title: Transcriptional effects of anti-inflammatory or anti-depressant drugs on primary human macrophages inflammatory response

city: Midlothian

first: Tim

last: Regan

address: Easter Bush Campus

department: Genetics and genomics

institute: The Roslin Institute, University of Edinburgh

summary:
The direct communication between our central nervous and inflammatory signalling systems is a well-recognised, yet poorly understood relationship. To increase our understanding of this relationship, we examined the metabolism of serotonin and its precursor tryptophan in macrophages under inflammatory settings. Both are involved in inflammatory signalling and known to play a major role in mood regulation. Tryptophan depletion by macrophages during inflammation can consequently result in a reduction of serotonin systemically and has been suggested to cause depression. Increased understanding of this system could help overcome the problem of treatment resistant depressed patients. To this end, we treated primary human monocyte derived macrophages with a range of anti-depressant/anti-inflammatory drugs and analysed their transcriptional profile under various inflammatory conditions. In addition to the classic endotoxic driver of inflammation, LPS, we also used IFNα which is a constitutive cytokine shown to directly induce depression when administered in high doses. The anti-depressant drugs were not found to have any significant effects on macrophage inflammatory signalling. However, the anti-inflammatories drugs were found to alter components of the serotonin/tryptophan metabolism pathways. This study increases our understanding of the intricacies of immune/mood cross-talk and offers into developing anti-inflammatories as co-treatment for depression.
We treated human primary macrophage cells with anti-inflammatory or anti-depressant drugs and analysed their transcriptional effects during inf.lammatory signaling within the context of tryptophan metabolism/kynurenic metabolism.

overall_design: Primary human CD14+ monocytes were isolated from the whole blood of 6 donors (3 male, 3 female). These were transformed in macrophages through CSF-1 stimulation over a week. Cells were then subject to inflammatory stimulus with LPS (10 ng/ml) or IFNa (50 U/ml) for 7 or 24 h or incubated for 24 h with no inflammatory stimulus. In each of these 5 conditions, cells were treated for the same amount of time with either vehicle control (DMSO), escitalopram (SSRI antidepressant), nortriptyline (tricyclic antidepressant), anti-TNFa (neutralising antibody anti-inflammatory), indomethacin (non-steroidal anti-inflammatory), prednisolone (steroidal anti-inflammatory) or left untreated.

first: Tom

last: Freeman


title: Gene expression profiles from murine BALB/c macrophages at the extremes of the M1 and M2 polarized phenotypes

status: Public on Jan 01 2018

city: Wuhu

first: Xueqin

last: Li

address: 2 Western Zheshan Road

country: China

institute: wannan medical college

summary:
Macrophages possess the hallmark feature of plasticity, allowing them to undergo a dynamic transition between M1 and M2 polarized phenotypes. The aim of the present study was to screen for differentially expressed genes (DEGs) that were associated with macrophage polarization.
The transcription profiles of three M1 and three M2 samples were obtained using microarray analysis. Based on the threshold of fold-change >2.0 and a p-value < 0.05, we screened a total of 1,253 DEGs, of which 696 were upregulated and 557 downregulated in M1 macrophages compared to that in M2 macrophages. Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were also performed. A gene-gene interaction network of the DEGs was constructed using the STRING database. GO annotation identified three categories, which included cellular component (CC), molecular function (MF), and biological process (BP), with 34 and 40 enrichment terms consisting of upregulated and downregulated DEGs, respectively. GO enrichment analysis of DEGs was mainly associated with protein binding, response to stimulus, cell differentiation, and regulation of biological process. KEGG enrichment identified 15 and four pathways involving upregulated and downregulated DEGs, respectively. Signaling pathway analysis showed that these DEGs were mainly involved in apoptosis, HIF-1 signaling pathway, innate immune system, TNF signaling pathway, cytokine-cytokine receptor interaction, and other signal transduction pathways. Interaction network analysis indicated that Tnf, Il6, Il1b, Socs3, Nos2, Hif1a, and other genes may play key roles in macrophage polarization. This study provides new insights into the role of genes in macrophage differentiation and polarization.

overall_design: Total RNA was prepared from bone marrow-derived macrophages of wild-type BALB/c mice treated in M1 or M2 conditions (n=3 replicates per condition originating from different mice)

first: Kun

last: Lv

first: Jiang


title: RNase 7 downregulates TH2 cytokine production by activated human T-cells

status: Public on Dec 31 2017

city: Hannover

first: Verena

last: Kopfnagel

address: Carl-Neuberg-Straße 1

department: Dermatology

country: Germany

institute: Hannover Medical School

summary: Isolated human CD3+ T-cells were stimulated with the a recombinant mutant of the antimicrobial peptide RNase 7 without ribonuclease activity (RNase 7M) and screened for possible effects by mRNA microarray analysis.

overall_design: RNase 7M induced gene expression in human CD3+ T-cells was analysed after 6h. Four independent experiments were performed using different donors. RNA of 2 donors was pooled. In order to enable inspection of intensity values, dual-colour results were integrated into a single-color GEO matrix.

first: Thomas

last: Werfel

first: Jürgen

last: Harder


title: Serotonin promotes the acquisition of an anti-inflammatory and pro-fibrotic profile in human macrophages via engagement of HTR7

city: Madrid

first: Angeles

last: Domínguez Soto

address: Ramiro de Maeztu

country: Spain

institute: CSIC

summary: Peripheral serotonin (5-hydroxytryptamine, 5HT) regulates cell growth and differentiation in numerous cell types through engagement of seven types of cell surface receptors (HTR1-7). Deregulated 5HT/HTR levels contribute to pathology in chronic inflammatory diseases, with macrophages being relevant targets for the physio-pathological effects of 5HT. In fact, 5HT skews human macrophage polarization through engagement of HTR2B and HTR7 receptors. We now report that 5HT primes macrophages for reduced pro-inflammatory cytokine production and IFN type I-mediated signalling, and promotes an anti-inflammatory and pro-fibrotic gene signature in human macrophages. The acquisition of the 5HT-dependent gene profile primarily depends on the HTR7 receptor and HTR7-initiated PKA-dependent signaling. In line with the transcriptional results, 5HT upregulates TGFb1 production by human macrophages in an HTR7- and PKA-dependent manner, whereas the absence of Htr7 in vivo results in diminished macrophage infiltration and collagen deposition in a mouse model of skin fibrosis. Our results indicate that the anti-inflammatory and pro-fibrotic activity of 5HT is primarily mediated through the HTR7-PKA axis, and that HTR7 contributes to pathology in fibrotic diseases.

overall_design: Macrophages were differentiated from peripheral blood monocytes from 3 healthy donors with M-CSF (M-MØ). Before treatment with 5HT, M-MØ macrophages were maintained in serum-free medium for 48 hours. Macrophages were untreated or 5HT-treated (10 uM) during 6 hours and global gene expression was analysed.

first: Miguel

middle: A

last: Vega

first: Ángel

middle: L

last: Corbí

last: Domínguez-Soto

first: Mateo

last: de las Casas-Engel


title: Transcriptional response of Scots pine trees to Heterobasidion annosum infection: analyses of antimicrobial protein Sp-AMP2

city: Helsinki

first: Tommaso

last: Raffaello

address: Latokartanonkaari 7 PO Box 27

department: Forest Sciences

country: Finland

institute: University of Helsinki

summary: Understanding of mechanisms of resistance of forest trees against microbial pathogens is an essential prerequisite for the development of sustainable forestry practices and for the improvement of commercially-grown trees via either conventional breeding or rational genetic engineering. We have studied the transcriptional response of Scots pine trees to Heterobasidion annosum infection under field conditions. By comparing responses of trees to wounding and to fungal inoculation we could identify a set of genes that were specifically responding to fungal infection. We have also investigated a contribution of Scots pine antimicrobial protein Sp-AMP2 to the host antimicrobial defense to evaluate the potential of Sp-AMP genes as molecular markers for resistance breeding.

overall_design: 6 Samples of Stem (bulk of xylem and phloem) were analysed. Three replicates of wounded (non-inoculated tree) and three replicates of infected stems (inoculated tree).

first: Emad

last: Jaber

first: Andriy

last: Kovalchuk

first: Susanna

last: Keriö

first: Teemu

last: Teeri

first: Fred

middle: O

last: Asiegbu


title: Gene expression change in the liver by luteolin treatment in rats with nonalcoholic steatohepatitis

city: Nagoya

first: Aya

last: Naiki-Ito

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

department: Department of Experimental Pathology and Tumor Biology

country: Japan

institute: Nagoya City University Graduate School of Medical Sciences

summary: Gene expression change in the liver of connexin dominant negative transgenic (Tg) and wild-type (Wt) rats fed methionine-choline deficient diet (MCDD) or MCDD with luteolin for 12 weeks.

overall_design: Cx32 dominant negative transgenic rats and wild-type rats at 10 weeks of age were given an intraperitoneal injection of diethylnitrosamine and fed MCDD or MCDD with luteolin for 12 weeks.


title: Gene expression profiles of E8.75, E9.5, E10.5 and E11.5 ureteric bud precursors

city: Kumamoto

first: Atsuhiro

last: Taguchi

state: Kumamoto

department: IMEG

institute: Kumamoto Univ.

summary: Understanding the early developmental processes of the kidney ureteric bud lienage is important for the regeneration of kidney in vitro. The combination of fluorescent activated cell sorting (FACS) plus microarray analysis offers a powerful, efficient and effective method for the creation of global gene expression profiles of the developing kidney precursors. Those gene expression data provides insights into not only the stage specific marker genes but also the signals working in each population, which should be informative for the directed differentiation of pluripotent stem cells in vitro.

overall_design: Hoxb7-GFP transgenic mice were used to isolate kidney ureteric bud (UB) precursor cells from embryos at E8.75, E9.5, E10.5 and E11.5. For isolation of the pure UB precursor population, dissociated embryos were sorted by the flow cytometry gating Hoxb7-GFP-positive  Flk1-negative population. To identify the differences between UB progenitors and neighboring nephron progenitor lineage precursors, the UB precursors were compared with E9.5 Wt1-GFP positive intermediate mesoderm cells, which give rise to the mesonephric and metanephric nephron progenitors.

first: Ryuichi

last: Nishinakamura


title: Expression analysis of Hsa-miR-145-5p overexpressed laryngeal squamous carcinoma cell line TU177

city: Taiyuan

first: Yongyan

last: Wu

state: Shanxi

address: No.85 South Jiefang Road, Taiyuan, Shanxi, China

department: Department of Otolaryngology Head & Neck Surgery, The First Hospital

institute: Shanxi Medical University

summary:
Investigation of whole genome gene expression level changes in laryngeal squamous carcinoma cell line TU177 in response to overexpressed miR-145-5p.
Differentially expressed protein-coding genes in the human laryngeal squamous carcinoma cells TU177 overexpressing miR-145-5p were identified by microarray analysis.

overall_design: The human laryngeal squamous carcinoma cells TU177 were transfected with Hsa-miR-145-5p mimic and negative control oligo  at a final concentration of 50 nM by using lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions, respectively. Three repeats were prepared for each panel. Total RNA was extracted after 48 h transfection, and six chip were used to analyze the gene expression changes.

first: Wei

last: Gao

first: Binquan

last: Wang

first: Qinli

last: Zhao

first: Qingqing

last: Liu

first: Huina

last: Guo

first: Jun

first: Xukuan

last: Qu


title: Differential expression of plasma miRNAs in immune thrombocytopenia

city: Suzhou

first: yang

last: he

state: Jiangsu

address: 1 Shizi Street

institute: Soochow University

summary: We investigated the expression profiles of plasma miRNAs in immune thrombocytopenia (ITP) patients. Peripheral blood plasma was used for Agilent miRNA expression microarray analysis to define miRNA profiles and to identify miRNAs with discriminatory levels for ITP and healthy controls. Results were further validated using quantitative realtime PCR on a larger cohort, enabling relative quantification of plasma miRNAs and defining miRNAs with diagnostic value for the disease.

overall_design: We analyzed expression profiles of plasma miRNAs from a total of individuals:  6 healthy controls and 10 ITP patients.

first: Bin

last: Zuo

first: Yunxiao

first: Jianfeng

last: Yang

first: Lan

last: Dai

first: Qingyu

first: Yang

last: He


title: miRNA expression profiling of Prostate Epithelial Cells (PrEc) with ESE3 knock-down

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

summary: Investigation of miRNA expression profiles of Prostate Epithelial Cells (PrEc) with ESE3 knock-down

overall_design: Two replicates for treated and control samples were performed

first: Cecilia

last: Dallavalle

first: Domenico

last: Albino

first: Gianluca

last: Civenni

first: Maurizia

last: Mello-Grand

first: George

last: Thalmann

first: Ramon

last: Garcia-Escudero

first: Giovanna

last: Chiorino

first: Carlo

middle: V

last: Catapano

first: Giuseppina

middle: M

last: Carbone


title: Transcriptomic analysis of glioblastoma cells bearing different IRE1a mutants

status: Public on Dec 09 2017

city: Athens

first: Aristotelis

last: Chatziioannou

address: 48 Vas. Constantinou Ave.

department: Institute of Biology, Medicinal Chemistry and Biotechnology

country: Greece

institute: National Hellenic Research Foundation

summary: Glioblastoma multiforme is the most lethal form of glioma with an overall survival at 5 years nearly null, which mainly results from acquired resistance to therapies. Large scale sequencing studies on human cancer biopsies defined IRE1alpha as the fifth most oncogenic mutated kinase in human cancer. IRE1alpha is a major component of the Unfolded Protein Response signaling and increasing evidence suggests that it is a central player in GBM development.

overall_design: U87-MG glioblastoma cells were transfected with different IRE1a mutants or a Dominant Negative form of IRE1a. Cells transfected with  Empty Vector were used as control. Cells were treated both in basal and stress conditions. For stress condition, tunicamycin (purchased from Calbiochem (Merck KGaA, Darmstadt, Germany)) was used at 0.5 µg/mL for 16 hrs. There are 3 replicates for each condition, except from the Dominant Negative (2 replicates).

first: Stéphanie

last: Lhomond

first: Konstantinos

last: Voutetakis

first: Olga

last: Papadodima

first: Marianthi

last: Logotheti

first: Eric

last: Chevet


title: Immunoglobulin class-switch recombination downregulates Blimp1-driven IL-10 production in IgM+CD138hi cells

status: Public on Sep 01 2017

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: To determine characterize IL-10 producing CD138hi cells, we compared the global gene expression of primary B220+ B cells in spleen, freshly isolated Venus+ CD138hi cells in bone marrow and spleen of IL-10 Venus reporter mice.

overall_design: B220+ and Venus+ CD138hi cells from spleen and bone marrow  of IL-10 Venus mice were sorted by flow cytometric cell sorting on a BD Aria III sorter (Becton Dickinson). Total RNA was purified using RNeasy Plus Mini Kit (QIAGEN). Total RNA was labeled with Cy5 using the Amino Allyl Message AMP II aRNA Amplification Kit (Applied Biosystems). The Cy5-labeled aRNA was fragmented and then hybridized to 3D-Gene Mouse Oligo chip 24k (Toray Industries Inc.). Hybridization signals were scanned with a 3D-Gene Scanner and processed by 3D-Gene Extraction software (Toray Industries). The raw data of each spot were normalized by subtraction with a mean intensity of the background signal determined by all blank spots' signal intensities of 95% confidence intervals. Detected signals for each gene were normalized by a global normalization method (the median of the detected signal intensity was adjusted to 25)

first: Nao

last: Yamazaki

last: Takaki


title: ChIP-chip analyses of PR- related pathway in human oncocytic thyroid tumor cell line XTC.UC1

status: Public on Nov 07 2017

city: TOULOUSE

first: Savagner

last: Frederique

address: Avenue Jean Poulhes

country: France

institute: Inserm

type: Genome binding/occupancy profiling by genome tiling array

summary:
ChIP-chip analyses of five transcription factors (ERR1, GABP, NRF1, CREB and YY1)  PRC coactivator and RNA polymerase II in XTC.UC1 cells compared to non specific IP (IgG or input)
seven factors studied: ERR1, GABP, NRF1, CREB, YY1, PRC, RNAPolII

overall_design: 10% of Serum induction for XTC.UC1 cells during 24h and 48h before ChIP chip analysis using  antibodies against transcription factors , PRC transcriptionnal coactivator and RNApolymerase II

first: F

last: Savagner

first: R

last: Houlgatte


title: Gene expression profiling of noncancerous prostate epithelial cells (RWPE-1) following pre-miR-424 transfection

first: Paola

last: Ostano

summary: MicroRNAs (miRNAs) play important roles in cell differentiation and self-renewal controlling post-transcriptional processing of mRNAs and attenuating production of the encoded proteins. Here, we unveil a novel oncogenic pathway leading to activation of STAT3 signaling through miRNA-mediated silencing of the E3 ubiquitin ligase COP1. miRNA profiling showed that miR-424 was upregulated in prostate cancer compared to normal prostate and specifically associated with reduced level of the ETS factor ESE3/EHF in an aggressive subgroup of tumors. MiR-424 was significantly elevated also in other epithelial cancers and amplified in 1-3% of various cancers. In normal prostate epithelial cells miR-424 was repressed by ESE3/EHF and when upregulated promoted oncogenic and cancer stem cell (CSC) properties. Conversely, ablation of miR-424 in metastatic prostate cancer cells reduced CSC self-renewal and prevented in vivo tumour initiation and metastatic spread. miR-424 targeted the 3' UTR of COP1 mRNA and reduced COP1 protein level. COP1 induced STAT3 ubiquitylation and degradation by the ubiquitin-proteasome system (UPS). Therefore, reduced levels of COP1 in prostate cancer cells, resulted in accumulation and increased STAT3 signaling. COP1 knockdown and over-expression phenocopied the effects of miR-424 deregulation on oncogenic phenotypes and STAT3 signalling, while STAT3 knockdown prevented the transforming effects of miR-424. Consistently, expression of EHF/ESE3 and RFWD2/COP1 were highly correlated in human prostate cancers and other epithelial tumors. Furthermore, miR-424 induced genes were enriched of STAT3 targets, converged with those induced by COP1 loss in mouse embryos and were associated with adverse prognosis in prostate and other epithelial cancers. In primary prostate tumours, low COP1 and high STAT3 protein level were also significantly associated and predictive of biochemical relapse. Collectively, this study reveals a novel miRNA-activated oncogenic axis in prostate cancer. Targeting miR-424 or miR-424 dependent pathways may represent a unique approach to attack a key node in tumorigenesis.

overall_design: Investigation of gene expression profiles of noncancerous prostate epithelial cells (RWPE-1) following pre-miR-424 transfection vs. control. Two technical replicates (dye swaps) were performed.

first: Cecilia

last: Dallavalle

first: Domenico

last: Albino

first: Gianluca

last: Civenni

first: Maurizia

last: Mello-Grand

last: Thalmann


title: Tet-Gabpα cKO ES cells: -Tet vs. +Tet

status: Public on Jul 01 2017

summary: We generated tetracycline-inducible myc-GABPα-expressing Gabpα conditional knockout embryonic stem cells (Tet-Gabbpα cKO ES cells), and then compared the transcriptional profiles between control (-Tet) and Gabpα-null (+Tet) cells by an oligo DNA microarray analysis.

overall_design: Tet-Gabpα cKO ES cells were cultured with or without Tet for 1 day. Total RNAs were isolated and subjected to microarray analysis.

first: Atsushi

last: Ueda

first: Tadayuki

last: Akagi

first: Takashi

last: Yokota


title: Evaluation of gene expression profiling in mouse selected populations of bone metastatasis derivatives

status: Public on Nov 15 2017

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

institute: Parc Taulí Research and Innovation Institute (I3PT)

summary: For many breast cancer (BCa) patients, symptomatic bone metastases appear after years or even decades of latency. How metastatic cells disseminate, and how micrometastatic lesions remain dormant and undetectable, are major questions in cancer research. Here we identify and functionally analyse a molecular mechanism involved in the bone metastatic latency of estrogen receptor (ER)+ BCa.

overall_design: Comparison of cells before and after residing in the mouse for 170 days. Gene expression was analyzed using Affymetrix Human Genome 133PM strip.

first: Sylwia

last: Gawrzak


title: Foot and mouth disease virus (FMDV) infection in Indian cattle (Bos indicus): Profiling of serum microRNAs

status: Public on Oct 20 2017

city: Bengaluru

first: Suresh

middle: H

last: Basagoudanavar

state: Karnataka

address: IVRI, Hebbal

department: FMD Research Laboratory

country: India

institute: Indian Veterinary Research Institute

summary: Profiling of miRNA in serum of FMDV infected cattle, to understand disease pathogenesis and to identify FMD specific miRNA biomarkers to aid early pre-clinical diagnosis

overall_design: Agilent  one-color miRNA experiment,Organism: Bos indicus,  Bovine miRNA 8x60K Microarray (AMADID: 072447)

first: Madhusudan

last: Hosamani

middle: P

last: Tamil Selvan

last: Venkataramanan


title: Characterizing transcriptional responses of the Ishikawa cell line to ethinyl estradiol (EE; CAS #57-63-6) following 72 hour exposure

city: RTP

first: Salil

middle: N

last: Pendse

state: NC

address: 6 Davis Drive

country: USA

institute: Scitovation

summary:
A toxicity pathway approach was taken to develop an in vitro assay using human uterine epithelial adenocarcinoma (Ishikawa) cells (ECACC cat#99040201) as a replacement for measuring an in vivo uterotrophic response to estrogens.
As part of validating the use of this cell line, gene arrays were performed to confirm functional transcriptional responses to ethinyl estradiol (EE)

overall_design: Ishikawa cells were treated with EE for 72 hours and then total RNA was isolated for gene expression anaylsis.  6 replicates were performed across 7 doses of EE.

first: Michelle

last: Miller


title: Transcriptional effects of soluble CD40 ligand on human immature dendritic cells

status: Public on Jun 08 2017

city: Spring House

first: Alice

last: Walsh

state: PA

address: Welsh & McKean Roads

department: Immunology

institute: Janssen R&D

summary: We performed microarray analysis of sCD40L-stimulated iDC to derive a signature of CD40 activation. Human monocytes from normal healthy donors were differentiated to iDCs with GM-CSF and IL4. FACS analysis demonstrated the immature status of these cells, illustrated by low expression of CD80, CD40, and CD86.  We confirmed that sCD40L induces the maturation of DCs, characterized by higher expression of CD80, HLA-DR, CD86, CD83 and CD40 and secretion of pro-inflammatory cytokines at 24hr post-stimulation. Cells were harvested at 1, 3 and 24hr post-stimulation for microarray analysis.

overall_design: Immature dendritic cells were derived from 5 healthy donors. Cells were treated with vehicle control or soluble CD40L for 1, 3, or 24hrs before RNA extraction and microarray processing with Affymetrix HT-HGU133 2 Plus PM arrays.

first: Yanxia

last: Guo


title: Distinctive transcriptome alterations of prefrontal pyramidal neurons in schizophrenia and schizoaffective disorder

status: Public on Jul 23 2017

city: Pittsburgh

first: David

last: Lewis

address: 3811 O'Hara St

department: Psychiatry and Neuroscience

institute: University of Pittsburgh

summary:
Schizophrenia is associated with alterations in working memory that reflect dysfunction of dorsolateral prefrontal cortex (DLPFC) circuitry. Working memory depends on the activity of excitatory pyramidal cells in DLPFC layer 3, and to a lesser extent in layer 5.
Although many studies have profiled gene expression in DLPFC gray matter in schizophrenia, little is known about cell type-specific transcript expression in these two populations of pyramidal cells. We hypothesized that interrogating gene expression specifically in DLPFC layer 3 or 5 pyramidal cells would reveal new and/or more robust schizophrenia-associated differences that would provide new insights into the nature of pyramidal cell dysfunction in the illness.

overall_design: Individual pyramidal cells in DLPFC layers 3 or 5 were captured by laser microdissection from 36 subjects with schizophrenia or schizoaffective disorder and matched normal comparison subjects.

first: Dominique

last: Arion

first: John

last: Corradi

first: Shaowu

last: Tang

first: Dibyadeep

last: Datta

first: Franklyn

last: Boothe

first: Aiqing

last: He

first: Angela

last: Cacace

first: Robert

last: Zaczek

first: Charles

middle: F

last: Albright

first: George

last: Tseng


title: TaqMan Human miRNA array profile of Mycobacterium tuberculosis H37Rv infected THP-1 differentiated macrophages cells.

status: Public on Apr 20 2017

city: Lucknow

first: Dr. Bhupendra

middle: Narain

last: Singh

state: Uttar Pradesh

address: Jankipuram Extension, Sec.-10, Sitapur Road

department: Microbiology

institute: CSIR-CDRI Lucknow

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

summary: Differentially regulated miRNA candidates in H37Rv infected THP-1 cells were analysed with respect to uninfected THP-1 reference samples. THP-1 cells are monocytes differentiated to macrophages after treatment with PMA for 48 hrs. Total RNA was isolated from infected THP-1 cells after 24 hrs of infection, cDNA was synthesized for TLDA real time PCR reaction using TaqMan MicroRNA Reverse Transcription kit and Megaplex Human Pool A and Pool B stem loop RT primers (version 3.0) as per manufacturer’s protocol. Further real time reaction was performed on QuantStudio 12K Flex Real-Time PCR System (Applied Biosystems) by using cDNA (without pre-amplification) on TLDA card A and card B (version 3.0).

overall_design: miRNA profile was obtained after Real Time PCR analyses using TLDA card from total RNA sample of H37Rv infected THP-1 macrophages (Treated) with respect to uninfected reference sample (Untreated).

first: Ashutosh

last: Tripathi

first: Bhupendra


title: Transcriptional effects of soluble CD40 ligand on human naïve B cells

summary: We performed microarray analysis to derive gene signatures down-stream of soluble CD40 ligand stimulation in human naive B cells. Naïve B cells were purified from healthy donor PBMC using negative selection beads (Miltenyi) and cultured with sCD40L at 2.5ug/ml for 6hr before microarray analysis. In the same study, cells were also harvested at day 5 post-stimulation to confirm sCD40L-induced B cell activation and proliferation. FACS analysis confirmed soluble CD40L induced up-regulation of CD86 and CD69 at 24hr. B cell proliferation was measured at day 4 post-stimulation by EdU incorporation.

overall_design: Naïve B cells were purified from peripheral blood of 6 healthy donors. Naïve B cells were then stimulated with sCD40L or mock-treated, and harvested at 6hr for microarray analysis. 2-4 replicates were available per donor and condition.


title: Gene expression profiles in human ES cells and human iPS cells

status: Public on Mar 26 2017

city: Kyoto

first: Kazuo

last: Takayama

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

institute: Kyoto University

summary: Genome editing research of human ES/iPS cells has been accelerated by clustered regularly interspaced short palindromic repeats/CRISPR-associated 9 (CRISPR/Cas9) and transcription activator-like effector nucleases (TALEN) technologies. However, the efficiency of biallelic genetic engineering in transcriptionally inactive genes is still low, unlike that in transcriptionally active genes. To enhance the biallelic homologous recombination efficiency in human ES/iPS cells, we performed screenings of accessorial genes and compounds. We found that RAD51 overexpression and valproic acid treatment enhanced biallelic-targeting efficiency in human ES/iPS cells regardless of the transcriptional activity of the targeted locus. Importantly, RAD51 overexpression and valproic acid treatment synergistically increased the biallelic homologous recombination efficiency. Our findings would facilitate genome editing study using human ES/iPS cells.

overall_design: Tic, YOW-iPS, Dotcom, KhES1, H9, H1 were pooled from three independent experiments, and then microarray analysis was performed.

first: Hiroyuki

last: Mizuguchi


title: Gene expression profile of cardiac macrophages at different timepoints after myocardial infarction

status: Public on Mar 27 2017

first: Satoshi

last: Kondo

summary:
Myocardial infarction (MI) causes sterile inflammation, which is characterized by recruitment and activation of innate and adaptive immune system cells. We have delineated the temporal dynamics of immune cell accumulation following MI by flow cytometry. Macrophages were numerically the predominant cells infiltrating the infarcted myocardium, increasing in number over the first week post-MI. Macrophages are functionally heterogeneous, and can be classified into M1 and M2 macrophages, respectively, based on surface-marker expression. M1 macrophages dominated at 1-3 days post-MI, whereas M2 macrophages represented the predominant macrophage subset after 5 days.
We used microarrays to examine the gene expression profiles of the macrophages sorted from the hearts at different timepoints after MI. We identified the kinetics of gene expression of cardiac macrophage after MI.

overall_design: To examine the expression profile of cardiac macrophages after MI, CD11b+F4/80+Ly-6G- macrophages were sorted and pooled from the hearts (Sham operation, Day1 after MI, Day3 after MI, Day7 after MI, Day14 after MI), followed by RNA extraction and microarrays.

first: X

last: Yan

first: M

last: Sano


title: Expression data from consecutive stages of human early in vitro T-cell differentiation

status: Public on Mar 08 2017

city: Utrecht

first: Jules

last: Meijerink

address: Uppsalalaan 8

country: Netherlands

institute: Princess Máxima Center for Pediatric Oncology

summary:
Human T-cell development is less well studied than its murine counterpart due to the lack of genetic tools and the difficulty of obtaining cells and tissues. However, recent technological advances allow identification of the transcriptional landscape of differentiating human thymocytes. Here we report the gene expression profiles of 11 immature, consecutive T-cell developmental stages. The changes in gene expression of cultured stem cells on OP9-DL1 match those of ex vivo isolated human thymocytes. These analyses led us to define evolutionary conserved gene signatures that represent pre- and post- αβ T-cell commitment stages. We found that loss of CD44 marks T-cell commitment in early CD7+CD5+CD45dim cells, before the acquisition of CD1a surface expression. The CD44-CD1a- post-committed thymocytes have initiated in frame TCR rearrangements and have completely lost the capacity to develop into myeloid, B- and NK-cells, unlike uncommitted CD44+CD1a- thymocytes. Therefore, loss of CD44 represents a previously unrecognized stage that defines the earliest committed T-cell population in the human thymus.
We used microarrays to detail the transcriptional program underlying human early T-cell differentiation, from CD34+ HSCs until the CD4+CD8+ DP stage.

overall_design: Throughout the differentiation of human HSC towards the T-cell lineage, we sorted T-cell fractions at 5 time points (days 0, 7, 12, 18, and 27) based on the expression of cell surface markers including CD45, CD34, CD7, CD5, CD1a, CD4 and CD8. Following the sorting of consecutive early T-cell development stages, the samples were then used for RNA extraction and hybridization on Affymetrix microarrays.

first: Rui

middle: D

last: Mendes

first: Kirsten

last: Canté-Barrett


title: MicroRNA profiling of human follicular fluid and MII oocytes

status: Public on Apr 25 2017

city: Catania

first: Cinzia

last: Di Pietro

address: via S.Sofia 87

department: Department of Biomedical and Biotechnological Sciences

institute: University of Catania

summary: This study is focused on microRNAs in ovarian follicles and their predicted role in the pathways involved in oocyte growth and maturation. We determined the expression profiles of microRNAs in human oocytes and follicular fluid by high-throughput analysis, and identified the most significant Biological Processes and the pathways regulated by microRNA validated targets.

overall_design: The aim of this study was to identify the miRNAs in the follicular microenvironment and position them within the different compartments of the ovarian follicle identifying the pathways regulated by miRNA targets. Human oocytes and follicular fluid (FF) samples were collected from healthy women undergone intracytoplasmic sperm injections (ICSI). FF of individual follicles was kept separated until decumulation of the oocytes to collect only the FF in which nuclear mature oocytes (metaphase II) had been identified. A total of 12 mature MII oocytes, two oocytes per woman, showing normal morphology, and 6 pools of FF were collected from individual follicles of 6 and 15 healthy women respectively, and used for miRNA expression profile analysis.

first: Rosalia

last: Battaglia

first: Vento

last: Elena

first: Borzì

last: Placido

first: Marco

last: Ragusa

first: Davide

last: Barbagallo

first: Desirée

last: Arena

first: Michele

last: Purrello


title: Pentraxin-3 is a PI 3-Kinase Effector that Regulates Stem-Cell-Like Traits in Basal-Like Breast Cancer

status: Public on Feb 28 2017

city: Boston

first: Antoine

middle: Elias

last: Karnoub

state: MA

address: 3 Blackfan Circle

department: Pathology

institute: Beth Israel Deaconess Medical Center and Harvard Medical School

summary:
MCF10A cells: control vs. PIK3CA mutant (H1047R)
Transcriptional profiling of MCF10A comparing control (expressing JP1520-PIK3CA-WT; Addgen plasmid #14570) and PIK3CA mutant (JP1520-PIK3CA-H1047R; Addgene plasmic#14572). Goal was to determine the effects of the PIK3CA H1047R mutation in the on global gene expression in MCF10A cells.

overall_design: Two-condition experiment, ES vs. TF-ES cells. Biological replicates: 4 control replicates, 3 transfected replicates.

first: Whitney

last: Henry

first: Alex

last: Toker


title: Gene expression data of QRsP-11 mouse fibrosarcoma cell line and its liver metastatic subline

first: Satoshi

last: Kondo

summary: Mouse QRsP-11 fibrosarcoma cells were injected into the spleens of mice to isolate sub-populations of tumor cells that colonize to the liver. Cells from liver metastatic nodules were established in vitro and subsequently injected intrasplenically for further cycles of selection. After 12 cycles of in vivo selection, the cell subline LV12 was established.  Intravenous injection of LV12 cells produced liver metastases than QRsP-11 cells, whereas the incidence of lung metastases was similar to that of QRsP-11 cells. LV12 cells exhibited adhesiveness to liver-derived but not to lung-derived endothelial cells. DNA chip analysis indicated that an amphoterin-induced gene and open reading frame 2 (Amigo2) was overexpressed in LV12 cells. Knockdown of Amigo2 expression by siRNA in LV12 cells attenuated liver endothelial cell adhesion. Ex vivo imaging showed that siRNA-mediated suppression of Amigo2 in luciferase-expressing LV12 cells reduced attachment to liver tissue to the same level as that observed with QRsP-11 cells.  Moreover, Amigo2-knockdown by siRNA inhibited liver metastasis. Amigo2 expression in human cancer cells was higher in liver metastatic lesions than in primary lesions of colon and gastric cancer specimens. These data indicated that Amigo2 is involved in tumor cell adhesion to liver endothelial cells and formation of liver metastases.

overall_design: Gene expression profiles of the parental QRsP-11 fibrosarcoma cell line and its liver metastatic LV12 subline were analyzed. Two samples.

first: Yusuke

last: Kanda

first: Mitsuhiko

last: Osaki

first: Kunishige

last: Onuma

first: Ayana

last: Sonoda

first: Masanobu

last: Kobayashi

first: Junichi

last: Hamada

first: Garth

last: Nicolson

first: Takahiro

last: Ochiya

first: Futoshi

last: Okada


title: Nanostring Immunology V2 panel comparing the transcriptional profile of GD2-CAR T-cells vs GD2-CAR.C7R T-cells after multiple tumor cell challenges.

status: Public on Oct 05 2017

city: Houston

first: Cliona

last: Rooney

state: Texas

address: 1102 Bates Street

institute: Baylor College of Medicine

summary: The purpose of the experiment was to compare the transcriptional profile of T-cells expressing a GD2-CAR construct or a GD2-CAR.C7R construct (where the GD2-CAR and the C7R construct are co-expressed), after the T-cells had been exposed to two serial tumor cell co-cultures. C7R is an engineered IL-7 receptor that has been rendered constitutively active. The sample replicates were generated using peripheral blood mononuclear cells (PBMCs) obtained from healthy human donors.

overall_design: There are 6 sample replicates for the GD2-CAR T-cell condition, and 6 sample replicates for the GD2-CAR.C7R T-cell condition. Samples 7546 and 7785 are from the same human donor (and were averaged together after normalization for the follow-up statistical analysis.

first: Thomas

last: Shum


title: Selective Degradation of Splicing Factor CAPER-alpha by Anticancer Sulfonamides

status: Public on Jan 20 2017

city: Tsukuba-shi

first: Taisuke

last: Uehara

state: Ibaraki

address: Tokodai 5-1-3

department: Oncology Business Group

institute: Eisai Co., Ltd.

summary: Target protein degradation is an emerging field in drug discovery and development. In particular, the substrate receptor proteins of the cullin ubiquitin ligase system play a key role in selective protein degradation, which is an essential component of the anti-myeloma activity of immunomodulatory drugs (IMiDs) represented by lenalidomide. Here, we demonstrate that a series of anticancer sulfonamides NSC 719239 (E7820), indisulam, and NSC 339004 (chloroquinoxaline sulfonamide, CQS) induce proteasomal degradation of the U2AF-related splicing factor CAPER-alpha via DCAF15-DDB1-CUL4 CRL4-DCAF15 mediated ubiquitination in human  cancer cell lines. Both CRISPR/Cas9-based knockout of DCAF15 and a single amino acid substitution of CAPER-alpha conferred resistance against sulfonamide-induced CAPER-alpha degradation and cell-growth inhibition. Thus, the these sulfonamides represent selective chemical probes for disrupting CAPER-alpha function and designate DCAFs as promising drug targets for promoting selective protein degradation in cancer therapy.

overall_design: Comparison of the siRNA-based genetic perturbation of CAPER/RBM39 (non-target siRNA vs. siRBM39, 20 nM, 48 hours, n = 3) and the E7820-based chemical perturbation of the protein (DMSO vs. E7820, 1 microM, 24 h, n = 3).

first: Mai

last: Uesugi


title: Anti-cancer effect and gene modulation of ET-743 in human biliary tract carcinoma preclinical models

status: Public on Feb 09 2017

first: Paola

last: Ostano

overall_design: Transcriptional profiling of EGI-1 xenografts and patient derived xenografts CHC001 PDX after treatment with ET-743 administrated by i.v. At the dose of 0.15 mg/Kg weekly for three administration

first: Caterina

last: Peraldo Neia

first: Giuliana

last: Cavalloni

first: Marco

last: Soster

first: Loretta

last: Gammaitoni

first: Serena

last: Marchiò

first: Francesco

last: Sassi

first: Livio

last: Trusolino

first: Andrea

last: Bertotti

first: Enzo

last: Medico

first: Lorenzo

last: Capussotti

first: Massimo

last: Aglietta

last: Leone


title: Identification of expression patterns after B2M restoration in deficient lung cancer cell lines

status: Public on Feb 27 2017

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

institute: IDIBELL

summary: We have employed microarray expression profiling to identify genes up- and down-regulated after the restitution of beta-2 microglobulin (B2M) gene in lung cancer cell lines.

overall_design: H2009 and H2135 non-small cell lung cancer (NSCLC) cell lines were infected with a plasmid carrying the B2M gene (wtB2M) or with the empty vector (mock).

first: Carolina

last: Pereira

first: Montse

last: Sánchez-Céspedes


title: Analysis of gene expression in TET1 depleted colorectal cancer HCT116 cells

status: Public on Jan 01 2017

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

institute: Sapporo Medical University

summary: We aimed to analyze the relationship between TET1 and aberrant CpG methylation in colorectal cancer (CRC). We established two stable TET1 knockdown clones and negative control clones of HCT116 cells, and carried out gene expression analysis with Agilent Human Gene Expression microarray kit.

overall_design: RNAi-induced TET1 knockdown was accomplished using a BLOCK-iT Pol II miR RNAi Expression Vector kit (Thermo Fisher Scientific). Two sets of oligonucleotides targeting TET1 were purchased from Invitrogen and ligated into a pcDNA6.2-GW/EmGFP-miR vector (Thermo Fisher Scientific). Cells were transfected with each TET1 knockdown vector or a pcDNA6.2-GW/EmGFP-miR-neg control plasmid (Thermo Fisher Scientific), after which they were selected with 1.0 mg/ml G418. GFP-positive colonies were isolated, and knockdown efficiencies were analyzed using RT-qPCR.


title: Analysis of gene expression in TET1 depleted colorectal cancer Colo320DM cells

summary: We aimed to analyze the relationship between TET1 and aberrant CpG methylation in colorectal cancer (CRC). We established three stable TET1 knockdown clones and negative control clones of Colo320DM cells, and carried out gene expression analysis with Agilent Human Gene Expression microarray kit.


title: Anti-proliferation activity of fucoidan on MKN45 gastric cancer cells and downregulation of phosphorylated ASK1, a cell-cycle-regulated cyclin-dependent kinase

city: Yonago

first: Miwa

last: Yoshimoto

address: 36-1 Nishi-cho

institute: Tottori University

summary: Fucoidan is a high-molecular polysaccharide whose main constituent is sulfated fucose. Extensive studies have demonstrated numerous interesting biological activities for fucoidan. We specifically focused on the anti-proliferation activity of fucoidan and examined the underlying mechanism in MKN45 gastric cancer cells. BrdU assay revealed that fucoidan impeded the MKN45 cell cycle by approximately 50%, and clonogenic assay also showed that fucoidan inhibited cell proliferation. Preliminary examinations of fucoidan using LDH assay showed no immediate cytotoxic effects at 24-h exposure. However, longer time courses revealed inhibition of cell growth at 4 days in a dose-dependent manner. Microarray analysis in MKN45 cells treated with fucoidan identified genes that were upregulated and downregulated in response to fucoidan, including MAP3K5, or ASK1 (apoptosis signal-regulating kinase), which was upregulated by 1.38-fold. Western blot confirmed that fucoidan increased ASK1 protein levels, while reducing the levels of phosphorylated ASK1. Reduction of ASK1 by siRNA decreased proliferation of MKN45 cells. Our findings show that fucoidan may suppress cellular proliferation and DNA synthesis in MKN45 cells by suppressing the ASK1-p38 signaling pathway through reduction of phosphorylated ASK1 levels.

overall_design: To identify potential genes involved in mediating the cellular effects of fucoidan, which is a high-molecular polysaccharide whose main constituent is sulfated fucose, total RNA was collected from cultured MKN45 gastric cancer cells and microarray expression analyses were performed using the Agilent Human microarray kit (Palo Alto, CA, US). A total of 20278 sequences were examined at DNA Chip Research Inc. (Kanagawa, Japan), and 496 genes were found to be upregulated and 774 genes were downregulated by fucoidan.

first: Masahide

last: Ikeguchi

first: Katsumi

last: Higaki

first: Eiji

last: Nanba


title: Using transcriptomics to evaluate thresholds in genotoxicity dose-response

status: Public on Dec 31 2016

city: Research Triangle Park

first: Rebecca

last: Clewell

department: Institute for Chemical Safety Sciences

institute: The Hamner Institutes for Health Sciences

summary: Several genotoxic chemicals have been reported to produce threshold-shaped dose-response curves for mutation and genotoxicity assays, both in vivo and in vitro.  These data challenge the current default practice for risk assessment of genotoxic chemicals, which assumes a linear dose-response below the lowest tested dose.  Due to the inherent challenges in data collection and analysis, statistical methods cannot determine whether a biological threshold exists with sufficient confidence to overturn this assumption of linearity.  Indeed, to truly define the shape of the dose-response curves, we must look to the underlying biology and develop targeted experiments to identify and measure the key processes governing cellular response at low doses. This chapter describes a series of studies aimed at defining the transcriptional responses to DNA damage in an effort to identify the key processes regulating low-dose DNA damage response.

overall_design: HT1080 cells were treated with multiple prototype compounds at a single chemical dose that led to a similar activation of p53-DNA damage pathway (1.5 fold increase in total p53)

first: Patrick

last: McMullen

first: Salil

last: Pendse

first: Yeyejide

last: Adeleye

first: Paul

last: Charmichael

first: Melvin

middle: E

last: Andersen


title: Chitosan promotes cancer progression and stem cell properties through Wnt signaling in colon and hepatocellular carcinoma cells

status: Public on Jan 18 2017

city: Chuo-ku

first: Keisuke

last: Sekine

state: Tokyo

address: 5-1-1 Tsukiji

department: Graduate School of Medicine

institute: National Cancer Center Research Institute, Japan

summary: Cancer stem cells (CSCs), a small population of cancer cells, have been considered to be the origin of cancer initiation, recurrence, and metastasis. Tumor microenvironment provides crucial signals for CSCs to maintain stem cell properties and promote tumorigenesis. Therefore, establishment of an appropriate cell culture system to mimic the microenvironment for CSC studies is an important issue. In this study, we grew colon and hepatocellular carcinoma (HCC) cells on chitosan membranes and evaluated the tumor progression by transwell migration, drug resistance, microarray, and RT-PCR analysis. We also evaluated the CSC properties by flow cytometry, sphere forming assay, luciferase reporter assay, western blot, and gene knockdown. Experimental results showed that culturing cancer cells on chitosan increased cell motility, drug resistance, quiescent population, self-renewal capacity, and the expression levels of stemness and CSC marker genes, such as OCT4, NANOG, CD133, CD44, and EpCAM. Furthermore, we demonstrated that chitosan might activate canonical Wnt/β-catenin-CD44 axis signaling in CD44positive colon cancer cells and noncanonical Wnt-STAT3 signaling in CD44negative HCC cells. In conclusion, chitosan as culture substrates activated the essential signaling of CSCs and promoted CSC properties. The chitosan culture system provides a convenient platform for the research of CSC biology and screening of anticancer drugs.

overall_design: Comparison of gene signatures of HT29 colon cancer cell line culture on normal cell culture dish,  Chitosan membrane, or HA-grafted Chitosan membrane.

first: Sekine

last: Keisuke

first: Edward

last: Chern


title: MicroRNA-24-3p is overexpressed in Hodgkin lymphoma and protects Hodgkin and Reed-Sternberg cells from apoptosis [ChIP-chip]

status: Public on Feb 26 2017

city: Groningen

first: Ye

last: Yuan

state: Groningen

address: Hanzeplein 1

department: pathology

institute: UMCG

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Micro (mi)RNAs not only play important roles in biological processes such as proliferation, metabolism, differentiation and apoptosis, but also in diseases such as cancers. We identified miRNAs with deregulated expression in Hodgkin lymphoma (HL) and investigated their role in the pathogenesis of HL. Small RNA sequencing revealed 84 significantly differentially expressed miRNAs in HL cell lines as compared to GC-B cells. Three upregulated miRNAs, miR-23a-3p, miR-24-3p and miR-27a-3p, were derived from one primary-miRNA transcript. Loss-of-function analysis for these miRNAs and their seed family members resulted in decreased growth upon miR-24-3p inhibition in three and of miR-27a/b-3p inhibition in one HL cell line. Apoptosis analysis indicated that the effect of miR-24-3p on cell growth is at least in part caused by an increase of apoptotic cells. Argonaute 2 (Ago2)-IP revealed 1,142 genes consistently targeted by miRNAs in at least three out of four HL cell lines. Furthermore, 52 out of the 1,142 genes were predicated targets of miR-24-3p. Functional annotation analysis revealed a function related to cell growth, cell death and/or apoptosis for 15 out of the 52 genes. Western blotting of the top-5 genes showed increased protein levels upon miR-24-3p inhibition for CDKN1B and MYC. In summary, we showed that miR-24-3p is upregulated in HL and its inhibition impaired cell growth possibly via targeting CDKN1B and MYC.

overall_design: Identification of miRNA targets (mRNAs and lcnRNAs) in Hodgkin lymphoma cell lines

first: Joost

last: Kluiver

first: Jasper

last: Koerts

first: Debora

last: de Jong

first: Bea

last: Rutgers

first: Fazlyn

last: Reeny Abdul Razak

first: Martijn

last: Terpstra

first: Boudewijn

last: Plaat

first: Ilja

last: Nolte

first: Arjan

last: Diepstra

first: Lydia

last: Visser

first: Klaas

last: Kok

first: Anke

last: van den Berg


title: Alkylating pyrrole-imidazole polyamide KR12 binding in colorectal cancer genomes (SW480)

status: Public on Nov 01 2016

city: Chiba

first: Jason

last: Lin

state: Chiba

address: 666-2 Nitona-cho, Chuo-ku

institute: Chiba Cancer Center Research Institute

summary: Pyrrole-imidazole polyamides are versatile DNA minor groove binders and attractive therapeutic options against oncological targets, especially upon functionalization with an alkylating agent such as endo-seco-CBI. These molecules also provide an alternative for oncogenes deemed “undruggable” at the protein level, where the absence of solvent-accessible pockets or structural crevices prevent the formation of protein-inhibitor ligands; nevertheless, the genome-wide effect of pyrrole-imidazole polyamide binding remain largely unclear to-date. Here we propose a next-generation sequencing-based workflow combined with whole genome expression arrays to address such issue using a candidate anti-cancer alkylating agent, KR12, against codon 12 mutant KRAS. Biotinylating KR12 enables the means to identify its genome-wide effects in living cells and possible biological implications via a coupled workflow of enrichment-based sequencing and expression microarrays. The subsequent computational pathway and expression analyses allow the identification of its genomic binding sites, as well as a route to explore a polyamide’s possible genome-wide effects. Among the 3,343 KR12 binding sites identified in the human LS180 colorectal cancer genome, the reduction of KR12-bound gene expressions was also observed. Additionally, the coupled microarray-sequencing analysis also revealed some insights about the effect of local chromatin structure on pyrrole-imidazole polyamide, which had not been fully understood to-date. A comparative analysis with KR12 in a different human colorectal cancer genome SW480 also showed agreeable agreements of KR12 binding affecting gene expressions. Combination of these analyses thus suggested the possibility of applying this approach to other pyrrole-imidazole polyamides to reveal further biological details about the effect of polyamide binding in a genome.

overall_design: For expression microarrays, samples were subject to 500 nM KR12 (treatment) or 0.05% DMSO (control) for 6 h followed by RNA extraction. For LS180, samples were prepared in 2 × 2 replicates for each treatment (DMSO as control compared to KR12 at 500 nM); for SW480, 3 replicates were performed for the control and treatment to determine effect of KR12 on gene expressions.

first: Kiriko

last: Hiraoka

first: Nagase

last: Hiroki


title: Differential gene expression profile of SCC13 tumor cells after TLR4 overexpression and LPS treatment

status: Public on Nov 16 2016

city: Zurich

first: Guergana

last: Iotzova-Weiss

address: Gloriastrasse 31

country: Switzerland

institute: Dermatology Clinic Zurich

summary: BACKGROUND & AIMS: TLR4 is an innate immune receptor with expression in human skin, keratinocytes as well as squamous cell carcinoma (SCC) of the skin. In the present study we investigate the role of TLR4 as a negative regulator of keratinocyte proliferation. We present here that the expression of TLR4 increased with the differentiation of cultured keratinocytes in a passage-dependent manner or under calcium-rich conditions. Moreover, the down-regulation of TLR4 by specific knockdown increased the proliferation of primary normal, SCC-derived and HaCaT keratinocytes in vitro. In addition, subcutaneously injected HaCaT keratinocytes with shTLR4 formed growing tumors in nude mice. In contrast, we observed lower proliferation and increased migration in vitro of the SCC13 cell line stably overexpressing TLR4 in comparison to SCC13 TLR4 negative cells. In vivo, SCC13 TLR4-overexpressing tumors showed delayed growth in comparison to TLR4 negative tumors. The overexpression of TLR4 in SCC13 tumor cells was followed by phosphorylation of ERK1/2 and JNK and increased expression of ATF3. In gene expression arrays, the overexpression of TLR4 in tumor cells correlated with gene expression of ATF-3, IL-6, CDH13, CXCL-1,  and TFPI. In summary, TLR4 negatively regulates the proliferation of primary keratinocytes and its overexpression reduces tumor growth of SCC cells.

overall_design: SCC13 tumor cells were stably transfected with pUNOTLR4 and pUNO (control) plasmids. SCC13 TLR4 cells and SCC13 pUNO were seeded in tetraplicates and treated with 10μg/ml ultrapure LPS for 24 hours. As controls untreated SCC13TLR4 and SCC13 pUNO cells were used.Gene expression comparison was performed between untreated SCC13TLR4 and control cells as well as between LPS treated cells.

first: G

first: M

middle: R

last: Lecca

first: H

last: Rehrauer


title: AhR links air pollution and atopic dermatitis via Artemin induction

status: Public on Nov 13 2016

city: Sendai

first: Eri

last: Kobayashi

state: Miyagi

address: 2-1 Seiryo-machi, Aobaku

department: Medical Biochemistry

institute: Tohoku University Graduate School of Medicine

summary: Atopic dermatitis is increasing worldwide, correlating with air pollutions. Various organic components of pollutants activate transcription factor AhR (aryl-hydrocarbon receptor). We have established AhR-CA mice, whose keratinocytes express constitutive-active AhR, and these mice developed atopic dermatitis-like frequent scratching and allergic inflammation. In this study we performed ChIP-seq analyses and identified keratinocyte-specific AhR target genes, including inflammatory cytokines Tslp and IL33, and neurotrophic factor Artemin. While AhR-CA mice exhibited epidermal hyperinnervation and alloknesis leading to hypersensitivity to pruritus, blockade of Artemin alleviated these phenotypes. AhR-CA mice showed scratching-induced barrier insufficiency and enhanced sensitization to epicutaneously-applied antigens, recapitulating human atopic dermatitis. Consistently, AhR activation and Artemin expression was detected in the epidermis of atopic dermatitis patients and keratinocytes exposed to air pollutants. Thus, AhR in keratinocytes senses the environmental stimuli and responds to them through moderating inflammation. We propose a mechanism in which air pollution induces atopic dermatitis through AhR activation.

overall_design: Gene expression in epidermis obtained from wild-type and AhRCA neonates. In AhRCA mice, constitutive active form of AhR transcription factor is expressed under the control of keratin 14 promoter. Three independent samplings were performed, and each sampling includes RNA from one AhRCA mice and one littermate wild-type mice, respectively.

first: Takanori

last: Hidaka

first: Eisaku

last: Ogawa

last: H. Kobayashi

first: Takafumi

last: Suzuki

first: Ryo

last: Funayama

first: Takeshi

last: Nagashima

first: Taku

last: Fujimura

first: Setsuya

last: Aiba

first: Keiko

last: Nakayama

first: Ryuhei

last: Okuyama

first: Masayuki

last: Yamamoto


title: The deubiquitinase USP22 stabilizes BMI1 polycomb ring finger oncoprotein to confer cancer stem cell traits and glioblastoma progression

city: Newhaven

first: Jiangbing

last: zhou

address: 310 Cedar Street, Ste LH 412A

institute: Yale university

summary: Glioblastoma (GBM) is the most common and aggressive primary brain tumor with limited therapeutic options, possibly because of the highly tumorigenic subpopulations of stem cell-like cells. Mechanisms that sustain cancer stem cells are crucial to tumor progression. The polycomb group protein BMI1 (BMI1 proto-oncogene, polycomb ring finger) maintains cancer hallmarks including the glioblastoma stem-like cell (GSC) state. Ubiquitin-specific protease 22 (USP22) is highly expressed in and required for the maintenance of cancer stem cells (CSCs). Previously, we observed that forced expressed microRNA-218 in glioblastoma cells led to suppressed BMI1 expression. However, the pathways engaged by USP22 or driving BMI1 accumulation in GSCs remained elusive. Here, we found USP22 to be a novel deubiquitylase of BMI1. USP22 directly deubiquitylates and stabilizes BMI1. USP22 protein levels are elevated in tumor neurosphere. USP22 depletion induces BMI1 destabilization, and results in the inhibition of GSCs self-renewal by regulating a broad range of genes involved in glioma stemness and progression. Xenograft analyses using U87MG cells showed that both USP22 and BMI1 depletion attenuated tumor growth. Clinically, the expression levels of USP22 and BMI1 were positively correlated with those common targets like POSTN, HEY2, or PDGFRA and inversely correlated with ATF3 in human glioblastoma specimens. Taken together, our data reveals that USP22 functions as a novel deubiquitylase of BMI1 and inhibits self-renewal of GSCs by stabilizing BMI1. These findings also indicate that the USP22-BMI1 axis has a critical role in glioma tumorigenesis and that targeting the axis may provide a new therapeutic approach for human glioblastoma.

overall_design: 3 Samples, one transduced with control shRNA, one with BMI1 shRNA and one with USP22 shRNA.

first: Weilin

last: Jin

first: Xingchun

last: Gao


title: Whole genome expression data from formalin-fixed parrafin embedded (FFPE) primary and metastatic melanomas

city: Callaghan

first: Nikola

last: Bowden

state: NSW

address: University Dr

department: School of Medicine and Public Health

country: Australia

institute: University of Newcastle

summary: The dominant genetic signature found in melanoma is C to T mutations due to UV radiation. Nucleotide excision repair (NER) recognises and repairs UV-induced DNA damage. We aimed to determine the effect of high UV exposure on the melanoma transcriptome and key NER transcripts in melanoma tumours in association with clinical and genetic features of the disease. 196 primary or metastatic melanomas were utilised for this study. Solar elastosis and transcriptome data was collected. mRNA transcript levels of NER components XPC, DDB1 and DDB2 were quantified and compared to clinical parameters. Solar elastosis negatively correlated with Breslow thickness (-0.251, p=0.017) and was significantly lower in BRAFV600E melanomas. Lower XPC expression was associated with BRAFV600E and NRASQ61R mutations, earlier age of diagnosis and poorer survival.  Transcriptome profiling identified an over-representation of DNA repair processes in high vs low solar elastosis. Further analysis revealed DNA repair and kinase activity related transcripts in the low XPC melanomas. XPC deficiency is associated with the presence of kinase mutations and an aggressive disease phenotype, both of which result from the hypermutability of melanoma.

overall_design: Formalin fixed paraffin embedded (FFPE) primary and metastatic melanoma tumours; collected for diagnostic purposes at the Hunter Area Pathology Service, NSW, Australia between 2004 and 2009; were used for this study. The Hunter New England Area Health Service Human Ethics Committee approved the study. 196 tumours were identified with sufficient tissue (>2mm width and length) and clinical information for the study. Departmental records where searched for melanoma cases reported between 2005 to 2009. The need to access sufficient tumour tissue to allow matching genomic sequencing, gene expression and immunohistochemical analysis required that cases with a thin primary melanoma (Breslow thickness less than 2mm) with only a small volume of metastatic disease (locoregional or distant metastases) were excluded from the study.  All cases utilised had stage 2 or greater disease as either metastatic lymph nodes or primary melanomas greater than 2mm were used. RNA and DNA was successfully extracted from 157 of the 196 tumours (80%).

first: Ricardo

last: Vilain

first: Katie

last: Ashton


title: Enzalutamide inhibits proliferation of gemcitabine-resistant bladder cancer cells with increased androgen receptor expression

status: Public on Nov 30 2016

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

institute: Toyohashi University of Technology

summary: Advanced bladder cancer is treated mainly with gemcitabine and cisplatin, but most patients eventually become resistance to these chemotherapeutic agents. Androgen receptor (AR) signaling has been implicated in bladder cancer as well as other types of cancer including prostate cancer. In the present study, we showed the expression and role of AR in gemcitabine-resistant bladder cancer cells and examined the potential of enzalutamide, an AR inhibitor, as a therapeutic for the chemoresistance. First of all, we established gemcitabine-resistant T24 cells (T24GR) from T24 bladder cancer cells and performed gene expression profiling and network analysis, which revealed increased AR expression and AR-related gene network in T24GR cells. Quantitative RT-PCR and Western blot analysis confirmed increased expression of AR in T24GR cells compared with parental T24 cells, which was associated with more potent transcriptional activity of AR in T24GR cells. The number of AR gene copy in T24GR cells was twice as many as that of T24 cells. Knockdown of AR expression by siRNA resulted in inhibition of proliferation of T24GR cells. Cell culture in charcoal-stripped serum and treatment with enzalutamide also inhibited growth of T24GR cells, which was accompanied by cell cycle arrest. Lastly, the AR transcriptional activity was found to be reduced in T24GR cells by enzalutamide treatment. Our results suggest that blockade of AR signaling by enzalutamide might be effective for patients with advanced gemcitabine-resistant bladder cancer with increased AR expression.

overall_design: T24 human bladder cancer cell line was obtained from RIKEN Cell Bank (Tsukuba, Japan).

first: Koji

last: Kameyama

last: Kato

first: Yasunori

last: Fujita

first: Kyojiro

last: Kawakami

first: Kosuke

last: Mizutani

first: Takashi

last: Deguchi

first: Masafumi

last: Ito


title: Expression profiling in blood from subjects with severe asthma, moderate asthma, and non-asthmatics collected in the U-BIOPRED study

status: Public on Dec 09 2016

city: Seattle

first: Jeannette

last: Bigler

state: WA

address: 3200 NE 92nd Street

institute: BJ Group, LLC

summary: Severe asthma is a collection of disease entities with varying pathophysiological characteristics (7) that result in symptoms of cough, wheeze and breathlessness, with frequent exacerbations. To address the problem of phenotypic difference and heterogeneity, the Unbiased Biomarkers for the Prediction of Respiratory Disease Outcomes (U-BIOPRED) project was set up as a public-private partnership within the framework of the Innovative Medicines Initiative (IMI), engaging academia, the pharmaceutical industry and patient groups. The goal of this investigation was to identify transcript fingerprints in whole blood that characterize patients with severe asthma and to determine whether subgroups of severe asthmatics can be identified. Furthermore, we were interested in elucidating the biological pathways that showed differences between subgroups.

overall_design: This is a cross-sectional study of severe asthmatics, moderate asthmatics, and healthy subjects. Blood was collected at baseline.

first: Marty

last: Timour

first: Michael

last: Boedigheimer


title: Alkylating pyrrole-imidazole polyamide KR12 binding in colorectal cancer genomes (LS180)

first: Jason

last: Lin

first: Kiriko

last: Hiraoka

first: Nagase

last: Hiroki


title: Cardiac reprogramming under defined conditions

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary:
FGF2, FGF10, and VEGF greatly promote cardiac reprogramming under defined serum-free conditions by enhancing the conversion of partially reprogrammed cells into fully reprogrammed functional iCMs.
Fibroblasts can be directly reprogrammed into cardiomyocyte-like cells (iCMs) by overexpression of cardiac transcription factors, including Gata4, Mef2c, and Tbx5; however, this process is inefficient under serum-based culture conditions, in which the conversion of partially reprogrammed cells into fully reprogrammed functional iCMs has been a major hurdle. Here, we report that a combination of fibroblast growth factor (FGF) 2, FGF10, and vascular endothelial growth factor (VEGF), termed FFV, promoted cardiac reprogramming under defined serum-free conditions, increasing spontaneously beating iCMs by 100-fold compared with those under conventional serum-based conditions. Mechanistically, FFV activated multiple cardiac transcriptional regulators and converted partially reprogrammed cells into functional iCMs through the p38 mitogen-activated protein kinase and phosphoinositol 3-kinase/AKT pathways. Moreover, FFV enabled cardiac reprogramming with only Mef2c and Tbx5 through the induction of cardiac reprogramming factors, including Gata4. Thus, defined culture conditions promoted the quality of cardiac reprogramming, and this finding provides new insights into the mechanism of cardiac reprogramming.

overall_design: In this study, we compared  the global gene expression patterns of MEFs, iCMs cultured under the indicated conditions (FBS, SF, FFV), and the hearts. The iCMs were sorted as aMHC-GFP+ cells at 2W and 4W weeks after GMT transduction. We also analyzed the iCMs induced by MT transduction, and iCMs induced from TTFs by GMTMM.

first: Masaki

last: Ieda

first: Hiroyuki

last: Yamakawa


title: Expression data from pancreatic ductal adenocarcinoma

status: Public on Oct 26 2016

city: Chengdu

first: Shikai

last: Zhu

address: No.32 West Second Section First Ring Road

institute: Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital

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

summary: Three PDAC tissue samples and their matched adjacent non-tumor samples were obtained and were used for microarray assay.

overall_design: Tissue samples were distributed into two experimental groups: control group and PDAC group which were taken during surgery, immediately frozen in liquid nitrogen, and stored at -80˚C for further analysis.

first: Yu

last: Zhou

first: Hongji

last: Yang


title: Human ESCs vs Human iPSCs & Human NSCs-ES vs Human NSCs-iPS

status: Public on Sep 29 2016

city: Newcastle upon Tyne

first: LILI

last: ZHU

address: Central Parkway

country: United Kingdom

institute: Newcastle University

summary:
Transcriptional profiling of Human ESCs vs Human iPSCs, Human NSCs-ES vs Human NSCs-iPS
iPSCs generated by using different method, and are not very good at Neural differentiation comapred with Human ESCs

overall_design: All adapted in the same culture condition for at least 5 passages; Four-condition experiment; Biological replicates: 2 of each sample

first: Lili

first: Majlinda

last: Lako

first: Lyle

last: Armstrong


title: Alkylating pyrrole-imidazole polyamide KR12 binding in colorectal cancer genomes

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

overall_design: Refer to individual Series


title: Transcriptome response of murine alveolar epithelial cells to infection by three unrelated respiratory viruses commonly studied in mouse models

city: Moscow

first: James

middle: Theodore

last: Van Leuven

state: ID

address: 709 S Deakin St

department: Center for Modeling Complex Interactions

institute: University of Idaho

summary: The severity and outcome of respiratory viral infections is partially determined by the cellular response mounted by infected lung epithelial cells. Disease prevention and treatment is dependent on our understanding of the shared and unique responses elicited by diverse viruses. We used microarray analysis to compare changes in gene expression of murine lung epithelial cells infected by one of three respiratory viruses causing mild (rhinovirus, RV1B), moderate (coronavirus, MHV-1), and severe (influenza A virus, PR8) disease in mice. The viruses prompted changes in host gene expression that differed in magnitude and timing. RV1B infection caused numerous gene expression changes, but the differential effect peaked at 12 hours post-infection. PR8 altered an intermediate number of genes whose expression continued to changes through 24 hours. MHV-1 had comparatively few effects on host gene expression. All three viruses elicited overlapping responses in antiviral defense systems, though MHV-1 induced a lower type I IFN response than the other two viruses. Our comparative approach identified signatures of each virus infection that can be used to discover mechanisms of pathogenesis in the respiratory tract.

overall_design: Microarray analysis of mouse epithial cells infected by one of three viruses. Infections done in triplicate. RNA extracted at 12 and 24 hours post infection.

middle: T

last: VanLeuven

first: Benjamin

middle: J

last: Ridenhour

first: Craig

last: Miller

first: Tanya

last: Miura


title: Gene expression profiling in 8 lung cancer in Xuanwei samples

status: Public on Oct 22 2016

city: Kunming

first: Yanliang

last: Zhang

state: Yunnan province

address: No. 295, Xichang Road

department: Department of Clinical Laboratory

institute: First Affiliated Hospital of Kunming Medical University

summary: In order to screen potential novel 'driver genes' in lung cancer in Xuanwei (LCXW), differentially expressed genes (DEGs) were detected on 8 paired LCXW and non-cancerous lung (NCL) tissues by gene expression microarrays. Statistically significantly expressed genes were identified using the mixed model analysis of variance with a false discovery rate (Benjamini-Hochberg test) adjusted p value of ≤ 0.05 and absolute fold-change values ≥ 2 or ≤ 0.5. A total of 5,129 genes were detected to be DEGs. Of these DEGs, 3,248 genes were upregulated, while another 1,881 genes were downregulated.

overall_design: 8 paired LCXW and NCL tissues were tested.

first: Yan

first: Qiuyue

last: Xue

first: Guo

middle: Q

last: Pan

first: Xiao

middle: Y

last: Tuo

first: Xue

last: Cai

first: Ya

last: Li

first: Tao

last: Huang

first: Xin

middle: C

last: Duan

first: Yong


title: Gene expression profiling and copy number alterations in 8 lung cancer in Xuanwei samples

type: Genome variation profiling by genome tiling array


title: RNA Splicing of the BHC80 gene Facilitates Neuroendocrine Prostate Cancer Progression

status: Public on Sep 15 2016

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

summary: By analysing RNA-sequencing data for a t-NEPC specific RNA splicing signature, we identified a BHC80 splice variant BHC80-2 that functions as a key facilitator for t-NEPC development.

overall_design: LNCaP cell were overexpressed control, BHC80-1 and BHC80-2 using lenti-virus and cultured in RPMI medium for 48 hours. Total RNA were isolated.

first: Yinan

first: Xuesen

last: Dong


title: Urinary Extracellular Vesicles RNA Profile in Clear Cell Renal Cell Carcinoma as Biomarker

status: Public on Sep 01 2016

city: Bari

first: Fabio

last: Sallustio

state: Bari

address: Piazza G. Cesare N°11

institute: University of Bari

summary:
Background: Renal cell carcinoma (RCC) accounts for about 2% of all cancers. Renal biopsy is the gold standard among the diagnostic tools, but it is invasive and not suitable for all patients. Therefore, new reliable and non-invasive biomarkers for ccRCC detection are required. Secretion of extracellular vesicles (EVs), containing RNA molecules that can be transferred between cells, seems to be a general characteristic of malignant transformation. Consistently, cancer-derived EVs are enriched in the blood, urine and various malignant effusions of cancer patients. Therefore, urinary samples can be a non-invasive approach for discovering diagnostic biomarkers.

Methods: We enrolled 33 clear-cell RCC (ccRCC) patients and 22 healthy subjects (HS), age and sex-matched, for urine collection and extracellular vesicles isolation by differential centrifugation. Transcriptional profiles of urinary EVs from 12 patients with ccRCC and 11 HS were generated using the Illumina HumanHT-12 v4 BeadChip oligonucleotide arrays. Microarray analysis led to the identification of RNA that were then validated using RT-qPCR.

Results: We showed for the first time that urinary exosomal shuttle RNA (esRNA) was significantly different in ccRCC patients compared to HS and we identified three EVs esRNA involved in the tumor biology that are potentially suitable as non-invasive biomarkers. GSTA1, CEBPA and PCBD1 RNA levels decreased in urinary EVs of patients compared to HS. After 1 month post-operation, the levels of RNA increased to reach the normal level.

Conclusions: This study suggests, for the first time, the potential use of the RNA content of urinary EVs to provide a non-invasive first step to diagnose the ccRCC.

overall_design: Total RNA obtained from urinary extracellular vesicles isolated from ccRCC patients and healthy subjects.

first: Giuseppe

last: De Palma

first: Francesco

last: Schena


title: Gene expression profiling of African-American prostate cancer

status: Public on Aug 31 2016

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: African-American (AA) men have both a higher incidence and significantly higher mortality rates from prostate cancer (PCa) than European American (EA) men. In this study we have carried out a detailed analysis of both CNAs and gene expression changes in PCas from AA men compared to their matched benign tissues. We have identified MNX1 as a novel androgen regulated oncogene that is upregulated to a greater degree in AA PCa compared to EA PCa. Furthermore, RGS12 is a novel tumor suppressor on 4p16.3 that is preferentially deleted in AA PCa which negatively regulates MNX1 expression.

overall_design:
In this study we have carried out a detailed analysis of gene expression changes in PCas from AA men compared to their matched benign tissues.
two-group comparison

first: Yiqun

first: Jianghua

last: Wang

first: Michael

last: Ittmann


title: An Indel Polymorphism within pre-miR3131 Confers Risk for Hepatocellular Carcinoma

status: Public on Aug 04 2016

city: Suzhou

first: wang

last: chaoqun

state: Jiangsu

address: Room 806-1, Engineering Building, North Campus ,Soochow University, No. 178, Ganjiang East Road, Gusu District

department: Department of Forensic Medicine

institute: Medical College of Soochow University

summary: Polymorphisms in pre-miRNAs may affect its expression, then having effect on its target mRNAs and be associated with cancer susceptibility. In the current study, we evaluated the association of a 3-base pair (3-bp) indel polymorphism (rs57408770) in pre-miR-3131 with hepatocellular carcinoma (HCC) susceptibility in a Chinese population. Logistic regression analysis showed that the insertion allele of rs57408770 was significantly associated with an increased risk for HCC occurrence in both case-control studies. To further investigated the molecular mechanism underlying the correlation between rs57408770 and the risk of HCC, overexpression of pre-miR-3131 in HCC cell line was performed. Human HCC cell lines Sk-Hep-1 was obtained from Shanghai Cell Bank of Chinese Academy of Sciences on 9 December 2013.The fragment of 366bp including the insert allele of rs57408770 in pre-miR-3131 was directly synthesized and cloned into BamHI and EcoRI sites of pEGFP-N1 yielding the wild-type vector (pEGFP-N1-miR3131-WT). The mutant-type vector (pEGFP-N1-miR3131-MT) including the delete allele of rs57408770 was generated using QuikChange Lightening Site-Directed Mutagenesis Kit. The resulting constructs were verified by direct sequencing. For overexpression experiments, cells were cultured in 6-well plates at a density of 200 000 cells per well the day before transfection. 2.5μg plasmids of empty vector pEGFP-N1, pEGFP-N1-miR3131-WT or pEGFP-N1-miR3131-MT were transfected into the growing cells (about 80%-90% confluent) using Lipofectamine2000. After 24 hours of the transfection, the cells were collected for subsequent experiments.And human genome-wide gene expression profile assay was used to screen the targets of miR-3131.

overall_design: For overexpression experiments, cells were cultured in 6-well plates at a density of 200 000 cells per well the day before transfection. 2.5μg plasmids of empty vector pEGFP-N1, pEGFP-N1-miR3131-WT or pEGFP-N1-miR3131-MT were transfected into the growing cells (about 80%-90% confluent) using Lipofectamine2000 (Invitrogen). After 24 hours of the transfection, the cells were collected for subsequent experiments. There are 3 samples in this experiment.

first: Yuzhen

last: Gao

first: Chaoqun


title: Placental mRNA Expression data from pregnant smokers and non-smokers

status: Public on Aug 08 2016

city: Boston

first: Manoj

last: Bhasin

state: MA

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

summary:
We used microarrays to determine the transcriptional profiles of placental tissue obtained from women who smoked during pregnancy and from women who did not smoke during pregnancy.
Fetal growth restriction is a frequent complication in mothers who smoke cigarettes during pregnancy. To evaluate novel pathways that regulate fetal growth affected by mothers who smoke, we isolated placental mRNA from smoking mothers with severe fetal growth restriction and compared them by microarray analysis to non-smoking mothers with appropriately grown fetuses. Bioinformatics analysis revealed distinct transcriptional patterns in the placentas of smoking mothers when compared to placentas from control non-smoking women. Analyses of the top upregulated and downregulated genes revealed several gene products such as secreted frizzled related protein 1 that was markedly upregulated in the placentas from women who smoked cigarettes during pregnancy.

overall_design: Total RNA was isolated from placental specimens obtained at time of delivery. RNA was hybridized to Affymetrix arrays, and analyzed.

first: Alice

first: Ananth

last: Karumanchi


title: Identification of expresion patterns after treatment with GC/RA and combination with AZA/SAHA in MYC amplified and BRG1 mutant lung cancer cell lines

status: Public on Sep 08 2016

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

institute: IDIBELL

summary: To development our gene expression approach , we have employed whole genome microarray expression profiling as a discovery platform to identify genes potentialy regulated by the treatment with glucocorticoids (GC) and retinoic acid (RA) alone and combined with AZA/SAHA and the relationship of these features with the status of BRG1 and MYC in lung cancer cell lines.

overall_design: MYC amplified cell lines and BRG1 mutant cell lines were treated with glucocorticoids (GC) and retinoic acid (RA) alone and combined with AZA/SAHA and their expression was then measured

first: Octavio

middle: A

last: Romero Ferraro

first: Manuel

last: Torres Diz

first: Montse

last: Sánchez-Céspedes


title: A phase 1b study of the Akt-inhibitor MK-2206 in combination with weekly paclitaxel and trastuzumab in patients with advanced HER2-overexpressing solid tumor malignancies

status: Public on Jul 31 2016

city: Novato

first: Christina

last: Yau

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute of Age Research

summary: 16 patients with HER2+ tumors were enrolled (12 breast, 3 gastric, 1 esophageal).  27 samples (12 primary + 15 metastatic) from the 16 unique patients were assayed on Agilent 60K expression microarrays, and association between expression and response data were evaluated to identify potential biomarker of MK2206 response

overall_design: We conducted a phase 1b study of MK-2206 in combination with weekly paclitaxel 80 mg/m2 and trastuzumab 2 mg/kg in patients with HER2+ malignancies.  Dose escalation was performed using a modified toxicity probability interval method. Molecular profiling of archived tissue samples and limited PK analyses were performed.

first: Amy

last: Chien

first: Alyson

last: Cockerill

first: Craig

last: Fancourt

first: Emmett

last: Schmidt

first: Mark

middle: M

last: Moasser

first: Hope

middle: S

last: Rugo

first: Michelle

last: Melisko

first: Andrew

last: Ko

first: R

middle: K

last: Kelley

first: W

last: Korn

first: Laura

last: Esserman

first: Denise

last: Wolf

first: Pamela

last: Munster


title: Initial development of a multigene 'omics-based exposure biomarker for pyrethroid pesticides

status: Public on Sep 30 2016

city: Cincinnati

first: mitch

last: kostich

state: Ohio

address: 26 W. Martin Luther King Dr

department: Office of Research and Development

institute: US Environmental Protection Agency

summary: This work describes the initial development of an omics based assay using 48Hr Pimephales promelas (FHM) larvae for identifying aquatic exposures to four pyrethroids (permethrin, cypermethrin, esfenvalerate and bifenthrin).  Gene expression classifiers were developed using the random forest algorithm for each exposure and evaluated first by cross-validation using hold out organisms from the same exposure experiment and then against test sets of each pyrethroid from separate exposure experiments.  Bifenthrin exposed organisms generated the highest quality classifier, demonstrating an empirical Area Under the Curve (eAUC) of 0.97 when tested against bifenthrin exposed organisms from other exposure experiments and 0.91 against organisms exposed to any of the pyrethroids.  Additionally, the bifenthrin classifier was able to successfully classify organisms from all other pyrethroid exposures at multiple concentrations, suggesting a potential utility for detecting cumulative exposures.  Considerable run-to-run variability was observed both in exposure concentrations and molecular responses of exposed fish across exposure experiments.  The application of a calibration step in analysis successfully corrected this, resulting in a significantly improved classifier.  Classifier evaluation suggested the importance of considering a number of aspects of experimental design when developing an expression based tool for general use in ecological monitoring and risk assessment, such as the inclusion of multiple experimental runs and high replicate numbers.

overall_design: Larval FHM were exposed to seven concentrations of each of four pyrethroids (permethrin, cypermethrin, esfenvalerate and bifenthrin) in order to establish dose response curves. Then, in three separate identical experiments, FHM were exposed to a single equitoxic concentration of each pyrethroid, corresponding to 33% of the calculated LC50.  All exposures were separated by weeks and all materials were either cleaned or replaced between runs.

first: Adam

last: Biales

first: Mitchell

last: Kostich

first: Angela

middle: L

last: Batt

first: Mary

last: See

first: Robert

middle: W

last: Flick

last: Gordon

first: Jim

last: Lazorchak

first: David

last: Bencic


title: Gene expression of developed cancer stem cells [OCC-hiPS]

status: Public on Aug 17 2016

city: Okayama

first: Akimasa

last: Seno

state: Okayama

address: 1-1, Tsushima-Naka, 1-chome, Kita-Ku

department: Applied Chemistry and Biotechnology

institute: Okayama University

summary: RNA expression of human induced cancer stem cells and human induced pluripotent stem cells were analyzed.

overall_design: We compared mRNA expression of human induced pluripotent stem cells and cancer stem cells which are induced from human iPS cells with a cancer cell culture medium. OCC: Okayama Cancer stem cell Collection

first: Tomonori

last: Kasai


title: Based on Molecular Profiling of Gene Expression, Palmoplantar Pustulosis and Palmoplantar Pustular Psoriasis are Highly Related Diseases that Appear to Be Distinct from Psoriasis Vulgaris

status: Public on Jun 30 2016

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

summary: There is a controversy surrounding the existence of palmoplantar pustulosis (PPP) and palmoplantar pustular psoriasis (PPPP) as separate clinical entities or as variants of the same clinical entity. We used gene expression microarray to compare gene expression in PPP and PPPP. PPP and PPPP could not be differentiated using gene expression microarray suggesting that they are not distinct clinical entities. Increased expression of GPRIN1, and ADAM23 in keratinocytes suggests that these proteins could be new therapeutic targets for PPP/PPPP.

overall_design: Skin biopsies from subjects with PPP (3), PPPP (6), psoriasis vulgaris (10) and acral skin from normal subjects (7) were analyzed using gene expression microarray. Principal component analysis showed that PPP and PPPP were different from psoriasis vulgaris and normal acral skin. However gene expression of PPP and PPPP clustered together and could not be used to differentiate PPP from PPPP. Gene-wise comparison between PPP and PPPP found no gene to be differentially expressed with a false discovery rate lower than 0.6. Surprisingly we found a higher expression of several genes involved in neural pathways (e.g. GPRIN and ADAM23) in PPP/PPPP as compared to psoriasis vulgaris and normal acral skin. Immunohistochemistry confirmed those findings and showed a keratinocyte localization for those proteins.

first: James

last: Krueger

last: Suárez-Fariñas

last: Bissonnette


title: Mouse bone marrow stromal cells: before or after total body irradiation

first: Satoshi

last: Kondo

summary:
Comprehensive gene expression analysis in BM-resident stromal cells was performed for an overview of BM environmental change caused by total body irradiation (TBI).
Total RNA samples collected from BM-resident stromal cells with or without TBI were subjected to high sensitivity DNA microarray assays

overall_design: Three-condition experiment: Unirradiated, 1 day after TBI and 3 days after TBI. Bone marrow stromal cells were obtained from C57BL/6 mice (n = 6) either non-irradiated or after 9.5 Gy irradiation at indicated times.

first: Sachie

last: Suzuki

first: Takashi

last: Ishida


title: Human embryonic stem cells vs. fibroblast-derived iPS cells

status: Public on Jun 22 2016

first: Takafumi

last: Hiramoto

address: 1959 NE Pacific Street, HSB K-260

department: Division of Hematology

institute: University of Washington

summary: Gene expression analysis by microarray between human ES cells and fibroblast derived iPS cells established by measles virus vector

overall_design: Total RNA derived from ES cells and iPS cells were extracted and analyzed for expression changes using oligomieroarray.

first: Kenzaburo

last: Tani


title: New non-transmissible measles virus vector for establishment of iPS cells


title: Role of Sirt1 in cardiomyocytes in the development of caloric restriction-induced cardioprotection

status: Public on May 05 2016

summary:
Comparison of transcriptional profiling in murine hearts obtained from the control mice fed ad libitium (AL) and treated with caloric restriction (CR).
Comparison of transcriptional profiling in murine hearts obtained from cardiomyocye-specific Sirt1 knockout mice fed ad libitium and treated with caloric restriction.

overall_design: Two-condition experiments, AL vs.CR and the control vs. cardiomyocyte-specific Sirt1 knockout mouse. A pair of murine heart samples per array.

first: Tunehisa

last: Yamamoto

first: Ken

last: Shinmura


title: Genes that are differentially expressed by 5AZA treatment and DNMT1 knockdown in intestinal tumor organoid

status: Public on May 23 2016

summary: Gene expression profiles after treatment with the DNA methylation inhibitor 5-Aza-CdR and DNMT1 knockdown were analyzed in tumor organoids derived from ApcMin mice.

overall_design: Tumor organoids were established from polyps of ApcMin mice. Treatment with 5-Aza-CdR and DNMT1 knockdown were performed and gene expression profiles were analyzed in tumor organoids.

first: Yoshimasa

last: Saito

first: Toshihide

last: Muramatsu


title: TGFβ signaling directs serrated adenomas to the mesenchymal colorectal cancer subtype [adenomas]

status: Public on Jun 01 2016

city: Amsterdam

first: Sander

middle: Roeland

last: van Hooff

address: Meibergdreef 9

department: Center for Experimental and Molecular Medicine (CEMM),

institute: AUMC

summary:
Colorectal cancer can be divided into four consensus molecular subtypes, which might associate with distinct precursor lesions. The aim of this study was to determine the subtype affiliation of two types of colorectal adenomas: tubular adenomas (TAs) and sessile serrated adenomas (SSAs) and to determine the activity of TGFβ signaling and the role of this cytokine in subtype affiliation.
Adenoma samples were collected in the Academic Medical Center (AMC), Amsterdam, The Netherlands. Tubular adenomas (TAs) were obtained from familial adenomatous polyposis (FAP) patients and sessile serrated adenomas (SSAs) were collected from serrated polyposis syndrome (SPS) patients.

overall_design: Gene expression was analyzed for 7 sessile serrated adenomas (SSA) and 9 tubular adenomas (TA).

first: Evelyn

last: Fessler

first: Jarno

last: Drost

first: Janneke

middle: F

last: Linnekamp

first: Xin

last: Wang

first: Marnix

last: Jansen

first: Felipe

last: De Sousa E Melo

first: Pramudita

last: Prasetyanti

first: Joep

last: Ijspeert

first: Marek

last: Franitza

first: Peter

last: Nürnberg

first: Carel

last: van Noesel

first: Evelien

last: Dekker

first: Louis

last: Vermeulen

first: Hans

last: Clevers

first: Jan

last: Medema


title: TGFβ signaling directs serrated adenomas to the mesenchymal colorectal cancer subtype [organoids]

summary:
The aim of this study was to determine the effects of TGFβ at the premalignant stage of CRC development.
Organoid cultures were isolated from normal colon and from tubular adenomas. One normal colon culture was genetically engineered using the CRISPR-Cas9 system to carry the BRAFV600E mutation.

overall_design: Organoid cultures of three different tubular adenomas and two normal colon samples, and one BRAFV600E-mutant organoid culture received TGFβ or control treatment after which gene expression was analyzed by microarray (Affymetrix U133+ PM Genechip Array).


title: TGFβ signaling directs serrated adenomas to the mesenchymal colorectal cancer subtype

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

overall_design: Refer to individual Series


title: Breast tumors: different structures of tumor cells [gene expression]

status: Public on Apr 29 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 morphologically-distinct structures of breast tumors: tubular, alveolar, solid, trabecular structures, and discrete groups of tumor cells in comparison with normal breast epithelium. The aim was to identify transcripts and cell signalling pathways which could be associated with the development of clinical relevant structures of tumor cells.

overall_design: Five types of morphological structures from breast tumors (n=3) vs. normal epithelial cells from tumor-adjacent normal tissues (n=3)

first: Evgeny

middle: V

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: Breast tumors: different structures of tumor cell

type:
Expression profiling by array
Genome variation profiling by array


title: Expression profile of Epstein Barr Virus infected mammary epithelial cells and Breast tumors

status: Public on May 04 2016

first: Gerburg

last: Wulf

address: 330 Brookline Ave

summary: Whether the human tumor virus, Epstein-Barr virus (EBV) promotes breast cancers remains controversial and a potential mechanism has remained elusive. Here we show EBV can infect primary mammary epithelial cells (MECs) that express the attachment receptor, CD21.  EBV infection leads to the expansion of early MEC progenitor cells with a stem cell phenotype and enforces a differentiation block. When MECs were implanted as xenografts, EBV infection cooperated with activated Ras and accelerated the formation of breast cancer. Infection in EBV-related tumors was of a latency type II pattern, including expression of latent membrane proteins 1 (LMP1) and 2 (LMP2), similar to nasopharyngeal carcinoma (NPC). A human gene expression signature for EBVness was generated based on the RNA expression profile of the EBV infected primary mammary epithelial cells, tumors. This was signature associated with high grade (40 vs 13.5%) estrogen-receptor-negative status (31.8 vs. 10.5%, p53 mutation (37.5 vs 14.5%) and poor survival. In 11/33 (33%) of tumors positive for EBVness EBV-DNA was found in tumor cells by fluorescent in situ hybridization for the viral LMP1 and BXLF2 genes, while only 4/36 (11%) of EBVness-negative tumors tested positive for EBV DNA. An analysis of the TCGA breast cancer data revealed a correlation of EBVness with presence of the APOBEC mutational signatures consistent with past viral infection. We conclude that a contribution of EBV to breast cancer etiology via a ‘hit-and-run’ mechanism is plausible, in which EBV infection predisposes mammary epithelial cells to malignant transformation, but is not required for the maintenance of the malignant phenotype.

overall_design: We incubated immortalized mammary epithelial cells (MCF-10A and HMECs) with GFP-labeled EBV and generated EBV infected mammary epithelial cells (EBV-MCF-10A, EBV-HMEC). The GFP control cells were also generated as GFP-MVF-10A, GFPHMEC. To test the hypothesis that EBV-infection of MECs cooperated with oncogenes to facilitate malignant transformation, we infected immortalized HMECs that expressed either GFP or GFP-EBV with Ras V12 or a matched retroviral vector control. At every step GFP-control HMECs were treated exactly like those infected with EBV. The resulting cell lines (EBV-GFP/RasV12/SV40-HMEC called EBV-HMEC-R, GFP/RasV12/SV40-HMEC called GFP-HMEC-R, EBV-GFP/RasV12/SV40-MCF-10A called EBV-MCF-10A-R and GFP/RasV12/SV40-MCF-10A called GFP- MCF-10A-R) were used for subsequent in vitro and xenotransplant experiments.  The HMEC line used to examine the effect of EBV infection on tumor formation in vivo was previously immortalized with telomerase (htert) and SV40 large T antigen. Eight tumors were generated, including four EBV tumor (EBV-tumor 1 to 4), four GFP tumor (GFP tumor 1 to 4).

first: Hai

last: Hu