MIC-1 gene.

overall_design: Two-condition experiment, HCT-8 vs. MIC-1-overexpressing HCT-8 cells.

first: Juil

first: Yuseok

last: Moon


title: Gene expression analysis during acute hepatitis C virus infection associates dendritic cell activation with viral clearance

status: Public on Jul 29 2016

city: Pamplona

first: Pablo

last: Sarobe

address: Avda. Pio XII, 55

country: Spain

institute: CIMA

summary:
Background and Aims: Viral clearance during acute hepatitis C virus (HCV) infection is associated with the induction of potent antiviral T-cell responses. Since dendritic cells (DC) are essential in the activation of primary T-cell responses our goal was to analyze gene expression in DC from patients during acute HCV infection.
Methods: By using microarrays, gene expression was compared in resting and activated peripheral blood plasmacytoid (pDC) and myeloid (mDC) DC from acute HCV resolving patients (AR) and from those who become chronically infected (ANR), as well as in HCV chronically infected patients (CHR) and healthy seronegative individuals (CTRL).
Results: For pDC, a high number of upregulated genes related to different functions and processes was found in AR patients, irrespective of DC stimulation. However, for mDC, most evident differences were detected after DC stimulation, again corresponding to upregulated genes in AR patients. Differences between AR and ANR were also observed when comparing their DC with those from CHR patients and CTRL individuals. Most differences corresponded to metabolism-associated genes, with upregulation in AR patients of genes belonging to pathways associated with DC activation and cytokine responses.
Conclusion: Our results show that upregulation of relevant genes in DC during acute HCV infection may determine viral clearance, suggesting that dysfunctional DC may be responsible for the lack of efficient T-cell responses which lead to chronic HCV infection.

overall_design: Gene expression was compared in resting and activated peripheral blood plasmacytoid (pDC) and myeloid (mDC) DC from acute HCV resolving patients (AR) and from those who become chronically infected (ANR), as well as in HCV chronically infected patients (CHR) and healthy seronegative individuals (CTRL)

first: Elizabeth

last: Guruceaga


title: Gene set enrichment analysis and ingenuity pathway analysis of metastatic clear cell renal cell carcinoma cell line

status: Public on Jun 17 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: In recent years, genome wide RNA expression analysis has become a routine tool that offers a great opportunity to study and understand the key role of genes that contribute to carcinogenesis. Various microarray platforms and statistical approaches are implemented to identify genes that might serve as prognostic bio-markers and used for anti-tumor therapies in future. Metastatic renal cell carcinoma (mRCC) is a serious life-threatening disease. There are few treatment options for metastatic RCC patients.  We performed one-color microarray gene expression (4X44K) analysis of metastatic RCC cell line Caki-1 and healthy kidney cell line ASE-5063. 1921 genes were differentially expressed in Caki-1 cell line (1023 up-regulated and 898 down-regulated). Gene set enrichment analysis (GSEA) and Ingenuity Pathway Analysis (IPA) approach was used to analyse these differentially expressed data from Caki-1.   The objective of this research is to identify complex biological changes that occur during metastatic development using Caki-1 as a model RCC cell line. Our data suggests that there are multiple de-regulated pathways associated with mccRCC including ILK Signaling, Leukocyte Extravasation Signaling, IGF-1 Signaling, CXCR4 Signaling, and PI3K/AKT Signaling. The IPA upstream analysis predicted top transcriptional regulators which are wither activated or inhibited such as ER, TP53, KDM5B, SPDEF, CDKN1A. The GSEA approach was used to further confirm enriched pathway data following IPA analysis.

overall_design: Comparative gene expression profiling of metastatic clear cell renal cell carcinoma with healthy kidney epithelial cells using GSEA and IPA analysis. Six independent microarrays was performed for two different cell type.

middle: I

first: Anna

middle: M

last: Czarnecka

first: Cezary

last: Szczylik


title: Proteasome inhibition and oxidative biochemistry are synergistic triggers of metabolic heme toxicity

status: Public on Aug 21 2016

city: Zurich

first: Christian

middle: Andreas

last: Schaer

address: Raemistrasse 100

country: Switzerland

institute: University Hospital Zurich

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

overall_design: Refer to individual Series


title: Gene expressions in Atg7- and Atg7 Nrf2-deficient livers

status: Public on Jun 21 2016

city: Niigata-shi

first: Tetsuya

last: Saito

state: Niigata

address: 757, Ichibancho, Asahimachidori, Chuo-ku

department: Biochemistry

institute: Niigata University school of medicine

summary: Nrf2-dependent expression of numerous genes in Atg7-deficient livers was observed.

overall_design: Three independent experiments were performed using different mice for each experiment.

first: Yasumasa

last: Nishito

first: Masaaki

last: Komatsu


title: microRNA expression profiling of xenografted tumors derived from human esophageal squamous cell carcinoma model treated with cisplatin

status: Public on Jun 16 2016

city: Guangzhou

first: Ai

middle: bin

last: Liu

address: 74 Zhongshan Road II

country: China

institute: SUN YAT-SEN UNIVERSITY

type: Non-coding RNA profiling by high throughput sequencing

summary: The plasticity of cancer stem cells (CSCs)/tumor-initiating cells (T-ICs) indicates that multiple CSC/T-IC subpopulations exist within a tumor and multiple oncogenic pathways collaborate to maintain the CSC/T-IC state.  Here, we aimed to enrich for T-ICs from clinical ESCC tissues. A chemoresistant human esophageal squamous cell carcinoma (ESCC) patient-derived xenograft model was employed to identify miRNA(s) that contribute to ESCC aggressiveness. We used microarrays to demenstrate the microRNA expression underlying  different pretreated conditions. NOG mice bearing subcutaneous tumor xenografts derived from clinical ESCC cells were intraperitoneally treated with CDDP or PBS twice weekly for three weeks.  Tumor cells were then isolated and re-inoculated subcutaneously into NOG mice for the next round of treatment.  In the 4th round of treatment, the volume of tumors in both CDDP- and PBS-treated groups were approximately the same, suggesting that the cells in CDDP-treated tumors were becoming resistant to CDDP.

overall_design: microRNA expression was measured by RNA extraction from cisplatin-treated tumors (EC-CR) or PBS-treated tumors(EC-UT) after 4 round of treatment,two microarrays were performed  for each sample.

first: Jun

last: Li

first: Aibin


title: miRNA expression profile of of mouse Lewis lung carcinoma cell line treated with single or fractionated ionizing radiation doses

status: Public on Jul 07 2016

city: Vilnius

first: Vaidotas

last: Stankevicius

state: Lithuania

address: Santariskiu 1

country: Lithuania

institute: National Cancer Institute

summary: Radiotherapy is one of the most common therapies for cancer. Approximately half of all cancer patients will receive radiotherapy at some point during treatment. Consequences of IR treatment are dose dependent and different sensitivity to IR of various types of cells is well established. To reduce the damage of IR to most sensitive cells of normal (noncancerous) tissue radiotherapy is administered as fractionated dose treatment applying radiation in ~2 Gy fractions every 24 hours, 5 times per week. However, during the therapy intrinsic and acquired tumor radioresistance may result in treatment failures. Comprehensive mechanisms of the resistance to irradiation as well as mechanisms of cellular response to fractionated dose IR remain unclear. Different gene expression patterns may be partially influenced by short ~22 nt non-coding RNA molecules called microRNAs (miRNAs) via translational regulation or RNA degradation mechanisms. Therefore, in the present study we evaluated global miRNA changes in murine Lewis lung carcinoma LLC1 cells following X-ray irradiation of single 2 Gy or 10 Gy and 2 Gy x 5 fractionated doses.

overall_design: Total RNA enriched in small noncoding RNAs was isolated from mouse Lewis lung carcinoma cells 4h after treatment of single (2 Gy or 10 Gy) or fractionated (5x2 Gy) ionizing radiation dose.

first: V

first: K

last: Suziedelis


title: Microarray analysis of CX3CR1high CD11b+ CD11c+ cells in murine intestinal lamina propria

status: Public on Jul 17 2016

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Several innate immune cell subsets have recently been identified to maintain gut homeostasis in both human and mice. Among these subsets, CX3CR1high CD11b+ CD11c+ cells contribute to intestinal tolerance through various mechanisms in mice. However, whether tolerogenic innate myeloid cells are present in the human intestine is not clearly defined. In this manuscript, we identified an intestinal myeloid cell subset possessing tolerogenic ability. HLA-DRhigh CD14+ CD163high cells in the human colon were divided into two subsets based on CD160 expression: CD163high CD160high and CD163high CD160low cells. Both cell subsets exhibited high levels of IL-10 production and high phagocytic activities. CD163high CD160high cells suppressed effector CD4+ T cell proliferation by a Foxp3+ Treg cell induction-independent mechanism. We further observed that the number and suppressive activity of these cells were profoundly decreased in patients with ulcerative colitis (UC). In addition, CD163high CD160high cells in the UC patients showed inflammatory phenotype, such as increased expression of IL6, CD80, and CD86, accompanied with decreased IL10RB expression. Our results highlight that a tolerogenic CD163high CD160high cell subset might be implicated in the prevention of UC development.

overall_design: Gene expression analysis of murine CX3CR1high cells (n=10) and murine blood Ly6c+ CD11b+ monocytes (n=6) were performed using Whole Mouse Genome Microarray Kit, 4x44K V2 (G4846A) as dye-swapped experiments.

first: Soumik

last: Barman

first: Hisako

last: Kayama

first: Kiyoshi

last: Takeda


title: Comparative Gene Profiling Study Between Pak1 Deficient Mouse and Human Breast Cancer Cells

first: Luis

last: Arias-Romero

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Toxoplasma gondii TgIST co-opts host chromatin repressors dampening STAT1-dependent gene regulation and IFN-γ-mediated host defenses.

status: Public on Jul 18 2016

city: LA TRONCHE

first: Mohamed-ali

last: HAKIMI

state: Grenoble

address: Domaine de la Merci, Campus Santé

country: France

institute: CNRS

summary: An early hallmark of Toxoplasma gondii infection is the rapid control of the parasite population by a potent multifaceted innate immune response that engages resident and homing immune cells along with pro- and counter-inflammatory cytokines. In this context, IFN-γ activates a variety of T. gondii-targeting activities in immune and nonimmune cells but can also contribute to host immune pathology. T. gondii has evolved mechanisms to timely counteract the host IFN-γ defenses by interfering with the transcription of IFN-γ-stimulated genes. We now have identified TgIST (T. gondii inhibitor of STAT1 transcriptional activity) as a critical molecular switch that is secreted by intracellular parasites and traffics to the host cell nucleus where it inhibits STAT1-dependent proinflammatory gene expression. We show that TgIST not only sequesters STAT1 on dedicated loci but also promotes shaping of a nonpermissive chromatin through its capacity to recruit the nucleosome remodeling deacetylase (NuRD) transcriptional repressor. We found that during mice acute infection, TgIST-deficient parasites are rapidly eliminated by the homing Gr1+ inflammatory monocytes, thus highlighting the protective role of TgIST against IFN-γ-mediated killing. By uncovering TgIST functions, this study brings novel evidence on how T. gondii has devised a molecular weapon of choice to take control over a ubiquitous immune gene expression mechanism in metazoans, as a way to promote long-term parasitism.

overall_design: HFF, 2fTGH (STAT1+/+) and U3A (STAT1-/-) human cells were left uninfected or infected for 24 hours with 76KGFP and 76KGFPΔTgIST Toxoplasma strains and stimulated with 100 U/ml IFN-γ for 6 hours before gene expression was measured. Three independent experiments were performed for each condition.

first: Gabrielle

last: Gay

first: Laurence

last: Braun

first: Marie-Pierre

last: Brenier-Pinchart

first: Julien

last: Vollaire

first: Véronique

last: Josserand

first: Rose-Laurence

last: Bertini

first: Aurélie

last: Varesano

first: Bastien

last: Touquet

first: Pieter-Jan

last: De Bock

first: Yohann

last: Coute

first: Isabelle

last: Tardieux

first: Alexandre

last: Bougdour

first: Mohamed

last: Hakimi


title: Advanced maternal age affects hippocampal gene expression in adult mouse offspring

status: Public on Jun 08 2016

city: Magdalenka

first: Adrian

middle: Mateusz

last: Stankiewicz

state: Mazovia

address: Jastrzebiec, ul. Postepu 36A

department: Animal Behaviour

summary:
Advanced Maternal Age (AMA) is a risk factor for neurological and neuropsychiatric disorders in offspring. We developed a mouse model to investigate whether pregnancy at advanced age may provoke behavioral and brain gene expression changes in offspring. Mice conceived by 15- to 18-month-old (15-18M) or 3M control females were delivered by cesarean section and were all fostered after birth by 3M dams. Genome-wide mRNA expression was analyzed using microarrays in the hippocampus of 4M male offspring. In conclusion, pregnancy at advanced age yields offspring with altered patterns of gene expression in the hippocampus, typical of human neuropsychiatric and neurodegenerative disorders. The effects were not reversed by the postnatal maternal care provided by young foster mothers. This suggests that prenatal conditions associated with AMA may negatively affect fetal brain development and hence postnatal behaviors.
This work was supported by the Polish National Science Center (2014/15/D/NZ4/04274 to SS and 2011/03/N/NZ29/05222 to AMS) and European Union Seventh Framework Programme (FP7/2007-2013-n 312097 to GEP). This work was also partially supported by Institute of Genetics and Animal Breeding of the Polish Academy of Sciences (S.III.1.3 to JAM) and by the Polish Ministry of Science and Higher Education (N N519 657940 to JG). SS, FZ and GEP are participating in the COST action FA1201 ‘Epiconcept’ - Epigenetic and Periconception Environment.

overall_design: We compared gene expression patterns of mice hippocampi harvested from male offspring of old versus young (control) mothers. Comparison was composed of 3 biological replicates in each group. Each biological replicate was a pool composed of equal amounts of 3 total RNA samples from hippocampi of mice belonging to a given group.

first: Joanna

last: Goscik

first: Federica

last: Zacchini

first: Agnieszka

last: Szostak

first: Artur

last: Swiergiel

first: Jacek

last: Modlinski

first: Grazyna

last: Ptak

first: Silvestre

last: Sampino


title: Antitumoral actions of 9-cis retinoic acid and mitotane in an adrenocortical xenograft model

status: Public on Jun 07 2016

city: Budapest

first: Zoltan

last: Nagy MD

state: Budapest

address: Szentkirályi str. 46.

department: 2nd Department of Medicine

country: Hungary

institute: Semmelweis University

summary: The actual drug treatment options for adrenocortical carcinoma (ACC) are rather narrow and intensive efforts are going on to find novel effective agents. In our previous functional genomics study, retinoid signaling via the retinoid X receptor (RXR) was detected as a major pathogenic pathway in ACC and we have demonstrated the in vitro activity of 9-cis retinoic acid (9-cisRA) acting via the RXR on NCI-H295R cells and also found that 9-cisRA has antitumoral effects in a small pilot xenograft study. In the present study our aim was to confirm the antitumoral effect of 9-cisRA on adrenocortical cancer in a large xenograft study involving both mitotane and 9-cisRA and their combination. 43 male SCID mice inoculated with NCI-H295R cells were treated in four groups (i. control – corn oil vehicle, ii. 5 mg/kg 9-cisRA, iii. 200 mg/kg mitotane, iv. 5 mg/kg 9-cisRA + 200 mg/kg mitotane) for 28 days. Regular tumor size follow-up, histological and immunohistochemical (Ki-67) analysis, tissue gene expression microarray have been performed. Quantitative real-time-PCR was used for the validation of the microarray results and to detect circulating and tissue microRNAs. To examine the proteome proteomics and Western-blot analysis were executed. We have found that both 9-cisRA and mitotane reduced tumor growth relative to control, but only the combination of the two agents resulted in significant tumor size reduction. The Ki-67 index was significantly reduced in both 9-cisRA and 9-cisRA+mitotane groups. Gene expression analysis revealed 483 genes with significant differences in expression, but only without Benjamini-Hochberg correction (APOA4 and PDE4A were validated).

overall_design: 43 SCID mice in four groups: 1) control, 2)mitotane, 3)9-cisRA, 4)combined treated. Treatment time: 28 days. Per os treatment

first: Zoltán

last: Nagy

first: Kornélia

last: Baghy

first: Éva

last: Hunyadi-Gulyás

first: Tamás

last: Micsik

first: Gergely

last: Rácz

first: Gábor

last: Nyír?

first: Pál

last: Perge

first: Ilona

last: Kovalszky

first: Katalin

last: Medzihradszky

first: Károly

first: Attila

last: Patócs

first: Peter

last: Igaz


title: Increased Protein Processing Gene Signature in HDACi-resistant cells predicts response to proteasome inhibitors.

status: Public on Jun 01 2016

first: Koren

last: Mann

summary: Epigenetic modifying enzymes are commonly mutated in diffuse large B cell lymphoma (DLBCL). Importantly, genetics abnormalities lead to inactivation of HAT, which tilt the balance in favor of decreased protein acetylation in DLBCL cells.  This suggests that protein acetylation regulation is an important factor in DLBCL pathogenesis and a potential target for therapy. We developed resistant cell lines to the histone deacetylase inhibitor (HDACi) vorinostat, in order to better define molecular mechanisms of action of HDACi in lymphoma cells. We found that cells resistant to HDACi have increased protein synthesis and proteasomal degradation.  Additionally, cells resistant to HDACi have acquired increased susceptibility to proteasome inhibitors and this correlates with activation of the unfolded protein response. Importantly, using transcriptional signatures found in our resistant lymphoma cell line model, we show that tumors from DLBCL patients treated but unresponsive to HDACi therapy undergo similar changes. Together, these data show, for the first time, that HDACi may be used to prime DLBCL for targeted therapy including proteasome inhibitors.

overall_design: Gene expression in U937 cells after 12h exposure to 2µM vorinostat and after development of resistance to 2 µM vorinostat, with and without vorinostat in the media.

first: Wilson

last: Miller Jr


title: Premalignant lesions of the bronchial epithelium

status: Public on May 25 2016

city: Tomsk

first: Aleksei

last: Sleptcov

state: Tomskaya oblasty

address: 10 Naberejnaya Ushaiki

country: Russia

institute: Research Institute of Medical Genetics

summary: Transcriptional profiling of hyperplastic, metaplastic, and dysplastic lesions of the bronchus in comparison with normal bronchial epithelium. The aim was to identify transcripts and cell signalling pathways associated with the development of isolated premalignant lesions and/or lesions combined with each other in the same bronchial epithelium.

overall_design: Basal cell hyperplasia (n=4), squamous metaplasia (n=4), and dysplasia (n=1) vs. normal bronchial epithelial cells (n=1)

first: Evgeny

middle: V

last: Denisov

first: Tatyana

middle: S

last: Gerashchenko

first: Valentina

middle: D

last: Yakushina

first: Nikolay

last: Skryabin

last: Sleptsov

first: Liubov

last: Tashireva

first: Olga

last: Pankova

first: Vladimir

last: Perelmuter


title: Identification of a novel PPARβ/δ / miR-21-3p axis in UV-induced skin inflammation [mouse miRNA]

status: Public on Jun 03 2016

city: Lausanne

first: Mark

last: Ibberson

address: Genopode building

department: Vital-IT

institute: SIB Swiss Institute of Bioinformatics

summary: Although excessive exposure to UV is widely recognized as a major factor leading to skin perturbations and cancer, the complex mechanisms underlying inflammatory skin disorders resulting from UV exposure remain incompletely characterized. The nuclear hormone receptor PPARβ/δ is known to control cutaneous repair and UV-induced cancer development. Here, we describe a novel PPARβ/δ-dependent molecular cascade involving TGFβ-1 and miR-21-3p, which is activated in the epidermis in response to UV exposure. We establish that the passenger miRNA miR-21-3p, that we identify as a novel UV-induced miRNA in the epidermis, plays a pro-inflammatory function in keratinocytes, and that its high level of expression in human skin is associated with psoriasis and squamous cell carcinomas. Finally, we provide evidence that inhibition of miR-21-3p reduces UV-induced cutaneous inflammation in ex vivo human skin biopsies, thereby underlining the clinical relevance of miRNA-based topical therapies for cutaneous disorders.

overall_design: 16 samples: 4 KO (Ppard-/-)and 4 WT (Ppard+/+) irradiated for 12 weeks; 4 KO and 4 WT without irratiation

first: Liliane

last: Michalik

first: Gwendoline

last: Degueurce


title: Gene expression profiling of tuberculosis patients from India

status: Public on May 24 2016

city: Bangalore

first: Nagasuma

last: Chandra

state: Karnataka

address: FB-04, New Biological Sciences, Indian Institute of Science

department: Department of Biochemistry

institute: Indian Institute of Science

summary: Whole genome microarray expression profiling was employed to identify differential gene expression profiles characteristic of tuberculosis patients in the South-Indian cohort. Whole blood samples were extracted from tuberculosis patients at the time of diagnosis and from healthy controls. The experiment served to validate computational predictions from a meta-analysis study of host transcriptional profiles in tuberculosis.

overall_design: Gene expression in human blood was measured from TB patients immediately after diagnosis and from corresponding healthy controls

first: Awanti

last: Sambarey

first: Abhinandan

last: Devaprasad

first: Shashidhar

last: Buggi

first: Krishnagoudar

last: BS

first: Priyanka

last: Tyagi

first: Amit

last: Singh


title: Gene expression signatures in cell cycle sorted cells [HeLa_mRNA_array]

status: Public on May 28 2016

first: Vince

middle: Kornél

last: Grolmusz

address: Szentkirályi 46.

summary: For the further examination of cell cycle dependent gene expression profile, DNA content based fluorescence activated cell sorting (cell cycle sort) was performed on human transformed cancer cell lines and primary, untransformed fibroblasts. Phase-dependent gene expression profiling was performed on G1, S and G2 phases. Results were validated by quantitative real-time PCR.

overall_design:
Phase-dependent gene expression profiling was performed on sorted human cancer (cervical - HeLa and adrenocortical - NCI-H295R) cells and primary untransformed fibroblasts (HDFa). G1, S and G2 phases were successfully sorted and analyzed.
HeLa_mRNA dataset

first: Attila

last: Patocs


title: Gene expression signatures in cell cycle sorted cells [H295R_mRNA_array]

overall_design:
Phase-dependent gene expression profiling was performed on sorted human cancer (cervical - HeLa and adrenocortical - NCI-H295R) cells and primary untransformed fibroblasts (HDFa). G1, S and G2 phases were successfully sorted and analyzed.
H295R_mRNA dataset


title: A Mixture Reflecting Polybrominated Diphenyl Ether (PBDE) Profiles   Detected in Human Follicular Fluid Significantly Affects Steroidogenesis   and Induces Oxidative Stress in a Human Granulosa Cell Line

city: Montréal

first: Pavine

middle: Lee

last: Lefevre

state: Québec

address: 3655 Promenade Sir-William Osl

department: Pharmacology and Therapeutics

institute: McGill University

summary: Brominated flame retardants (BFRs) are incorporated into consumer products to prevent flame propagation. These compounds leach into the domestic environment, resulting in chronic exposure and contamination. Pregnancy failure is associated with high levels of BFRs in human follicular fluid, raising serious questions regarding their impact on female fertility. Our goal was to elucidate effects of a mixture reflecting human follicular fluid levels of polybrominated flame retardants (PBDEs), the major class of BFRs, on an immortalized human granulosa cell line, the KGN cell line. We showed that cell viability was altered and oxidative stress was induced, as reflected by increased reactive oxygen species formation, at 20 µM of the PBDE mixture. Transcriptomic analysis revealed that several genes showing an altered expression after the PBDE treatment were involved in oxidative stress signaling pathways. Significant dose-dependent reduction of progesterone and estradiol levels was measured after PBDE treatment; expression of genes involved in steroid hormone metabolism, namely CYP1A1, was significantly affected by PBDEs. Treatment with the PBDE mixture also modified genes encoding for members of the transforming growth factor β superfamily like inhibins and cytokines, including the pro-inflammatory factor, interleukin-6 (IL6). Concentration of IL-6 in KGN cell culture media was consistently increased after treatment with the PBDE mixture. Our results clearly demonstrate that the PBDEs detected in human follicular fluid alter human granulosa cell functions by inducing oxidative stress, disrupting steroidogenesis and triggering an inflammatory response. This strengthens the fact that PBDEs are detrimental to ovarian functions and thus, to women’s reproductive health.

overall_design: KGN cells were exposed to 0, 1, 5 and 20 µM of a PBDE mixture for 48h; n=6 in triplicates for each experiments except for samples at 5 µM of a PBDE, for which there are 5 replicates.

middle: L

first: Michael

last: Wade

first: Bernard

last: Robaire

first: Cindy

last: Goodyer

first: Barbara

middle: F

last: Hales


title: Identification of Novel Changes in Human Skeletal Muscle Proteome following Roux-en-Y Gastric Bypass Surgery

status: Public on May 22 2016

city: Tucson

first: Dawn

middle: K

last: Coletta

state: AZ

address: 1501 N. Campbell Ave

department: Medicine

country: USA

institute: UNIVERSITY OF ARIZONA

summary: The mechanisms of metabolic improvements following Roux-en-Y gastric bypass (RYGB) surgery are not entirely clear. Therefore, the aim of our study was to investigate the role of obesity and RYGB on the human skeletal muscle proteome.

overall_design: Basal muscle biopsies were obtained from seven obese (BMI >40 kg/m2) female subjects (45.1±3.6 years) pre- and 3 months post-RYGB, and euglycemic-hyperinsulinemic clamps were used to assess insulin sensitivity.


title: Expression data from fetal sheep immunocytes

status: Public on May 03 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 the initiation of systemic inflammatory signaling in fetuses exposed to TLR-4 agonist lipopolysaccharides from E.coli.
Microarray was used to determine the inflammatory transcriptome in circulating fetal immunocytes.

overall_design: Fetal sheep at 92d GA were catheterised prior to intra-amniotic exposure of saline or lipopolysaccharides for 48h prior to euthanasia.

first: M

middle: W

last: Kemp

first: T

middle: J


title: Gene expression signatures in cell cycle sorted cells [HDFa_mRNA_array]

overall_design:
Phase-dependent gene expression profiling was performed on sorted human cancer (cervical - HeLa and adrenocortical - NCI-H295R) cells and primary untransformed fibroblasts (HDFa). G1, S and G2 phases were successfully sorted and analyzed.
HDFa_mRNA dataset


title: ORA47 binding cis-element prediction

city: Taipei

first: Hsing-Yu

last: Chen

address: No. 1, Sec. 4, Roosevelt Rd.

department: Institute of Plant Biology

institute: National Taiwan University

summary: To find genes directly regulated by ORA47, the P35S:ORA47-GR transgenic line was grown in the normal condition, treated with DEX and as well cycloheximide (CYC), prevented secondary transcriptional regulation downstream of ORA47 regulation by blocking protein synthesis.  Gene expression patterns were then analyzed by microarray.

overall_design: To exclude genes that were induced by DEX, CYC, and the transgenic plant background, seven-day-old ORA47-GR transgenic T2 and WT seedlings were separated into two subgroups: (1) 35S:ORA47-GR transgenic T2 and WT seedlings treated with 50 μM CYC and 20 μM DEX, and WT plants were used as control. (2) 35S:ORA47-GR transgenic T2 seedlings treated with 50 μM CYC and 20 μM DEX, and ORA47-GR seedlings treated with 50 μM CYC only were used as controls. Seedlings were treated with CYC for 1 h followed by DEX treatment for 2 h before harvesting. Total RNA of each group was isolated and prepared for microarray assay. There were two independent replicates for each group. The common up-regulated genes obtained from these two datasets were considered as the putative ORA47 direct downstream genes. The one kb promoter regions of the 100 most highly up-regulated genes (fold change greater than 4.1) were analyzed by the eTFBS program.

first: Tsan-Piao

last: Lin

first: Chien-Yu


title: Transcriptome of human NSCLC tissues

status: Public on May 18 2016

city: Borstel

first: Sebastian

last: Marwitz

address: Parkallee 3a

department: Histology

country: Germany

institute: Research Center Borstel - Leibniz Lung Center

summary: RNA from patient samples was isolated to examine the TGFb pathway expression between matching pairs of tumor-free lung and NSCLC specimen

first: S

first: O

last: Ammerpohl

last: Reck

first: U

last: Klingmueller

last: Goldmann


title: TSLP-Induced Gene Expression Signature in Primary CRLF2 B-ALL

city: Loma Linda

first: Kimberly

last: Payne

state: CA

address: 11085 Campus Street, Mortensen Hall, First Floor

institute: Loma Linda University

summary: The cytokine TSLP stimulates in vitro proliferation of human fetal B cell progenitors. Genetic alterations that cause overexpression of the TSLP receptor component, CRLF2, lead to B cell acute lymphoblastic leukemia (CRLF2 B-ALL) with poor outcome. The in vivo role of TSLP in normal human B cell development and its contribution to CRLF2 B-ALL are unknown. In classic xenograft models CRLF2-mediated signaling is unlikely to be activated by mouse TSLP, based on data from engineered cellular models. Here, we show that mouse TSLP does not induce activation of the CRLF-2 downstream pathways (JAK/STAT and AKT/mTOR) that are induced by human TSLP (hTSLP) in CRLF2 B-ALL cells. Based on this, we developed a novel human-mouse xenograft model system comprised of mice that produce hTSLP (+T mice) to activate human CRLF2-mediated signaling and mice that lack hTSLP (–T mice). Normal serum levels of hTSLP were achieved in +T mice, while hTSLP was undetectable in –T mice. hTSLP produced by stroma induced JAK/STAT and AKT/mTOR pathway activation and showed functional in vivo effects on normal human B cell progenitors and primary CRLF2 B-ALL cells. Whole genome microarray of primary CRLF2 B-ALL showed an induction of mTOR regulated gene expression and preservation of TSLP responsiveness in cells expanded in +T mice as compared to –T mice.

overall_design: TSLP-induced gene expression in primary CRLF2 B-ALL cells was measured in cells that were expanded in +TSLP and -TSLP mice for 9 weeks. TSLP-induced gene expression was also measured in primary CRLF2 B-ALL cells that were harvested from the bone marrow of +TSLP and -TSLP mice and cultured for 3 days in vitro with or without commercially available exogenous human TSLP.

first: Olivia

last: Francis


title: Breast tumors: different structures of tumor cells [cnv]

status: Public on Apr 29 2016

first: Aleksei

middle: A

last: Sleptcov

summary: Cytogenetic profiling of morphologically-distinct structures of breast tumors: tubular, alveolar, solid, trabecular structures, and discrete groups of tumor cells. The aim was to identify chromosomal aberrations which could be associated with the development of clinical relevant structures of tumor cells.

overall_design: Five types of morphological structures from three regions of breast tumors (n=3) vs. human female DNA (Agilent Technologies, Inc., USA)

first: Evgeny

last: Denisov

first: Nikolay

last: Skryabin

first: Tatyana

last: Gerashchenko

first: Liubov

last: Tashireva

first: Jochen

last: Wilhelm

first: Michail

last: Buldakov

last: Sleptsov

first: Marina

last: Zavyalova

first: Nadezhda

last: Cherdyntseva

first: Vladimir

last: Perelmuter


title: Gene expression of myeloma patient samples under hypoxia

status: Public on Apr 22 2016

city: Akita

first: Sho

last: Ikeda

address: Hondo 1-1-1

department: Hematology

country: Japan

institute: Akita univ.

summary: We conducted whole genome gene screening against the MM patients bone marrow (sorted by CD38++) cells that were subjected by chronic hypoxia condition.

overall_design: We compared four primary myeloma samples cultured under hypoxia with cultured under normoxia (48hr) to find new anti-apoptotic gene of myeloma.

first: Hiroyuki

last: Tagawa


title: Conditional liver NIPP1 KO micro array on total liver RNA

status: Public on Mar 27 2016

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: The goal is to investigate genes that are more or less expressed due to the removal of NIPP1 in mouse epithelial liver cells. In this way we hope to unravel the function of NIPP1 in vivo.

overall_design: 4 control and 4 conditional knockout mice were sacrificed. No replicates were performed. Samples were analyzed using the Mouse GE 4x44K v2 Microarray (gene expression microarray).

first: Aleyde

last: Van Eynde

first: Mathieu

last: Bollen

first: Shannah

last: Boens


title: Abnormalities in hair follicles of Pla2g2e knockout mice

status: Public on Apr 20 2016

city: Setagaya

first: Kei

last: Yamamoto

state: Tokyo

address: 2-1-6 kamikitazawa

department: Lipid Metabolism Project

institute: Tokyo Metropolitan Institute of Medical Science

summary: Pla2g2e is dominantly expressed in hair follicles. Microarray gene profiling showed modest changes in the steady-state expression of a subset of skin genes.

overall_design: Pla2g2e knockout mice and littermate controls (C57BL/6 background); 33-day old; skin; pooled from 4 mice for each genotype.

first: Yasumasa

last: Nishito

first: Makoto

last: Murakami


title: Comparison of gene expression profiles of FCRL5+/CD21-/lo/CD27- and FCRL5-/CD21-/lo/CD27- peripheral B cells from healthy donors

status: Public on Apr 26 2016

city: Silver Spring

first: Mate

last: Tolnay

state: MD

address: 10903 New Hampshire Ave.

department: Office of Biological Product

institute: FDA/CDER

summary: To compare gene expression profile of FCRL5+ and FCRL5- tissue-like memory B cells (CD21-/lo/CD27-/CD19+), we have employed whole genome microarray expression profiling to identify differentially regulated genes in these two B cell subgroups. B cells freshly isolated from leukapheresis of healthy donors were used in the experiment.

overall_design: PBMC from leukapheresis of healthy donors were obtained by Ficoll-Hypaque centrifugation, and B cells were then isolated from PBMC by negative magnetic bead-based selection. Cells were then stained, and sorted by flow cytometry to get the FCRL5- and FCRL5+ tissue-like memory B cells. RNA purified from these two groups of cells from three healthy donors was used in microarray analysis.

first: Hui-Fang

last: Li


title: Whole-genome microarray analysis of human skin fibroblasts

status: Public on Apr 14 2016

city: Örebro

first: Anita

last: Koskela von Sydow

address: Södra Grev Rosengatan 32

country: Sweden

institute: Örebro University

summary: Connective tissue growthfactor (CTGF/CCN2) is a matricellular protein induced by transforming growth factor-beta (TGF-beta) and intimately involved with tissue repair and overexpressed in various fibrotic conditions. We have previously shown that keratinocytes in vitro downregulate TGF-beta induced expression of CTGF in fibroblasts by an interleukin-1 alfa (IL-1alfa) dependent mechanism. With this study we want to get a better overall perspective who fibroblasts respond on TGF-beta and in a TGF-Beta stinulated system, what effect addition of IL-1 alfa have. This to understand the expression of CTGF in human fibroblasts which in turn have implications for the pathogenesis of fibrotic conditions involving the skin.

overall_design: Microarray was performed on human skin fibroblast RNA from one patient, Fibroblasts were seeded in vitro as a control (Control, C), TGF-beta were added to fibroblasts and incubated for 16 h (addition of TGF-beta, T) and  both IL-1alfa and TGF-beta were added to fibroblasts for 16 h (addition of IL-1alfa and TGF-beta, IT). Each condition (C,T and IT) were done in three replicates.

first: Chris

last: Janbaz

first: Caroline

last: Kardeby

first: Dirk

last: Repsilber

first: Mikael

last: Ivarsson


title: High-efficiency cellular reprogramming with microfluidics

status: Public on Apr 10 2016

city: Bologna

first: Camilla

last: Luni

address: Via Terracini 28

department: DICAM

country: Italy

institute: University of Bologna

summary: We report that the efficiency of reprogramming human somatic cells to induced pluripotent stem cells (hiPSCs) can be dramatically improved in a microfluidic environment. Microliter-volume confinement resulted in a 50-fold increase in efficiency over traditional reprogramming by delivery of synthetic mRNAs encoding transcription factors. In these small volumes, extracellular components of the TGF-β and other signaling pathways exhibited temporal regulation that appears critical to acquisition of pluripotency. The high quality and purity of the resulting hiPSCs (μ-hiPSCs) allowed direct differentiation into functional hepatocyte- and cardiomyocyte-like cells in the same platform without additional expansion.

overall_design: We performed cell reprogramming of human foreskin BJ fibroblasts, seeded on a feeder layer of inactivated human newborn foreskin fibroblasts NuFF-RQs, by modified mRNA (mmRNA) daily transfections of OCT4, SOX2, KLF4,c-MYC, NANOG, LIN28, and nuclear GFP for 18 days.  The process was performed in parallel in 6-well plates and within a microfluidic system. 48 hours after last reprogramming mmRNA transfection, 4 freshly derived colonies of comparable size were selected both from the microfluidic system and from a parallel reprogramming experiment in well. After a 24 h conditioning in StemMACS Brew XF medium, each colony was split in two halves: one was stopped at passage p0 and used for total RNA extraction, the other one was further expanded in feeder-free conditions for 3 passages (p3) in well before total RNA extraction from another sectioned colony of comparable size. Thus, the overall study includes: (i) N=4 p0 hiPS colonies reprogrammed in well, (ii) N=4 p0 hiPS colonies reprogrammed in microfluidics, (iii) N=4 p3 hiPS colonies (the same as in (i)) expanded in well, (iv) p3 hiPS colonies (the same as in (ii)) expanded in well.


title: RNA binding protein TIA1 cytoplasmic expression as an Independent Prognostic Factor in Human Esophageal Squamous Cell Carcinoma (ESCC).

status: Public on Mar 31 2016

city: Tokushima

first: Kiyoshi

last: Masuda

address: 3-18-15 Kuramoto-cho

department: Department of Human Genetics

institute: Institute of Biomedical Sciences, Tokushima University Graduate School

summary: T-cell intracellular antigen-1 (TIA1) is an RNA-binding protein modulating many regulatory aspects of target mRNA metabolism. Despite several reports referring to the role of TIA1 in carcinogenesis, little is known about the significance of its expression and function in human cancers including esophageal squamous cell carcinoma (ESCC). In the present study, we found that ectopic localization of overexpressed TIA1 in the cytoplasm was observed in a cohort of 143 ESCC patients using immunohistochemistry, and the cytoplasmic TIA1 was an independent prognosticator for worse overall survival. Moreover, we revealed that TIA1 was overexpression in many ESCC cell lines, and silencing of TIA1 in those cells inhibited cell growth with an accumulation of cells in G0–G1 and sub-G1 phases. The human TIA1 gene generates two major protein isoforms, TIA1a and TIA1b. Expression of TIA1a isoform tended to be higher than that of TIA1b in ESCC cells, and TIA1a was expressed both in the nucleus and cytoplasm but TIA1b was expressed mainly in the nucleus. Further studies revealed that each isoform showed opposite effects on cell proliferation through ectopically introducing each gene: TIA1a promotes anchorage-dependent and independent cell proliferation, whereas TIA1b inhibits cell proliferation and/or induces cell death. The ribonucleoprotein immunoprecipitation followed by a microarray analysis or massive-parallel sequencing identified a set of TIA1-associating mRNAs including enriched cell cycle-associated genes. Among them, SKP2 and CCNA2 mRNA were shown to be interacted with TIA1 protein through their different regions, and SKP2 and CCNA2 protein levels were positively regulated by TIA1 through suppression of mRNA decay and translational induction, respectively. These findings provide new insights into the previously unknown role of TIA1 and its isoforms as tumor-promoting molecules regulating a set of downstream oncogenic proteins, and implicate their potential application as a useful marker of malignant potential and a therapeutic target in ESCC.

overall_design: To investigate the target molecules regulated by TIA1 in esophageal squamous cell carcinoma cell line (KYSE180), the expression levels of mRNAs (total) and transcripts captured by RIP with TIA1 antibody (TIA1_RIP) were analyzed using microarray.

first: Junichi

last: Hamada

first: Katsutoshi

last: Shoda

first: Takuya

last: Naruto

first: Yuji

last: Fujita

first: Tomohiro

last: Komoto

first: Yuko

last: Miyagami

first: Yasusei

last: Kudoh

first: Daisuke

last: Ichikawa

first: Eigo

last: Otsuji

first: Issei

last: Imoto


title: Microarray of IVM susceptable and resistant Haemonchus contortous

status: Public on Mar 25 2016

city: Glasgow

first: Victoria

last: Gillan

address: bearsden road

country: United Kingdom

institute: University of Glasgow

summary: Anthelmintic resistance is a major problem in the global fight against parasitic nematodes., Most previous studies have focused on the analysis of potential candidate genes that may have a role in resistance. Here we take a novel approach in the important parasite, Haemonchus contortus, by investigating changes in microRNA expression between resistant and susceptible parasites. The resistant worms included two geographically distinct strains and two lines generated by multiple rounds of backcrossing between susceptible and resistant parents, with ivermectin selection. All four resistant strains showed increased abundance of a single miRNA, hco-miR-9551, compared to the susceptible strain. hco-miR-9551 is enriched in female worms, is likely to be located on the X chromosome and is found only in clade V parasitic nematodes. Approximately 5-10% of the genomes of the resistant parental strains are introgressed into the respective backcrosses, suggesting that hco-miR-9551, or genes regulated by the miRNA, may be genetically linked to a locus that determines resistance. Genes containing predicted binding sites for hco-miR-9551 were identified computationally and refined based on differential expression in a transcriptomic dataset. These findings advance our conceptual understanding of the molecular mechanisms of anthelmintic resistance in H. contortus and indicate that altered miRNA expression may be linked with drug resistance.

overall_design: All samples were carried out using three biological replicates

first: Kirsty

last: Maitland

first: Roz

last: Laing

first: Henry

last: Gu

first: Alan

last: Winter

first: David

last: Bartley

first: Alison

last: Morrison

first: Philip

last: Skuce

first: Andrew

last: Rezansoff

first: John

last: Gilleard

first: Axel

last: Martinelli

first: Collette

last: Britton

first: Eileen

last: Devaney


title: Gene expression of myeloma cell lines under hypoxia

status: Public on Apr 12 2016

first: Sho

last: Ikeda

summary: By using myeloma cell lines (RPMI8226, KMS-11, KMS-12BM, and MM.1S), we conducted whole genome gene screening against the cells that were subjected by chronic hypoxia condition.

overall_design: We compared four myeloma cell lines (RPMI8226, KMS-11, KMS-12BM, and MM.1S) cultured under hypoxia with cultured under normoxia (48hr) to find new anti-apoptotic gene of myeloma.

first: Hiroyuki

last: Tagawa


title: Effects of a Closed Space Environment on Gene Expression in Hair Follicles of Astronauts in the International Space Station

city: Tsukuba

first: Masaya

last: Seki

state: Ibaraki

address: Sengen 2-1-1

department: JEM Utilization Center

institute: Japan Aerospace Exploration agency

summary:
In recent times, long-term stay has become a common occurrence in the International Space Station (ISS). However, adaptation to the space environment can sometimes pose physiological problems to the astronauts after their return.
Therefore, it is important to develop healthcare technologies for astronauts. In this study, hair, an easy-to-obtain sample, was identified as the candidate. In order to investigate the genetic changes in human hair during space flight, the hair follicles of 10 astronauts were analyzed by DNA microarray and real time q-PCR analyses.

overall_design: Space environment induced gene expression of hair follicles of astronaut was measured 6 differnent times included 2 in flight on orbit. Ten independent experiments were performed on differing astronauts. and the sampling day was differed for each astronaut because of their schedules.

first: Masahiro

last: Terada


title: Inhibition of AK4 expression increases drug sensitivity and elevates mitochondrial ATP synthesis

city: Ube

first: Koichi

last: Fujisawa

state: Yamaguchi

address: 1-1-1, minami-kogushi

department: Department of Gastroenterology and Hepatology

institute: Yamaguchi University Graduate School of Medicine

summary: Adenylate kinase 4 (AK4) is localized in the mitochondrial matrix, and is believed to be involved in stress, drug resistance, the malignant transformation of cancer, and ATP regulation. We produced AK4 knockdown HeLa cells by using shRNA and used these to analyze resistance, and found that sensitivity to hypoxia and drugs increased.

overall_design: 3 samples of HeLa cells haboring AK4 shRNA plasmids and 4 samples of HeLa cells haboring control shRNA plasmid.

first: Shuji

last: Terai

first: Takafumi

last: Noma

first: Taro

last: Takami

first: Naoki

last: Yamamoto

first: Isao

last: Sakaida


title: Microarray analysis of regulatory and inflammatory macrophages differentiated with glycolysis inhibitor

status: Public on Mar 07 2016

city: Kawasaki-shi

first: Hiroaki

last: Suzuki

state: Kanagawa

address: 1-1, Suzuki-cho, Kawasaki-ku

institute: Ajinomoto Pharmaceuticals Co., LTD.

summary: The gene expression patterns of macrophages were analyzed to understand how glycolysis inhibitor affects macrophage differentiation. Human monocytes derived from peripheral blood were cultured in vitro in the presence of macrophage colony-stimulating factor (M-CSF) to yield regulatory macrophages (M-Mφs), or M-CSF plus interferon-gamma to yield inflammatory macrophages (Mγ-Mφs). 2-deoxy-D-glucose (2-DG), a glycolysis inhibitor, was added during macrophage differentiation. Gene expression patterns of monocytes, M-Mφs and Mγ-Mφs diffrentiated with or without 2-DG were analyzed by microarray analysis.

overall_design: Gene expression patterns of monocytes, M-Mφs and Mγ-Mφs differentiated with or without 3 mM 2-DG for 6-days were analyzed. For each condition, equal amounts of RNA from 3 individuals were mixed and provided for microarray analysis.

first: Tadakazu

last: Hisamatsu

first: Sayako

last: Chiba

first: Kiyoto

last: Mori

first: Mina

middle: T

last: Kitazume

first: Katsuyoshi

last: Shimamura

first: Nobuhiro

last: Nakamoto

last: Matsuoka

first: Hirotoshi

last: Ebinuma

first: Makoto

last: Naganuma

first: Takanori

last: Kanai


title: SNP-array profiling of 21 novel primary and metastatic colorectal cancer cell lines [Illumina HumanExome-12 v1.2 BeadChip]

status: Public on Feb 29 2016

city: Singapore

first: Arnoud

last: Boot

state: Singapore

address: 8 college road

country: Singapore

institute: Duke-NUS Medical School

summary:
Background: In vitro models are an essential tool towards understanding the molecular characteristics of colorectal cancer (CRC) and the testing of therapies for CRC. To this end we established 21 novel CRC cell lines of which six were derived from liver metastases. Extensive genetic, genomic, transcriptomic and methylomic profiling was performed in order to characterize these new cell lines and all data is made publically available. Additionally, sensitivity of oxaliplatin was tested as a measure for chemotherapy resistance.
Results: By combining mutation profiles with CNA and gene expression profiles we constructed an overview of the alterations in the major CRC-related signalling pathways. The mutation profiles, along with the genome, transcriptome and methylome data of these cell lines will be made publically available . This combined dataset puts these cell lines among the best characterized CRC cell lines, allowing researchers to select appropriate cell line models for their particular experiment, making optimal use of these novel cell lines as in vitro model for CRC.
Conclusions: By combining mutation profiles with CNA and gene expression profiles we constructed an overview of the alterations in the major CRC-related signalling pathways. The mutation profiles, along with the genome, transcriptome and methylome data of these cell lines will be made publically available . This combined dataset puts these cell lines among the best characterized CRC cell lines, allowing researchers to select appropriate cell line models for their particular experiment, making optimal use of these novel cell lines as in vitro model for CRC.

overall_design: SNP-array analysis of 21 novel CRC cell lines; 16 with Illumina HumanExome-12 v1.2 BeadChip and 5 with Illumina HumanExome-12 v1.0.

first: A

first: T

last: van Wezel


title: Development of gene set for IL-6-dependent RB inactivation signature

status: Public on Mar 19 2016

city: Tokyo

first: Shunsuke

last: Kitajima

address: 3-8-31 Ariake, Koto

institute: Japanese Foundation for Cancer Research

summary: Our findings suggested that tamxofen resistance induced by RB depletion depends on increased IL-6 production. To elucidate molecular mechanism, we employed whole genome microarray expression profiling as a discovery platform to identify IL-6-dependent RB inactivation signature. RB depleted MCF7 and control MCF7 were cultured with 2 ug/ml anti-IL-6 antibody or IgG, and a 35-gene signature upregulated by RB depletion in an IL-6 dependent manner was identified. This gene set was highly enriched in genes involved in mitochondrial respiration chain. These data revealed that activation of mitochondrial respiration contribute to RB-depletion induced tamoxifen resistance.

overall_design: RB-depletion induced gene expression in MCF-7 cells was measured in the presence of anti-IL-6 antibody or IgG. Three independent experiments were performed.

first: Chiaki

last: Takahashi


title: SNP-array profiling of 21 novel primary and metastatic colorectal cancer cell lines [Illumina HumanExome-12 v1.0 BeadChip]

summary:
Background: In vitro models are an essential tool towards understanding the molecular characteristics of colorectal cancer (CRC) and the testing of therapies for CRC. To this end we established 21 novel CRC cell lines of which six were derived from liver metastases. Extensive genetic, genomic, transcriptomic and methylomic profiling was performed in order to characterize these new cell lines and all data is made publically available. Additionally, sensitivity of oxaliplatin was tested as a measure for chemotherapy resistance.
Results: DNA copy-number alterations (CNA) were compared between primary and metastasis derived cell lines. In concordance with previous studies copy-number gain of chr20, and loss of chr8p were found highly specific for liver metastases. Previously reported BRAF-mutation associated DNA methylation profiles could be validated on the genome-wide DNA methylation profiles of these cell lines. 47.6% of the loci previously reported to associate with BRAF mutation status were reproduced in this dataset. When examining the gene expression profiles in conjunction with these DNA methylation results, we identified 20 genes of which the gene expression correlated with the DNA methylation status, including MEIS1, LRAT and STC2. These genes have previously been reported to be subject to transcriptional regulation through DNA hypermethylation, validating our approach.
Conclusions: By combining mutation profiles with CNA and gene expression profiles we constructed an overview of the alterations in the major CRC-related signalling pathways. The mutation profiles, along with the genome, transcriptome and methylome data of these cell lines will be made publically available . This combined dataset puts these cell lines among the best characterized CRC cell lines, allowing researchers to select appropriate cell line models for their particular experiment, making optimal use of these novel cell lines as in vitro model for CRC.

overall_design: SNP-array analysis of 21 novel CRC cell lines; 16 with Illumina HumanExome-12 v1.2 BeadChip and 5 with Illumina HumanExome-12 v1.0 BeadChip.


title: ARPE-19_adriamycin_gene_expression

status: Public on Mar 01 2016

city: Hangzhou

first: Yuchen

last: Lin

address: 866 Yuhangtang Road

institute: Zhejiang University School of Medicine

summary: This study compared the gene expression change of ARPE-19 cells before and after adriamycin treatment

overall_design: ARPE-19 cells were treated with 1μM adriamycin for 24 h compared with control


title: BRAF-mutation associated DNA methylation in novel CRC cell lines

type: Methylation profiling by genome tiling array

overall_design: 21 CRC cell lines were analyzed


title: The effects of RED GREEN and BLUE LED light on human normal healthy fibroblast cell lines

status: Public on Feb 18 2016

city: hatyai

first: pongsathorn

last: chotikasemsri

state: songkhla

address: kajanavanich rd

department: faculty of medicine

country: Thailand

institute: prince of songkhla university

summary: The purpose of this study is to investigate whether LED light at different wavelength can improve wound healing in normal fibroblast. In this study, both diabetic and normal fibroblast cell lines were cultured and created some artificial wounds with pipette tips. After LED irradiation and microarray analysis, we found that GPCR Class A, a rhodopsin-like-structure gene, was significantly up regulated in all treated groups. Besides, for normal cell treated groups, the expression of other genes relevant to defense response to virus became strongly higher. However, in diabetic cells, genes relating to acute inflammatory response and mitotic cell cycle were highly expressed. Researchers also found that diabetic cells significantly respond to wound healing better than normal cells because inflammatory response, cell migration, cell proliferation, cell adhesion, and regulation of mitosis pathways can be instantly activated by red and green LED light according to gene expression profiles.

overall_design: Normal cell lines were irradiated with different wavelength (red/green/blue) LED color and compare their gene expression with the control groups.

first: Pongsathorn

last: Chotikasemsri


title: Gene expression profile in HIV-1 and HIV-2 infected PBMC

status: Public on Feb 01 2016

first: Indira

last: Hewlett

state: Maryland

address: 10903 New Hampshire Ave

department: DETTD

institute: CBER/FDA

summary: Analyzed the effects of HIV-1 (MN) and HIV-2 (ROD) infection on the expression of host factors in PBMC at the RNA level using the Agilent Whole Human Genome Oligo Microarray.

overall_design: RNA samples from PBMC isolated from 3 independent donors productively infected with HIV-1 MN or HIV-2 ROD were used to obtain gene expression data from Agilent microarrays.

first: Krishnakumar

last: Devadas

first: Santanu

last: Biswas


title: Targeting the lineage-specific long non-coding RNA LINC01212 as an effective anti-melanoma therapeutic strategy [2]

status: Public on Jan 15 2016

city: Gent

first: Pieter

last: mestdagh

address: De Pintelaan 185

institute: Center for Medical Genetics

summary: Focal amplifications of 3p13-3p14 occur in about 10% of melanoma and are associated with poor prognosis. The melanoma-specific oncogene MITF resides at the epicenter of this amplicon1. However, whether other loci present in this amplicon also contribute to melanomagenesis is unknown. Here we show that the recently annotated long non-coding RNA gene LINC01212 is consistently co-gained with MITF. In addition to being amplified, LINC01212 is a target of the lineage-specific transcription factor SOX10 and, consequently, it is expressed in more than 90% of human melanomas, but not in normal adult tissues. Whereas exogenous LINC01212 functions in trans to increase melanoma clonogenic potential LINC01212 knock-down dramatically decreases the viability of melanoma cells irrespective of their transcriptional cell state, BRAF, NRAS or TP53 status, diminishes melanoma growth and increases their sensitivity to MAPK-targeting therapeutics both in vitro and in patient-derived melanoma xenograft mouse models. Mechanistically, LINC01212 functions as a lineage addiction oncogene by interacting with and modulating the cellular localization and function of two proteins, XRN2 and p32, involved in nucleolar and mitochondrial rRNA processing, ribosome biogenesis and protein synthesis. LINC01212 targeting, especially in combination with BRAFV600E-inhibitors, is expected to deliver highly effective and tissue-restricted antimelanoma therapeutic responses.

overall_design: Five GapmeR3 treated and four control treated patient derived xenografts were analysed.

last: Mestdagh

first: Jo

last: Vandesompele


title: Targeting the lineage-specific long non-coding RNA LINC01212 as an effective anti-melanoma therapeutic strategy

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

overall_design: Refer to individual Series


title: Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA-dependent repair pathways

city: Lausanne

first: Mark

last: Ibberson

address: Genopode building

department: Vital-IT

institute: SIB Swiss Institute of Bioinformatics

summary: The mammalian heart has poor regenerative capacity following injury. In contrast, certain lower vertebrates such as zebrafish retain a robust capacity for regeneration into adult life. Here we use an integrated approach to identify evolutionary conserved regenerative miRNA-dependant regulatory circuits in the heart. We identified novel miRNA-dependant networks involved in critical biological pathways, which are differentially utilized between the infarcted mouse heart and the regenerating zebrafish heart.

overall_design: 2 conditions, 4 biological replicates per condition

first: Stefania

last: Crippa

first: Samir

last: Ounzain

first: Mohammed

last: Nemir

first: Corinne

last: Berthonneche

first: Alexandre

last: Sarre

first: Gaëlle

last: Boisset

first: Keith

last: Harshman

first: Ioannis

last: Xenarios

first: Dario

last: Diviani

first: Daniel

last: Schorderet

first: Thierry

last: Pedrazzini


title: Comparison of expression data between control and Bdh2 morphant zebrafish embryos, as well as Bdh2 morphant zebrafish embryos expressing ectopic Bdh2

status: Public on Jan 21 2016

city: Cleveland

first: Zhuoming

last: Liu

state: OH

address: 2103 Cornell Road

institute: Case Western Reserve University

summary: Bdh2 morphants displayed mitochondrial dysfunction and degradation by autophagy, which could be restored by ectopic Bdh2 overexpression.

overall_design: Total RNAs from control and Bdh2 morphant zebrafish embryos, as well as Bdh2 morphant zebrafish embryos expressing ectopic Bdh2 were isolated at 72 hpf using the RNeasy Mini kit (Qiagen). RNA samples were processed as per manufacturer’s instructions (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetric, Inc., Santa Clara, CA, USA) at Case Comprehensive Cancer Center Microarray Core Facility. Experiments were performed in duplicate for control and Bdh2 morphant zebrafish embryos, and in singlet for Bdh2 morphant zebrafish embryos expressing ectopic Bdh2.

first: Laxminarayana

last: Devireddy

first: Gangarao

last: Davuluri

first: Takuya

last: Sakaguchi


title: Comparison of expression data between control, Atg7, Bdh2, Atg7 and Bdh2 dual morphant zebrafish embryos

summary: Bdh2 morphants displayed mitochondrial dysfunction and degradation by autophagy, as well as hypohemoglobinization. Suppression of Atg7 expression in Bdh2 morphants diminished mitochondrial clearance and partly corrected their hemoglobinization defect.

overall_design: Total RNAs from control, Atg7, Bdh2, Atg7 and Bdh2 dual morphant zebrafish embryos were isolated at 72 hpf using the RNeasy Mini kit (Qiagen). RNA samples were processed as per manufacturer’s instructions (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetric, Inc., Santa Clara, CA, USA) at Case Comprehensive Cancer Center Microarray Core Facility. Experiments were performed in triplicate for control, Atg7, Atg7 and Bdh2 dual morphant zebrafish embryos, and in singlet for Bdh2 morphant zebrafish embryos.


title: LncVSM (AK098656) down-regulation in Vascular Smooth Muscle cells

status: Public on Jan 12 2016

city: Beijing

first: Lei

last: Yang

address: No.8 Gongtinanlu

department: Medical Research Center

institute: Beijing Chaoyang Hosptial, Capital Mediacal Unversity

summary: The full length of LncVSM transfected into Vascular Smooth Muscle cells to down-regulation for screening differential expression prolifes of LncVSM effecting.The empty vector transfected Vascular Smooth Muscle cells as controls.

overall_design: Eight Samples analyzed.

first: Cai

last: Jun

first: Geng

last: Bin

first: Qinghua

last: Cui


title: The effects of RED GREEN and BLUE LED light on both human diabetic fibroblast cell lines

first: pongsathorn

last: chotikasemsri

summary: The purpose of this study is to investigate whether LED light at different wavelength can improve wound healing in both diabetic fibroblast. In this study, both diabetic and normal fibroblast cell lines were cultured and created some artificial wounds with pipette tips. After LED irradiation and microarray analysis, we found that GPCR Class A, a rhodopsin-like-structure gene, was significantly up regulated in all treated groups. Besides, for normal cell treated groups, the expression of other genes relevant to defense response to virus became strongly higher. However, in diabetic cells, genes relating to acute inflammatory response and mitotic cell cycle were highly expressed. Researchers also found that diabetic cells significantly respond to wound healing better than normal cells because inflammatory response, cell migration, cell proliferation, cell adhesion, and regulation of mitosis pathways can be instantly activated by red and green LED light according to gene expression profiles.

overall_design: Diabetic fibroblast cells were irradiated with different wavelength (red/green/blue) LED color and compare their gene expression with the control groups.

first: Pongsathorn

last: Chotikasemsri


title: Blood transcriptomic markers in patients with late-onset major depressive disorder

status: Public on Jan 14 2016

city: Maebashi

first: Shigeo

last: Miyata

address: 3-39-22 Showa-machi

institute: Gunma University Graduate School of Medicine

summary: Search for the biomarkers of major depressive disorder (MDD) has facilitated from the genes expressed in the patient’s blood cells. Because the severity of depressive symptoms and characteristics in patients with MDD are differed by the age at onset of first depressive episode, the potential transcriptomic markers in blood cells may also be different by the age at onset of MDD. In this study, we searched the transcriptomic markers of late-onset (onset ages ≥ 50 years) MDD (LOD) from the expressed genes in blood cells, and identified state-dependent biomarkers in the patients. We assessed the expressed genes in blood cells by the microarray and found that the expression levels of 3,066 probes were state-dependently changed in the blood cells of patients with LOD.

overall_design: Elderly (age ≥50 years) outpatients and inpatients with MDD corresponding to a DSM-IV diagnosis of the melancholy type of MDD episodes were studied. The depressive state was measured using the Structured Interview Guide for the Hamilton Depression (SIGH-D) rating scale. Syndromal remission was defined as a stage in which a participant did not meet the diagnosis of a MINI major depressive episode for a period of 2 consecutive months and had a SIGH-D score of less than 8. Twelve healthy individuals were also recruited. Blood was obtained from the participants and analyzed using an Agilent SurePrint G3 Human GE 8×60K v2 Microarray (Design ID: 039494).

first: Yoshiko

last: Okano

first: Noriko

last: Sakurai

first: Keisuke

last: Takahashi

first: Kosuke

last: Narita

first: Masato

last: Fukuda

first: Masahiko

last: Mikuni


title: Downstream genes regulated by TSHZ2 in MCF-7 cells

status: Public on Jan 11 2016

city: Nagakute

first: Kenji

last: Kasai

state: Aichi

address: 1-1 Yazakokarimata

department: Department of Pathology

institute: Aichi Medical University School of Medicine

summary: To clarify downstream genes regulated by TSHZ2, MCF-7 cells were lentivirally transduced by TSHZ2 and its control LacZ and served their RNA samples for gene expression analysis using AGILENT human 8x60K cDNA microarray.

overall_design: Array analysis of MCF-7 cells expressing either TSHZ2 or LacZ. 1 color method was employed.

first: M

last: Riku

first: K

first: S

last: Inaguma

first: H

last: Ito

last: Ikeda


title: A Luminal, Steroid Receptor-Positive Breast Cancer Stem Cell that Generates Intratumoral Heterogeneity is Preserved by Progesterone and Depleted by Estradiol

status: Public on Jan 31 2016

city: Aurora

first: Aaron

last: Knox

state: Colorado

department: School of Medicine, Division of Endocrinology

institute: UCDenver

summary: Most breast cancers are luminal, depending on estrogens for growth. The remainder lack estrogen receptors, are hormone-resistant and basal-like. It is thought that breast cancers arise from self-renewing normal stem cells that have undergone malignant transformation. However currently reported cancer stem cells are hormone insensitive and generate basal, rather than luminal tumors. We now describe true luminal hormone-responsive breast cancer stem cells that express estrogen and progesterone receptors. Their self-renewal capacity is protected by progesterone. Stem cell levels are depleted by estrogens as tumors transition into differentiated and homogeneous luminal states. But, if added to estrogens, progesterone promotes heterogeneity and “rescues” the stem cells. By keeping luminal cancer stem cells “safe”, progesterone, widely used for contraception and hormone replacement, could be harmful to breast cancer survivors or women with occult disease.

overall_design: The cytokeratin 5 (CK5) and CD28 studies each contains 2 sample groups (CK5+, CK5–, CD28+, CD28-) assayed in triplicate, generating 12 individual samples (12 arrays).  CK5+ and CK5- samples were generated from T47Dco cells maintained in 1nM β-Estradiol + 10nM Progesterone for 5 days. For CK5-staining, single cell suspensions were permeabilized and fixed with RNAlater (Ambion Inc.), and incubated with 2 µg anti-CK5 mAb (Novocastra; NCL-L-CK5) labeled with Zenon Alexa Fluor 488 (Invitrogen; Z-25002). Stained cells were centrifuged and resuspended in RNAse-free NST buffer containing DAPI and FACS sorted (Beckman Coulter XDP-100 MoFlo) based on CK5+ vs. CK5– expression. RNA was extracted using the PicoPure RNA isolation kit (Arcturus). RNA from T47Dco-derived CK5+ and CK5– cells were obtained in triplicate and expression profiled using Agilent 4x44K chips at MOgene LC (www.mogene.com). To isolate CD28+ and CD28- cell populations, T47Dco cells were treated with E+P for 5 days, stained for CD28 (Invitrogen; CD2801), FACS sorted and mRNA was extracted. CD28+ and CD28– gene profiles were generated as described above.

first: Abdel-Hafiz

last: Hany

first: Kathryn

middle: B

last: Horwitz

first: Huaping

last: Fan


title: Oncogenic roles of SETDB2 histone methyltransferase in gastric cancer

status: Public on Feb 21 2016

city: Yushima

first: Nishikawaji

last: Taketo

address: 1-5-45 Bunkyo-ku

department: Molecular Oncology

institute: Tokyo Medical and Dental University

summary: Histone H3 lysine 9 tri-methyltransferases (H3K9me3) are related to transcriptional gene silencing. Although SETDB2 has H3K9me3 activity, it is unknown whether SETDB2 is linking to carcinogenesis. Here, we studied alterations and functions of SETDB2 in gastric cancers (GCs). In human clinical samples, overexpression of SETDB2 protein was observed in 30 of 72 (41.7%) primary GC tissues compared with their normal counterparts, and significantly associated with poor prognosis of the patients (P<0.05). SETDB2 protein was significantly detected in late stage of GCs. Moreover, SETDB2 protein was strongly expressed in four (30.8%) of 13 GC cell lines, and knockdown of SETDB2 led to decrease the cell proliferation, migration and invasion. According to the microarray analysis on a GC cell line after knockdown of SETDB2, the expression of WWOX and CADM1 tumor suppressor genes was significantly up-regulated. ChIP analysis showed that the H3K9me3 levels at the promoter regions of WWOX and CADM1 genes were closely regulated by the SETDB2 in GC cells. We also found that SETDB2 bound to the promoter regions after SETDB2 overexpression. Our data suggest that SETDB2 is associated with transcriptional repression of WWOX and CADM1, through H3K9me3, and hence overexpression of SETDB2 may contribute to gastric progression.

overall_design: Transfection of SETDB2 siRNA into MKN74 cells were performed by electroporation. After 48hrs, cells were harvested. Total RNA was used for cDNA microarray.

first: T

last: Nishikawaji

first: Y

last: Akiyma

last: Shimada

last: Yuasa

last: Tanaka


title: Difference of gene expression between LPS-stimulated monocytes cultured in the presence NRBCs and those cultured in the absence of NRBCs

status: Public on Dec 31 2015

city: Fukuoka

first: Cui

middle: Li

last: Li

department: Pediatrics

institute: Kyushu university

summary: We found that human cord blood nucleated red blood cells (NRBCs) have a regulatory function in the innate immune reaction. NRBCs suppressed the production of inflammatory cytokines including TNF-a and IL-1b from monocytes in response to lipopolysaccharide (LPS). NRBCs exerted the regulatory function even without cell-to-cell contact with monocytes. On the other hand, IL-10 production from monocytes by the stimulation of LPS in the presence of NRBCs was higher than that of LPS-stimulated monocytes cultured in the absence of NRBCs. Addition of an anti-IL-10 receptor blocking antibody restored the inflammatory cytokine production from monocytes, suggesting that the functional change of monocytes caused by the interaction of NRBCs was characterized and mediated by the increased IL-10 production. Whole-genome microarray analysis revealed that monocytes expressed increased amounts of IL-10 superfamily genes after the interaction with NRBCs. IL-19, one of the IL-10 superfamily, enhanced IL-10 production from monocytes, which suggested cooperative role of IL-10 superfamily in the suppression of inflammatory cytokine production from monocytes. Arginase which was reported to play an important role in the suppressive function of NRBCs on monocytes in mice was found to play no significant role in human monocytes. NRBCs seem to have a regulatory role to suppress vigorous innate immune reaction which can be harmful to the fetuses via some unknown soluble factor which enhances the production of IL-10 and IL-10 family cytokines in monocytes.

overall_design: Human LPS-stimulated monocytes were collected after culture in a condition without and with NRBCs in transwell culture system. Only one experiment was performed.

first: Lili

last: Cui

first: Hidetoshi

last: Takada


title: THP-1 human monocytes Transcriptome following exposure to S-nitrosoglutathione (GSNO)

city: nancy

first: Olivier

last: Joubert

address: 2 allée guinier

department: Dpt 4

institute: Université de lorraine

summary: To further study the transcriptome of THP-1 human monocytes after exposure to of S-nitrosoglutathione (GSNO), we investigate whole genome microarray expression to identify genes regulated by exposure to GSNO (1.4 or 6 µM).

overall_design: Changes in gene expression in THP-1 cells incubated without (control) or with (1.4 or 6 µM) of GSNO for 4 h were measured. Four biological replicates were performed as controls: C1; C2; C3; C4. Four biological replicates were performed in 1,4 or 6 µM GSNO-exposed cells: G1; G2; G3; G4 and G5; G6; G7; G8; respectively.

first: Ramia

last: Safar

first: Chloé

last: Puisney

first: Bertrand

middle: H

last: Rihn

middle: R


title: Mdm2 enhances stemness-promoting chromatin modifications through the Polycomb Repressor Complex 2 in a p53-Independent Manner [HCT116 microarray]

city: Goettingen

first: Magdalena

last: Wienken

address: Justus-von-Liebig-Weg 11

institute: University Medical Center Goettingen

summary: The Mdm2 oncoprotein ubiquitinates and antagonizes p53 but may also carry out p53-independent functions. Here we report that Mdm2 is required for the efficient generation of induced pluripotent stem cells (iPSCs) from murine embryonic fibroblasts, in the absence of p53. Similarly, Mdm2 depletion in the context of p53 deficiency also promoted the differentiation of human mesenchymal stem cells and diminished clonogenic survival of cancer cells. Most of the Mdm2-controlled genes also responded to the inactivation of the Polycomb Repressor Complex 2 (PRC2) and its catalytic component EZH2. Mdm2 physically associated with EZH2 on chromatin, enhancing the trimethylation of Histone 3 at lysine 27 and the ubiquitination of Histone 2A at lysine 119 (H2AK119) at its target genes. Removing Mdm2 simultaneously with the H2AK119 E3 ligase Ring1B/RNF2 further induced these genes and synthetically arrested cell proliferation. In conclusion, Mdm2 supports the Polycomb-mediated repression of lineage specific genes independent of p53.

overall_design: microarray analysis in HCT116 p53-/-cells

first: Matthias

last: Dobbelstein


title: Altered branched-chain amino acid metabolism due to boron deficiency

status: Public on Dec 25 2015

city: Oeiras

first: Marta

last: Alves

address: Av. da República, Apartado 127

country: Portugal

institute: ITQB

summary: The importance of boron (B) for living organisms is a puzzling matter. Despite the long established essential micronutrient role of B for vascular plants, only recent research gave insights on the mechanisms of its uptake, transport and direct participation in cell-wall formation. Despite that its precise role in plant metabolism remains elusive. In an attempt to clarify the role of B in plant metabolism the gene expression profile of a persistent response to B suppression was evaluated. For that purpose, the transcriptional profile of Arabidopsis thaliana subjected to 2 days of B deficiency was analyzed and the genes that kept responding 4 days after B deficiency were selected. The gene expression profile of Arabidopsis plants submitted to Ca deficiency was also evaluated and this data cross-compared with the 2 days transcriptional profile obtained under B deficiency.

overall_design: Plants were grown on perlite, which has a low B content. After a period of 2 days at 4 ºC, the containers were transferred to a growth chamber at a temperature of 16/22 ºC (night/day), with a 16 h photoperiod and a light intensity of 150 µmol m-2 s-1, PAR. The plants were watered every other day with a complete nutrient solution in which the B concentration was 25 µM and the Ca concentration of 3 mM. Boron or Ca deficiencies were imposed 19 days after sowing by daily watering the plants with a B-free nutrient solution or with a Ca-free nutrient solution corrected for the nitrate content with magnesium and potassium salts. The gene expression profiles of the plants grown under B deficiency for 2 and 4 days or Ca deficiency for 2 days was analysed with Affymetrix ATH1 Genome Array.The expression profile of the selected genes was further evaluated by RT-qPCR.

first: Alves

last: Marta

first: Saibo

last: Nelson

first: Jackson

last: Phil

first: Ricardo

last: Cândido


title: High throughput screening of lipopolysaccharide treatment in nasal fibroblast

city: Seoul

first: Heung-Man

last: Lee

address: 148, Gurodong-ro, Guro-gu

department: Department of otorhinolaryngology

country: South Korea

institute: Korea universitiy guro hospital

summary: To evaluate effect of lipopolysaccharide in nasal fibroblast, we have employed whole genome microarray expression profiling as a discovery platform. Nasal fibroblasts were exposed to LPS (10 μg/mL) for 12 h. Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA). For control and test RNAs, synthesis of target cRNA probes and hybridization were performed using the Low RNA Input Linear Amplification kit (Agilent Technology, Santa Clara, CA). Hybridized images were scanned using a DNA microarray scanner and quantified using Feature Extraction Software (Agilent). All data normalization and selection of fold-change of the genes were performed using GeneSpringGX 7.3 (Agilent).

overall_design: Nasal fibroblasts were exposed to LPS (10 μg/mL) for 12 h. After exposure for 12hr with LPS, the untreated nasal fibroblasts and LPS-treated nasal fibroblasts were harvested and measured. Double independent experiments were performed at each time (0 or 12 hours) using different nasal fibroblasts for each experiment. So these data are duplicated.

first: Jung-Sun

last: Cho


title: Comparison of gene expression by sheep and human blood stimulated with the TLR4 agonists lipopolysaccharide and monophosphoryl lipid A

status: Public on Dec 16 2015

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

sample_organism:
Homo sapiens
Ovis aries

platform_organism:
Homo sapiens
Ovis aries


title: Investigating heterogeneity within T follicular helper cells (TFH) population.

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

institute: Centre for Immunity, Infection and Evolution

summary:
T follicular helper cells (TFH) are heterogenic population of CD4+ T cells, expressing CXCR5+ and PD-1+ on their surface. Their role is linked to supporting formation of germinal centres (GC) and these cells are thought to express high levels of PD-1 marker. Two models of immunisation were used to investigate the role of PD-1 low TFH. In Salmonella enterica infection high frequency of T follicular helper cells expressing low levels of PD-1 surface molecule are observed within first week of infection but GC do not appear until much a later stage (week 7-8). Sheep red blood cell immunisation (SRBC) gives rise to both TFH and GC B cells within first week of response and these TFH express low to high level of PD-1 molecule.
Microarray analysis was applied in order to investigate the relationship between and characteristics of different TFH populations in order to elucidate their role in GC support, developmental stage and contributions to memory T cell pool.

overall_design: Extensive FACS sorting was undertaken to separate populations of TFH from S. enterica or SRBC immunised mice (day 6 p.i.) form the effector cells. In SRBC model TFH cells were further separated into PD-1 high and PD-1 low TFH, based on the expression of PD-1 surface molecule. As a control population, effector cells were isolated from immunised mice and naive CD4+ T cells from naive mice.

first: David

last: Gray

last: Trüb


title: Transcriptome study of Caco-2 human intestinal cells following exposure to empty or S-nitrosoglutathione-loaded polymeric nanoparticles

last: Joubert

summary: To further study the transcriptome of Caco-2 human colon epithelial-like cells after exposure to S-nitrosoglutathione (GSNO, 1.4 μM), or Eudragit RL PO polymeric nanoparticles (NP-ERL, 50 μg/mL) or GSNO loaded nanoparticles (NP-GSNO, 50 μg/mL corresponding to (1.4 μM GSNO) we investigate whole genome microarray to identify genes regulates by exposure or not to GSNO (1.4 μM) or Eudragit RL PO polymeric nanoparticles (NP-ERL, 50 μg/mL) or GSNO loaded nanoparticles (NP-GSNO, 50 μg/mL corresponding to (1.4 μM GSNO).

overall_design: Changes in gene expression in Caco-2 cells incubated without (control) or with GSNO or nanoparticles for 4 h, were measured. Four biological replicates were performed as controls: S46_1_4 ; S46_1_3 ; S35_1_4 ; S35_1_3. Four biological replicates were performed for each conditions : wtih GSNO (1.4 µM) exposed cells (S46_2_2 ; S46_2_1 ; S35_2_2 ; S35_2_1), with NP-ERL (50 μg/mL) exposed cells (S46_1_2 ; S46_1_1 ; S35_1_2 ; S35_1_1) with NP-GSNO (50 μg/mL corresponding to 1.4 µM GSNO) exposed cells (S46_2_4 ; S46_2_3 ; S35_2_4 ; S35_2_3)

first: Luc

last: Ferrari


title: Microarray characterization of Vhl; Vhl, Hif1a; Vhl, Hif2a and Vhl, Hif1a, Hif2a deficient primary kidney cells

status: Public on Jan 08 2016

city: Zurich

first: Michal

last: Rajski

address: Winterthurerstrasse 190

department: Institute of Physiology

country: Switzerland

institute: University of Zurich

summary: To unravel the potential cooperative roles of oxygen-regulated signaling pathways; von Hippel-Lindau (VHL) tumor suppressor protein and hypoxia-inducible factor (HIF) transcription factors, we have generated mutant mice with; Vhlh, Vhlh/Hif1α, Vhlh/Hif2α and Vhlh/Hif1α/Hif2α gene alleles floxed. Subsequently primary kidney cells were isolated, cultured and infected with Adenoviruses bearing either Cre/GFP or GFP expression only. Agilent cDNA microarrays were utilized to compare the gene expression profiles of the kidney epithelial cells from aforementioned cell cultures to gain insight about the molecules and signaling pathways that drive aberrant cellular proliferation in clear cell renal cell carcinoma (ccRCC).

overall_design: 24 independent biological samples from 4 genetic experimental conditions were hybridized in two- color format on 13 Mouse GE 4x44K v2 Microarray Kit (Design ID 026655) arrays. Eventual dye specific hybridization effects were controlled with dye swap on biological replicates. For an each experimental condition 3 arrays were use, except of one where 4 arrays were used (one sample combination in repetition with a dye swap). For the final analysis the gene expression levels were dye effect corrected and values for biological replicates were averaged to obtain a matrix with gene expression levels for 4 independent biological (1. Vhlh-/-, 2. Vhlh-/-/Hif1α-/-, 3. Vhlh-/-/Hif2α-/- and 4. Vhlh-/-/Hif1α-/-/Hif2α-/-) conditions.

first: Désirée

last: Schönenberger

first: Sabine

last: Harlander

first: Robert

last: Jacobs

first: Anne-Kristine

last: Lundby

first: Tomas

last: Hejhal

first: Mojca

last: Adlesic

first: Peter

last: Wild

first: Carsten

first: Ian

last: Frew


title: Regulation of blood group gene expression by miRNAs

status: Public on Jan 06 2016

city: Dresden

first: Romy

last: Kronstein-Wiedemann

address: Blasewitzer Str. 68-70

department: Institute for experimental transfusion medicine

institute: Medical faculty Carl Gusatv Carus TU-Dresden

summary: To determine the miRNA expression pattern in RBCs, we isolated miRNA from RBCs of healthy blood donors, who were homozygous or heterozygous carriers of different AB0 blood groups. We first analyzed miRNA expression by microarray chip analysis. In average, we found 873 miRNAs to be present in RBCs with a partially differential expression pattern depending on the blood group genotype. 148 out of these 873 miRNAs were significantly up- or downregulated in RBCs of blood group 0 and of heterozygous genotypes, as compared to homozygous genotypes.

overall_design: For each blood group genotype erythrocyte concentrates of three different donors were used for microarray analysis.

first: Torsten

last: Tonn


title: Fibrocyte-like cells mediate acquired resistance to anti-angiogenic therapy with bevacizumab

status: Public on Dec 03 2015

city: Tokushima

first: atsushi

last: mitsuhashi

address: 3-18-15 Kuramoto-cho

department: Department of Respiratory Medicine and Rheumatology

institute: Tokushima university

summary: Bevacizumab represents anti-angiogenic effect in cancer patients by inhibiting vascular endothelial growth factor (VEGF). However, its use is still limited due to the resistance to the initial response. Such resistance could be regulated by various cell types and soluble factors, although the underlying mechanisms, especially cell-based mechanisms, remain incompletely understood. Here, we identified bone marrow-derived fibrocytes as a novel contributor for the acquired resistance to bevacizumab, defined as alpha-1 type I collagen-positive and CXCR4-positive cells. In mouse models of lung cancer and malignant pleural mesothelioma, fibrocytes mediated the resistance to bevacizumab as a main producer of fibroblast growth factor 2. Using clinical specimens of lung cancer that were surgically resected after bevacizumab treatment, we demonstrated that the number of fibrocytes was significantly increased in bevacizumab-treated tumor, and was correlated with the number of treatment cycles as well as CD31-positive vessels. Our results identify fibrocytes as a promising cell biomarker and a potential therapeutic target to overcome resistance to anti-VEGF therapy.

overall_design: In this study, it was found that long term treatment of bevacizumab induce the recruitment of fibrocytes and acquirement of resistance in tumor tissue.  In order to determine the mechanism by which fibrocytes were recruited into the tumor environment, we performed global analysis by using human malignant mesothelioma (Y-MESO-14) tumor tissue in orthotopic implantation mouse model. Y-MESO-14 bearing mice were treated with bevacizumab or vheicle continuously and tumor tissue were retrieved on day28. Gene expression profiles were analyzed and compared with both groups using Agilent4 ×44K ver. 2.0 Micro Arrays .

first: Atsushi

last: Mitsuhashi

first: Hisatsugu

last: Goto

first: Hideaki

last: Horikawa

first: Yasuhiko

last: Nishioka