title: Effect of p38 MAPK inhibitor SB203580 on gene expression in monocytic THP-1 cells stimulated with HIV gp120 or LPS.

city: La Jolla

first: Roy

last: Williams

state: CA

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

summary: Human monocytic THP-1 cells were exposed to HIV envelope protein gp120 or bacterial LPS in the presence and absence of a pharmacological inhibitor of the p38 mitogen-activated protein kinase (MAPK) for 4 and 24 hours. A microarray analysis was performed in order to assess differential gene expression at the RNA level.

overall_design: Human monocytic THP-1 cells were pre-treated for 15 min with 10 µM SB203580 followed by exposure for 4 h or 24 h to 1 nM HIV gp120SF162 or 1 µg/ml LPS. 0.1 % DMSO and 0.001 % BSA served as vehicle controls for SB203580 and gp120, respectively. The experimental samples were 1) control 4 h, 2) gp120 4 h, 3) LPS 4 h, 4) SB203580 (SB) 4 h, 5) SB+gp120 4 h, 6) SB+LPS 4 h, 7) control 24 h, 8) gp120 24 h, 9) LPS 24 h, 10) SB 24 h, 11) SB+gp120 24 h, 12) SB+LPS 24 h. RNA was isolated from three biological replicates for each experimental condition using an RNeasy kit commercially available from Qiagen (Valencia, CA). Roughly 2 X 106 cells were collected to obtain 500 ng – 2 µg RNA. RNA quality (A260/A280 ratio ~1.8-2.0) was tested using the NanoDrop system from Thermo Scientific (Rockford, IL). High quality RNA was then provided to the Microarray/ QPCR Facility Core at Sanford-Burnham Medical Research Institute and DNA microarray was performed using the whole genome gene-expression analysis HumanHT-12 v4 Expression BeadChip kit from Illumina (San Diego, CA). Microarray results were further analyzed by Dr. Roy Williams (Bioinformatics Core, Sanford-Burnham Medical Research Institute) using the GeneSpring GX platform

first: Kathryn

last: Medders

first: Marcus

last: Kaul


title: Role of HCV-induced immune responses on the establishment of operational tolerance following liver transplantation in humans

status: Public on Dec 23 2014

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: Immune responses induced by ongoing and/or past infections prevent the establishment of transplantation tolerance in experimental animal models. How host-pathogen interactions influence allograft tolerance in humans has not been investigated before. The spontaneous development of operational tolerance in liver transplant recipients with chronic hepatitis C virus (HCV) infection constitutes a unique setting to address this question. We conducted a clinical trial of immunosuppression withdrawal in stable HCV-infected liver recipients to elucidate: i) the mechanisms through which allograft tolerance is established in the presence of an ongoing inflammatory response; and ii) how is influenced by anti-HCV heterologous immune responses. Enrolled patients gradually discontinued their immunosuppressive drugs over 6-9 months, and those who maintained normal allograft status 12 months after drug withdrawal were considered operationally tolerant. Successful drug withdrawal was associated with intra-hepatic over-expression of type I interferon and immune-regulatory genes, and correlated with an expansion of exhausted PD1/CTLA4/2B4-positive HCV-specific circulating CD8+ T cells. These findings were already present before immunosuppression was discontinued and were specific for HCV infection. In contrast, the magnitude of HCV-induced inflammatory gene expression and the scope of anti-HCV effector T cell responses did not influence drug withdrawal outcome. Our data indicate that in humans persistent viral infections do not necessarily preclude the development of transplantation tolerance. At least in HCV-infected liver allografts, mechanisms associated with the capacity of the virus to evade adaptive immunity could contribute to the restraining of alloimmune responses and the establishment of transplantation tolerance.

overall_design: Transcriptomic study from the following liver tissue samples: 12 tolerant before immunosuppression (IS), 13 non-tolerant before IS, 4 from non-tolerant at the time of rejection, 13 from tolerant patients 12 months after IS discontinuation. Additionally, 8 liver tissue samples obtained from healthy living liver donors undergoing partial hepatectomy were included as non-transplanted controls.

first: F

last: Bohne

first: M

middle: C

last: Londoño

first: C

last: Benitez

first: R

last: Miquel

last: Martinez-LLordella

first: A

last: Rimola

first: J

middle: J

last: Sanchez-Fueyo


title: B-Raf inhibitors induce epithelial differentiation in BRAF mutant colorectal cancer cells

status: Public on Dec 21 2014

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

summary: Mutations in the BRAF proto-oncogene, which encodes the B-Raf kinase, are associated with more aggressive, less-differentiated and therapy-resistant colorectal cancers (CRC). However, the molecular mechanisms responsible for these correlations remain unknown. Here, we report the characterization of human isogenic CRC cell line models (Caco-2, HT29, Colo-205) in which we modulate the expression of the B-RafV600E oncoprotein either by conditional cDNA or shRNA expression. Using these models in conventional and three dimensional tissue culture systems, we demonstrate that genetic depletion of endogenous B-RafV600E decreases cellular motility and invasion, while it induces hallmarks of differentiated epithelia such as the formation of functional adherens and tight junctions. Importantly, these effects are recapitulated by exposing these lines to B-Raf (PLX4720, vemurafenib, dabrafenib) or MEK inhibitors (trametinib). Furthermore, loss of endogenous B-RafV600E in HT29 xenografts does not only stall tumor growth, but also induces epithelial structures with marked expression of Cdx-2, a prognostic marker and master regulator of intestinal morphogenesis. By performing the first transcriptome profiles of B-Raf inhibitor treated 3D cultures of a primary adenocarcinoma and a metastasis derived CRC cell line, we establish functional links between B-RafV600E and proteins of known and potentially new prognostic relevance. We propose that B-Raf/MEK/ERK pathway inhibitors could be used to induce CRC differentiation and thereby to limit metastatic disease.

overall_design: To measure the time resolved gene responses, RNA was isolated from PLX4720 or DMSO treated Colo-205 and HT29 3D culture cell lysates at days 1,3 and 10 and days 1,3, and 8, respectively. The time points for HT29 cells were taken in biological duplicates.

first: Melanie

last: Boerries

first: Ricarda

last: Herr

first: Tilman

last: Brummer


title: Molecular patterns in human ulcerative colitis and correlation with response to infliximab

status: Public on Dec 22 2014

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

summary: Background & Aims. As a T cell-mediated disease of the colonic epithelium, ulcerative colitis (UC) is likely to share pathogenic elements with other T cell-mediated inflammatory diseases. Recently we showed T cell-mediated rejection of kidney and heart transplants share large scale molecular changes. We hypothesized that UC would manifest a similar disturbance, and that these features would correlate with response to infliximab.   Results. UC biopsies manifested coordinate transcript changes resembling rejecting transplants, with T cell, IFNG-induced, macrophage, and injury transcripts increasing while parenchymal transcripts decreased. The disturbance expressed as principal component 1 correlated with conventional assessments e.g. Mayo scores, serum albumin, and lymphoplasmacytic infiltrate. When assessed in published microarray studies, the disturbance predicted response to infliximab: patients with intense disturbance did not achieve clinical response, although quantitative improvement was usually seen even in non-responders. Similar changes were seen in Crohn’s colitis (CDc).  Conclusions. The molecular phenotype of UC manifests a large scale coordinate disturbance reflecting changes in inflammatory cells and parenchymal elements that correlates with conventional features and predicts response to infliximab.

overall_design: We studied 56 colon biopsies from patients with colitis, including 43 with UC, characterizing the clinical and histological features, and defined the mRNA phenotype with Affymetrix expression microarrays. We measured the expression of previously defined pathogenesis-based transcript sets representing effector T cells, macrophages, IFNG effects, and parenchymal injury response and dedifferentiation. We also studied 48 microarray files from human colon biopsies from the Gene Expression Omnibus database, classified by response to infliximab therapy to look for molecular changes that predict unresponsiveness.

first: Brendan

middle: P

last: Halloran

first: Philip

middle: F


title: YAP conveys an invasive phenotype to clear cell renal cell carcinoma cell lines via endothelin-2

city: Bonn

first: Moritz

last: Kebschull

address: Welschnonnenstr. 17

department: Department of Periodontology

institute: University of Bonn

summary: To determine the biological mechanisms underlying the oncogenic properties of YAP in ccRCC the human ccRCC cell line MZ1774 was transduced with lentivirus containing a shRNA-cassette targeting YAP-mRNA. Expression profiles of MZ1774 YAP knockdown cells were compared to mock-transduced control cells.

overall_design: Total RNA from MZ1774 cells stably expressing shRNA directed against YAP compared to mock-transduced MZ1174 cells

first: Georg

last: Feldmann

first: Ute

last: Schütte


title: The TMAO Generating Enzyme Flavin Monooxygenase 3 is a Central Regulator of Cholesterol Balance

status: Public on Dec 19 2014

city: Winston-Salem

first: Jeff

last: Chou

state: NC

address: Medical Center Blvd

country: USA

institute: Atrium Health Wake Forest Baptist

summary: Circulating levels of the gut microbe-derived metabolite trimethylamine-N-oxide(TMAO) have recently been linked to cardiovascular disease (CVD) risk. Here we performed transcriptional profiling in mouse models of altered reverse cholesterol transport (RCT), and serendipitously identified the TMAO-generating enzyme flavin monooxygenase 3 (FMO3) as a powerful modifier of cholesterol metabolism and RCT. Knockdown of FMO3 in cholesterol-fed mice alters biliary lipid secretion, blunts intestinal cholesterol absorption, and limits the production of hepatic oxysterols and cholesteryl esters. Furthermore, FMO3 knockdown stimulates basal and liver X receptor (LXR)-stimulated macrophage RCT, thereby improving cholesterol balance. Conversely, FMO3 knockdown exacerbates hepatic ER stress and inflammation in part by decreasing hepatic oxysterol levels and subsequent LXR activation. FMO3 is thus identified as a central integrator of hepatic cholesterol and triacylglycerol metabolism, inflammation, and ER stress. These studies suggest that the gut microbiota-driven TMA/FMO3/TMAO pathway is a key regulator of lipid metabolism and inflammation.

overall_design: To identify potential regulators of macrophage reverse cholesterol transport (RCT), liver was isolated from two independent mouse models where the non-biliary RCT pathway known as transintestinal cholesterol excretion (TICE) was either chronically (NPC1L1-liver-transgenic mice) or acutely (ACAT2 antisense oligonucleotide treatment) stimulated. Total RNA was isolated and gene expression levels were profiled on the Affymetrix GeneAtlas MG-430 PM Array Strip (Affymetrix; Santa Clara, CA, USA)

first: Manya

last: Warrier

first: Diana

middle: M

last: Shih

first: Amy

last: Burrows

first: Daniel

last: Ferguson

first: Anthony

middle: D

last: Gromovsky

first: Amanda

middle: L

last: Brown

first: Stephanie

last: Marshall

first: Allison

last: McDaniel

first: Rebecca

last: Schugar

first: Zeneng

last: Wang

last: Sacks

first: Xin

last: Rong

first: Thomas

last: de Aguiar Vallim

first: Pavlina

middle: T

last: Ivanova

first: David

middle: S

last: Myers

first: H

middle: A

first: Richard

middle: G

last: Lee

first: Rosanne

last: Crooke

first: Mark

last: Graham

first: Xiuli

last: Liu

first: Paolo

last: Parini

first: Peter

last: Tontonoz

first: Aldon

last: Lusis

first: Stanley

last: Hazen

first: Ryan

middle: E

last: Temel


title: Genome wide analysis of the host antiviral response to dengue virus infection in primary human monocyte-derived dendritic cells

status: Public on Dec 18 2014

city: Port Saint Lucie

first: John

last: Hiscott

state: Florida

address: 9801 SW Discovery Way

department: Infectious Diseases

institute: Vaccine and Gene Institute-Florida

summary: Analysis of the host response to dengue virus at gene expression level. The hypothesis tested in the present study was that dengue virus triggers and regulate different pathaway with different kinetics controlling the antiviral, the inflammatory and the apoptotic response in primary human DC. Results provide important information of the response to DC to dengue virus showing that antioxidant genes are early stimulated after denv infection reflecting an early production of reactive oxygen species. Interestingely, we demonstrated that ROS production and antiviral and apoptotic responses intersect since chemical inhibition of ROS impairs antiviral and apoptotic responses in these cells.

overall_design: Total RNA obtained from in vitro dengue infected primary human dendritic cells at 0, 6, 12, 18, 24 hours compared to uninfected cells at time 0

last: Olagnier

first: Courtney

last: Steel

first: Cindy

last: Chiang

first: Nadine

last: VanMontfoort

first: Vladamir

last: Beljanski

first: Zhong

last: He

first: Carmen

last: Nichols

first: Rongtuan

last: Lin

first: Siddharth

last: Balachandran

first: Suraj

last: Peri

first: Stephanie

last: Richards


title: MCT4 knockdown in pancreatic cancer cells

status: Public on Dec 17 2014

city: Dallas

first: Erik

last: Knudsen

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Gene expression levels were determined with control or MCT4 knockdown pancreatic cancer cells.

overall_design: MiaPaca2, Capan-2, and PL45 cells were transfected with non-specific or MCT4-specific RNAi. RNA was harvested at 72 hours post transfection and analyzed on Illumina microarrays.

first: Agnieszka

last: Witkiewicz


title: Normal counterpart in the identification of a molecular signature for leukemic promyelocytes

city: Modena

first: Enrico

last: Tagliafico

state: MO

address: Via Campi 287

department: Center for Genome Research

country: Italy

institute: University of Modena and Reggio Emilia

summary: Gene expression profiles of 8 samples of CD34+derived normal promyelocytes

overall_design: We collected RNA from CD34+cells from healthy blood donors cultured in serum-free medium with G-CSF, IL-3 and GM-CSF

first: Alexis

last: Grande

first: Rossella

last: Manfredini

first: Elena

last: Tenedini


title: Transcriptome analysis of LXR regulated genes in early differentiating and mature human macrophages

city: Luxembourg

first: Anke

middle: K.

last: Wienecke-Baldacchino

address: 162a, Avenue de la Faiencerie

country: Luxembourg

institute: University of Luxembourg

summary: The objective of the study was to figure out the impact of LXR signaling on human macrophages. Primary human macrophages in an early differentiating and a mature differentiation state were treated with the LXR agonist T091317 for 4 and 24 h and transcriptome-wide expression analysis were performed.  As LXRa is highly induced during macrophage differentiation and 68% of all LXRs targets change their expression during this process, we suggest that LXRs have essential functions in macrophage development. More than 238 genes are regulated in early as well as mature macrophages by activation of LXRs; most of them are up-regulated. LXRs administrate differentiation state specific as well as common macrophages functions related primarily to lipid homeostasis, immune response and cell fate. Interestingly, almost only genes related to lipid and cholesterol metabolism are overrepresented among early induced genes, whereas genes related to immune functions respond later, implying the existence of indirect mechanisms of control. Furthermore, in early differentiating macrophages cell proliferation and cell death associated genes are induced after 24 h of LXR activation, whereas in mature macrophages, showing high LXRa expression, the same functional cluster respond far earlier (4 h) after LXR ligand treatment. In conclusion, our data suggest that LXRs are modulators of macrophage differentiation, operating principally as positive transcriptional regulators of genes involved in lipid and cholesterol metabolism and by this indirectly influencing the immunophenotype of macrophages.

overall_design: CD14 positive cells of healthy donors were isolated by magnetic separation and differentiated in the presence of human serum to macrophages. At an early differentiating state (16 h after isolation) and at in mature differentiating state (day 11 after isolation) the cells were treated with the synthetical LXR agonist T091317 respective its solvent DMSO for 4 and 24 h. RNA was isolated and a whole genome microarray was performed.


title: Molecular classification of non-melanoma skin cancer by gene expression profiling

status: Public on Dec 13 2014

city: Suwon

first: Hyun Goo

last: Woo

address: 164 Worldcup-ro Yeongtong-gu

country: South Korea

institute: Ajou University School of Medicine

summary: Non-melanoma skin cancers (NMSC) including basal cell carcinoma (BCC) and squamous cell carcinoma (SCC) are more common kinds of skin cancer. Although these tumors share common pathological and clinical features, their similarity and heterogeneity at molecular levels are not fully elaborated yet. Here, by performing comparative analysis of gene expression profiling of BCC, SCC, and normal skin tissues, we could classify the BCC into three subtypes of classical, SCC-like, and normal-like BCCs. Functional enrichment and pathway analyses revealed the molecular characteristics of each subtype.

overall_design: The analysis of gene expression profiling among non-melanoma skin cancer types

first: H


title: Gene expression regulated by HBV mRNAs

status: Public on Dec 12 2014

city: Beijing

first: Jun

last: Hu

address: No. 1 West Beichen Road, Chaoyang District

department: CAS Key Laboratory of Pathogenic Microbiology and Immunology

country: China

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: HBV mRNAs harboring miR-122 response elements were found to bind and sequester endogenous miR-122. This microarray experiment was carried out to find out differentially expressed genes in Huh7 cells expressing HBV mRNAs.

overall_design: RNA was extracted from Huh7 cells transfected with pcDNA3.1 plasmid containing HBV mRNA with wild type (WT) or mutant (Mut) miR-122 response elements in its 3’-UTR or the empty pcDNA3.1 vector (3.1) as a mock. Total RNA was then extracted and processed on Affymetrix microarrays in biological duplicate.

first: Songdong

last: Meng


title: Genome-wide analysis of control and MMP-14 (MT1-MMP) expressing MCF-7 cells growing in three-dimensional (3D) type I collagen gels versus monolayer cell culture conditions

status: Public on Dec 15 2014

city: Liège

last: Maquoi

address: Tour de Pathologie, B23 Sart-Tilman

country: Belgium

institute: University of Liège

summary: In order to investigate the impact of MMP-14 (MT1-MMP) and three-dimensional (3D) culture conditions on the transcriptomes of a human breast adenocarcinoma cell line, we performed a microarray analysis from RNAs isolated from MCF-7 cells expressing either an empty vector (CTRL) or human MMP-14 cDNA (MT1) in monolayer (2D) and 3D collagen (3D Col) growth conditions.

overall_design: MCF-7 cells were stably transfected with either an empty vector (pcDNA3.1/Zeo) or human MMP-14 cDNA (pcDNA3.1-MMP-14/Zeo). Cells were grown for 24, 48 and 72 hours in three-dimensional (3D) type I collagen gels or in monolayer culture conditions. Cells were then lysed in TRIzol and total RNA was isolated. For each experimental condition, total RNAs isolated from 4 independant biological replicates were pooled.

first: Delphine

last: Assent

first: Agnès

last: Noël


title: chronic temporal lobe epilepsy: biopsy hippocampus

status: Public on Dec 04 2014

first: Albert

last: Becker

address: Sigmund-Freud Str. 25

department: Neuropathology

institute: University of Bonn Medical Center

summary: Analysis of biopsy hippocampal tissue of patients with pharmacoresistant temporal lobe epilepsy (TLE) undergoing neurosurgical removal of the epileptogenic focus for seizure control. Chronic TLE goes along with focal hyperexcitability. Results provide insight into molecular mechanisms that may play a role in seizure propensity

overall_design: 129 human hippocampus samples


title: Expression profile of Hepatocellular Carcinoma

status: Public on Dec 10 2014

city: Singapore

first: Lee

middle: Guat Lay

last: Caroline

address: 11 Hospital Drive

department: Department of Biochemistry, National University of Singapore

country: Singapore

institute: National Cancer Centre Singapore

summary: Expression profiling of tumor and adjacent non-tumorous tissues of Hepatocellular Carcinoma (HCC) patients. Illumina HumanHT-12 V4.0 expression beadchip was used to obtain expression profiles across more than 31,000 annotated genes. Samples included 59 tumors and 59 adjacent non-tumorous samples.

overall_design: Total RNA obtained from the 39 tumors and 39 adjacent non-tumorous samples

first: Way-Champ

last: Mah

first: Thomas

last: Thurnherr

first: Caroline

last: Lee

first: Pierce

middle: K

last: Chow

first: Alexander

middle: Y

last: Chung

first: London

last: Ooi

first: Han

last: Toh

first: Bin

last: Teh

first: Yogen

last: Saunthararajah


title: Gene expression profiles of CD4+CD25+ regulatory T cells during acute and chronic viral infection

status: Public on Dec 05 2014

city: Seoul

first: Sang-Jun

last: Ha

address: 50 Yonsei-ro, Science Research Center, Room S423

department: Biochemistry

institute: Yonsei University

summary: Regulatory T (Treg) cells act as terminators in the case of T cell immunity during the acute phase of viral infection. However, their roles in chronic viral infection are not completely understood. We compared the phenotype and function of Treg cells during acute and chronic viral infection using lymphocytic choriomeningitis virus-infected mouse models. Chronic infection, unlike acute infection, led to induction of Treg cells and upregulation of various inhibitory receptors. Treg cells isolated from chronically infected mice (chronic Treg cells) displayed greater suppressive capacity for inhibiting T cell proliferation and subsequent cytokine production than those from naïve (naive Treg cells) or acutely infected mice (acute Treg cells). These gene expression profiles provided evidence that chronic Treg cells display characteristics distinct from either naive or acute Treg cells.

overall_design: Mouse splenic CD4+CD25+ regulatory T cells were analyzed at 0 day and 16 day after acute or chronic viral infection with LCMV Arm or CL13, respectively.

first: Hyo

last: Park

first: Joon


title: Increased CD226 Expression on CD8+ T cells in Patients with Systemic Sclerosis

status: Public on Dec 06 2014

city: Fukuoka

first: Masahiro

last: Ayano

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Medicine and Biosystemic Science

country: Japan

institute: Kyushu University Graduate School of Medical Sciences

summary: Systemic sclerosis (SSc) is an autoimmune disease characterized by vascular damage, and fibrosis of the skin and internal organs. Because activated and oligoclonally expanded CD8+ T cells can be detected in peripheral blood and lung of SSc patients, effector memory CD8+ T cells may play a critical role for organ involvement in SSc; however, the pathogenic functions of effector memory CD8+ T cells remain incompletely understood. Here we performed DNA microarray analysis of the sort-purified effector memory CD8+ T cells from SSc patients and healthy controls, and showed that the expression of genes related to immune response and cell adhesion, including CD226 (also known as DNAX accessory molecule-1, DNAM-1), was significantly altered. Moreover, detailed analysis of CD226 revealed that CD226highCD8+ T cells were increased in SSc patients (mean, 50.7%) compared with healthy controls (32.9%) and were appreciably associated with the severity of skin sclerosis and interstitial lung disease. Further, CD226highCD8+ T cells from SSc patients produced abundant IL-13 and were positively correlated with the cytotoxic capacity of CD8+ T cells against HUVECs. Finally, the neutralization of CD226 impaired IL-13 production and cytolysis against HUVECs. These findings indicate that upregulated CD226 expression on CD8+ T cells reflects disease severity and are involved in SSc pathogenesis via the production of profibrotic IL-13 and endothelial cell injury, and that CD226 may be a useful target in the treatment of SSc.

overall_design: We first purified effector memory CD8+ T cells (CD3+CD8+CD45RO+CD62L+ cells) from peripheral blood by cell sorting and subsequently performed cDNA microarray analysis of the sort-purified effector memory CD8+ T cells from 9 SSc patients and 5 healthy controls.

first: Hiroshi

last: Tsukamoto


title: Alarmins MRP8 and MRP14 induce stress-tolerance in phagocytes under sterile inflammatory conditions

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Hyporesponsiveness by phagocytes, a well-known phenomenon in sepsis, is frequently induced by low-dose endotoxin-stimulation of Toll-like-receptor-4 (TLR4) but can also be found under sterile inflammatory conditions. We now demonstrate that the endogenous alarmins myeloid-related protein (MRP) 8 and MRP14 induce phagocyte hyporesponsiveness via chromatin modifications in a TLR4-dependent manner resulting in enhanced survival during murine septic shock. Also during sterile inflammation, polytrauma and burn patients present with initially high MRP serum concentrations identifying these proteins as obvious candidates for triggering secondary hyporesponsiveness in these patients. Interestingly, increased peripartal MRP concentrations prime human neonatal phagocytes for hyporesponsiveness, which was confirmed in murine neonatal endotoxinemia in wildtype and MRP14 -/- mice. Using a comparative bioinformatics analysis between genome-wide response patterns of MRP- and LPS- tolerized monocytes we demonstrated no difference in global gene expression between samples pretreated with either MRP8-MRP14 or LPS. Our data indicate that alarmin-triggered phagocyte tolerance represents a novel regulatory mechanism for the susceptibility of neonates to systemic infections and during sterile inflammation.

overall_design: Human blood monocytes prestimulated with MRP8-MRP14 or LPS and afterwards activated with LPS were selected for RNA extraction and hybridization on Illumina microarrays.

first: J

last: Austermann

last: Friesenhagen

first: S

last: Fassl

first: T

last: Ortkras

last: Burgmann

first: B

last: Petersen

first: K

last: Barczyk-Kahlert

first: E

last: Faist

last: Zedler

first: C

last: Spiekermann

last: Pirr

last: Rohde

last: Müller-Tidow

first: M

last: von

last: Flohé

last: Ulas

last: Roth

last: Vogl

first: D

last: Viemann


title: Response to a LNA miR-92a inhibitor in immortalized human bronchial epithelial cells.

city: San Antonio

first: Alexander

last: Pertsemlidis

address: 8403 Floyd Curl Drive, MC 7784

department: Pediatrics and Cellular & Structural Biology

institute: UT Health Science Center at San Antonio

summary: Lung cancer is the leading cause of cancer-related fatalities. Recent success developing genotypically-targeted therapies, with potency only in well-defined subpopulations of tumors, suggests a path to improving patient survival. We utilized a library of oligonucleotide inhibitors to microRNAs, a class of post-transcriptional gene regulators, to identify novel synthetic lethal interactions between miRNA inhibition and molecular mechanisms in NSCLC. Two inhibitors, those for miR-92a and miR-1226*, produced a toxicity distribution across a panel of 27 cell lines that correlated with loss of p53 protein expression. Notably, depletion of p53 was sufficient to confer sensitivity to otherwise resistant telomerase-immortalized bronchial epithelial cells. We found that both miR inhibitors cause sequence-specific down-regulation of the miR-17~92 polycistron, and this down-regulation was toxic only in the context of p53 loss. Mechanistic studies indicated the selective toxicity of miR-17~92 polycistron inactivation was the consequence of derepression of vitamin D signaling via suppression of CYP24A1; a rate limiting enzyme in the 1α,25-dihydroxyvitamin D3 metabolic pathway. Of note, high CYP24A1 expression significantly correlated with poor patient outcome in multiple lung cancer cohorts. Our results indicate that the screening approach utilized in this study can identify clinically relevant synthetic lethal interactions, and that vitamin D receptor agonists may show enhanced efficacy in p53-negative lung cancer patients.

overall_design: 2 cell lines, 2 conditions per cell line, 3 replicates per condition, RNA collected 48 hours post transfection

first: Michael

last: White


title: Tumor infiltrating IL-33 producing effector-memory CD8+ T cells in resected hepatocellular carcinoma prolong patient survival

status: Public on Dec 08 2014

city: Regensburg

first: Stefan

last: Brunner

address: Franz-Josef-Strauss-Allee 11

institute: Univeritaetsklinikum Regensburg

summary:
Background: IL-33, a cytokine with pleiotropic functions, is elevated in serum of patients with hepatocellular carcinoma (HCC). This study investigated effects of local IL-33 expression in resected HCC on patient survival and on immunological and molecular tumor microenvironment.

Methods: Tissue of resected HCCs was stained for H&E, masson trichrome, alpha smooth muscle actin, IL-33, CD8 and IL-13 and analysed by flow cytometry. Besides histomorphologic evaluation, the immunohistochemical stainings were analysed for the respective cell numbers separately for tumor area, infiltrative margin and distant liver stroma. These findings were correlated with clinical data and patient outcome. Further, gene expression of different HCC risk groups was compared using Micro Arrays.

Results: In multivariable analysis, infiltration of HCCs by IL-33+ cells (P=0.032) and CD8+ cells (P=0.014) both independently were associated with prolonged patient survival. Flow cytometry demonstrated that cytotoxically active CD8+CD62L-KLRG1+CD107a+ effectory-memory cells are the main producers of IL-33 in these HCC patients. Using infiltration by IL-33+ and CD8+ cells as two separate factors, a HCC immune score (HCCIS) was designed and evaluated that stratified patient survival (P=0.0004). This HCCIS identified high and low risk patients who differ in gene expression profiles (P<0.001).

Conclusion: Infiltration of HCCs by IL-33+ and CD8+ cells is independently associated with prolonged patient survival. We suggest that this is due to an induction of highly effective cytotoxically active CD8+CD62L-KLRG1+CD107a+ effector-memory cells producing IL-33. Based on these two independent factors we established a HCC immune score that provides risk stratification for HCC patients and can be used in the clinical setting.

To investigate if  HCCIS 0 high risk and HCCIS 2 low risk tumors exhibit a distinct molecular environment and gene expression pattern, RNA from fresh tumor tissue was isolated and analyzed by whole genome Microarray

overall_design: 4 patients with low risk tumors (HCCIS 2) were compared to 4 patients with high risk tumors (HCCIS 0).

first: Christoph

last: Rubner

first: Rebecca

last: Kesselring

first: Maria

last: Martin

first: Petra

last: Ruemmele

first: Thomas

last: Stempfl

first: Andreas

last: Teufel

first: Hans

last: Schlitt

last: Fichtner-Feigl


title: Predominance of MAPK reactivation in early resistance to debrafenib/trametinib combination therapy of BRAF mutant metastatic melanoma.

status: Public on Dec 03 2014

city: Westmead

first: Gulietta

last: Pupo

state: NSW

address: Darcy Road

country: Australia

institute: University of Sydney

summary: One third of BRAF-mutant metastatic melanoma patients treated with combined BRAF and MEK inhibition progress within six months. Treatment options for these patients remain limited. Here we analyse twenty BRAFV600 mutant melanoma metastases derived from 10 patients treated with the combination of debrafenib and trametinib for resistance mechanisms and genetic correlates of response. Resistance mechanisms are identified in 9/11 progressing tumors and MAPK reactivation occurred in 9/10 tumors, commonly via BRAF amplification and mutations activating NRAS and MEK2. Our data confirming that MEK2C125S, but not the synonymous MEK1C121S protein confers resistance to combination therapy, highlight the functional differences between these kinases and the preponderance of MEK2 mutations in combination therapy-resistant melanomas. Exome sequencing did not identify additional progression-specific resistance candidates. Nevertheless, most melanomas carried additional oncogenic mutations at baseline (e.g. RCA1 and AKT3) that activate the MAPK and P13K pathways and are thus predicted to diminish response to MAPK inhibitors.

overall_design: Total RNA obtained from fresh frozen melanoma tumors treated with a combination of dabrafenib and trametinib

first: Helen

last: Rizos


title: Hepatocellular Carcinoma

first: Lee

last: Caroline

type:
Expression profiling by array
Methylation profiling by array

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

overall_design: Refer to individual Series


title: Genome-wide microarray analysis of human fibroblasts in response to indomethacin and nimesulide.

status: Public on Dec 01 2014

city: Gdańsk

first: Magdalena

last: Gabig-Cimińska

address: Wita Stwosza 59

department: of Medical Biology and Genetics

country: Poland

institute: University of Gdańsk

summary: Establishment of a transcriptomic profile of human cells treated with genistein with particular emphasis on signature of genes coding for enzymes involved in glycosaminoglycan synthesis stands for the present study. The hypothesis tested was that indomethacin and nimesulide influence expression of some genes among which are those coding for enzymes required for synthesis of different GAGs being pathologically accumulated in mucopolysaccharidoses. Results provide important information concerning the extent of action of indomethacin and nimesulide at the molecular level in terms of modulation of gene expression by these substances.

overall_design: Total RNA obtained from Human Dermal Fibroblasts adult (HDFa) and Mucopolysaccharidosis type II (MPS II) cell lines subjected to 24 or 48 hours in vitro exposure to 2 or 10 µM indomethacin, 5 or 25 µM nimesulide, or 0.05% DMSO (K).


title: Regulation of skeletal muscle energy/nutrient-sensing pathways during metabolic adaptation to fasting in healthy humans

status: Public on Dec 02 2014

city: Leiden

first: Bruno

last: Guigas

address: P.O.Box 9600, Postzone L40-Q

department: Parasitology

country: Netherlands

institute: Leiden University Medical Center

summary: The aim of the study was to investigate how short-term fasting affects whole-body energy homeostasis and skeletal muscle energy/nutrient-sensing pathways and transcriptome in humans. For this purpose, twelve young healthy men were studied during a 24-hour fast. Skeletal muscle biopsies were collected and analyzed at baseline and after 4, 10 and 24h of fasting. As expected, fasting induced a time-dependent decrease in plasma insulin and leptin levels, whereas levels of ketone bodies and free fatty acids increased. This was associated with a metabolic shift from glucose towards lipid oxidation. Transcriptome profiling identified genes that were significantly regulated by fasting in skeletal muscle at both early and late time-points. Collectively, our study provides a comprehensive map of the main energy/nutrient-sensing pathways and transcriptomic changes during short-term adaptation to fasting in human skeletal muscle

overall_design: Total RNA obtained from skeletal muscle biopsies collected at 1.5, 4 10 and 24h post-meal in healthy men subjected to a 24h-fast

first: Peter-Bram

last: 't Hoen


title: Genome-wide gene expression analysis of upper airway (i.e., nasal) epithelial cells (i.e., RPMI 2650) exposed to fresh welding fumes

city: Iowa City

first: Aditya

last: Stanam

state: Iowa

address: 500 Newton Road

department: Pathology

institute: University of Iowa

summary: Inhaled welding fumes are deposited on all parts of the respiratory system, with the nasal cavity being the initial point of contact. We investigated the influence of fresh welding fumes on nasal epithelial model, i.e., RPMI 2650 cells, at the transcriptome level. Spark-generated welding fumes at two different concentrations (85 µg/m3 - low; 760 µg/m3 - high) were exposed to RPMI 2650 cell monolayers at air-liquid-interface continuously for 6h, followed by zero hours (or) four hours post-exposure incubation.

overall_design:
Total RNA was isolated from:
1. unexposed (i.e., incubator control) RPMI 2650 cells (or)
2. cells exposed to particle-free clean air for 6h with 0h (i.e., 6h) post-exposure incubation (or)
3. cells exposed to particle-free clean air for 6h with 4h (i.e., 6-4h) post-exposure incubation (or)
4. cells exposed to welding fumes at each concentration (85 µg/m3 - low; 760 µg/m3 - high) for 6 hours with 0 hours (i.e., 6h) post-exposure incubation (or)
5. cells exposed to welding fumes at each concentration (85 µg/m3 - low; 760 µg/m3 - high) for 6 hours with 4 hours (i.e., 6-4h) post-exposure incubation

first: Jae

middle: H

last: Park

last: Peters

first: Peter

last: Thorne

first: Andrean

last: Simons


title: Global gene expression profiling identifies new therapeutic targets in acute Kawasaki disease

first: Ahmad Nazri

last: Mohamed Naim

address: 60 Biopolis Street, Genome, #02-01

department: Infectious disease

institute: Genome institute of Singapore

summary: Transcriptional profile in Kawasaki patients at acute and convalescent phase with different clinical outcomes were investigated.

overall_design: To gain further insight into the molecular mechanisms underlying KD, we investigated the acute and convalescent whole blood transcriptional profiles of 171 KD subjects and compared them with the transcriptional profiles of pediatric patients with confirmed bacterial or viral infection, and with healthy control children. We also investigated the transcript abundance in patients with different intravenous immunoglobulin treatment responses and different coronary artery outcomes.

first: Long

last: Hoang

first: Martin

last: Lloyd Hibberd


title: Effect of donor age on the proportion of mesenchymal stem cells derived from anterior cruciate ligaments

first: Dae-Hee

last: Lee

address: 126-1, Anam-dong 5-ga, Seongbuk-gu

department: Department of Orthopaedic Surgery

institute: Korea University College of Medicine

summary: Analysis of gene expression profiles of ACL-MSCs derived from total knee arthroplasty (TKA) and ACL reconstruction patients. We hypothesized that the proportion of MSCs in ACL samples correlates negatively with donor age, i.e., the proportion of MSCs in ACL samples are higher in younger patients undergoing ACL reconstruction than in older patients undergoing TKA. Results provide additional information on the the effect of age on MSC properties, in particular, the differential regulation of genes encoding components of the extracellular matrix (ECM).

overall_design: Total RNA was isolated from second-passage ACL-MSCs derived from TKA and ACL reconstruction patients

first: Dae-hee

first: Joanne

last: Ng

first: Sang-Beom

last: Kim

first: Chung-hee

last: Sonn

first: Seung-Beom

last: Han

first: Kyung-Mi


title: Endometrial expression profiling in women with recurrent early pregnancy loss

city: Chicago

first: Gulum

last: Kosova

address: 920 E 58th Street

department: Human Genetics

institute: University of Chicago

summary: Pregnancy loss is the most common complication of human pregnancy. Recurrent early  pregnancy loss (REPL) has multiple etiologies, including endometrial dysregulation leading to  “suboptimal” implantation. Although the implantation process is tightly regulated in Eutherian  (placental) mammals, the molecular factors contributing to dysregulated endometrial gene  expression patterns in women with REPL are largely unknown. We hypothesized that genes  that gained novel expression in the endometria of mammals that evolved in the Eutherian stemlineage,  coincident with the evolution of pregnancy, are likely essential for establishment and  maintenance of normal pregnancy and are, therefore, good candidates for genes whose  expression may be dysregulated in disorders such as REPL. To test this hypothesis, we took an  evolutionary forward genomics approach to characterize gene expression profiles of midsecretory  endometria from women with REPL associated with abnormal endometria based  either on histology or molecular expression of cyclin E. We identified 58 genes that were  differentially expressed (P<0.001) between women with out-of-phase histological dating vs  normal histology, and 81 genes that were differentially expressed (P<0.001) between women  with abnormally elevated cyclin E levels vs normal cyclin E. Remarkably, genes that were  recruited into endometrial expression during the evolution of pregnancy in Eutherian mammals  were significantly enriched for dysregulated genes (P=0.002 for histology, P=0.021 for cyclin E),  as well as for immune and signaling pathways with essential roles in endometrial biology. Thus,  our novel evolutionary-based forward genomics approach identified genes whose dysregulation  during the mid-secretory phase likely contributes to the molecular etiologies of recurrent early  pregnancy loss.

overall_design: Total RNA obtained from mid luteal phase endometrium (two replicates per biopsy) from women with recurrent early pregnancy loss (REPL). Endometrial gene expression levels were compared 1) between women with out-of-phase (n=10) and normal histological dating (n=22), 2) between women with abnormally elevated (n=9) and normal (n=23) cyclin E levels. For 5 additional women with abnormally high cyclin E levels, biopsy samples were collected before and after progesterone treatment to investigate the gene expression profiles in response to progesterone.

first: Mary

last: Stephenson

first: Vincent

last: Lynch

first: Carole

last: Ober


title: Expression of imprinted non-coding RNAs from the DLK1-DIO3 locus in human embryonic stem cells advantages neural lineage differentiation

city: Taipei

first: Kang-Yu

last: Tai

address: Yonglin Biomedical Engineering Hall, No.49, Fanglan Rd.

department: Genome and Systems Biology Degree Program

country: Taiwan

institute: National Taiwan University

summary: Pluripotent stem cells are increasingly used for therapeutic models, including transplantation of neural progenitors derived from human embryonic stem cells (hESCs). Recently, long non-coding RNAs (lncRNAs), including Maternally Expressed Gene 3 (MEG3) that is derived from DLK1-DIO3 imprinted locus, were found to be expressed during neural developmental events. Their deregulations are associated with various neurological diseases. The DLK1-DIO3 imprinted locus encodes abundant non-coding RNAs (ncRNAs) that are regulated by differential methylation on the locus. The aim of our research is to study the correlation between the DLK1-DIO3 derived ncRNAs and the capacity of hESC neural lineage differentiation. We classified hESCs into MEG3-ON and MEG3-OFF based on the expression levels of MEG3 as well as its downstream miRNAs by qRT-PCR. Initial embryoid body (EB) formation was conducted  to examine the three germ layer differentiation  ability. cDNA microarray was used to analyze the gene expression  profiles of hESCs. Directed neural lineage differentiation was performed, followed by analysis of neural lineage marker expression levels and neurite formation via qRT-PCR and immunocytochemistry methods to investigate the capacity of neural differentiation in MEG3-ON and MEG3-OFF hESCs

overall_design: To study the correlations between the DLK1-DIO3 derived ncRNAs and differentiation capacity of hESC toward neural lineage, we classified hESCs into MEG3-ON and MEG3-OFF based on the expression levels of MEG3 by qRT-PCR and validated the methylation patterns of DLK1-DIO3 locus by bisulfite-sequencing. Then we conducted transcriptome analysis of these two groups of hESCs by cDNA microarray. This set contained 12 microarray samples, including 4 MEG3-ON hESCs, 7 MEG3-OFF hESCs, and 1  embryoid body as the negative control of pluripotentcy for pluritest.

first: Chu-Fan

last: Mo

first: Shau-Ping

last: Lin


title: Molecular diversity of breast cancers at the time of endocrine resistance

city: Cambridge

first: Alexey

last: Larionov

state: Cambridgeshire

address: Box 238, Lv 6 Addenbrooke's Treatment Centre, Cambridge BioMedical Campus

department: School of Clinical Medicine

country: United Kingdom

institute: The University of Cambridge

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


title: Ectopic microRNA-150 transcription mimics GR therapy response in GC sensitive MM1S multiple myeloma cells but fails to overcome GC resistance in MM1R cells

city: Edegem

first: Ken

last: Op de Beeck

address: Universiteitsplein 1

institute: University Of Antwerp

summary: Glucocorticoids (GCs) are commonly used to treat patients suffering from lymphoid malignancies i.e.  leukemia and multiple myeloma. Although GCs are known to be strong inducers of apoptosis in lymphoid cells, the molecular determinants of GC therapy resistance are poorly understood. Although GC treatment triggers important changes in gene expression, few studies have addressed the regulatory role of small regulatory microRNAs (miRNAs) in GC therapy response. Only recently, aberrant microRNA expression has been linked to the development of haematological malignancies and microRNAs have become master regulators of drug resistance. We identified GC inducible mRNA and microRNA transcription profiles in GC sensitive MM1S as compared to GC resistant MM1R cells. Transcriptome analysis revealed that GCs regulate multiple genes involved in cell cycle control, cell organization and cell death in MM1S, which remain unaffected in MM1R cells. Correspondingly, GCs selectively trigger cell death in MM1S but not in MM1R. Out of 32 microRNAs responsive to GC in MM1S cells but not in MM1R cells, mir-150 was identified as the most persistent GC responsive microRNA. Furthermore, Ingenuity Pathways Analysis (IPA) revealed that ectopic transfection of a synthetic mir-150 mimics GC therapy response in MM1S cells, associated with selective changes in mRNA levels of typical GR transactivated and transrepressed target genes. Although mir-150 largely mirrors GC responsive changes in gene expression of the transcription factor Myb, GR chaperone FKBP5, cell cycle modulator proteins (IL23A, SKP2, CDKN1A), chemokine signaling proteins (CXCR4, CX3CR1, CCL3) and mTOR/UPR stress related proteins (DDIT4, TXNIP), we also observed mir-150 selective effects on transcription factors (NR3C2 (MR), Myb, Fos, Jun, C/EBP-beta, IRF4, NFE2L1, ATF3, ATF4,), chaperone molecules HSPA8, HSP90AB1), the sodium channel SCNN1G and UPR stress proteins (TRIB3, DDIT3). Remarkably, mir-150 overexpression was not able to overcome GC therapy resistance, since we could not detect GC like effects of mir-150 in GR (NR3C1) deficient MM1R cells. Altogether GC-inducible mir-150 adds a novel complex layer of regulation for fine tuning GC specific therapeutic responses in multiple myeloma.

overall_design: 2 myeloma cellines, resistant (MM1R) and sensitive (MM1S), were treated  treated with dexamethasone for 72hrs and compared to their untreated counterparts or transfected with synthetic mir-150-5p for 72hrs and compared to their mock transfected counterparts.

first: Ajay

last: Palagani

first: Stefan

last: Naulaerts

first: Jolien

last: Diddens

first: Chandra

last: Sekhar Chirumamilla

first: Guy

last: Van Camp

first: Kris

last: Laukens

first: Karen

last: Heyninck

first: Sarah

last: Gerlo

first: Pieter

last: Mestdagh

first: Joke

last: Vandesompele

first: Wim

last: Vanden Berghe


title: Molecular diversity of breast cancers at the time of endocrine resistance [mRNA]

summary:
Dataset containing whole-genome expression profiles of breast cancers at the time of endocrine resistance. It has been used to identify five distinctive phenotypes with different expression of gene clusters associated with ER-signalling, stromal rearrangement and cytokine-signalling. Pathway-focused analysis suggested individual tumours with active ER-signalling (24/55, 44%), PIK3CA-signalling (18/55, 32%), RAS (12/55, 22%) and MYC-signalling (11/55, 20%). 3 or 4 of the above pathways were simultaneously active in 6/55 (11%) cases. Results provide important information about prevalence of different mechanisms of endocrine resistance in clinical samples of breast cancer.

Please note that the tumor samples are clinically quite homogeneous: all are post-menopausal ER+ve breast cancers, endocrine treated and growing on treatment. The main purpose of collecting these data was not to compare transcriptional profiles with clinical parameters, but rather to use the transcriptional profiles of these clinically homogeneous tumours for identifying intrinsic subgroups within endocrine resistance. However, the relevant clinical data was also provided as Series supplementary file (ClinicalData_AL28Jan2014.xlsx).

overall_design: Total RNA extracted from 60 fresh-frozen clinical biopsies of breast cancer at the time of endocrine resistance has been profiled with Illumina HT-12 whole-genome expression micro-arrays.  The profiles have been analysied using un-supervised and pathway-focused bioinformatics techniques to study diversity between tumours and potential mechanisms of resistance for individual tumours.


title: Disruption of FAT10-MAD2 binding inhibits tumor progression

first: Caroline

last: Lee

address: 14 Medical Drive

institute: National University of Singapore

summary: FAT10 interacts with MAD2 and caused tumor progression. The hypothesis tested in the present study was FAT10 induces tumor progression through its binding to MAD2 and Disruption of this binding restored its global gene expression

overall_design: Total RNA obtained from wild-type HCT116, stable FAT overexpressed HCT116, and FAT10 mutants, where its binding with MAD2 was disrupted or abolished.

first: Steven

last: Theng


title: Genome-wide analysis of transcriptome and translatome following eIF4A1 knockdown in MCF7 cells [Array]

first: Roslin

last: Russell

address: Robinson Way

institute: Cambridge Research Institute, Cancer Research UK

summary: To identify which genes were regulated by mRNA helicase activity, the effect of eIF4A1 knockdown on the MCF7 cell transcriptome and translatome was determined. eIF4A1-dependent mRNAs were highly enriched for several classes of genes with oncogenic potential, which leads to a model whereby dysregulation of mRNA unwinding contribues to the malignant phenotype in breast cancer cells via preferential translation of a subset of genes.

overall_design: Total, subpolysomal and polysomal RNA was isolated from MCF7 cells treated with either control siRNAs or siRNAs directed against eIF4A1 (48h post-transfection).

first: Angelika

last: Modelska


title: Gene expression and cytokine profile correlate with mycobacterial growth in a human BCG challenge model

city: Oxford

first: Magali

last: Matsumiya

address: Roosevelt Drive

department: Jenner Institute

institute: University of Oxford

summary: Bacille Calmette Guerin (BCG) is the most widely administered vaccine in the world yet its mechanism of action remains unclear. In this study, we have used samples from a human mycobacterial challenge study in which previously BCG-vaccinated or BCG-naïve UK adults were challenged intradermally with a standard dose of BCG vaccine. BCG remaining at the site of vaccination was quantified by polymerase chain reaction from a skin biopsy sample taken two weeks post-challenge and was used as a measure of BCG growth and functional anti-mycobacterial immunity. Using gene expression microarrays and flow cytometric analysis of intracellular cytokine production, we show that the magnitude of the immune response is greater in previously vaccinated volunteers and that this correlates with reduced mycobacterial growth but increased scarring at the vaccination site. In particular the IFNγ and IL-17 pathways are strongly induced in previously vaccinated volunteers and correlate with reduced mycobacterial growth in this population. This study supports the use of BCG challenge as a tool for evaluating vaccine efficacy and identifying mechanisms of anti-mycobacterial immunity

overall_design: Two groups of volunteers were recruited: BCG naïve (group A, n=11) and those with had previously been vaccinated with BCG (group C, n=13). Volunteers were challenged with a standard dose of SSI BCG on day of challenge (0) and a punch biopsy taken from the site 14 days later (day 14). BCG remaining at the site (present in the biopsy) was quantified by qPCR. BCG was quantified once for each volunteer, at day 14. PBMC were collected from volunteers on days 0, 2, 7 and 14. Gene expression was determined in unstimulated (U) and BCG-stimulated (B) PBMC for the volunteers at each timepoint.


title: Profiling the successful response to infection with West Nile virus

status: Public on Nov 24 2014

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

summary: Individual variations in immune status and function determine responses to infection and contribute to disease severity and outcome. Patients exhibit considerable variation in clinical responses to infection with West Nile virus. We have undertaken a comprehensive characterization of the immune responses of a stratified cohort of patients with a history of West Nile virus infection to identify key mechanisms of resistance and susceptibility. We provide molecular profiles of cellular mechanisms of primary human immune cells defined through multifaceted interrogation including multiplexed gene expression analysis integrated with highly sensitive multidimensional flow cytometry. The availability of reliably curated patient cohorts and data-sharing and data mining techniques of high-throughout investigations should accelerate identification of critical elements of immune resistance to important pathogens

overall_design: Differential gene expression by human PBMCs and macrophages from asymptomatic and severe patients with WNV infection or Poly I:C were generated by microarray.

first: Ruth

last: Montgomery

first: Feng

last: Qian

last: Kleinstein


title: HOXB7 is an ERα cofactor in the activation of HER2 and multiple ER target genes leading to endocrine resistance

status: Public on Nov 25 2014

city: Baltimore

first: Saraswati

last: Sukumar

state: MD

address: 1650 Orleans St, CRB 1, Rm 132

department: Breast Cancer Program

institute: Johns Hopkins School of Medicine

summary: Why breast cancers become resistant to tamoxifen despite continued expression of the estrogen receptor alpha (ERα) and what factors are responsible for high HER2 expression in these tumors remains an enigma. HOXB7 ChIP analysis followed by validation showed that HOXB7 physically interacts with ERα, and that the HOXB7-ERα complex enhances transcription of many ERα target genes including HER2. Investigating strategies for controlling HOXB7, our studies revealed that MYC, stabilized via phosphorylation mediated by EGFR-HER2 signaling, inhibits transcription of miRNA-196a, a HOXB7 repressor. This leads to increased expression of HOXB7, ER-target genes and HER2.  Repressing MYC using small molecule inhibitors reverses these events, and causes regression of breast cancer xenografts. The MYC-HOXB7-HER2 signaling pathway is eminently targetable in endocrine-resistant breast cancer.

overall_design: MCF7 cell lines stably transduced with either vector control of HOXB7. Array ran in duplicates.

first: Kideok

last: Jin

first: Soonweng

last: Cho


title: Wild type and Neuregulin 4 (Nrg4) knockout mouse livers

status: Public on Nov 17 2014

city: Ann Arbor

first: Jiandie

last: Lin

state: MI

address: 210 Washtenaw Avenue

department: Life Sciences Institute

institute: University of Michigan

summary:
Nrg4 is a brown fat-enriched adipokine that binds to the liver and preserves metabolic homeostasis during chronic energy excess. Adipose tissue Nrg4 expression is reduced in mouse and human obesity. Nrg4 deficient mice develp more severe insulin resistance and hepatic fat accumulation upon high-fat diet feeding.
We used microarrays to elucidate the metabolic pathways that are regulated by Nrg4 in the liver.

overall_design:
Wild type and Neuregulin 4 (Nrg4) knockout mice were fed high-fat diet (Research Diets D12492) for eight weeks. Tissues were harvested under ad lib condition for RNA isolation and microarray hybridization using Affymetrix Mouse MG-430 PM Strip arrays. Three independent pools of WT and KO mouse liver RNA were included in the study.
Manuscript title: A brown fat-enriched secreted factor preserves metabolic homeostasis through attenuating hepatic lipogenesis, (journal information TBD)

first: Guo

middle: X

last: Wang

first: Xu

last: Zhao

first: Zhuo

first: Matthias

last: Kern

first: Arne

last: Dietrich

first: Zhimin

last: Chen

first: Zoharit

last: Cozacov

first: Dequan

last: Zhou

first: Adewole

last: Okunade

first: Xiong

last: Su

first: Siming

last: Li

last: Blüher


title: Comparison of parental and CDKi-resistant ovarian cancer cell lines

status: Public on Nov 22 2014

city: Los Angeles

first: Wolf

last: Wiedemeyer

state: California

address: 8700 Beverly Blvd.

department: BMS

institute: Cedars-Sinai

summary: High-grade serous ovarian cancers (HGSOC) are genomically complex, heterogeneous cancers with a high mortality rate, due to acquired chemoresistance and lack of targeted therapy options. Cyclin-dependent kinase inhibitors (CDKi) target the retinoblastoma (RB) signaling network, and have been successfully incorporated into treatment regimens for breast and other cancers. Here, we have compared mechanisms of response and resistance to three CDKi that target either CDK4/6 or CDK2 and abrogate E2F target gene expression. We identify CCNE1 gain and RB1 loss as mechanisms of resistance to CDK4/6 inhibition, whereas receptor tyrosine kinase (RTK) and RAS signaling is associated with CDK2 inhibitor resistance. Mechanistically, we show that ETS factors are mediators of RTK/RAS signaling that cooperate with E2F in cell cycle progression. Consequently, CDK2 inhibition sensitizes cyclin E1-driven but not RAS-driven ovarian cancer cells to platinum-based chemotherapy. In summary, this study outlines a rational approach for incorporating CDKi into treatment regimens for HGSOC.

overall_design: For parental HEY, two replicates per condition (control=10%, SNS032-treated, PD0332991-treated) were analyzed. For CDKi-resistant cells, two individual subclones derived from single cells were analyzed, except OAW28 sublines (two polyclonal populations per subline), OV90-PD/SNS-R (two polyclonal populations) and OV90-SNS-R-1 (polyclonal population, whereas OV90-SNS-R-2 is derived from a single colony).

first: Barbie

last: Taylor-Harding

middle: R


title: Genome-wide analysis of gene expression in M. bovis BCG infected THP-1 cells subjected to Metformin treatement

city: Singapore

first: Michael

last: Poidinger

address: #04-06, 8A Biomedical Grove

department: Bioinformatics

institute: Singapore Immunology Network

summary: Analysis of Metfromin induced changes in mycobacteria infected cell at gene expression level. The hypothesis tested in the present study was whether metformin has any effect on the host immune response in mycobacteria infected cells? Results provide important information on the effect of metformin on the inflammatory response and immune activation associated with mycobacterial infection. In conclusion, Metfromin normalizes the effect of infection in THP1 cells.

overall_design: Total RNA obtained from M. bovis BCG infected cells subjected to 4 or 48h of invitro treatment with 2mM metformin. This was compared to uninfected cells and, untreated infected cells.

first: Amit

last: Singhal

first: Francesca

last: Zolezzi

first: Jinmiao

first: Gennaro

last: De Libero


title: Robust expansion of human pluripotent stem cells: integration of bioprocess design with transcriptomic and metabolomic characterization

status: Public on Nov 13 2014

city: Oeiras

first: Marta

middle: Marques

last: Silva

state: Oeiras

address: Apartado 12

department: Animal Cell Technology Unit

country: Portugal

institute: iBET - Instituto de Biologia Experimental e Tecnológica

summary: Human embryonic stem cells (hESC) have an enormous potential as a source for cell replacement therapies, tissue engineering and in vitro toxicology applications.  The lack of standardized and robust bioprocesses for hESC expansion in relevant quantities while maintaining their pluripotency has hindered the application of hESC and their derivatives in clinical setting. Here, we developed a scalable and well-characterized bioprocess for hESC expansion under fully-defined conditions and explored the potential of transcriptomic and metabolomic tools to evaluate the impact of culture system on hESC phenotype. Two different hESC lines (feeder-dependent and feeder-free lines) were efficiently expanded on xeno-free microcarriers in stirred culture systems. Moreover, both hESC lines maintained the expression of stemness markers such as Oct-4, Nanog, SSEA-4 and TRA1-60, and the ability to spontaneously differentiate into the three germ layers. Whole-genome transcriptome profiling revealed a phenotypic convergence between both hESC lines along the expansion process in stirred-tank bioreactor cultures, providing strong evidence on the robustness of the cultivation process to homogenize cellular phenotype. Under low oxygen tensions, results showed a metabolic rearrangement with the up-regulation of the glycolytic machinery favoring an anaerobic glycolysis Warburg-effect like phenotype, with no evidence of hypoxic stress response, in contrast to 2-dimensional culture. Overall, we report a scalable and fully-defined bioprocess for the propagation of hESC while guaranteeing product quality. Furthermore, the “omics” tools herein used provided relevant findings on the physiological/metabolic changes during the hESC expansion in environmentally-controlled stirred-tank bioreactors, which can contribute for more standardized production systems.

overall_design: 11 samples, comprising time-profile analysis of two hESC cell lines during expansion

first: Ana

last: Rodrigues

first: Cláudia

last: Correia

first: Marcos

last: Sousa

first: Catarina

last: Brito

last: Coroadinha

first: Margarida

last: Serra

first: Paula

last: Alves


title: Gene Expression data in whole blood from 121 Puerto Rican children

status: Public on Nov 08 2014

city: Pittsburgh

first: Jerom

last: Lin

state: Pennsylvania

address: 4401 Penn Ave

institute: University of Pittsburgh

summary: Puerto Ricans are a racially admixed population, that consists of European, African and Native American ancestrie. Understanding eQTL patterns in Puerto Ricans should help us elucidate both regulation of gene expression and disease causation in racially admixed populations in general, and in Hispanic subgroups in particular.

overall_design: Total RNA was extracted from additional whole-blood samples collected in PaxGene tubes for the 121 study participants.

first: Juan

last: Celedon


title: Loss of BRMS1 promotes a mesenchymal phenotype through regulation of Twist1

status: Public on Nov 12 2014

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: Analysis of BRMS1 KD-induced EMT in non-samll cell lung cancer at gene expression level. The hypothesis tested in the present study was that BRMS1 KD induces EMT through differential regulation of EMT genes and Twist1 KD restores the epithelial phenotype in cells with BRMS1 KD. Results provide important information of biological functions in lung cancer which BRMS1 KD involves in, such as EMT, signaling, biological adhesion, immune system process, response to stimulus, and so on.

overall_design: Total RNA obtained from NSCLC H1993 cells infected with lentivirus encoding shRNA BRMS1 or shRNA BRMS1/shRNA Twist1, compared to shRNA control sequence. Illumina microarry were performed using Human HT-12 in duplicates.

first: David

last: Jones

first: Yuan

last: Liu

first: Marty

middle: W

last: Mayo

first: Aizhen

last: Xiao

first: Emily

last: Hall

first: Elianna

middle: B

last: Amin

first: Prasad

last: Adusumilli


title: Hepatic regeneration gene expression signature predicts late recurrence of hepatocellular carcinoma

status: Public on Nov 03 2014

city: Houston

first: Sangbae

last: Kim

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

summary: While we and others have uncovered and validated several genomic predictors for metastatic recurrences, a molecular or genomic predictor that can reliably identify high-risk patients for late de novo recurrence has not been firmly established. We analyzed previously reported gene expression data from human livers that underwent partial hepatectomy or transplantation, which were representative physiological conditions that trigger liver regeneration signals. We generated gene expression data from tumor and matched non-tumor surrounding tissues of 72 hepatocellular carcinoma (HCC) patients who underwent surgical resection as the primary treatment. We used these gene expression data to develop a new prognostification model for recurrence of HCC after surgery.

overall_design: We generated gene expression data from tumor and matched non-tumor surrounding tissues of 72 HCC patients who underwent surgical resection as the primary treatment.

first: JiHoon

first: KooJeong

last: Kang

first: Ju-Seog

last: Lee

first: Yun-Yong

last: Park


title: Genome-wide transcriptional profiling of primary human AML samples with distinct susceptibilities to telomerase inhibition

status: Public on Nov 11 2014

city: Herston

first: Steven

last: Lane

address: 300 Herston Road

institute: QIMR Berghofer Medical Research Institute

summary:
Analysis of gene expression profiles of human AML patient samples. The hypothesis tested was that AML patient samples showing a higher sensitivity to subsequent telomerase inhibition would already harbour a telomerase deficiency gene expression signature before treatment that may be useful to predict therapeutic efficacy.
The results provide a clear separation of AML patient samples based on a telomerase deficiency gene signature that is correlated with subsequent sensitivity to pharmacologic telomerase inhibition assessed in a xenograft transplantation system in vivo.

overall_design: Total RNA from sorted viable human CD45+ expressing AML patient cells expanded in an NSGS xenograft transplantation assay in vivo.

first: Claudia

last: Bruedigam

first: Frederik

middle: O

last: Bagger


title: Loss of non-coding RNA expression from the DLK1-DIO3 imprinted locus correlates with reduced neural differentiation potential in human embryonic stem cell lines

status: Public on Nov 05 2014

city: Taipei City

first: Shau-Ping

last: Lin

state: select a state

address: 4F, No. 81, Chang-Xing St.,

department: Institute of Biotechnology

first: Chu-Fan

last: Mo

first: Kang-Yu

last: Tai


title: M12-8: MRX34 Biomarker study in animals bearing Hep3B orthotopic liver tumors [Illumina]

city: Austin

first: Christopher

last: Daige

address: 2150 Woodward street, suite 100

institute: Mirna Therapeutics

summary: To identify direct tumor mRNA targets of miR-34a, tumor RNAs isolated from whole tumors from animals treated with negative control and MRX34

overall_design:
Hep3B cells were surgically implanted into the livers of Nod/Scid mice and allow to grow for multiple weeks.  Once serum AFP levels reached levels consistent with tumor growth of ~80-100 mg,
animals were subjected to a single IV injection of MRX34.  Twenty-four hours later animals were sacrificed, tumors resected and RNA isolated for subsequent microarray analysis.

first: Chris

first: David

last: Brown


title: FACS–array profiling of helper T cell subtypes from human peripheral blood.

city: Sendai

first: Chiaki

last: Ono

state: Miyagi

address: 2-1 Seiryo-machi, Aoba-ku

department: International Research Institute of Disaster Science

institute: Tohoku University

summary: Gene expression analysis of Th1(CD4+/CXCR3+/CCR4-) and Th2 ((CD4+/CCR4+/CXCR3-) cells by FACS-array

overall_design: 12 Th1 and 12 Th2 samples

first: Hiroaki

last: Tomita


title: Transcriptomic profiling facilitates classification of response to influenza challenge

status: Public on Nov 06 2014

first: Emma

middle: Elisabeth

last: Davenport

address: Hinxton

institute: Wellcome Sanger Institute

summary: Despite increases in vaccination coverage, reductions in influenza-related mortality have not been observed. Better vaccines are therefore required and influenza challenge studies can be used to test the efficacy of new vaccines. However, this requires the accurate post-challenge classification of subjects by outcome, which is limited in current methods that use artificial thresholds to assign “symptomatic” and “asymptomatic” phenotypes. We present data from an influenza challenge study in which 22 healthy adults (11 vaccinated) were inoculated with H3N2 influenza (A/Wisconsin/67/2005). We generated genome-wide gene expression data from peripheral blood taken immediately before the challenge and at 12, 24, and 48 hours post-challenge. Variation in symptomatic scoring was found among those with laboratory confirmed influenza. By combining the dynamic transcriptomic data with the clinical parameters this variability can be reduced. We identified four subjects with severe laboratory confirmed flu that show differential gene expression in 1,103 probes 48 hours post-challenge compared to the remaining subjects. We have further reduced this profile to 6 genes that can be used to define these subjects. We have used this gene set to predict symptomatic infection from an independent study. This analysis gives further insight into host-pathogen interactions during influenza infection. However, the major potential value is in the clinical trial setting by providing a more quantitative method to better classify symptomatic individuals post influenza challenge.

overall_design: Twenty two healthy volunteers were enrolled for an influenza challenge study. Eleven were vaccinated thirty days before challenge with H3N2 influenza. Whole blood was collected in PAXgene tubes prior to influenza challenge and then at three further timepoints (12, 24 and 48 hours post-challenge).

first: Richard

middle: D

last: Antrobus

first: Patrick

middle: J

last: Lillie

first: Sarah

last: Gilbert

first: Julian

middle: C

last: Knight


title: Global gene expression analysis comparing wild type and beta catenin deficient BxPC3 pancreatic adenocarcinoma cells.

status: Public on Nov 07 2014

city: Oslo

first: Petter

middle: Angell

last: Olsen

address: Gaustadalleen 34

department: Dep. of Microbiology

country: Norway

institute: Oslo University Hospital - Rikshospitalet

summary: Goal:obtaing an overview of gene expression changes in BxPC3 cells rendered deficient in beta-catenin protein due to a zinc-finger nuclease mediated disruption of the beta-catenin gene (CTNNB1).

overall_design: Total RNA from exponentially growing cells were harvested and subjected to further analysis

middle: A

first: Kaja

last: Lund


title: Expression profiling of human CD34+ cells derived from mobilized peripheral blood samples after overexpression of MEIS1B or MEIS1D

city: Amsterdam

first: Daphne

middle: C.

last: Thijssen-Timmer

address: Plesmanlaan 125

department: Hematopoiesis

institute: Sanquin Blood Supply

summary: MEIS1 is a transcription factor expressed in hematopoietic stem and progenitor cells (HSPC) and in mature megakaryocytes. In contrast to its role in leukemogenesis, the role of MEIS1 in normal hematopoiesis is largely unknown. We show that MEIS1 can direct human hematopoietic progenitors towards a megakaryocyte-erythroid progenitor (MEP) fate. Ectopoic expression of MEIS1 in CD34+ cells resulted in increased erythroid differentiation at the expense of granulocyte and monocyte (GM) differentiation. MEIS1 overexpression not only skewed differentiation of CMPs towards the erythroid lineage but also reprogrammed GM progenitors towards erythrocyte differentiation. Expression profiling was used to determine the transcriptional changes induced by MEIS1 that lead to the oberved phenotype. A transcriptional program enriched for erythrocytic and megakaryocytic genes was detected.

overall_design: Three independent experiments were performed. Total RNA was isolated from lentivirally transduced human CD34+ cells, 48 hours after transduction. Transductions were performed for the two MEIS1 splice variants MEIS1B and MEIS1D. An empty vector was taken along as a control.

first: Sabrina

last: Zeddies


title: Radial glia require PDGFD/PDGFRB signaling in human but not mouse neocortex

city: San Francisco

first: Michael

last: Oldham

state: CA

address: 35 Medical Center Way #0525

institute: UCSF

summary: Analysis of gene expression over serial 150um sections of a single gestational week 14.5 human neocortical specimen. The hypothesis tested with this dataset was that a transcriptional signature of radial glia (neural stem cells) could be isolated via unsupervised gene coexpression analysis due to variation in the abundance of this cell type from section to section. This dataset is the first of its kind generated using this method (Gene Coexpression Analysis of Serial Sections, or GCASS).

overall_design: Total RNA obtained from serial sections of a single GW14.5 human neocortical specimen.


title: Effect of TGF-β on gene expression of human prostate cancer cells PC-3

status: Public on Nov 01 2014

city: Indianapolis

first: Pierrick

middle: GJ

last: Fournier

state: IN

address: 980 West Walnut Street

department: Medicine

institute: Indiana University

summary:
Transforming growth factor-β (TGF-β) is a key factor for the development of prostate cancer metastases in bone. In breast cancer and melanoma, studies have shown how TGF-β regulates gene expression to allow cancer cells to adapt to the bone microenvironment.
We used microarray analyses to characterize the effect of TGF-β on gene expression in prostate cancer cells in vitro.

overall_design: Human prostate cancer cells, PC-3, were cultured in the presence or absence of TGF-β. Total RNA was extracted for hybridization on Affymetrix microarray analyzed with Microarray Analysis Suite 5.0.

first: Theresa

last: Guise

first: Gregory

last: Clines

middle: G


title: Genome wide gene expression analysis of chronic granulomatous disease patients

city: Turku

first: Tiina

middle: Kelkka

last: Ilona

address: Tykistökatu 6A

department: Medicity

country: Finland

institute: University of Turku

summary: Whole blood was collected from chronic granulomatous patients, carriers and healthy controls.

overall_design: RNA was isolated from whole blood and globin removal was performed for all samples. The cells were not selecter or stimulated ex vivo.

last: Kelkka

first: Deborah

last: Kienhöfer

first: Markus

last: Hoffmann

first: Marjo

last: Linja

first: Kajsa

last: Wing

first: Outi

last: Sareila

first: Malin

last: Hultqvist

first: Essi

last: Laajala

first: Zhi

last: Chen

first: Paulo

last: Rodriques-Santos

first: Júlia

last: Vasconcelos

first: Esmeralda

last: Neves

first: Margarida

last: Guedes

first: Laura

last: Marques

first: Gerhard

last: Krönke

first: Merja

last: Helminen

first: Leena

last: Kainulainen

first: Peter

last: Olofsson

first: Harri

last: Lähdesmäki

first: Sirpa

last: Jalkanen

first: Riitta

last: Lahesmaa

last: Souto-Carneiro

first: Rikard

last: Holmdahl


title: Gene expression profiling of myxoid liposarcomas

status: Public on Oct 30 2014

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

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

overall_design: Refer to individual Series


title: Analysis of blood myelomonocytic cells from RCC patients

first: Michael

last: Poidinger

summary: Myelomonocytic cells (i.e., monocytes or macrophages) play a key role in tumor progression as revealed by numerous mice tumor model studies. However, their contribution in human tumor progression is not well-studied. Using  Renal Cell Carcinoma (RCC) as a model for human cancer, we performed a transcriptomal profiling of blood monocytes from RCC patients to investigate the contribution of these cells in cancer progression. As compared to monocytes from healthy donors (Mo), transcriptome analysis of monocytes from RCC patients (RCC-Mo) showed a distinct gene expression signature consisting of cytokines, chemokines and various inflammation-related genes. Validation of these genes by qPCR as well as other functional assays indicated RCC-Mo possess an inflammatory and tumor promoting phenotype.

overall_design: Blood monocytes from RCC patients (with early or metastatic disease) or healthy donors (controls) were isolated, and then differential gene expression was detected with Limma.

first: Subhra

middle: K

last: Biswas


title: Transcriptome data for bacterial and fungal keratitis compared to cadaver cornea

status: Public on Oct 31 2014

city: London

first: Jaya

middle: Devi

last: Chidambaram

address: Keppel Street

department: Clinical Research Department

institute: London School of Hygiene and Tropical Medicine

summary: Microbial keratitis is a major cause of blindness worldwide. An excessive host inflammatory response can occur even after adequate antimicrobial treatment. This results in tissue damage with corneal thinning and even perforation, which may require corneal transplantation. In this study we investigated the pathways involved in the pathophysiology of this disease by comparing the human transcriptome profile of tissue from culture-proven bacterial and fungal keratitis (n=7 and n=8 respectively) with normal non-infected cadaveric corneal tissue (C, n=12) using Illumina HT12 v4 microarrays. The causative organisms were Streptococcus pneumoniae (n=6) and Pseudomonas aeruginosa (n=1) for bacterial keratitis (BK). Fungal keratitis (FK) was caused by Fusarium sp. (n=5), Aspergillus sp. (n=2, A. flavus and terreus) and Lasiodiplodia sp. (n=1). Differential expression (DE) analysis revealed 2310 significantly altered probes in the BK v C comparison, and 1813 probes for FK v C.  The most highly upregulated gene in both comparisons was MMP9 with fold changes (FC) of 64 (fdr-adjusted p<6 x10-11) for FK v C and 89 for BK v C (fdr-adjusted p<4 x10-11) respectively. Network co-expression analyses revealed the defense response, inflammatory response and extracellular matrix mechanisms to be the main functional pathways involved. Microarray results were validated by performing real-time quantitative PCR (RTqPCR) for 46 DE genes using RNA extracted from the same samples. There was a high correlation between log2 FC values from microarray and RTqPCR. Further studies are needed to evaluate the most highly differentially expressed genes as possible biomarkers of disease progression or therapeutic targets.

overall_design: Case - control study design. Corneal ulcer tissue from 8 bacterial and 9 fungal ulcers was excised at the time of corneal transplantation surgery and immediately preserved in RNALater. Non-infected corneal tissue from 13 cadaver corneas were the control tissue. Transcriptome profile generated using Illumina HT12 v4 beadchips. Differential expression analysis was performed with pairwise comparisons: bacterial ulcers versus controls, fungal ulcers versus controls and bacterial versus fungal ulcers. Microarray results validated with RTqPCR.

first: Namperumalsamy

middle: V

last: Prajna

first: Palepu

last: Srikanthi

first: Shruti

last: Lanjewar

first: Prajna

last: Lalitha

first: Shanmugam

last: Elakkiya

first: Julien

last: Bauer

first: Martin

last: Holland

first: Matthew

last: Burton


title: Potentiation of neurotoxicity in double mutant mice with Pink1 ablation and A53T-SNCA overexpression

status: Public on Nov 04 2014

city: Tuebingen

middle: H.

last: Walter

address: Calwer Str. 7

department: Department of Medical Genetics

country: Germany

institute: University of Tuebingen

summary: As the second most frequent neurodegenerative disorder of old age, Parkinson’s disease (PD) can result from autosomal dominant causes like increased alpha-synuclein (SNCA) dosage, or from autosomal recessive causes like PINK1 loss-of-function. Interactions between these triggers and their potential convergence onto shared pathways are crucial to understand, but currently conflicting evidence exists. Here, we crossed previously characterized mice with A53T-SNCA overexpression and mice with PINK1 deletion to generate double mutants (DM). We studied their lifespan and behavior, together with histological and molecular anomalies at late and early ages, respectively. DM animals showed potentiated phenotypes in comparison to both single mutants (SM), with markedly reduced survival after age 450 days and strongly reduced spontaneous movements from age 3 months onwards. A considerable part of DM animals manifested progressive paralysis at ages >1 year and also exhibited protein aggregates with immunoreactivity for pSer129-SNCA, p62, and ubiquitin in spinal cord and basal brain, contrasting with absence of such features from SM. A brain proteome quantification of ubiquitination sites documented altered degradation of SNCA and the DNA-damage marker H2AX at age 18 months. Global brain transcriptome profiles and qPCR validation experiments identified many consistent transcriptional dysregulations already at age 6 weeks, which were absent from SM. The observed downregulations for Dapk1, Dcaf17, Rab42 and upregulations for Dctn5, Mrpl9, Tmem181a, Xaf1 reflect changes in ubiquitination, mitochondrial / synaptic / microtubular dynamics, and DNA damage. Thus, our study confirmed that SNCA-triggered neurotoxicity is exacerbated by the absence of PINK1, and identified a novel molecular signature that is detectable early in the course of this double pathology.

overall_design: Factorial design comparing Pink1 knock-out/A53T-SNCA double transgenic mice with appropriate wild-type controls (129SvEv+FVB/N) in three different tissues (cerebellum, midbrain, striatum)

first: Gispert

last: Suzana

first: Brehm

last: Nadine

first: Walter

last: Michael

first: Auburger

last: Georg


title: Differential gene expression in erythroid progenitor cells from β-thalassaemia patients and healthy controls [Bioconductor/limma R analysis]

status: Public on Oct 28 2014

city: Perth

first: Luke

last: Forster

state: WA

address: Hopsital Ave

department: Haematology

institute: PathWest

summary: This study uses microarray technology to examine the erythroid progenitor mRNA of patients with transfusion dependent β-thalassaemia and compare it to erythroid progenitor mRNA from healthy controls. We observed no statistical difference in gene expression between the groups following 7 days in culture. However, following 14 days in culture we observed differential expression of 161 genes.

overall_design: Haematopoietic cells from the peripheral blood of 6 β-thalassaemia patients and 6 healthy controls was grown in semi-solid media. After 7 and 14 days in culture cells of erythroid origin were isolated. Total RNA was isolated from these for microarray gene expression analysis

first: John

last: McCooke

last: BellGard

first: Jill

last: Finlayson

first: Reza

last: Ghassemifar


title: Differential Gene Expression Analysis in Early and Late Erythroid Progenitor Cells in β-thalassaemia


title: Genome-wide profiling of whole blood from patients with defects in Toll-like receptors (TLRs) and IL-1Rs (the TIR pathway) signaling

status: Public on Oct 26 2014

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

country: USA

institute: Baylor Institute for Immunology Research

summary: The objective of this study is to: 1) Characterize the innate immune responsiveness of patients with inborn errors in Toll-IL1 receptor signaling pathway (IRAK4, MyD88 deficiencies) compared to healthy subjects, through the analysis of blood leukocytes' transcriptional profiles after stimulation with ligands for the whole set of Toll-like receptors and IL-1Rs plus whole bacteria.  2) Understand the redundancies in TLR pathway in humans. 3) Explore the use of blood profiling approaches to assess the immune status of an individual by using Primary Immune Deficiencies as a proof of principle.

overall_design: A total of 22 blood samples were collected from three groups of subjects: 4 patients with complete MYD88 deficiency, 4 patients with complete IRAK4 deficiency, and 14 healthy donors. Mutations from IRAK4 and MYD88 patients are loss-of-function. The subjects were recruited in two different batches: first set includes 4 healthy controls, MYD88 P1 and P2, IRAK4 P1 and P2 patients. Second set includes 10 different healthy controls, MYD88 P3 and P4 and IRAK4 P3 and P4. Healthy individuals are considered so based on past medical history (no recurrent infections). They were also healthy at the time of sampling.     From each subject, peripheral blood was drawn into sodium heparin vacuum tubes on clinic site (Necker Hospital, Paris). Right away, 500µl whole blood was diluted with the same amount of RPMI before adding different stimulus. Diluted whole blood was activated with a wide range of ligands (16 conditions total, see below) in a volume of 50 µl, for 2 hours along with 10µg/ml of polymyxin B to clear LPS contamination in reagents. Whole blood was lysated with Tempus solution (from Tempus tubes, Applied Biosystems) to stabilize the RNA at 1:3 ratio after restimulation. The lysates were kept at -80ºC temperature until mRNA extraction. A total of 365 samples were analyzed. Choice of agonists: PAM3 (TLR1/2) and PAM2 (TLR2/6), 100 ng/ml final concentration, Invivogen®; poly(I:C) 25 µg/ml final concentration, Invivogen® (TLR3); LPS 100 ng/ml final concentration, Sigma®  (TLR4); Flagellin 100 ng/ml final concentration, Invivogen® (TLR5); 3M13 (TLR7) and 3M2 (TLR8), 3µg/ml final concentration, 3M pharmaceuticals®; R848 3µg/ml final concentration, Invivogen® (TLR7/8); CpG-D19 and CPG C (TLR9), 3µg/ml final concentration, from collaborator. Agonists for IL-1R: IL-1b 20ng/ml final concentration, IL18 and IL33 50ng/ml final concentration, from RaD systems®; agonist for TNFa receptor, TNFa, 20ng/ml final concentration, from RaD systems®; PMA 25 ng/ml + Ionomycin 1µg/ml final concentration, Sigma®; heat killed whole bacteria: 3 pneumococcal strains (R6, 5.106 partical/ml final concentration; R8450 108 partical/ml final concentration; R11470, 5.106 partical/ml final concentration, heat killed at 65°C for 15 min) from collaborator, and Staphylococcus aureus (SAC), 107 partical/ml final concentration, from Invivogen®. No stimulation serves as negative control and PMA/ionomycin stimulation as positive control.


title: Gene expression profiling of myxoid liposarcomas (validation set INT-B)

first: Loris

last: De Cecco

country: Italy

summary: FUS-CHOP and EWS-CHOP balanced translocations characterize myxoid liposarcoma which encompasses myxoid (ML) and round cell (RC) variants initially believed to be distinct diseases. Currently, myxoid and RC liposarcoma are regarded to represent the well differentiated and the poorly differentiated ends, respectively, within spectrum of myxoid liposarcoma where the fusion proteins blocking lipogenic differentiation play a role in tumor initiation while molecular determinants associated to progression to RC remain poorly understood. Activation of AKT pathway sustained by PIK3CA and PTEN mutations and growth factor receptor signalling such as RET and IGF1R have been recently correlated with the increasing of aggressiveness and RC.  Aim of the present study is to elucidate molecular events involved in driving round cell progression analyzing two small series of MLS selected to be representative of the two end of the gamut: the pure myxoid (0% of RC component) and RC with high cellular component (≥80%).

overall_design: The validation series (INT-B) consisted of cryopreserved samples obtained from 12 patients. Six cases were pure myxoid and six were pure RC. The diagnoses were confirmed by means of FISH analysis, which revealed CHOP rearrangement, or by RT-PCR searching for the transcript type. Different molecular variants of the fusion transcript have been described by Powers MP et al. (Mod Pathol. 2010).

first: L

first: S

last: Pilotti


title: Expression data from ZBP1-expression and ZBP1 nonexpression breast tumors.

status: Public on Oct 24 2014

city: Shantou

first: Wei

last: Gu

state: GuangDong

address: 22 Xing-Lin Road

department: Pathophysiology

institute: Shantou University Medical College

summary:
ZBP1/IMP1 is an mRNA binding protein that post-transcriptionally regulates the expression of a handful mRNAs, implicated in maintaining cell polarity and adhesion. We have previously shown that ZBP1 was able to inhibit proliferation and invasiveness of breast carcinoma cells in vitro. In the current study, we utilized orthotopic breast fat pad xenografts to further investigate the ZBP1-mediated functions in breast tumorigenesis and metastasis in vivo.
We used microarrays to identify important gene for breast tumor growth and metastasis in response to ZBP1 expression

overall_design: Total RNA was extracted from breast tumor generated from ZBP1-expression and ZBP1-nonexpression MDA231 cells and used for hybridization on Affymetrix microarrays. We sought to obtain gene expression profiles from the individual tumors and identify what genes are up-regulated or down-regulated in the presence of ZBP1. The microarray experiments and data analysis were performed in 'Gene Company Limited' in Senzheng, China. G-10 and G-13, Tumors generated from MDA231/GFP cells; I-5 and I-6, tumors generated from MDA231/ZBP1-GFP cells.

first: Zhengqiang

last: Huang


title: Time dependent salicylate treatment effect on human embryonic kidney cell line

city: Seoul

first: Jun-Seok

last: Lee

address: 39-1 Hawolgok-dong Seungbuk-gu

institute: Korea Institute of Science and Technology (KIST)

summary: Analysis of HEK293 cells treated with salicylate. 50 mM final concentration of sodium salicylate was treated to HEK293 cells, and their mRNA expression perturbation was observed time-dependent manner.

overall_design: Total RNA obtained from HEK293 cells was compared after salicylate treatment (30 min and 60 min).

first: Young-Hwa

last: Yoo


title: Differential gene expression in erythroid progenitor cells from β-thalassaemia patients and healthy controls [BRB-ArrayTools analysis]

summary: This study uses microarray technology to examine the erythroid progenitor mRNA of patients with transfusion dependent β-thalassaemia and compare it to erythroid progenitor mRNA from healthy controls. We observed no statistical difference in gene expression between the groups following 7 days in culture. However, following 14 days in culture we observed differential expression of 277 genes.

first: David

last: Joske


title: Impact of mutant p53 on TNF-induced gene expression

status: Public on Oct 27 2014

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

institute: ICGEB

summary: MDA-MB-231 are a metastatic triple-negative breast cancer cell line that bears a missense p53 mutation (R280K). We depleted endogenous mutp53 in MDA-MB-231 cells by siRNA transfection, and treated the cells with Tumor Necrosis Factor (TNF)-alpha. Microarray analysis was performed to evaluate the impact of mutant p53 on the transcriptional response triggered by TNFα in these cells.

overall_design: MDA-MB-231 cells transfected with control or p53 siRNA were treated with TNFα for 20 hrs or left untreated. The study comprises four experimental points, each in triplicate.

first: Giulio

last: Di Minin

first: Arianna

last: Bellazzo

first: Licio

last: Collavin


title: Experimental gene expression analysis of 12 cancer cell lines

status: Public on Jan 27 2015

city: Moscow

first: Larisa

last: Venkova

address: Miklukho-Maklaya, 16/10

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

type:
Expression profiling by array
Third-party reanalysis

summary:
The accurate choice of anti-cancer drugs is important problem of modern medicine. We developed a new method for the selection of targeted drugs based on detection of specific intracellular signaling and metabolic pathways in the bioinformatic system termed OncoFinder before the treatment.
We obtained transcriptomic data 12 human cancer cell lines (NT2/D1, Tera-1, NGP, HepG2, BT474, Skov-3, T3M4, HeLa, A549, MCF-7, Jurkat, BxPc1) before a treatment. In our research for gene expression quantile normalization of the experimental data of all 12 cell lines together, we used separately eleven gene expression datasets corresponding to different normal human tissues profiled on Illumina HT-12v3-4 platform, 4-33 samples per dataset (from GEO). Normalization datasets used for the processing of the experimental transcriptomic data: GSE17822 (GSM444688, GSM444689, GSM444690, GSM444691, GSM444692, GSM444693), GSE26852 (GSM661123, GSM661124, GSM661125, GSM661126, GSM661127, GSM661128, GSM661130), GSE32124 (GSM796359, GSM796360, GSM796361, GSM796362, GSM796363, GSM796364, GSM796365, GSM796366, GSM796367, GSM796368, GSM796369, GSM796370, GSM796371, GSM796372, GSM796373, GSM796374, GSM796375, GSM796376, GSM796377, GSM796378, GSM796379, GSM796380, GSM796381, GSM796382, GSM796383, GSM796384, GSM796385, GSM796386, GSM796387, GSM796388, GSM796389, GSM796390, GSM796391), GSE34074 (GSM841415, GSM841419, GSM841423, GSM841427, GSM841431, GSM841435), GSE37013 (GSM908514, GSM908515, GSM908516, GSM908517, GSM908518, GSM908519, GSM908520), GSE40645 (GSM998797, GSM998798, GSM998799, GSM998800, GSM998801, GSM998802, GSM998803, GSM998804, GSM998805, GSM998806, GSM998807, GSM998808, GSM998809, GSM998810), GSE42656 (GSM1047460, GSM1047462, GSM1047463, GSM1047467), GSE52130 (GSM1260102, GSM1260103, GSM1260104, GSM1260105, GSM1260106, GSM1260107, GSM1260108), GSE54563 (GSM1318920, GSM1318921, GSM1318922, GSM1318923, GSM1318924, GSM1318925, GSM1318926, GSM1318927, GSM1318928, GSM1318929, GSM1318930, GSM1318931, GSM1318932, GSM1318933, GSM1318934, GSM1318935, GSM1318936, GSM1318937, GSM1318938, GSM1318939, GSM1318940, GSM1318941, GSM1318945, GSM1318946, GSM1318947), GSE57218 (GSM1380887, GSM1380888, GSM1380956, GSM1380957, GSM1380958, GSM1380959), GSE60709 (GSM1486145,  GSM1486146, GSM1486160, GSM1486161, GSM1486162, GSM1486163, GSM1486164, GSM1486165, GSM1486166, GSM1486167, GSM1486168, GSM1486169, GSM1486170, GSM1486171, GSM1486172, GSM1486173).  Normalization of the 12 new cell line data was performed independently 11 times together with the data from the GSM ID numbers listed above. For GSM1486145, data for replicate samples 34 and 35 were used.  For sample GSM1486146, data for replicate sample 36 was used.

overall_design: Total RNA obtained from NT2/D1, Tera-1, NGP, HepG2, BT474, Skov-3, T3M4, HeLa, A549, MCF-7, Jurkat, BxPc1 cell lines.

first: Anton

last: Buzdin


title: Proteomic signatures of extracellular vesicles secreted by non-mineralizing and mineralizing human osteoblasts and stimulation of tumor cell growth

city: Rotterdam

first: Jeroen

last: van de Peppel

address: 's Gravendijkwal 230

institute: ErasmusMC

summary: Beyond forming bone, osteoblasts play pivotal roles in various biological processes, including hematopoiesis and bone metastasis. Extracellular vesicles (EVs) have recently been implicated in intercellular communication via transfer of proteins and nucleic acids between cells. Here, we focused on the proteomic characterization of non-mineralizing (NMOBs) and mineralizing (MOBs) human osteoblast (SV-HFOs) EVs and investigated their effect on human prostate cancer (PC3) cells by microscopic, proteomic and gene expression analyses. Proteomic analysis showed that 97% of the proteins were shared among NMOB and MOB EVs, and 30% were novel osteoblast-specific EV proteins. Label-free quantification demonstrated mineralization stage-dependent five-fold enrichment of 59 and 451 EV proteins in NMOBs and MOBs, respectively. Interestingly, bioinformatic analyses of the osteoblast EV proteomes and EV-regulated prostate cancer gene expression profiles showed that they converged on pathways involved in cell survival and growth. This was verified by in vitro proliferation assays where osteoblast EV uptake led to two-fold increase in PC3 cell growth compared to cell-free culture medium-derived vesicle controls. Our findings elucidate the mineralization stage-specific protein content of osteoblast-secreted EVs, show a novel way by which osteoblasts communicate with prostate cancer, and open up innovative avenues for therapeutic intervention.

overall_design: PC3 cells were treated with extracellular vesicles from non-mineralizing and mineralizing SV-HFOs for three different incubation times (4hrs, 24hrs, 48hr)

first: Jess

last: Morhayim

first: Hans

last: van Leeuwen