title: Expression data from infected mice bladder and kidney tissue

status: Public on Aug 27 2016

city: Lund

first: Ines

last: Ambite

address: Klinikgatan 28

department: Laboratory Medicine

country: Sweden

institute: Lund University

summary: Acute cystitis is rapidly becoming a therapeutic enigma, as antibiotic resistance is reducing the options to a minimum. Fortunately, new insights are now making it possible to explore immune response modifiers as alternatives to antibiotics. In patients with acute cystitis, infection triggers a rapid and potent inflammatory response in the bladder mucosa and clinical symptoms include pain, urgency and frequency of urination. The molecular basis of these symptoms is not well understood, but bacterial interactions with the bladder epithelium have been shown to create inflammatory cascades.  This study examined how innate immune response genes influence the outcome of bladder infection and the pathogenesis of acute cystitis with a particular focus on IL-1β. C57BL/6 mice were intravesically infected with relevant uropathogenic Escherichia coli strain, CFT073. Acute cystitis in infected bladders was defined by macroscopic inspection of edema, hyperemia and purulent discharge followed by histology and immunohistochemistry, after 24 hours and seven days. Genetic determinants of transient bladder inflammation versus severe disease were subsequently identified using C57BL/6 mice with specific inflammasome gene deletions (Il1b-/-, Casp1-/-, Asc-/- and Nlrp3-/-). Using genome-wide transcriptomic analysis to characterize genes regulated by infection in the bladders of these mice, we identified acute cystitis as an IL-1β-driven, hyper-inflammatory disease. Consistent with such a role, Il1b-/- mice were protected from infection and pathology. In contrast Asc-/- and Nlrp3-/- mice developed progressive IL-1β-driven bladder inflammation and severe pathology, caused by a new, non-canonical IL-1β processing mechanism, involving the metalloproteinase MMP-7. Using IL-1β and MMP-7 as targets for immunotherapy, we succeeded in protecting susceptible Asc-/- mice against acute cystitis, confirming the potential of immunotherapy for this indication.  The results reproduce important aspects of human cystitis in the murine urinary tract infection (UTI) model and provide a comprehensive molecular framework for the pathogenesis and immunotherapy of acute cystitis, one of the most common bacterial infections in man.

overall_design: Mouse were infected intravesically with E. coli CFT073 and bladder and kidney samples were collected after 7 days. Isolated RNA was subjected to Affymetrix whole genome transcriptomic analysis.

first: Manoj

last: Puthia

first: Catharina

last: Svanborg


title: Study the function of miR-195 and miR-30d in prostate cancer cell (LNCap and DU145)

status: Public on Aug 23 2016

city: Guangzhou

first: Yifeng

last: Luo

state: Guangdong

address: 58 Zhongshan 2nd Road

department: Institute of Respiratory Diseases of Sun Yat-sen University

country: China

institute: The First Affiliated Hospital of Sun Yat-sen University

summary:
miRNAs are related with the initiation and development of prostate cancer. We discover the miR-195 and miR-30 can be as a biomarker of prognosis of prostate cancer in clinical patients. miRNA functions through affecting the mRNA degradation by binding the mRNA 3’UTR. So we test the change of transcriptional profile of miR-195 and miR-30d cell line respectively to further study the function of miR-195 and miR-30d.
To study the function of miR-195 and miR-30d in prostate cancer, we setup the over-expression cell line of the miR-195 and miR-30d respectively in prostate cancer cell(LNCap and DU145), then study the change of transcriptional profile in cell line by microarray experiment (Affymetrix PrimeView human gene expression).

overall_design: We order the over-expression plasmid of vector, miR-195 and miR-30d from System Biosciences company (Cat No: Scramble Vector PMIRH000PA-1 as Control, miR-195 PMIRH195PA-1, miR-30d PMIRH30dPA-1), and packaged the virus and construct the stable cell line (LNCaP_Control, LNCaP_mir195, LNCaP_mir30d,DU145_Control, DU145_mir195, DU145_mir30d,).    We test the transcriptional profile in cell line by microarray experiment (Affymetrix PrimeView human gene expression).

first: Wei-de

last: Zhong

first: Fu-neng

last: Jiang


title: Jumonji Demethylase Inhibitor GSK-J4 treated Multiple Myeloma JJN3 and RPMI

status: Public on Aug 21 2016

city: Oxford

first: Udo

last: Oppermann

state: Oxfordshire

address: Botnar Research Centre, Nuffield Orthopaedic Centre, Windmill Road

department: Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences

country: United Kingdom

institute: University of Oxford

summary: Analysis of Multiple Myeloma Cell lines JJN-3 and RPMI gene expression following treated with GSK-J4 or Bortezomib

overall_design: Total RNA extracted from cells after 6 or 24 hour treatment with either GSK-J4, GSK-J5, Bortezomib or vehicle

first: Edward

middle: S

last: Hookway


title: APOL1 renal-risk variants induce mitochondrial dysfunction (Illumina)

city: Winston Salem

first: Lijun

last: Ma

state: NC

address: 1 Medical Center Blvd

department: Nephrology

country: USA

institute: Wake Forest School of Medicine

summary: To elucidate pathways whereby apolipoprotein L1 gene (APOL1) G1 and G2 variants facilitate kidney disease in African Americans, human embryonic kidney cells (HEK293) were used to establish doxycycline-inducible (Tet-on) cell lines stably expressing reference APOL1 G0 and its G1 and G2 renal-risk variants. Illumina human HT-12-v4 arrays and Affymetrix HTA 2.0 arrays were employed to generate global gene expression data with doxycycline induction. Significantly altered pathways identified through bioinformatics involved mitochondrial function; results were validated using immunoblotting, immunofluorescence and functional assays.

overall_design: Global gene expression profiles were performed on HEK293 Tet-on G0, G1, G2 and empty vector cells with and without Dox induction using Illumina human HT-12 v4 arrays. Another independent gene expression array system, Affymetrix HTA 2.0, was used to verify the results of Illumina arrays. Pair-wise and pattern-based analyses were applied to detect the mostly impacted pathways due to overexpression and by APOL1 genotypes.

first: Jeff

middle: W

last: Chou

first: James

middle: A

last: Snipes

first: Manish

last: Bharadwaj

first: Ann

middle: L

last: Craddock

first: Dongmei

last: Cheng

first: Allison

last: Weckerle

first: Snezana

last: Petrovic

first: Pamela

middle: J

last: Hicks

first: Ashok

middle: K

last: Hemal

first: Gregory

last: Hawkins

first: Lance

middle: D

last: Miller

first: Anthony

last: Molina

first: Carl

last: Langefeld

first: Mariana

last: Murea

first: John

last: Parks

first: Barry

middle: I

last: Freedman


title: The expression patterns correlated with disease severity of adrenoleukodystrophy via microarray analysis

status: Public on Aug 19 2016

city: Seoul

first: Dong-Wook

last: Kim

address: 50-1 Yonsei-ro, Seodaemun-gu

department: Dept. of Physiol.

country: South Korea

institute: Yonsei University College of Medicine

summary: To gain molecular insight into the inflammatory phenotype of childhood cerebral adrenoleukodystrophy (CCALD), we performed microarray-based transcriptional profiling analysis of human embryonic stem cells (hESCs), control-induced pluripotent stem cells (iPSCs), adrenomyeloneuropathy (AMN)-iPSCs and CCALD-iPSCs.

overall_design: 200 ng of total RNA from purified hESCs (P35–45), control-iPSCs (P10-20), CCALD-iPSCs (P10–20), AMN-iPSCs (P10–20) was transcribed to yield biotinylated complimentary RNA (cRNA) according to the manufacturer’s instructions.

first: Jiho

last: Jang


title: Circular non-coding RNA ANRIL modulates ribosomal RNA maturation and atherosclerosis in humans.

status: Public on Aug 22 2016

city: Munich

first: Bernd

middle: Henrik

last: Northoff

address: Marchioninistr. 15

department: Institute of Laboratory Medicine

country: Germany

institute: Ludwig-Maximilians-University Munich

summary:
Circular RNAs (circRNAs) are broadly expressed in eukaryotic cells, but their role in human health and disease remains obscure. Here, we show that circular antisense non-coding RNA in the INK4 locus (circANRIL), which is transcribed at a locus of atherosclerotic cardiovascular disease on chromosome 9p21, confers athero-protection by controlling ribosomal RNA (rRNA) maturation and modulating pathways of atherogenesis.
At the molecular level, circANRIL competes with precursor rRNA (pre-rRNA) for binding to pescadillo homolog 1 (PES1), an essential 60S-preribosomal assembly factor, thereby impairing exonuclease-mediated pre-rRNA processing and ribosome biogenesis. As a consequence, circANRIL induces nucleolar stress and p53 activation, resulting in the induction of apoptosis and inhibition of proliferation, which are key athero-protective cell functions within the arterial wall. Collectively, these findings identify circANRIL as a prototype of a circRNA regulating ribosome biogenesis and conferring athero-protection, thereby unveiling a therapeutic potential of certain circRNAs in human disease.

overall_design: Analysis of transcriptome-wide expression level in HEK293 cells with stable overexpression of circular ANRIL (n=3) compared to a vector control (n=3).

first: Lesca

middle: M

last: Holdt

middle: H


title: Comparative gene expression profiling of serum-free and FBS treated colorectal TIC cultures

status: Public on Aug 20 2016

city: Heidelberg

first: Taronish

last: Dubash

institute: National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ)

summary: To induce a differentiated phenotype, primary colorectal TIC cultures were grown in 10% FBS containing conditions. To analyze gene expression changes upon induction of a differentiated phenotype, total RNA of cells cultured in FBS containing conditions and  control cells cultured under serum-free conditions was isolated and comparative gene expression profiling was performed.

overall_design: RNA was obtained from five different patient derived spheroid cultures grown in serum-free or 10% FBS containing culture medium.

first: Dubash

last: Taronish

first: Ball

middle: R

last: Claudia


title: Gene expression analysis of bone marrow stromal cells from multiple myeloma patients and controls

first: Seon Young

address: 101 Daehak-ro, Jongno-gu,

institute: Seoul National University College of Medicine

summary: Multiple myeloma is hematologic malignancies result from clonal proliferation of plasma cells. Recently, increasing evidence supports the hypothesis that microenvironment cells play important roles in the proliferation, survival, and drug resistance of clonal plasma cells. The aim of this study is to culture stromal cells from bone marrow aspirates of patients with multiple myeloma, and to investigate expression profiles of bone marrow stromal cells and their relationships with the clinical characteristics of patients.

overall_design: RNA was extracted cultured bone marrow stromal cells from 15 patients with plasma cell neoplasms, and bone marrow stromal cells from 13 control patients with 9 B-cell lymphoma patients with no evidence of BM involvement and 4 patients with mild-to-moderate cytopenia without evidence of hematologic malignancies

first: Seon

middle: Y

first: Dong

last: Lee


title: Endothelial cell response to trophoblastic debris

city: AUCKLAND

first: Larry

last: Chamley

address: 85 Park Road

department: Obstetrics and Gynaecology

country: New Zealand

institute: The University of Auckland

summary:
The human placenta is covered by a single multinucleated fetal cell, the syncytiotrophoblast, which is bathed in maternal blood. During all pregnancies, membrane enclosed extracellular vesicles derived from the syncytiotrophoblast are extruded into the maternal blood.The large size of these extracellular vesicles (diameter larger than 10µm) is referred to as trophoblastic debris in this study. We have shown in the past that endothleial cells are involved in clearence of this trophoblastic debris and induction of immune tolerence by trophoblastic debris.This study aimed to characterise the transcriptional changes that occur in human vascular endothelial cells following exposure to trophoblastic debris from normal first trimester placentae.
Microarrays were used to probe transcriptomic changes 2 and 21 hours after exposure of endothelial cells (Human microvascular endothelial cell line,HMEC-1) to trophoblastic debris from normal first trimester placentae

overall_design: Trophoblastic debris were isolated by low speed centrifugation from three individual first trimester human placentae (three biological replicates). The protein content in trophoblastic debris was measured by BCA assay. HMEC-1 was co-cultured with trophoblastic debris (60ug/ml total debris protein contents) for either 2 or 21 hours before RNA extraction. Untreated HMEC-1 at 2 and 21 hours were used as controls.In total, 12 samples were analyzed.

first: Jia

last: Wei


title: Neutralizing Antibody Mediated Protection Against Mucosal Simian-Human Immunodeficiency Virus Challenge Includes Systemic Clearance of Distal Virus

status: Public on Sep 01 2016

city: Cleveland

first: Rafick

last: Pierre-Sekaly

state: OH

address: 2103 Cornell Avenue

department: Pathology

institute: Case Western Reserve University

summary: The purpose of this study was to investigate the anatomic sites and mechanisms of antibody-mediated protection.  In particular, to determine whether bNAbs completely block virus at the local portal of entry following mucosal virus challenge.

overall_design: We performed comprehensive necropsies following intravaginal SHIV-SF162P3 challenge of rhesus monkeys that had received a fully protective dose of the potent V3 glycan-dependent bNAb PGT121.  This bNAb has been shown to protect robustly against SHIV-SF162P3, SHIV-AD8, and SHIV-DH12

first: Jian

last: Liu

first: Khader

last: Ghneim

first: Devin

last: Sok

first: William

last: Bosche

first: Yuan

last: Li

first: Elizabeth

last: Chipriano

first: Brian

last: Berkemeier

first: Kelli

last: Oswald

first: Erica

last: Borducchi

first: Crystal

last: Cabral

first: Lauren

last: Peter

first: Amanda

last: Brinkman

first: Mayuri

last: Shetty

first: Jessica

last: Jeminez

first: Jade

last: Mondesir

first: Benjamin

first: Patricia

last: Giglio

first: Abishek

last: Chandrashekar

first: Arnaud

last: Colantonio

first: Courtney

last: Gittens

first: Chantelle

last: Baker

first: Wendeline

last: Wagner

first: Mark

middle: G

last: Lewis

first: Wenjun

first: Rafick-Pierre

last: Sekaly

first: Jeffrey

last: Lifson

first: Dennis

last: Burton

first: Dan

last: Barouch


title: Microarray Analysis of chemosensitivity in Laryngeal Squamous Cell Carcinoma

status: Public on Aug 16 2016

city: Beijing

first: Jugao

last: Fang

address: No. 1 Dongjiao Min Xiang, Dongcheng District

institute: Capital University of Medical Sciences attaches to Beijing Tongr

summary: OBJECTIVE: To investigate the differentially expressed genes related to the chemosensitivity of laryngeal squamous cell carcinoma （LSCC）by microarrays arrays.   METHODS: 1. A total number of 11 patients who underwent induction chemotherapy for primary hypopharyngeal squamous cell carcinoma (7 patients are sensitive to chemotherapy ,and others are not) were recruited for microarray and miRNA array gene expression analysis  2. Bioinformatics analysis of differentially expressed genes screened by microarrays : The differential gene cluster analysis was applied in biological processes, cellular components and molecular functions by GO database; The differential gene enrichment analysis was applied in signaling pathways by KEGG database, and the differentially expressed and biologically meaningful core genes would be screened.  RESULTS: 1. Analyzed by microarrays, there were 1554 genes significantly related to the sensitivity to chemotherapy; Among these 1554genes, 777 showed a higher expression in the tissue from patients who are sensitive to chemotherapy , while 785 presented the contrasting pattern.   CONCLUSIONS: The research revealed a gene expression signature of chemosensitivity in laryngeal squamous cell carcinoma by microarrays arrays. The result will contribute to the understanding of the molecular basis of laryngeal squamous cell carcinoma and help to improve diagnosis and treatment.

first: Qian

last: Shi

first: Meng

last: Lian


title: The effect of IKKβ on estrogen receptor positive breast cancer phenotypes

status: Public on Aug 17 2016

city: Chicago

first: Jonna

last: Frasor

state: IL

address: 835 S. Wolcott MC901

department: Physiology and Biophysics

institute: University of Illinois at Chicago

summary:
Estrogen receptor α (ER) is a good prognostic marker expressed in ~75% of breast tumors. Women with ER+ tumors will receive endocrine therapy, yet ~50% will experience relapse and late recurrence ~5-20 years after primary diagnosis.
The recurrent tumors are often aggressive, resistant, and metastatic. A growing body of evidence suggests that an inflammatory microenvironment and the activation of the NF-ĸB pathway are highly associated with the progression of ER+ tumors
to more aggressive stages. However, it is unknown whether NF-ĸB is a driver or a consequence of aggressive ER+ disease. In order to study this, we developed multiple ER+ breast cancer cell lines expressing a Doxycycline-inducible, constitutively
active form of IĸB kinase β (CA-IKKβ), a key kinase in the canonical NF-ĸB pathway. This allowed us to specifically activate the canonical arm of the NF-ĸB pathway in a controlled fashion.

overall_design: Constitutively active IKK β-MCF-7 cells are treated with Estrogen (E2), Doxycycline (Dox) or E2+Dox for 72 hrs.The study includes four groups: Vehicle, E2, Dox and E2+Dox with three replicates per group.

first: Lamiaa

last: El-Shennawy


title: Hormonal and nutritive control of HCC1937 basal cell line plasticity

status: Public on Aug 12 2016

city: Lyon

last: VIGNERON

address: 28 rue Laennec

country: France

institute: Cancer Research Center of Lyon

summary: Analysis of glucocorticoid and retinoic acid effects on gene expression of HCC1937

overall_design: Total RNA obtained from HCC1937 cells treated 16 hours with dexamethasone (200nM) alone or with retinoic acid (1µM) and compared to untreated control.

last: Vigneron

first: Ebticem

last: Nouri


title: Analysis of gene expression change due to knockdown of Slug expression in a basal-subtype breast cancer cell line, MCFDCIS.

status: Public on Aug 11 2016

city: Dallas

first: Xiaoyu

last: Wang

state: Texas

address: ND3 200, 6001 Forest Park Rd

department: Cancer Center

institute: Ut Southwestern Medical Center

overall_design: Total RNA isolated from MCFDCIS cells transfected with control or Slug specific siRNA.

first: Gray

last: Pearson


title: Regulation of nuclear gene expression by PK 11195, a ligand specific for the mitochondrial 18 kDa translocator protein (TSPO) (15, 30, and 45 minutes of exposure)

city: Haifa

first: nasra

middle: mohamed

last: yasin

address: Bat Galim haifa- rappaport

department: neuropharmacology

country: Israel

institute: technion

summary:
It is known that application of TSPO ligands as well as knockdown of the mitochondrial 18 kDa translocator protein (TSPO) modulate viability, proliferation, adhesion, and migration of glioblastoma cells, as well as angiogenesis. To study the ability of the TSPO to regulate gene expression in relation to these functions we applied microarray analysis of gene expression to U118MG glioblastoma cells. Seen at the time points of 15, 30, and 45 minutes,  the TSPO ligand PK 11195 induced changes in expression of immediate early genes and transcription factors. These changes  also included gene products that are part of the canonical pathway for modulation of general gene expression.  These changes peaked at 30 minutes. Thus, it appears that the TSPO is part of the retrograde mitochondrial-nuclear signaling pathway for modulation of gene expression.  Consequently, our data indicate that this is a major venue whereby TSPO may drive its numerous functional effects. Keywords: modulation of nuclear gene expression, mitochondrial 18 kDa translocator protein (TSPO), TSPO ligand, PK 11195, 2-Cl-MGV-1, retrograde mitochondrial-nuclear signaling pathway, microscopy, mitochondria, cell nucleus
abstract of annual meetingof the israel society for neuroscience, section B, abstract # 98.

overall_design: The aim of the study was to compare the gene expression profile using human expression beadchip of 4 experimental groups in triplicates: Vehicle (Base line (BL) - Without any treatment), 15 min after stimulus, 30 min after stimulus and 45 min after stimulus. The experiment design was to compare the change in expression during a time course of 0,15,30,& 45 min with 3 replicates for each time point. First of all, U118MG cells (1.3 × 10^6) were seeded in Petri dishes (i.e. 28.5 × 10^3 cells / cm2) and allowed to proliferate for 3 days in full medium. Experiments for gene expression assayed with microarray typically consisted of three experimental groups and a vehicle control group (n = 3 for each group). After seeding and proliferation, serum deprived medium was applied for 24 hrs, in the experimental groups ending with the inclusion a choice of various PK 11195 exposures i.e. either 15 min, 30 min, or 45 min. Exposure to PK 11195 implies serum deprived medium with 1% alcohol (vehicle) and PK 11195 (25 µM final concentration) for the required time period. 25 µM of PK 11195 is the optimal concentration for these types of experiments with U118MG cells (Kugler et al., 2008). The cells were collected by trypsinization, washed by centrifugation in phosphate buffered saline (PBS) (400 × g, 5 min), and lysed [RLT lysis buffer provided with the RNeasy Mini Kit diluted with β-mercaptoethanol (1 : 100)], according to the manufacturer's instructions. Lysates were stored at -70oC.

first: N

last: Yasin

first: L

last: Veenman

first: M

last: Gavish


title: Illumina HT-12 v4 expression array data for Ovarian Cancer Samples

city: Vancouver

first: Kelsie

last: Thu

state: British Columbia

address: 675 West 10th Avenue

country: Canada

institute: BC Cancer Research Centre

summary: This study aimed to generate a new panel of comprehensively, genomically characterized high-grade serous ovarian carcinoma (HGSOC) cell line and xenograft models. Multidimensional genomic data were generated and compared between cell lines/xenografts and the tumours they were derived from, indicating the cell lines/xenografts are highly similar to their patient-matched tumours. Cell line/xenograft data were also compared to TCGA ovarian tumours to show the cell lines are good models of clinical HGSOC.

overall_design: Illumina HT-12 v4 arrays were performed according to the manufacturer's directions on total RNA extracted from i) tumour cells purified from ovarian tumour ascites, and ii) established cell lines. Evaluation of the similarity in copy number/methylation/gene expression/mutational profiles of cell lines/tumours/xenografts was performed.

first: Adi

middle: F

last: Gazdar


title: Expression in liver tissue of wildtype (wt) or hepatocyte specific Klf6 knockout (DeltaKLF6) after partial hepatectomy

status: Public on Aug 10 2016

city: Essen

first: Lars

middle: P

last: Bechmann

address: Hufelandstr. 55

department: Gastroenterology and Hepatology

institute: University Hospital Essen

summary:
Krüppel-like factor 6 (KLF6) is a transcription factor and tumor suppressor. Loss or reduction of KLF6 is linked with progression of experimental and human hepatocellular carcinoma. Despite its important contributions to liver homeostasis and growth, there are no data characterizing the involvement of KLF6 to hepatic regeneration.
Microarray data from wildtype and DeltaKlf6 mice were used to identify regulating mechanisms and potential mediators within liver regeneration

overall_design: Wildtype and hepatocyte specific Klf6 knockout mice (DeltaKlf6) were employed for 70% partial liver resection/hepatectomy (PHx) in order to analyse liver regeneration. Twelve hours after partial hepatectomy animals were scrificed and remnant liver tissue was used for further experiemnts. For the overall study we used 6 animals per group, and included RNA from liver tissue of 3 wildtype and 3 DeltaKlf6 animals for the microarray analysis. Wildtype animals were used as controls.

first: Svenja

last: Sydor


title: AKT Isoform Specificity Downstream of PIK3CA Mutation Impacts Estradiol and PI3K Inhibitor Response in Breast Cancer Cells

city: Indianapolis

first: Guanglong

last: Jiang

state: IN

department: Medical and Molecular Genetics

institute: Indiana University School of Medicine

summary: Background: PIK3CA mutations are observed in >30% of breast cancers, which are more common in estrogen receptor (ERα)-positive breast cancer compared with ERα-negative breast cancer. AKT1, 2, and 3 isoforms, major isoforms downstream of PI3K, modulate ERα activity. It is unknown whether PIK3CA mutation leads to preferential activation of specific AKT isoforms with an ability to modulate ERα function.  Methods: Gene expression arrays were performed on parental, AKT1 knockdown or AKT2 knockdown MCF-7 breast cancer cells with or without estradiol treatment for three hours.  Results: AKT1 had a dominant role in ERα:estradiol-dependent gene expression and proliferation. We have identified a unique gene expression signature that is dependent on ERα, estradiol, AKT1 and the pioneer factor FOXA1. Overexpression of this signature was associated with better outcome in patients with ERα-positive breast cancer. In contrast, AKT2 controlled global gene expression.

overall_design: Cells were maintained in phenol red free MEM with 5% charcoal dextran treated fetal calf serum for four days and then treated with ethanol or 0.1 nM estradiol for three hours. RNA was prepared using RNeasy kit (Qiagen, Valencia, CA, USA) Microarray with biological triplicates was performed using Illumina HumanHT-12 V4 expression beadchip. Genes that showed statistically insignificant signals in majority of samples were removed from the microarray data, and only those probes that showed statistically significant signal in at least half of samples of at least one group were retained. The probe level data was then collapsed to gene level data by retaining only the probes, which showed a maximal coefficient of variation across all samples. The data was imported into partek genomics suite for differential expression analysis. ANOVA analysis was performed to identify genes differentially expressed between AKT1KD vs. pLKO, AKT2KD vs. pLKO, and AKT1KD vs. AKT2KD groups. Stratagene Universal Human Reference RNA (Illumina Catalog # 740000) was used as quality control specimen

first: Harikrishna

last: Nakshatri


title: A Transcriptomic Reporter Assay Employing Neutrophils to Measure Immunogenic Activity of Septic Patients' Plasma (Expt. 3)

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

summary: The wide array of molecules carried by plasma regulates critical immune functions and constitutes valuable biomarkers and therapeutic targets. In recent years the introduction of “systems approaches” has provided investigators with powerful means for assessing immune responses in patient samples on a global scale. However, while the use of genome-wide profiling technologies has become widespread, measuring the plasma proteome still presents considerable challenges. An alternative approach that consists in measuring transcriptome responses in reporter cells exposed in vitro to patient plasma has been successfully employed in a limited number of studies. Here we devised such a “Transcriptomic Reporter Assay” system to assess the immunogenicity of plasma from septic patients and evaluate its potential for biomarker discovery. Sepsis is a common, severe systemic infectious process for which physicians still lack efficient diagnostic or prognostic tools. Of the three different cell reporter systems tested, neutrophils were identified as the most capable “plasma sensor”. Compared to peripheral blood mononuclear cells and dendritic cell preparations neutrophils were best able to discriminate between plasma from septic and control subjects and responded by upregulating a robust immune transcriptional program. Additionally, the amplitude of the neutrophil transcriptomic response was shown to be associated with disease severity in two additional sets of patients. Overall, our results demonstrate both the suitability and potential clinical relevance of a neutrophil reporter assay for assessing immunopathogenic processes in a complex and severe condition such as sepsis.

overall_design: Polymorphonuclear neutrophils (PMNs) were isolated a healthy donor. Plasma samples were obtained from a first set of patients with culture-confirmed sepsis (n=35) and from uninfected controls (n=19). PMNs were cultured for 6 h in medium alone, plasma from patients with sepsis, plasma from uninfected controls, and LPS using a final concentration of 20%. Transcriptional profiles were acquired using Illumina HumanHT12 V4 BeadChips.

first: Prasong

last: Khaenam

first: Darawan

last: Rinchai

first: Laurent

last: Chiche

first: Matthew

middle: C

last: Altman

first: Surachat

last: Buddhisa

first: Chidchamai

last: Kewcharoenwong

first: Duangchan

last: Suwannasaen

first: Michael

last: Mason

first: Elizabeth

last: Whalen

first: Wattanachai

last: Susaengrat

first: Kimberly

last: O’Brien

first: Quynh-Ahn

last: Nguyen

first: Vivian

last: Gersuk

first: Peter

last: Linsley

first: Ganjana

last: Lertmemongkolchai


title: Expression profiling of fibroblasts treated with melanosomes

status: Public on Aug 09 2016

city: Tel Aviv

first: Carmit

last: Levy

address: Ramat Aviv

department: Human Genetics and Biochemistry

institute: Tel Aviv University

summary: mRNA profiling was performed on primary fibroblasts treated with melanosomes and untreated fibroblasts as control. The aim of this study was to explore whether melanoma-derived mature melanosomes functionally affect primary fibroblasts. A functional gene set enrichment analysis based on the resulting mRNA profiles predicted that an uptake of mature melanosomes by fibroblasts causes increased cell proliferation and cell motility.

overall_design:
Expression profiling was performed for 3 replicates of primary human fibroblasts that were treated with mature melanosomes, 1 replicate of fibroblasts treated with early melanosomes and 3 replicates of untreated fibroblasts as controls. Melanosomes were extracted from the human melanoma cell line MNT-1. Fibroblasts were treated with melanosomes for 24h. Fold changes were calculed for fibroblasts treated with mature melanosomes vs. controls. The sample of fibroblasts treated with early melanosomes was considered for the normalization, but not for further analyses.
Microarray Unit of the Core Facility Genomics and Proteomics DKFZ

first: Laureen

last: Sander

first: Jörg

last: Hoheisel


title: Melanoma miRNA trafficking triggers the tumor primary niche formation

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

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

overall_design: Refer to individual Series


title: Tumour sampling method can significantly influence gene expression profiles derived from neoadjuvant window studies I

status: Public on Aug 08 2016

city: Edinburgh

first: Dominic

middle: Andrew

last: Pearce

address: University of Edinburgh Cancer Research UK Centre (ECRC)

department: Institute of Genetics and Molecular Medicine

institute: The University of Edinburgh

summary: Background: Gene expression profiling has been used extensively within breast cancer research. Patient matched transcriptomic studies of tumour samples before and after treatment offer great potential and have been initiated, but tend not to include a control group. Here we examine gene expression changes between patient-matched core biopsies and surgical resection samples in the absence of treatment, to consider sampling methods and tumour heterogeneity.   Patients and Methods: Illumina BeadArray technology was used to measure dynamic changes in gene expression from thirty-seven paired baseline and surgically excised breast tumour samples obtained from women receiving no treatment prior to surgery.   Results: Patient-matched sample pairs had significantly higher correlations than samples between different individuals, demonstrating that tumour heterogeneity and intra-tumour differences are less prominent than inter-tumour/patient differences. Perhaps surprisingly, consistent changes in gene expression were identified during the diagnosis-surgery interval, despite a lack of treatment. 50 genes were significantly differentially expressed (48 up, 2 down; FDR 0.05) in a manner that appears independent of both subtype and the sampling-interval length. Gene set enrichment analysis using four independent treated datasets has implicated the tumour sampling method as the likely cause of these expression changes which include increases in early growth response genes such as EGR1, 2 and 3 along with DUSP1 and FOS. Our data does not support the idea that there is a significant wounding or immune response.  Conclusion:  This is the largest cohort of patient-matched transcriptome profiling of tumours from patients receiving no treatment between diagnosis and surgery to date. It has revealed that consistent changes in gene expression do exist between diagnostic core biopsy and the surgical excision sample. We have confirmed these findings in a number of published breast cancer datasets. Ultimately, researchers should be aware of the potential for the tumour sampling method to introduce a confounding factor in future neoadjuvant studies.

overall_design: 37 paired patient-matched whole-transcriptome profiled primary breast tumours from patients receiving no treatment between diagnosis and surgery. Superseries is a product of two integrated individual batches.


title: Tumour sampling method can significantly influence gene expression profiles derived from neoadjuvant window studies


title: Tumour sampling method can significantly influence gene expression profiles derived from neoadjuvant window studies II

middle: A


title: Mitofusin 2 expression in muscle decreases during aging and generates a gene signature characteristic of aged muscle

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

summary: Mitochondrial fusion and fission proteins regulate mitochondrial quality control and mitochondrial metabolism. In turn, mitochondrial dysfunction is associated with aging, although its causes are still under debate. Here, we show that aging is characterized by a progressive reduction of Mitofusin 2 (Mfn2) in mouse skeletal muscle and that skeletal muscle Mfn2 ablation in mice generates a gene signature linked to aging. Furthermore, muscle Mfn2-deficient mice show unhealthy aging characterized by altered metabolic homeostasis and sarcopenia. Mfn2 deficiency impairs mitochondrial quality control, which contributes to an exacerbated age-related mitochondrial dysfunction. Surprisingly, aging-induced Mfn2 deficiency triggers a ROS-dependent retrograde signaling pathway through induction of HIF1 transcription factor and BNIP3. This pathway ameliorates mitochondrial autophagy and minimizes mitochondrial damage. Our findings reveal that repression of Mfn2 in skeletal muscle during aging is determinant for the loss of mitochondrial quality, contributing to age-associated metabolic alterations and loss of muscle fitness.

overall_design: Quadriceps muscle from four mice per genotype were used (Control young (6 month-old), Mfn2KO young (6-month-old), control old (22-month-old) and Mfn2KO old (22-month-old)

first: David

last: Sebastian


title: Combining bevacizumab and chemoradiation in rectal cancer. Translational results of the AXEBeam trial.

status: Public on Aug 02 2016

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: Objective: Insights about differences in tumor vasculature and how it reacts to VEGF inhibition is limited, but nevertheless of major relevance to anti-angiogenic therapy. In this study we therefore characterize the effect of bevacizumab combined with chemoradiotherapy (CRT), and explore molecular and genetic markers for response prediction to this combination treatment. Material and Methods: In an academic multicentric randomized phase II study, patients with advanced rectal cancer have been treated with bevacizumab (5mg/kg) in combination with capecitabine (1650mg/m2/day) and radiotherapy (45Gy; 1.8Gy/day) with (50mg/m2) or without oxaliplatin prior to surgery. Of 59 patients, tumor tissue and blood samples were collected before treatment and after the first loading dose of bevacizumab but before CRT (week 3). First, cDNA micro-arrays were performed on the biopsies to investigate differences in gene expression of tumors from patients with and without a pathological complete response (pCR) before start of treatment and to identify biological processes affected by bevacizumab delivery. The paraffin embedded tissue was stained for blood vessels (CD31/CD34) combined with α-SMA (pericytes) and CA-IX (hypoxia). To explore candidate blood-based biomarkers ELISA’s were performed for PDGF-AA, PDGF-BB, THBS-1, IL-8, CYR61 and Ang-2. The expression of all markers was correlated with the pathological response of the patients. Results: Differences in tumoral gene expression are observed between patients with and without a pCR, with the first response group presenting a more angiogenic phenotype before start of treatment and changes in angiogenic processes after bevacizumab delivery. One dose of bevacizumab leads to a decrease in the number of pericyte covered blood vessels, a decrease in circulating PDGF-AA, PDGF-BB and Thrombospondin-1. Patients showing a pCR having less pericyte covered blood vessels, more hypoxia, and less circulating PDGF-BB compared to patients who did not have a pCR after bevacizumab treatment with chemoradiation and bevacizumab. Conclusions: The translational data demonstrate that tumors with an angiogenic expression profile respond better to bevacizumab combined with CRT and points towards a possible role for PDGF, CA-IX and pericyte covered blood vessels for the early response prediction to this treatment. Our findings suggest a role for mural cell recruitment and vessel maturation for the susceptibility of the tumor vasculature to bevacizumab treatment. Further validation of our biological observations and hypothesis generating data in randomized trials is needed.

overall_design: This study involves samples of patients enrolled in the AXEbeam trail that were analysed by Primeview microarray (Affymetrix).  Biopsies were taken at two different timepoints: before treatment (tumor and normal mucosa) and after the first loading dose of bevacizumab but before chemoradiation (only tumor, week 3). Patients were classified into two groups: with a complete pathological response at time of surgery (Responders=R) or non-responders (NR). For the responders, we collected 21 samples in total (7 tumor samples and 8 normal mucosa samples taken before treatment and 6 tumor samples collected at week 3). From the non-responders we had 26 samples in total (9 tumor and 10 mucosa samples before treatment and 7 tumor samples at week 3 after a single dose of bevacizumab). Microarrays were run in two batches (15xxx versus 16xxx CEL file samples; indicated in the description field). Three samples (NJ 04/003 T1, RVS 09/002 M and NJ 04/003 W3) were put twice on the array (15897+16789; 15893+16790; 15898+16791) to verify and exclude batch effects.  Please note that, due to these three technical repeats the total number of microarray CEL files is 50 (21 Responders, 26 Non-responders and 3 repeats).

first: Maud

last: Verstraete

first: Jeroen

last: Dekervel

first: Annelies

last: Debucquoy

first: Eric

last: Van Cutsem

first: Karin

last: Haustermans

first: Jos

last: van Pelt


title: TLR9 re-expression in cancer cells extends the S-phase and stabilizes p16INK4a protein expression.

city: LYON

first: FLORENCE

last: LE CALVEZ-KELM

address: 150 Cours Albert Thomas

department: Genetics

institute: International Agency for Research on Cancer

summary: Using Illumina HumanHT-12 v4 Expression BeadChips, providing a genome-wide coverage of over 24,000 genes, we have analysed gene expression variation in HNSCC 136 cells transduced with pLVUT’ TLR9 or GFP where the same number of cells  were harvested and RNA extracted after 36 h treatment with doxycyline.

overall_design: Total RNA obtained HNSCC 136 cells transduced with pLVUT’ TLR9 or GFP as controls where the same number of cells  were harvested and RNA extracted after 36 h treatment with doxycyline.Diffrential expression analysis was conducted with GFP replicates as reference group.

first: Uzma

last: Hasan

first: Florence

last: Le Calvez-Kelm


title: Upregulation of HLA expression in primary Uveal Melanoma by infiltrating leukocytes

status: Public on Aug 07 2016

city: Leiden

first: Theodorus

middle: Huibertus

last: van Essen

address: Albinusdreef 2

country: Netherlands

institute: Leiden University Medical Center

summary: Uveal melanoma (UM) with an inflammatory phenotype, characterized by infiltrating leukocytes and increased human leukocyte antigen (HLA) expression, carry an increased risk of death due to metastases. These tumors shoud be ideal for T-cell based therapies, yet it is not clear why prognostically-infaust tumors have a high HLA expression. We set out to determine whether the level of HLA molecules in UM is associated with other genetic factors, HLA transcriptional regulators, or microenvironmental factors.   28 enucleated UM were used to study HLA class I and II expression, and several regulators of HLA by immunohistochemistry, PCR microarray, qPCR and chromosome SNP-array. Fresh tumor samples of eight primary UM and four metastases were compared to their corresponding xenograft in SCID mice, using a PCR microarray and SNP array.   Increased expression levels of HLA class I and II showed no dosage effect of chromosome 6p, but, as expected, were associated with monosomy of chromosome 3. Increased HLA class I and II protein levels were positively associated with their gene expression and with raised levels of the peptide-loading gene TAP1, and HLA transcriptional regulators IRF1, IRF8, CIITA, and NLRC5, revealing a higher transcriptional activity in prognostically-bad tumors. Implantation of fresh human tumor samples into SCID mice led to a loss of infiltrating leukocytes, and to a decreased expression of HLA class I and II genes , and their regulators.  Our data provides evidence for a proper functioning HLA regulatory system in UM, offering a target for T-cell based therapies.  NB: Here we show the PCR microarray (Illumina array).

overall_design: Total RNA was isolated from (malignant) uveal melanoma cells is from stored tissue of surgically removed specimen.

first: Sake


title: Functional tissue specific MSC in lung-transplanted patients with and without bronchiolitis obliterans syndrome (BOS) - a potential source for cell-therapy?

status: Public on Aug 01 2016

city: Lund

first: Sara

last: Rolandsson Enes

address: BMC, C12

department: EMV

institute: Lund University

summary:
Background: Mesenchymal stromal cells (MSC) have been proposed as a future cell based therapy for lung diseases like bronchiolitis obliterans syndrome (BOS). Theoretically, it might be beneficial to use lung resident MSC already adapted to the pulmonary environment. We therefore aimed to compare lung MSC with the well-characterized bone marrow MSC. Furthermore, MSC isolated from lung-transplanted patients with BOS were compared to MSC isolated from good outcome recipients.
Methods: MSC were isolated from bone marrow (BM) and adult/fetal lung tissues and compared by a comprehensive panel of assays.
Results:The gene expression profiles of adult lung derived and fetal lung derived MSC were very similar compared to BM derived MSC, with only 235 and 338 genes, respectively, being significantly differently expressed. Out of the 235 genes that were significantly different between adult lung derived and BM derived MSC, 90 genes were higher expressed in the lung derived MSC. In case of fetal lung derived MSC, 166 genes were higher expressed compared to the BM derived MSC. Interestingly, only, 89 genes were found to be expressed differently when comparing BM derived MSC to both, fetal and adult lung derived MSC, indicating that these genes are lung specific. Next, we went on to evaluate if MSC isolated from biopsies of lung-transplanted patients with BOS differed compared to patients without BOS, i.e. good outcome recipients. Here we found that four genes (Sox9, FAR2, LOC728855 and NDUFS5) were significantly higher expressed in MSC isolated from BOS patients
Conclusions: This data demonstrates that lung resident MSC possess lung specific properties that should be taken into considerations when using MSC for cell-based therapy in severe lung disorders like BOS. These results also show that MSC isolated from lung-transplanted patients with BOS do not have an altered phenotype.

overall_design: Comparison of gene expression of MSC isolated from bone marrow, adult lung and fetal lung.

first: Annika

last: Andersson Sjöland

first: Ingrid

last: Skog

first: Lennart

last: Hansson

first: Hillevi

last: Larsson

first: Katarina

last: Le Blanc

first: Leif

last: Eriksson

last: Bjermer

first: Stefan

last: Scheding

first: Gunilla

last: Westergren-Thorsson


title: Identification of cell signaling pathway associated miRNAs in cancer cells using a systems biological approach: potent RNAi response in cancer using novel 2’-OMe-phosphorodithioated modified siRNAs

city: Houston

first: Sangbae

last: Kim

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

summary: MicroRNAs (miRNAs) are single-stranded, non-coding RNA molecules and on average only 22 nucleotides long that regulate gene expression at the post-transcriptional level. Target predictions of miRNA based on sequence are limited due to too many candidates resulting in high false positives. We generated the Association score matrix and miRNA-pathway association map. To validate our approach, we used miR-500 as an example to investigate the hypothetical target regulation mechanisms. We confirmed in-vitro that mir-500 highly is associated with ERK signaling pathway in breast cancer cells. Furthermore, we found PPFIA1 might be one of direct targets of miR-500 to regulate activating the ERK pathway. In conclusion, we developed a model system to systematically predict potential miRNA functional targets which play critical roles in cell signaling pathways from the NCI-60 genomic and proteomic data at whole genomic scale.

overall_design: Two groups of samples  are included: 1. siControl treated control-miRNA  and 2. mimic miR-500 treated two cells: MCF7 and MDA-MB-231. Gene expression profiles of mimic miR-500 treated cells were compared to that of control treated cells.

first: Ju-Seog

last: Lee


title: Identification of differentially expressed genes in Fibrogenesis imperfecta ossium via Global microarray analysis

status: Public on Jul 31 2016

city: Postgraduate Institute of Medical Education & Research

first: sanjay

middle: kumar

last: bhadada

state: sec-12, chandigarh

address: room no: 2, 4th floor, Block:F,Nehru hospital

department: Endocrinology

country: India

institute: Postgraduate Institute of Medical Education and Research

summary:
Global microarray was performed from Trans-Iliac Bone biopsy from the patient with clinically characterized Fibrogensis imperfecta ossium (FIO).   A 40-year-old male patient with clinically characterized Fibrogensis imperfecta ossium (FIO) includes fragility fracture with osteomalacia (Losser’s zone).  On examination, his height was 158 cm, weight 47 kg, body mass index (BMI) 16.5, and his  blood pressure was 120/80 mmHg.  He had no palpable goiter, neck masses or lymphadenopathy.  He had no exostosis or bony deformity. He had difficulty in getting up from squatting position and needed a stick to help with walking.  The hip joint movements were painful and restricted..  The rest of the examination including abdomen was  other wise normal or non-contributory.  His laboratory evaluation was as follows: hemoglobin 13.2gm/dl, total WBC 7200/mm3 and erythrocyte sedimentation rate12 mm for 1st hour.  Mean ± SD (3 values) serum  calcium (Ca) adjusted for albumin was 9.5 ± 1.3 mg/dl (reference range: 8.5 - 11mg/dl).  Serum phosphate (PO4) was 3.5 ± 0.3 mg/dl (reference range 3.5-5.0 mg/dl), serum magnesium 1.6mg/dl (reference range 1.58-2.55 mg/dl), total alkaline phosphatase (AP) 39.6 ± 2.6 KA Units (reference range: 3 – 13 KA Units), serum creatinine (Cr) was 1.1 mg/dl.  Liver function tests were normal.  Twenty four hour mean urine Ca, and phosphorus was 65.3 and 563  mg/d, respectively. The renal tubular handling of phosphate was normal (TmP/GFR 4.2 mg/dl – normal 2.4-4.2).    The serum intact parathyroid hormone (iPTH) level by immunochemilunometry  was 19 pg/ml  (reference range: 10-69 pg/ml).Serum 25-hydroxyvitamin D level was 59.9( reference range 9 – 37 ng/ml). Serum 1,25-hydroxyvitamin D level was 76.6 ng/ml (reference range  – 3 ng/ml). Arterial blood gases and urine pH were within normal range.  Thyroid function tests were normal. Serum tissue transglutaminase antibody (tTG) titre was negative. Urine for Bence  Jones protein was negative and serum electrophoresis was normal.   Radiographs of the skull and hands were normal. The lumbar spine showed “rugger –jersey” spine with osteopenia . Views of the pelvis showed bilateral coxa vera and  bilateral femur neck fracture with “fishnet appearance”. The  chest radiograph showed multiple Looser zones with  fractures of several ribs.  The lower end of tibia showed “fishnet appearance”, tendon calcification and new bone formation. Ultrasonography of the neck did not reveal any abnormality in the thyroid or parathyroid glands. Ultrasonography of the abdomen and KUB region was normal. A 99mTc sestamibi scan was normal.  Bone mineral density (BMD) of the hip with a T-score of -2.2 SD.  Magnetic resonance imaging of pelvis showed fracture of bilateral neck and hypointense marrow on T1W and T2W sequences . A 99mTc MDP bone scan showed increased radiotracer uptake bilaterally in the shoulders, elbows, wrists, small joints of hands, multiple sites at bilateral ribs, the entire vertebral column, and lower end of tibia but not the skull (beheaed scan).   Transiliac bone biopsy showed thickened bony trabeculae with obliteration of marrow spaces and at places, focal areas of exaggerated osteoclastic activity. There was prominent osteoblastic proliferation as well as osteoid like areas were also seen. At places it showed sclerosis, eaten up edges of bone and foci of new calcification (bone formation). With the above mentioned clinical and investigation proile a diagnosis of FIO was considered most likely
FIO may easily be misdiagnosed because of its superficial similarity to axial osteomalacia  osteoporosis, and other metabolic bone disorders with pathological fractures. Bone pain or pathological fractures in a previously healthy adult should lead to radiological and biochemical investigation. Generalized increase in radiological bone density may indicate myelofibrosis or fluorosis but an increased level of alkaline phosphatase favours Paget’s disease or osteomalacia. Bone biopsy suggests gross  osteomalacia until the nostic process  is rarely logical, but it would not be so delayed if bone sections were always examined under polarized light.  There are many unsolved problems in this crippling condition. Apart from complete ignorance of the cause, yet it is not known, what is replacing the mature collagen of bone, why other collagen-containing tissues are apparently unaffected. Why patients commonly have circulating paraprotein and whether there is any effective treatment. Till date, there is no literature has been reported exploring the genes involved in the pathogenesis of FIO. Hence, aim of present study is identification of various genes involved in the regulation of various signaling pathways involved in pathogenesis of FIO.

overall_design: Total RNA was isolated from Trans-Iliac Bone biopsy (Control Individual (n=1) & Patient (n=1)) using TRIZOL method and global microarray was performed on Affymetrix Genechip HumanPrimview platform. The array was performed on duplicate.

first: Sanjay

last: Bhadada

first: Vandana

last: Dhiman

first: Akhilesh

last: Kumar

first: K

last: Rajagopal

first: Ashutosh

last: Arya

first: Sameer

last: Aggarwal

first: DC

last: Sharma

first: Yashpal

last: Gogate

first: Anil

last: Bhansali

first: DS

last: Rao


title: Gene expression data from peripheral blood leukocytes of Amish and Hutterite schoolchildren

status: Public on Aug 05 2016

first: Carole

last: Ober

state: Illinois

address: 920 E 58th St

department: Human Genetics

institute: University of Chicago

summary: The Amish and Hutterites are U.S. farming populations with remarkably similar lifestyles. However, the Amish follow traditional farming practices, while the Hutterites employ modern farming techniques, and also show striking differences in asthma prevalence. Little is known about immune responses underlying these differences. To address this, we obtained genome-wide gene expression data in peripheral blood leukocytes from Amish and Hutterite schoolchildren.

overall_design: The study includes data from whole blood samples from age- and sex-matched Amish and Hutterite schoolchildren.  Written consent was obtained from the parents and written assent was obtained from the children. One mL of whole blood was drawn into a TruCulture tube containing media alone, and incubated upright on a dry heat block at 37°C for 30 hours. Cells were isolated and total RNA was extracted using Qiagen AllPrep DNA/RNA Mini Kits. RNA concentration was assayed with a Nanodrop ND-100 Sepectrophotometer; RNA quality was assessed with an Agilent 2100 Bioanalyzer. Samples underwent cDNA synthesis and were then hybridized on the Illumina HumanHT-12 v4 Expression BeadChip arrays at the Functional Genomics Core at the University of Chicago.

first: Michelle

last: Stein


title: Transcriptomics response to miR-644 overexpression in three breast cancer cell lines

status: Public on Jul 25 2016

city: Basel

first: Jitao David

last: Zhang

address: Grenzacherstrasse 124

department: Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel

country: Switzerland

institute: F. Hoffmann-La Roche

summary: The goal of the study is to investigate the effect of microRNA-644 overexpression by chemical mimics on gene expression in breast cancer cell lines. To this purpose control and microRNA-644 mimics are used to transfect MDA-MB-231 cells, SK-BR-3 cells, and MCF-7 cells respectively. Transcriptomics profiling was performed with Illumina HumanHT-12 V4.0 BeadChip microarray.

overall_design: Three cell lines are treated with scramble microRNA mimic (control herein) and microRNA-644 mimic (miR-644 herein), with two replicates per condition. mRNA expression is compared between miR-644 and control treatment within each cell line, respectively.

first: Stefan

last: Uhlmann

first: Jitao

first: Özgür

last: Sahin


title: Epidermal Growth Factor Receptor inhibition triggers Type 1 Interferon signature in human keratinocytes

city: Rome

first: Saveria

last: Pastore

address: via Monti di Creta 104

country: Italy

institute: Istituto Dermopatico dell'Immacolata, IRCCS

summary: The Epidermal Growth Factor Receptor (EGFR)/ligand system is centrally involved in multiple homeostatic functions of the epithelia. Epithelial cells are the primary targets of humanized antibodies and small molecule inhibitors against this system, whereby the constellation of skin-specific side effects of these drugs stems from a profound disturbance of keratinocyte biology. So far, the molecular mechanisms underlying these toxic events have been investigated only broadly. Here we show that keratinocyte response to anti-EGFR drugs comprises the development of a type 1 interferon (IFN) molecular signature including enhanced expression of IFN-kappa. Mechanistically, nuclear accumulation of IRF1 precedes this signature as well as the enhanced expression of a chemokine cluster we previously identified as a relevant pro-inflammatory component of EGFR inhibition. In fact, either silencing of IRF1 transcript expression, or antibody-mediated blockade of type 1 IFN receptor function and consequent abrogation of STAT1 activation, leads to impairment of this gene transcription profile. High levels of IRF1 and IFN-kappa can be clearly observed in the early skin lesions of patients treated with cetuximab. Type 1 IFN signaling could be crucially implicated in the triggering of the inflammatory mechanisms active in the skin of patients under treatment with anti-EGFR drugs.

overall_design: Normal human keratinocyte cultures were treated with Tumor Necrosis Factor (TNF) alpha (50 ng/ml) alone (SAMPLES #4-6), or with  the concomitant administration of the small-molecule EGFR inhibitor PD168393 (2 microM) (SAMPLES #7-9) for 6 hours. Cultures were performed in triplicate and include untreated controls (SAMPLES #1-3).

first: Daniela

last: Lulli

first: Maria

middle: L

last: Carbone

first: Andrea

last: Cavani


title: Heterogeneous niche activity of ex-vivo cultured MSCs as a parameter for outcomes in MSC-based cell therapy for hematopoietic recovery

city: Daejeon

first: Bic-Na

last: Song

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea

department: Korean Bioinformation Center

institute: Korea Research Institutue of Bioscience & Biotechnology

summary: Ex-vivo expanded mesenchymal stromal cells (MSCs) are increasingly used for paracrine support of hematopoietic stem cell (HSC) regeneration, but inconsistent outcomes have been the huddle for on-going clinical trials. Here, we hypothesized that the heterogeneity in the niche activity of manufactured MSCs can be a parameter for variable outcomes in MSC-based cell therapy. We first screened MSC culture medium and found that serum batches caused larger variations in colony forming unit-fibroblast (CFU-F) content of MSCs than individual donor variations. The culture conditions supporting high (stimulatory) and low (non-stimulatory) CFU-F caused distinct niche activity of MSCs; MSCs under stimulatory condition exhibited higher level expression of cross-talk molecules (Jagged-1 and CXCL-12) and higher support for HSCS during long-term culture than MSCs under non-stimulatory culture.  Moreover, the effects of MSCs enhancing hematopoietic engraftment were only visible when HSCs were co-transplanted with MSCs expanded under stimulatory, but not non-stimulatory conditions. However, these differences of MSCs were readily reversed by switching the culture mediums, indicating their distinct functional state, rather than clonal heterogeneity. Accordingly, transcriptomic analysis showed distinct gene set enrichment between the different MSCs and revealed distinct upstream signaling pathways such as inhibition of P53 and activation of ATF4 for MSCs under stimulatory conditions. Taken together, our study shows that the heterogeneity in the niche activity of MSCs can be created during ex-vivo expansion to cause a difference in the hematopoietic engraftment and raise the possibility that MSCs can be pre-screened for more predictable outcomes in clinical trials of MSCs.

overall_design: Total RNA obtained from isolated human mesenchymal stromal cells. To compare stimulatory (SS) serum and non-stimulatory (NSS) serums, MSCs had been maintained in each serum media were sub-cultured for at least two passages before analysis.

first: Il-Hoan

last: Oh


title: Different responses of Caco-2 and MCF-7 cells to silver nanoparticles are based on highly similar mechanisms of action

status: Public on Jul 30 2016

city: Wageningen

first: Meike

last: van der Zande

address: Akkermaalsbos 2

institute: Wageningen University & Research

summary: The mode of action of silver nanoparticles (AgNPs) is suggested to be exerted through both Ag+ and AgNP dependent mechanisms. Ingestion is one of the major NP exposure routes, and potential effects are often studied using Caco-2 cells, a well-established model for the gut epithelium. MCF-7 cells are epithelial breast cancer cells with extensive well-characterized toxicogenomics profiles. In the present study we aimed to gain a deeper understanding of the cellular molecular responses in Caco-2 and MCF-7 cells after AgNP exposure in order to evaluate whether epithelial cells derived from different tissues demonstrated similar responses. These insights could possibly reduce the size of cell panels for NP hazard identification screening purposes. AgNPs of 20, 30, 60, and 110 nm, and AgNO3 were exposed for 6h and 24h. AgNPs were shown to be taken up and dissolve intracellularly. Compared with MCF-7 cells, Caco-2 cells showed a higher sensitivity to AgNPs, slower gene expression kinetics, and absence of NP size-dependent responses. However, on a molecular level, no significant differences were observed between the two cell types. Transcriptomic analysis showed that Ag(NP) exposure caused (oxidative) stress responses, possibly leading to cell death in both cell lines. There was no indication for effects specifically induced by AgNPs. Responses to AgNPs appeared to be induced by silver ions released from the AgNPs. In conclusion, differences in mRNA responses to AgNPs between Caco-2 and MCF-7 cells were mainly related to timing and magnitude, but not to a different underlying mechanism.

overall_design:
In total 73 samples are analyzed (24 different samples all n=3; except for 1 sample with n=4).
Twelve of the 24 different samples are extracted from Caco-2 cells, 6 samples at t=6h and 6 at t=24h
The other 12 different of the 24 samples are extracted from MCF-7 cells, 6 samples at t=6h and 6 at t=24h
For each cell type and each timepoint one of the 6 samples was a negative control sample

first: Anna

middle: K

last: Undas

first: Evelien

last: Kramer

first: Marco

last: Monopoli

first: Ruud

middle: J

last: Peters

first: David

last: Garry

first: Elsa

last: Antunes Fernandes

first: Peter

last: Hendriksen

first: Hans

last: Marvin

first: Ad

last: Peijnenburg

last: Bouwmeester


title: Extraneous Genes of Mentally Retarded Subject in Terms of Microarray a gene expression profiling technology

status: Public on Jul 22 2016

city: Chennai

first: Thulasi

middle: bai

last: K

state: Tamilnadu

address: 39 Vellalar Street,

department: Bioinformatics

institute: Loyola College

summary: Searching for new genes involved in Mental Retardation. This research has also leaded to the identification of set of extraeneous up and down regulated genes of mentally retarded male and female subjects by comparing with normal reference.

overall_design: Total RNA was extracted using NucleoSpin® RNA Blood Midi kit, Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit, 750 ng of labeled cRNA samples were hybridized to each Human HT12 expression v.4 bead array for 16-18 h at 58°C, Arrays were scanned with an Illumina bead array Reader confocal scanner, All data analysis and visualization of differentially expressed genes was conducted using R 2.15.0.

first: K

last: Thulasibai

first: D

last: Sudarsanam

first: V

last: Ganesan


title: Transcriptional profiling of HT-29 cells stimulated with pairwise combinations of TNF, EGF, and insulin

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

institute: University of Virginia

summary:
The objective of this study was to investigate the link between signaling-network activation and transcriptional regulation downstream of tumor necrosis factor (TNF), epidermal growth factor (EGF), and insulin.
Microarrays were used to capture the transcriptional responses to TNF, EGF, and insulin at intermediate-to-late times after stimulation.

overall_design: Nine combinations of TNF, EGF, and insulin were evaluated at three time points after stimulation in biological duplicate.

first: Zeinab

last: Chitforoushzadeh

first: Rebecca

last: Fry


title: Conversion of Human Gastric Epithelial Cells to Multipotent Endodermal Progenitors using Defined Small Molecules [array]

status: Public on Jul 24 2016

city: Beijing

first: Jinhua

last: Qin

address: Taiping Road

institute: Beijing Institute of Transfusion

summary: Endodermal stem/progenitor cells have diverse potential applications in research and regenerative medicine, so a readily available source could have widespread uses. Here we describe derivation of human induced endodermal progenitor cells (hiEndoPCs) from gastrointestinal epithelial cells using a cocktail of defined small molecules along with support from tissue-specific mesenchymal feeders. The hiEndoPCs show clonal expansion in culture and give rise to hepatocytes, pancreatic endocrine cells, and intestinal epithelial cells when treated with defined soluble molecules directing differentiation. The hiEndoPC-derived hepatocytes are able to rescue liver failure in Fah-/-Rag2-/- mice after transplantation, and, unlike hESCs, transplanted hiEndoPCs do not give rise to teratomas. Since human gastric epithelial cells are readily available from donors of many ages, this conversion strategy can generate clonally expandable cell populations with a variety of potential applications, including personalized drug screening and therapeutic strategies for liver failure and diabetes.

overall_design: Human gastric epithelial cells (hGECs) and gastric subepithelial myofibroblasts (GSEMFs) are isolated from human stomach, and human duodenum epithelial cells (hDECs) are isolated from human duodenum. Human induced endodermal progenitor cells (hiEndoPCs) were reprogrammed from hGECs/hDECs by small molecules with the support of GSEMFs. Definitive endoderm cells (DEs) are derived from human embryonic stem cells by differentiation. Totally, 13 samples including two samples of hDECs, one sample of hGECs, two clones of D-hiEndoPCs, one clone of G-hiEndoPCs, four samples of DEs and three samples of GSEMFs were analyzed using microarray.

first: Shuyong

last: Wang

first: Wencheng

last: Zhang

first: Yunfang


title: Network analysis identifies proinflammatory plasma cell polarization for secretion of ISG15 in human autoimmunity

city: York

first: Matthew

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

department: Department of Biology

institute: The University of York

summary: Plasma cells (PCs) as effectors of humoral immunity produce immunoglobulins to match pathogenic insult. However, emerging data suggests more diverse roles for PCs as regulators of immune and inflammatory responses via secretion of factors other than immunoglobulins. The extent to which such responses are pre-programmed in B-lineage cells or can be induced in PCs by the microenvironment is unknown. Here we dissect the impact of IFNs on the regulatory networks of human plasma cells. We show that core PC programs are unaffected, while PCs respond to IFNs with distinctive transcriptional responses. The ISG15-system emerges as a major transcriptional output induced in a sustained fashion by IFN-α in PCs and linked both to intracellular conjugation and ISG15 secretion. This leads to the identification of ISG15-secreting plasmablasts/PCs in patients with active SLE. Thus ISG15-secreting PCs represent a distinct pro-inflammatory PC subset providing an immunoglobulin-independent mechanism of PC action in human autoimmunity

overall_design: B-cells were isolated from the peripheral blood of three adult donors and differentiated in vitro (see individual samples for culture conditions)

first: Nicholas

last: Barnes


title: GE expression profile of PBMCs in healthy subjects and MS patients after extra virgin olive oil (EVOO) intake - PART 3 - MS Patients

status: Public on Jul 19 2016

city: Bari

first: Antonio

last: Moschetta

address: Via Orazio Flacco, 65

institute: IRCCS Ospedale Oncologico di Bari

summary: Gene expression profiles of PBMCs in patients with MS following extra virgin olive oil intake. The aim of the present study was to investigate the whole-genome gene and miRNA profiles of after EVOO intake. Results provide the information of changes in PBMCs transcriptome following EVOO intake.

overall_design: RNA obtained from PBMCs of the same patients before and after extra virgin olive oil intake (paired samples). Comparisons: T0 vs. T1 (paired samples)

first: Simona

last: D'Amore

first: Andria

last: D'Orazio

first: Giusi

last: Graziano

first: Michele

last: Vacca


title: Genome-wide analysis of PIAS1 on AR gene expression in MDA-MB453

status: Public on Jul 18 2016

city: Kuopio

first: Sari

last: Toropainen

address: Yliopistonranta 1 E

department: School of Medicine

country: Finland

institute: University of Eastern Finland

summary: The majority of breast cancer subtypes express androgen receptor (AR) in addition to estrogen receptor α (ERα). Depending on the breast cancer subtype androgen signaling has either stimulatory or inhibitory roles in breast cancer cell growth. We have mapped AR cistrome in ERα negative human molecular apocrine breast cancer MDA-MB453 cells and analyzed it in relation to the androgen-regulated transcriptome in the same cells. We have also examined the effect of silencing of the coregulator SUMO ligase PIAS1 on the androgen-regulated transcriptome and AR cistrome in MDA-MB453 cells. Our results show that the MDA-MB453 cells share with VCaP prostate cancer cells a core AR cistrome and target gene signature linked to cancer cell growth and that PIAS1 acts as an AR target gene-selective coregulator in MDA-MB453 cells.

overall_design: MDA-MB453 cells were transfected with control siRNA (siNON) or PIAS1 siRNA (siPIAS1) for 72 h and treated 16 h with 10 nM R1881 or vehicle (ethanol). Total RNA was isolated and biological triplicate samples were analyzed by microarray.

first: Marjo

last: Malinen

first: Tiina

last: Jääskeläinen

first: Biswajyoti

last: Sahu

first: Olli

last: Jänne

first: Jorma

last: Palvimo


title: Serum Conditions Do Not Abolish The Tumorigenicity of Glioma Stem Cells

status: Public on Jul 21 2016

city: Oslo

first: Biljana

last: Stangeland

address: Sognsvannsveien 20

department: Institute of Surgical Research

country: Norway

institute: Oslo University Hospital

summary: The subset of GBM patient samples gives rise to adherent cultures even in sphere culture conditions. Most samples in this subset are tumorigenic and exhibit a hybrid expression profile when tested with the marker panel. Cultures from these samples have a predominantly mesenchymal character based on substrate adherence, morphology, differentiation potential and gene expression.

overall_design: Total RNA isolated from glioblastoma stem cells (GSC) cultured as spheres was compared to that from adherent GSCs cultured in sphere culture conditions that exhibited both GSC and mesenchymal properties.


title: Comparison of CLL and MCL primary cells obtained from a patient with MCL variant Richter syndrome

status: Public on Jul 13 2016

city: Prague 2

first: Vojtěch

last: Kulvait

address: U Nemocnice 5

department: Institute of Pathological Physiology

country: Czech Republic

institute: Charles University in Prague - 1st Faculty of Medicine

overall_design:
CLL and MCL samples are labeled CLL and MCL, respectively.
This dataset contains 2 Illumina array spots with a samples of interest from the 12 spot array.

first: Pavel

last: Klener


title: Global gene expression analysis between cetuximab-sensitive and cetuximab-resistant colorectal cancer cells

status: Public on Jul 17 2016

first: Zhen

last: Fan

address: 1515 Holcombe Blvd.

department: Experimental Therapeutics

institute: UT MD Anderson Cancer Center

summary:
Cetuximab is an epidermal growth factor receptor (EGFR)-blocking antibody approved for treatment of metastatic colorectal cancer. We examined differences in global gene expression between the syngeneic DiFi colorectal cancer cells, and a subline of DiFi cells with acquired resistance to cetuximab (DiFi5).
We used Affymetrix HG-U133A array to compare the expression pattern of genes that are up-regulated or down-regulated between the parental DiFi colorectal cancer cells and the cetuximab-resistant DiFi5 cells.

overall_design: We generated a cetuximab-resistant DiFi subline, termed DiFi5, by chronic exposure of parental DiFi cells to serially increased doses of cetuximab (from 0.5 nM to 5 nM) for over 1 year. The resulting DiFi5 subline exhibits significant resistance to cetuximab-induced apoptosis. After we confirmed that the phenotype was stable over a period of time of more than 6 months, the RNA from DiFi and DiFi5 cells were extracted and hybridized to an Affymetrix HG-U133A array according to the manufacturer’s instructions. Following the hybridization, the array was scanned using a laser confocal scanner, and microarray image data were analyzed using DNA-Chip Analyzer (dChip), version 1.3, by the Sequencing and Microarray Facility at MD Anderson Cancer Center.

first: Yang

last: Lu


title: Gene expression profile of PBMCs in healthy subjects and MS Patients after extra virgin olive oil (EVOO) intake - Part 1 (Controls)

summary: Gene expression profiles of PBMCs in healthy subjects following extra virgin olive oil intake. The aim of the present study was to investigate the whole-genome gene and miRNA profiles of after EVOO intake. Results provide the information of changes in PBMPs transcriptome following EVOO intake.

overall_design: RNA obtained from PBMCs of the same subjects before and after extra virgin olive oil intake (paired samples). Comparisons: T0 vs. T1 (paired samples) - Controls


status: Public on Jul 12 2016

city: London

first: Ai

last: Nagano

state: --- Select a state ---

address: John Vane Science Centre, Charterhouse Square

department: Centre for Molecular Oncology

country: United Kingdom

institute: Barts Cancer Institute

overall_design:
Identifying the differentially expressed genes between ADI-PEG20 resistant and parental Ju77 cell line
2x10 ^ 5 cells were plated in a 6-well plate and RNA extracted the following day using the RNeasy kit (Qiagen).

first: Sarah-Anne

last: Martin

first: Matthew

last: Locke


title: Transcriptional profiling of inducible GATA6L-overexpressing HT-29 cells stimulated with TNF

first: Kevin

last: Janes

country: USA

summary:
The objective of this study was to investigate the role of GATA6L with or without TNF stimulation.
Microarrays were used to capture the transcriptional response to GATA6L overpexression at intermediate times after TNF stimulation.

overall_design: Cells were induced for GATA6L overexpression and evaluated at two hours after stimulation with saturating TNF in biological triplicate.

first: Zeinab

last: Chitforoushzadeh


title: Effects of lactoferrin, sophorolipids and lactoferrin-sophorolipids-assembly on gene expression of human dermal fibroblasts (HDFn)

status: Public on Jul 08 2016

city: Davis

first: Rulan

last: Jiang

state: CA

address: One Shields Ave.

institute: University of California, Davis

summary: The aim of this study is investigate effects of lactoferrin on human dermal fibroblasts and if sophorolipids influence effects of lactoferrin on human dermal fibroblasts.

overall_design: Human dermal fibroblasts (HDFn) were treated with lactoferrin, sophorolipids or lactoferrin-sophorolipids-assebly for 24 hours. Total RNA was isolated for microarray assays.

first: Yasushi

last: Suzuki

first: Xiaogu

last: Du

first: Bo

last: Lönnerdal


title: Analysis of global gene expression profiles of A549 cells treated with TOP1 siRNA under basal conditions

status: Public on Jul 11 2016

city: New York

first: Ivan

last: Marazzi

address: 1468 Madison Avenue

department: Department of Microbiology

institute: Icahn School of Medicine at Mount Sinai

summary: Untransfected (no siRNA), control siRNA or TOP1 siRNA treated A549 cells were analyzed for gene expression differences under basal conditions

overall_design: 3 Biological Replicates per condition

middle: S

last: Miller

first: Alexander

last: Rialdi

first: Jessica

last: Ho

first: Luis

last: Martinez-Gil

first: Natasha

last: Moshkina

first: Micah

last: Tilove

first: Ana

last: Maestre

first: Olivier

last: Bequerel

first: Alicia

middle: R

last: Feagins

first: Christopher

last: Basler

last: Fernandez-Sesma

first: Martin

last: Lavin

first: Harm

last: van Bakel


title: Transcriptomic analysis reveals abnormal repair and remodeling in survivors of critical illness with sustained muscle weakness

city: Toronto

first: Claudia

last: dos Santos

state: Ontario

address: 30 Bond St.

department: Intensive Care

institute: St. Michael's Hospital

summary: ICU acquired weakness (ICUAW) is a complication of critical illness characterized by structural and functional impairment of skeletal muscle that may persist for years after ICU discharge with many survivors developing  protracted courses with few regaining functional independence. Elucidating molecular mechanisms underscoring sustained ICUAW is crucial to understanding outcomes linked to different morbidity trajectories as well as for the development of novel therapies.  Quadriceps muscle biopsies and functional measures of muscle strength and mass were obtained at 7 days and 6 months post-ICU discharge from a cohort of ICUAW patients. Unsupervised co-expression network analysis of transcriptomic profiles identified discrete modules of co-expressed genes associated with the degree of muscle weakness and atrophy in early and sustained ICUAW. Modules were enriched for genes involved in skeletal muscle regeneration and extracellular matrix deposition. Collagen deposition in persistent ICUAW was confirmed by histochemical stain. Modules were further validated in an independent cohort of critically ill patients with sepsis-induced multi-organ failure and a porcine model of ICUAW, demonstrating disease-associated conservation across species and peripheral muscle type. Our findings provide a pathomolecular basis for sustained ICUAW, implicating aberrant expression of distinct skeletal muscle structural and regenerative genes in early and persistent ICUAW.

overall_design: Total RNA was extracted from approximately 200mg of quadriceps muscle (vastus lateralis) tissue in patients with Intensive care unit (ICU) acquired weakness (ICUAW) at day 7 post-ICU discharge (D7) and month 6 post-ICU discharge (M6), and from healthy controls (C)

last: Walsh

first: Jane

last: Batt

first: Margaret

last: Herridge

first: Sunita

last: Mathur

first: Gary

middle: D

last: Bader

first: Pingzhao

last: Hu


title: Analysis of global gene expression profiles of A549 cells treated with TOP1 siRNA upon Influenza A/PR/8/34(ΔNS1) Infection

first: Ivan

last: Marazzi

summary: Untransfected (no siRNA), control siRNA or TOP1 siRNA treated A549 cells were infected with A/Puerto Rico/8/1934(ΔNS1) for 12 hours

first: Matthew

last: Miller

first: Alexander

last: Rialdi

last: Ho

last: Martinez

first: Zuleyma

last: Peralta

first: Justine

last: Noel

first: Camilla

last: Melegari

middle: M

first: Panagiotis

last: Mitsopoulos

first: Joaquín

last: Madrenas

first: Sven

last: Heinz

first: Chris

last: Benner

first: John

last: Young


title: hESC vs NSC transcriptome comparison

city: San Diego

first: Laurence

middle: M.

last: Brill

address: 10420 Wateridge Circle

institute: Intertek Pharmaceutical Services

summary: Pluripotent human embryonic stem cells were compared with essentially pure multipotent neural stem cell derivatives.

overall_design: Gene expression profiles were compared between replicates of human embryonic stem cells and derived human neural stem cells

first: Andrew

last: Crain

first: Gustavo

last: Guiterrez

first: Ilyas

last: Singec


title: Whole blood transcriptional analysis of vaccine combination administration in infants

status: Public on Jul 20 2016

city: Edinburgh

first: Paul

last: Dickinson

address: 49 Little France Crescent

department: Division of Infection and Pathway Medicine

institute: University of Edinburgh

summary: We aimed to identify the gene network and pathway biology associated with response to vaccine administration by determining genome-wide alterations in host RNA in children

overall_design:
Samples were obtained from children before and after vaccine administration.
RNA was extracted from whole blood samples with PAXgene blood RNA reagent, followed by clean-up and DNase I treatment with QIAGEN PAXgene blood RNA kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

first: Peter

last: Ghazal


title: Expression data from HCT116 wild-type and RAP1-knockdown cells

city: Chicago

first: Yongyong

last: Yang

address: 303 E Superior ST

department: Department of Urology

institute: Northwestern University

summary:
knockdown of RAP1 decreased colorectal cancer cell migration by downregulation of Vimentin
We used microarrays to detail the global programme of gene expression underlying HCT116 wild-type and RAP1-knockdown cells and identified disparate classes of regulated genes during this process.

overall_design: HCT116 cells were selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain a disticnt impact of RAP1 on colorectal cancer cells. To that end, we selected HCT116 cells, which were infected with lentivirus sh-negative-control and lentivirus sh-RAP1-4#, separately.


title: Study of differentiation of human adipocytes using SBGS cells in vitro.

city: Rovereto

first: Mario

last: Lauria

state: TN

address: Piazza Manifattura 1

institute: COSBI

summary: This data set consists of a time series of transcriptional profiles of differentiating human adipocytes in vitro.

overall_design: In this study the adipogenesis process of human SBGS pre-adipocyte cells in vitro was monitored by obtaining gene expression profiles at beginning of experiment and at different time points after induction of differentiation. The resulting transcriptomic data set includes six time points (0, 6, 48, 96, 192, 384 hours), with three to nine replicates per time point, for a total of 26 profiles. The platfom used for the profiling was Illumina Human HT-12 v4 Expression BeadChip (Ilumina, Inc., San Diego, CA).

first: Isar

last: Nassiri

first: Rosario

last: Lombardo

first: Melissa

last: Morine

first: Petros

last: Moyseos

first: Vijayalakshmi

last: Varma

first: Greg

middle: T

last: Nolen

first: Bridgett

last: Knox

first: Daniel

last: Sloper

first: Jim

last: Kaput

first: Corrado

last: Priami


title: Gene Expression Network Analyses in Response to Air Pollution Exposures in the Trucking Industry

city: New Haven

first: Jen-hwa

last: Chu

state: CT

department: Pulmonary, Critical Care and Sleep Medicine

institute: Yale University School of Medicine

summary: To investigate the cellular responses induced by air pollution exposures, we performed genome-wide gene expression microarray analysis using whole blood RNA sampled at three time-points across the work weeks of 63 non-smoking employees in the trucking industry. Our objective was to identify the genes and gene networks differentially activated in response to micro-environmental measures of occupational exposure to three pollutants: PM2.5 (particulate matter ≤ 2.5 microns in diameter) and elemental carbon (EC) and organic carbon (OC).

overall_design: Subjects were recruited from 10 trucking terminals in the northeastern US. The participants included workers whose job duties were characterized by different patterns of exposure: pick-up and delivery (P&D) drivers, dock workers, and office workers. Whole blood samples were collected using PaxGene RNA tubes, three times from each subject: (1) before the first shift of the workweek (first day, AM draw); (2) at the end of the first shift (8-12 hours later) on the same day (first day, PM draw); and (3) at the end of the last work shift of the same workweek (last day, PM draw). Micro-environmental samples of PM2.5, and EC and OC in PM1.0 were collected over the full workweek (24 hours/day for 6-9 days) at each of the 10 terminals. The final data set included 165 samples from 63 subjects.

first: J

middle: E

last: Hart

first: D

last: Chhabra

first: E

last: Garshick

first: B

last: Raby

first: F

last: Laden


title: A novel histone variant H2A.J accumulates in senescent human cell with persistent DNA damage and promote inflammatory gene expression

status: Public on Jul 04 2016

city: Evry Cedex

first: Robert

last: Olaso

address: 2 rue Gaston Cremieux

department: CNRGH

institute: CEA-DRF

summary: The senescence of mammalian cells is characterized by a proliferative arrest in response to stress and the expression of an inflammatory phenotype. We discovered that H2A.J, a poorly studied H2A variant found only in mammals, accumulates in human fibroblasts in senescence with persistent DNA damage. Knock-down of H2A.J interfered with the derepression of a set of inflammatory genes that contribute to the senescent-associated secretory phenotype (SASP), and over-expression of H2A.J increased the expression of some of these genes in proliferating cells. H2A.J accumulation may thus promote the signaling of senescent cells to the immune system.

overall_design: 41 samples analysed

first: Jean-Francois

last: Deleuze

first: Carl

last: Mann


title: Functional Connection with Cardiac Tissues Confers Maturation Phenotypes in hPSC-Derived PHOX2B::GFP Expressing Sympathetic Neurons

status: Public on Jul 01 2016

city: Baltimore

first: Gabsang

last: Lee

state: MD

address: 733 North Broadway

institute: The Johns Hopkins University

summary: Neurons derived from human pluripotent stem cells (hPSCs) are a remarkable tool for modeling human neural development and diseases. However, it remains largely unknown whether the hPSC-derived neurons can be functionally coupled with their target tissues in vitro, which is essential for understanding inter-cellular physiology and further translational studies. Here, we demonstrate that hPSC-derived sympathetic neurons can be obtained from hPSCs and that the resulting neurons form physical and functional connections with cardiac muscle cells. By use of multiple hPSC reporter lines, we recapitulated human autonomic neuron development in vitro, and successfully isolated PHOX2B::eGFP+ neurons exhibiting sympathetic marker expression, electrophysiological properties, and norepinephrine secretion. With pharmacological and optogenetic manipulations, the PHOX2B::eGFP+ neurons controlled the beating rates of cardiomyocytes, and their physical interaction led to neuronal maturation. Our study lays a foundation for the specification of human sympathetic neurons and for the hPSC-based neuronal control of end organs in a dish.

overall_design: Using the four genetic reporter systems (OCT4::eGFP, SOX10::eGFP, ASCL1::eGFP, and PHOX2B::eGFP reporter hESC lines), we were able to purify discrete cell populations at four differentiation stages, recapitulating the sympathoadrenal differentiation process in vitro with purified and defined populations in four specific differentiation stages. We performed transcriptome analysis of OCT4::eGFP+ cells (3 biological replicates, representing undifferentiated hESCs), SOX10::eGFP+ cells (3 biological replicates, multi-potent neural crest), ASCL1::eGFP+ cells (3 biological replicates, putative sympathoadrenal progenitors), and PHOX2B::eGFP+ cells (2 biological replicates, putative sympathetic neuronal precursors).

first: Yohan

last: Oh


title: Genome-wide analysis of gefitinib short-term resistance gene expression in the NSCLC cell line PC9 in co-culture

city: Heidelberg

first: Sajo

last: Kaduthanam

state: BW

address: Im Neuenheimer Feld 460

department: Molecular Genetics

institute: DKFZ

summary: Analysis of gefitinib short-term resistance at gene expression level. The hyposthesis tested in the present study was that short-term resistance towards gefitinib in NSCLC cells influences pathways that associates with resistance towards EGFR-TKI treatment. Results provide important information of the response of EGFR mutant NSCLC cells to gefitinib and also to resistance towards gefitinib resistance, up-or down-regulated specific resistance pathways and cellular functions.

overall_design: Total RNA obtained from PC9 cell line (n=3), co-cultured PC9 (with MRC-5 cells)(n=3), gefitinib treated (0.5µM) PC9 (n=3), and co-cultured (MRC-5) + gefitinib treated PC9 cells (n=3) for 48h after gefitinib treatment


title: Pandemic H1N1 Influenza A Directly Induces a Robust and Acute Inflammatory Gene Signature in Primary Human Bronchial Epithelial Cells Downstream of Membrane Fusion

first: Longsi

last: Ran

state: ON

address: 101 College Street

department: Division of Experimental Therapeutics

institute: Toronto General Research Institute

summary: Pandemic H1N1 influenza A (H1N1pdm) elicits stronger pulmonary inflammation than previously circulating seasonal H1N1 influenza A (sH1N1), yet mechanisms of inflammatory activation in respiratory epithelial cells during H1N1pdm infection are unclear.  We investigated host responses to H1N1pdm / sH1N1 infection and virus entry mechanisms in primary human bronchial epithelial cells in vitro.  H1N1pdm infection rapidly initiated a robust inflammatory gene signature (3 h post-infection) not elicited by sH1N1 infection.  Protein secretion inhibition had no effect on gene induction.  Infection with membrane fusion deficient H1N1pdm failed to induce robust inflammatory gene expression which was rescued with restoration of fusion ability, suggesting H1N1pdm directly triggered the inflammatory signature downstream of membrane fusion.  Investigation of intra-virion components revealed H1N1pdm viral RNA (vRNA) triggered a stronger inflammatory phenotype than sH1N1 vRNA.  Thus, our study is first to report H1N1pdm induces greater inflammatory gene expression than sH1N1 in vitro due to direct virus-epithelial cell interaction.

overall_design: Total RNA obtained from Normal Human Bronchial Epithelial Cells (NHBEC) at 3 hours or 24 hours post-infection with either 0.9 MOI A/Mexico/4108/2009 (H1N1) or 0.9 MOI A/Brisbane/59/2007 (H1N1).  Total RNA was also collected at 0 hours from uninfected NHBEC for each infection.  Changes in gene expression relative to uninfected cells were then investigated.

first: David

last: Kelvin


title: Multi-organ mapping of cancer risk

city: Memphis

last: Finkelstein

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Cancers are distributed unevenly across the body; but the importance of cell intrinsic factors such as stem cell function in determining organ cancer risk is unknown.  Therefore, we used cre-recombination of conditional lineage tracing, oncogene and tumour suppressor alleles to define populations of stem and non-stem cells in mouse organs, and test their life-long susceptibility to tumorigenesis.  We show that cancer risk is determined by the life-long generative capacity of mutated cells. This relationship held true in the presence of multiple genotypes and regardless of developmental stage, strongly supporting the notion that stem cells dictate organ cancer risk.  Using the liver as a model system, we further show that damage-induced activation of stem cell function markedly increases cancer risk.  Therefore, we propose that a combination of stem cell mutagenesis and extrinsic factors that enhance the proliferation of these cell populations, creates a ‘perfect storm’ that ultimately determines organ cancer risk.

overall_design: Long-term lineage tracing and conditional oncogenic targeting of Prom1-expressing cells in various mouse organs.

first: Liqin

last: Zhu

first: Culian

last: Gao

first: Lei

last: Shi

first: Yongdong

last: Wang

first: Dolores

last: López-Terrada

first: Kasper

first: Sarah

last: Utley

first: Stanely

middle: B

last: Pounds

first: Geoffrey

last: Neale

middle: W

last: Ellison

first: Arzu

last: Onar-Thomas

first: Richard

last: Gilbertson


title: Genome-wide analysis of gefitinib short-term resistance gene expression in the NSCLC cell line HCC827 in co-culture

overall_design: Total RNA obtained from HCC827 cell line (n=3), co-cultured HCC827 (with MRC-5 cells)(n=3), gefitinib treated (0.5µM) HCC827 (n=3), and co-cultured (MRC-5) + gefitinib treated HCC827 cells (n=3) for 48h after gefitinib treatment


title: Gene expression profiling of SHSY5Y cells exposed to manganese

city: Nagpur

first: Dr. saravana

last: devi

state: Maharashtra

department: Environmental Health Division

institute: CSIR-National Environmental Engineering Research Institute

summary: The trace element manganese is essential for normal development for all the organisms. Overexposure of manganese may leads to multiple neuronal disorders such as Parkinson, manganism. To explore the molecular mechanism of manganese induced neurotoxicity, gene expression profiling was performed on human neuroblastoma SHSY-5Y cells. Cells were exposed to sub-lethal concentration of manganese (100 μM) for 24 hrs. Our result demonstrates that manganese alter multiple biological pathways including chromatin assembly, neurogenesis and apoptotic pathways.Cells grown in  75mm2 flask. three replicates for each sample

overall_design:
SHSY5Y cells grown in MEM:F12 media (1:1) were treated with manganese and total RNA was isolated from cells after 24 hour exposure
Three replicate were used for the experiment

first: Deepa

last: Gandhi

first: S

last: Devi

first: K

last: Krishnamurthi


title: JQ1 modulates inflammatory related-genes in  human renal tubular epithelial cells

city: Oviedo

first: Beatriz

last: Suarez-Alvarez

state: Oviedo

address: Celestino Villamil s/n

institute: Hospital Universitario Central de Asturias

summary: Selective bromodomains inhibitors block the interaction between diverse bromodomains and extraterminal domains (BET) proteins and acetylated proteins. These inhibitors have shown beneficial effects in cancers malignancies and experimental inflammation in mouse models, but data on renal diseases are scarce. We have investigated the effect of the BET proteins inhibitor JQ1 in a mice model of unilateral ureteral obstruction. Treatment with JQ1 diminished renal damage, the presence of inflammatory cell infiltration and the upregulation of proinflammatory genes. The in vitro evaluation of JQ1 on TNF-α inducible genes in renal cells showed that BET inhibition modulated several biological processes, including inflammation or immune response. Moreover, gene-silencing experiments showed that BRD4 regulates several proinflammatory genes (IL-6, CCL-2 and CCL-5) and chromatin immunoprecipitation techniques demonstrated that BRD4 specifically binds to acetylated histone H3 in the promoter region of those genes. The nuclear factor-B (NF-B) pathway regulates renal inflammation. The RelA NF-B subunit is activated by acetylation of lysine 310. In damaged kidneys and in TNF-α-treated renal cells, JQ1 blocked the nuclear translocation of RelA/NF-B and NF-B-mediated gene expression. Additionally, obstructed kidneys showed an activation of the Th17 immune response, which was diminished by JQ1 treatment. Our results demonstrate that the BET inhibition decreases renal inflammation by 3 independent mechanisms: 1) chromatin remodelling in the promoter regions of specific genes, 2) blocking NF-B pathway activation, and 3) modulating the Th17 immune response. These results suggest that BET inhibitors could have important therapeutic applications in inflammatory renal diseases.

overall_design: HK2 cell line was  treated with JQ1 or its enantiomer JQ1(-) (500nM) for 1 hour before stimulation or not with TNF-α (5ng/ml) for additional 3h. We analized the genes up- and down-regulated by TNF-α vs unstimulated cells, and further the genes downregulated or unaffected by JQ1 compared to the cells treated with the enantiomer (-) JQ1.

first: José

last: Morgado-Pascual

first: Sandra

last: Rayego-Mateos

first: Ramón

last: Rodríguez

first: Ana

last: Sanz

first: Jesus

last: Egido

first: Alberto

last: Ortiz

first: Carlos

last: Lopez-Larrea

first: Marta

last: Ruiz-Ortega


title: Genome-wide analysis of gefitinib short-term resistance gene expression in EGFR mutant NSCLC cell lines

first: Sajo

last: Kaduthanam

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

overall_design: Refer to individual Series


title: Immune Responses to Influenza-Like Illness

city: palo alto

first: weiqi

last: wang

state: ca

address: 1291 welch road

institute: stanford

summary: To investigate the nasal transcriptional response and peripheral plasmablast response in acute influenza infection

overall_design: 1. To investigate the nasal transcriptional response with real time PCR. 2. To measure plasmablast response by PPAb analysis.

first: Harry

last: Greenberg


title: Transcription profile of fetal human CD140a-defined OPC differentiation in vitro

city: Buffalo

first: Fraser

middle: James

last: Sim

state: NY

address: 3435 Main Street

department: Pharmacology

institute: University at Buffalo

summary: Human fetal dissociates from 19-22 week gestational age were magnetically sorted for CD140a antigen. CD140a-defined OPCs were plated into serum free conditions and allowed to differentiate in the absence of growth factors or mitogens. RNA was extracted from cells immediately following isolation and every day for 4 days. To block differentiation, matched cells were cultured in the presence of PDGF-AA (10ng/ml). This treatment prevents the acquisition of O4-positive oligodendrocyte cell fate and delays MBP mRNA expression by human CD140a-sorted OPCs.

overall_design: 29 samples, 4 time points, 2 media conditions, at least three biological replicates per time point and media condition

first: Suyog

middle: U

last: Pol

first: Melanie

middle: A

last: O'Bara

first: Bansi

middle: H

last: Vedia