title: Lysophosphatidic Acid Receptor 4 is transiently expressed during cardiac differentiation and critical for repair of the damaged heart

status: Public on Jun 17 2016

city: Seoul

first: Choon-Soo

last: Lee

address: 28 Yongon-Dong, Jongno-gu

institute: Seoul National University Hospital

summary: Efficient differentiation of pluripotent stem cells (PSCs) into cardiac cells is essential for the development of new therapeutic modalities to repair damaged heart tissue. We identified a novel cell surface marker, the G protein-coupled receptor lysophosphatidic acid receptor 4 (LPAR4), specific to cardiac progenitor cells (CPCs) and determined its functional significance and therapeutic potential. During in vitro differentiation of mouse and human PSCs toward cardiac lineage, LPAR4 expression peaked after 3−7 days of differentiation in cardiac progenitors and then declined. In vivo, LPAR4 was specifically expressed in the early stage of embryonal heart development, and as development progressed, LPAR4 expression decreased and was non-specifically distributed. We identified the effective agonist octadecenyl phosphate and a p38 MAPK blocker, as the downstream signal blocker. Sequential stimulation and inhibition of LPAR4 using these agents enhanced the in vitro efficiency of cardiac differentiation from mouse and human PSCs. Importantly, in vivo, this sequential stimulation and inhibition of LPAR4 reduced the infarct size and rescued heart dysfunction in mice. In conclusion, LPAR4 is a novel CPC marker transiently expressed only in heart during embryo development. Modulation of LPAR4-positive cells may be a promising strategy for repairing myocardium after myocardial infarction.

overall_design: 12 samples are analyzed (4 groups, triplicates) and 1 group (piPS cell_0day) is control.

first: Jin-Woo

first: Yong-Rim

last: Ryu

first: Jaewon

first: HyunJu

last: Son

first: Hyun-Jai

last: Cho

first: Hyo-Soo

last: Kim


title: Identification of genes controlled by Ikaros and IL-7 in the mouse Ikaros-deficient pre-B cell line BH1

status: Public on Nov 30 2013

city: Illkirch

first: Susan

last: Chan

address: 1, rue Laurent Fries

country: France

institute: IGBMC

summary: The aim of the experiment was to compare to single and combined effect of Ikaros activation and IL-7 withdrawal in the Ikaros-null pre-B cell line BH1

overall_design: The mouse BH1 pre-B cell line was transduced with retroviruses encoding Bcl2 and an Ikaros-estrogen receptor fusion protein. Doubly transduced cells were purified by FACS (BH1-Bcl2-Ik1ER). The transcriptome of these cells was analyzed at time 0, and after 6h and 24h of induction of Ikaros activity with 4-hydroxytamoxifen (4OHT) and/or withdrawal of IL-7. Samples from 2 independent experiments were analyzed (exp1 and exp2).

first: Philippe

last: Kastner


title: The Hematopoietic System - Myeloid arm

status: Public on Jan 01 2014

city: Copenhagen

first: Nicolas

last: Rapin

address: Ole Maaloes vej 5

department: Finsen Laboratory

country: Denmark

institute: Copenhagen University

summary: We used microarray to create a normal cell landscape for the myeloid arm of the hematopoietic system.

overall_design:
Mononuclear bone marrow cells from heathly donors were enriched for 34+ and hematopoietic stem and progenitor cells were sorted by FACS.
Bone marrow cells were aspirated from the posterior iliac crest of healthy subjects, according to the standard protocol of the Department of Hematology, Rigshospitalet University of Copenhagen (Denmark), and in accordance with the Declaration of Helsinki. All samples were obtained after informed consent according to guidelines established by the local ethics committee, which are in accordance with the Declaration of Helsinki. Hematopoietic stem cells (HSCs) and hematopoietic progenitors (HPCs) with the following immunophenotypes were purified essentially as described in earlier1-3 paper using a FACS Aria I cell sorter (BD Bioscience): HSCs: Lin−, CD34+, CD38−, CD90+, CD45RA−, multipotent progenitors (MPPs): Lin−, CD34+, CD38−, CD90−, 45RA−), common myeloid progenitors (CMPs; Lin−, CD34+, CD38+, CD45RA−, CD123+), megakaryocyte-erythroid progenitors (MEPs; Lin−, CD34+, CD38+, CD45RA−, CD123−) and granulocyte-macrophage progenitors (GMPs; Lin−, CD34+, CD38+, CD45RA+, CD123+).  BM populations representing early and late promyelocytes (Early_PMs, Late_PMs), myelocytes (MYs), metamyelocytes (MMs), band cells (BCs), and bone marrow polymorphonuclear neutrophil granulocytes (BM_PMNs) were isolated by flow cytometry-based cell sorting :
Eraly_PM( LIN neg,  FSC hi,  SSC int,  CD34 neg,  CD15 int,  CD49d hi,  CD33 hi,  CD11b neg,  CD16 neg )
Late_PM( LIN neg,  FSC hi,  SSC hi,  CD34 neg,  CD15 hi,  CD49d hi,  CD33 hi,  CD11b neg,  CD16 neg )
MY( LIN neg,  FSC hi,  SSC hi,  CD34 neg,  CD15 hi,  CD49d hi,  CD33 hi,  CD11b hi,  CD16 neg)
MM( LIN neg,  FSC hi,  SSC hi,  CD34 neg,  CD15 hi,  CD49d neg,  CD33 neg,  CD11b hi,  CD16 neg)
BC( LIN neg,  FSC hi,  SSC hi,  CD34 neg,  CD15 hi,  CD49d neg,  CD33 neg,  CD11b hi,  CD16 int )
PMN( LIN neg,  FSC hi,  SSC hi,  CD34 neg,  CD15 hi,  CD49d neg,  CD33 neg,  CD11b hi,  CD16 hi )

first: Johan

last: Jendholm

first: Kim

last: Theilgaard-Mönch

first: Helena

last: Mora Jensen


title: Individual letters of the RNA polymerase II CTD code govern distinct gene expression programs in fission yeast

status: Public on Mar 13 2014

city: London

first: Danny

middle: Asher

last: Bitton

address: Darwin Building, Gower Street

department: Department of Genetics, Evolution & Environment

country: United Kingdom

institute: University College London

type: Expression profiling by high throughput sequencing

summary: The primary structure and phosphorylation pattern of the tandem YSPTSPS repeats of the RNA polymerase II CTD comprise an informational code that coordinates transcription, chromatin modification, and RNA processing. To gauge the contributions of individual CTD coding “letters” to gene expression, we analyzed the poly(A)+ transcriptomes of fission yeast mutants that lack each of the four inessential CTD phosphoacceptors: Tyr1, Ser2, Thr4, and Ser7. There was a hierarchy of CTD mutational effects with respect to the number of dysregulated protein-coding RNAs, with S2A (n=227) >> Y1F (n=71) > S7A (n=58) >> T4A (n=7). The majority of the protein-coding RNAs affected in Y1F cells were coordinately affected by S2A, suggesting that Tyr1-Ser2 constitutes a two-letter code “word”. Y1F and S2A elicited increased expression of genes encoding proteins involved in iron uptake (Frp1, Fip1, Fio1, Str3, Str1, Sib1), without affecting the expression of the genes that repress the iron regulon, implying that Tyr1-Ser2 transduces a repressive signal. Y1F and S2A cells had increased levels of ferric reductase activity and were hypersensitive to phleomycin, indicative of elevated intracellular iron. The T4A and S7A mutations had opposing effects on the phosphate response pathway. T4A reduced the expression of two genes encoding proteins involved in phosphate acquisition (the Pho1 acid phosphatase and the phosphate transporter SPBC8E4.01c), without affecting the expression of known genes that regulate the phosphate response pathway, while S7A increased pho1+ expression. Meiotic genes were enriched among those up-regulated in S7A cells. These results highlight specific cellular gene expression programs that are responsive to distinct CTD cues.

overall_design: Interrogation of the S. pombe transcriptome using polyA+ strand specific RNA sequencing (Illumina HiSeq 2000) in cultures. A total of 16 samples were analysed: two biological repeates of each WT, Y1F, S2A, T4A, S7A,Y1F-S7A, S2A-S7A and T4A-S7A strains

first: Beate

last: Schwer

middle: A

first: Jürg

last: Bähler

first: Stewart

last: Shuman

first: Sandra

last: Codlin

first: Samuel

last: Marguerat


title: Global Gene Expression Profiling in wildtype and PAI-1 Knockout Murine Heart and Kidney.

status: Public on Apr 23 2014

city: Des Moines

first: Chunfa

last: Jie

state: IA

address: 3200 Grand Ave

country: USA

institute: Des Moines University

summary: Fibrosis is defined as an abnormal matrix remodeling and loss of tissue homeostasis due to excessive synthesis and accumulation of extracellular matrix proteins in tissues. At present, there is no effective therapy for organ fibrosis. Previous studies demonstrated that aged plasminogen activator inhibitor-1(PAI-1) knockout mice develop spontaneously cardiac-selective fibrosis without affecting any other organs including kidney. Therefore, the PAI-1 knockout model of cardiac fibrosis provides an excellent opportunity to find the igniter(s) of cardiac fibrosis and its status in unaffected organs. We hypothesized that differential expressions of profibrotic and antifibrotic genes in PAI-1 knockout hearts and unaffected organs lead to cardiac selective fibrosis. In order to address this prediction, we have used a genome-wide gene expression profiling of transcripts derived from aged PAI-1 knockout hearts and kidneys. The variations of global gene expression profiling were compared within four groups: wildtype heart vs. knockout heart; wildtype kidney vs. knockout kidney; knockout heart vs. knockout kidney and wildtype heart vs. wildtype kidney. Analysis of illumina-based microarray data revealed that several genes involved in different biological processes such as immune system processing, response to stress, cytokine signaling, cell proliferation, adhesion, migration, matrix organization and transcriptional regulation were affected in hearts and kidneys by the absence of PAI-1, a potent inhibitor of urokinase- and tissue-type plasminogen activator. Importantly, the expressions of a number of genes, involved in profibrotic pathways were upregulated or downregulated in PAI-1 knockout hearts compared to wildtype hearts and PAI-1 knockout kidneys. To our knowledge, this is the first comprehensive report on the influence of PAI-1 on global gene expression profiling in the heart and kidney and its implication in several biological processes including fibrogenesis.

overall_design: Total RNA was extracted from hearts and kidneys derived from three PAI-1 knockout (12- month old) and three wild-type mice (12-month old) using RNeasy Fibrous Tissue Mini Kit (Qiagen, Valencia, CA) following the manufacturer’s instructions. The quality of RNA (RNA Integrity, RIN) in all 12 samples (3 wildtype hearts; 3 PAI-1 KO hearts; 3 wildtype kidneys; and 3 PAI-1 KO kidneys) was checked using the bioanalyzer. We have used a genome-wide gene expression profiling of transcripts derived from aged PAI-1 knockout hearts and kidneys. The variations of global gene expression profiling were compared within four groups: wildtype heart vs. knockout heart; wildtype kidney vs. knockout kidney; knockout heart vs. knockout kidney and wildtype heart vs. wildtype kidney.

first: Asish

middle: K

last: Ghosh


title: RNA expression data from kidneys lacking von Hippel-Lindau (VHL) protein in tubular epithelial cells

status: Public on Jan 17 2014

city: Nashville

first: Navid

last: Farsijani

state: Tennesee

address: 1161 21st Avenue South

institute: Vanderbilt University

summary: The cellular response to low oxygen supply is mediated by hypoxia-inducible factors (HIF). Under hypoxic conditions, HIF is stabilized and target genes are induced. Under normoxia, however, HIF is ubiquitinated through the von Hippel-Lindau protein (VHL), which results in proteasomal degradation. HIF activation leads to induction of genes involved in erythropoiesis, angiogenesis, and cell survival. Furthermore, HIF orchestrates a metabolic shift from oxidative phosphorylation to glycolysis to facilitate ATP production under low oxygen conditions. We used microarrays to detail gene expression changes in kidneys with stable HIF activation in renal tubules, which was achieved by tubule-specific VHL ablation.

overall_design: Three week old Pax8-rtTA;LC-1;Vhl-floxed mice (n=4) and control littermates (n=4) were treated with doxycyline in drinking water for two weeks and put back on normal drinking water for one week. Six weeks old mice were sacrificed and kidneys harvested. Total RNA was extracted and hybridized on Affymetrix microarrays.

first: N

middle: M

first: V

middle: H

last: Haase


title: Influenzavirus serotype association to global whole blood transcriptional changes

status: Public on Apr 01 2014

city: Singapore

first: Ahmad Nazri

last: Mohamed Naim

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

department: Infectious disease

country: Singapore

institute: Genome institute of Singapore

summary: Febrile patients PCR positive for H1N1 swine flu, seasonal H1N1  and seasonal H3N2 in nasal swabs and  controls consisting of febrile patients with rhinovirus infection or febrile patients of non-viral etiology (nasal swabs PCR negative for common respiratory viruses and blood PCR negative for dengue and parvovirus B19) were assessed consecutively for global transcriptional changes in whole blood

overall_design: Peripheral whole blood collected in PAX-gene tubes and extracted for total RNA

first: Ahmad

middle: N

last: Naim

first: Chee

middle: G

last: Foo

first: Thomas

last: Tolfvenstam

first: Martin

middle: L

last: Hibberd


title: Gene expression of hepatocyte cell line (HepG2) treated with H2O2 to induce senescence relative to control untreated cells

status: Public on Jan 01 2015

city: Cambridge

first: Nicholas

middle: B

last: Shannon

address: Robinson Way

department: Oncology

institute: Cambridge Research Institute

summary: We used microarrays to identify a transcriptional signature of oxidative stress induced senescence in a hepatocyte cell line (HepG2) by globally assessing differential gene expression after treatment with 0.5mM of H2O2 for 60 minutes, compared to nontreated cells as a control.

overall_design: We performed genome-wide comparison of gene expression and identified genes that are differentially expressed in senescent HepG2 cells relative to untreated cells, 4 biological replicates per condition

first: Aloysious

last: Aravinthan


title: High resolution comparative genomic hybridisation analysis of ductal carcinoma in situ of the breast

status: Public on Oct 15 2013

city: Bethesda

first: Sean

last: Davis

state: MD

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

type: Genome variation profiling by genome tiling array

summary: In a previous study of ductal carcinoma in situ (DCIS) of the breast (see GEO accession #GSE7882) we identified six genes at chromosome 17q21.33 that were over-expressed in high grade cases, and showed a correlation between expression level and gene copy number. The aim of this study was to determine whether potential drivers of high grade breast cancer growth could be identified at 17q21.33. High resolution comparative genomic hybridisation was used to interrogate genomic aberrations in laser capture microdissected samples of ductal carcinoma in situ.

overall_design: Amplified DNA from laser capture microdissected ductal carcinoma in situ (DCIS) was hybridised with amplified male DNA are a reference.

middle: R

first: Lucy

last: Webster

first: Rosemary

last: Balleine

first: Pamela

middle: J

last: Provan

first: Dinny

last: Graham

first: Karen

last: Byth

first: Robert

last: Walker

first: Adrienne

last: Morey

first: Robyn

last: Ward

last: Hawkins

first: Christine

last: Clarke

first: Paul

middle: S

last: Meltzer


title: Expression data from peripheral blood

status: Public on Feb 15 2014

city: Shenzhen

first: Xinchun

last: Chen

address: No.29, Bulan Road

country: China

institute: Shenzhen Third People's Hospital

summary:
C1q expression increases significantly in the peripheral blood of patients with active tuberculosis compared to healthy controls and individuals with latent TB infection. The percentage of C1q-expressing CD14 positive cells is significantly increased in active TB patients. C1q expression in the peripheral blood correlates with sputum smear positivity in tuberculosis patients and is reduced after anti-tuberculosis chemotherapy. Notably, receiver operating characteristic analysis showed that C1qC mRNA levels in peripheral blood efficiently discriminate active from latent tuberculosis infection and healthy controls. Additionally, C1qC protein level in pleural effusion shows improved power in discriminating tuberculosis from non-tuberculosis pleurisy when compared to other inflammatory markers, such as IL-6 and TNF-α
C1q expression correlates with active disease in human tuberculosis. C1q could be a potential diagnostic marker to discriminate active tuberculosis from latent tuberculosis infection as well as tuberculosis pleurisy from non-tuberculosis pleurisy.

overall_design: Complement gene expression in peripheral blood mononuclear cells of tuberculosis patients and controls were determined using whole genome transcriptional microarray assays. The mRNA and protein levels of three C1q components, C1qA, C1qB, and C1qC, were further validated by qRT-PCR and enzyme-linked immunosorbent assay, respectively. The percentages of C1q expression in CD14 positive cells were determined by flow cytometry.  Finally, C1qC protein level was quantified in the pleural fluid of tuberculosis and non-tuberculosis pleurisy.

first: Yi

last: Cai


title: T lymphocytes from Chronic HCV-infected patients express unique pro-apoptotic gene signature.

status: Public on Aug 19 2013

city: Beijing

first: Binbin

last: Zhao

address: No. 9 Dong Dan San Tiao, Dongcheng District

institute: Institute of Pathogen Biology, CAMS&PUMC

summary:
Although extensive studies have demonstrated the gene expression patterns of antigen-specific CD4+ and CD8+ T-cells during chronic hepatitis C virus (HCV) infection, the transcriptional profiles of global CD4+ and CD8+ T-cells remains unclear. In this report, we recruited 10 long-term (~20 years) treatment-naïve chronic HCV (CHC) patients and 5 healthy donors (HDs) to investigate differences in global CD4+ and CD8+ T-cells gene expression profile.
Global CD4+ and CD8+ T-cells showed unique transcriptional profiles in the expression of apoptosis-related genes. We identified BCL2, PMAIP1, and CASP1 in CD4+ T-cells and IER3 and BCL2A1 in CD8+ T-cells from CHC patients as HCV-specific gene signatures. The unique apoptosis-related gene expression profilesin global CD4+ and CD8+ T-cells  programmed by chronic HCV infection seemed to enhance activation-induced apoptosis, which was suffered by  global CD4+ and CD8+ T-cells.

overall_design: We obtained 15 blood samples to identify the gene expression signatures of global CD4+ and CD8+ T-cells due to chronic HCV infection. The samples included: 5 samples from high HCV viral load patients (HCV-h), 5 samples from low HCV viral load (HCV-l) and 5 samples from healthy donors (HD). HCV patients were all Ab+ and treatment-naive prior to the study. Samples were taken once from each individual. Global CD4+ and CD8+ T-cells were enriched by microbeads, and total RNA were used in gene chip analysis.

first: Bin-Bin

first: Su-Jun

last: Zheng

first: Lu-Lu

last: Gong

first: Yu

last: Wang

first: Cai-Feng

first: Wen-Jing

last: Jin

first: Ding

last: Zhang

first: Xiao-Hui

last: Yuan

first: Jian

last: Guo

first: Zhong-Ping

last: Duan

first: You-Wen

last: He


title: Caco-2 cells cultured in the presence of Lactobacillus fermentum strains AGR1485 or AGR1487

status: Public on May 01 2013

city: Palmerston North

first: Wayne

last: Young

address: Tennent Drive

country: New Zealand

institute: AgResearch

summary: Transcriptional profiling of Caco-2 cells co-cultured with L. fermentum AGR1487 (isolated from IBD patient), Caco-2 cells co-cultured with L. fermentum AGR1485 (isolated from healthy volunteer), or Caco-2 cells alone (Control).

overall_design: Three-condition experiment with dye swap, A vs B, A vs C, B vs C, 8 biological replicates: A = Control, B = AGR1487, C = AGR1485

first: Rachel

last: Anderson


title: Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome.

status: Public on Jan 11 2013

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

type: Methylation profiling by high throughput sequencing

summary: Cytosine methylation is involved in various biological processes such as silencing of transposable elements (TEs) and imprinting.  Multiple pathways regulate DNA methylation in a sequence specific manner. What factors regulate DNA methylation at a given site in the genome largely remains elusive. Here by generating single nucleotide resolution maps of DNA methylation we have surveyed the effect of mutations in a comprehensive list of genes involved in gene silencing in Arabidopsis. We find that DNA methylation is site-specifically regulated by different factors. Furthermore, we have identified novel regulators of DNA methylation. We have generated a comprehensive resource to further understanding the control of DNA methylation patterning.

overall_design: Whole genome methylation maps of 86 silencing mutants involved in gene silencing and chromatin modifications were generated using BS-seq (Cokus et al., Nature 2008 ). Wild type replicate 1 dataset can be found at GSM938370.


title: Affymetrix SNP array data for pediatric rhabdomyosarcoma (RMS)

status: Public on Aug 12 2013

city: Tokyo

first: Riki

last: Nishimura

address: 7-3-1, Hongo, Bunkyo-ku

country: Japan

institute: University of Tokyo

type: Genome binding/occupancy profiling by SNP array

summary: To elucidate the pathogenesis of rhabdomyosarcoma (RMS), particularly for different subgroups, we performed a SNP array-based copy number analysis of 54 RMS specimens from primary cases with ERMS (N = 30), ARMS (N = 14), unclassified RMS (N = 1), and RMS of unknown histology (N = 3) together with 7 RMS-derived cell lines. The ERMS subtype was characterized by hyperploidy and was significantly associated with gains of chromosomes 2, 8, and 12, whereas majority of ARMS cases exhibited near-diploid copy number profiles.  Recurrent loss of heterozygosity (LOH) of chromosomes 3 (28.6%) and 15q (35.7%) was detected in ARMS. Uniparental disomy/polysomy of 11p was commonly found in both tumor types.  Focal gains/amplifications were associated mostly with PAX3-FOXO1 (5/10) or PAX7-FOXO1 (6/6) fusions, but novel amplified regions were also found, including the IRS2 in 2 ARMS.  Gain of 13q was significantly associated with good patient outcome in ERMS.  These findings not only illustrate genetic differences between ARMS and ERMS but also provide novel insights into the pathogenesis of RMS.

overall_design: Copy number analysis of Affymetrix 50K/250K SNP arrays was performed for 54 RMS samples.

last: Nishimrua

first: Junko

last: Takita

first: Aiko

last: Sato-Otsubo

first: Motohiro

last: Kato

first: Katsuyoshi

last: Koh

first: Ryoji

last: Hanada

first: Yukichi

last: Tanaka

first: Masashi

last: Sanada

first: Yasuhide

last: Hayashi

first: Seishi

last: Ogawa


title: Whole blood transcriptional signature distinguishes viral infection from bacterial infection in febrile young children.

status: Public on Oct 15 2012

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

summary: Viral infections are among the most common causes for fever without an apparent source (FWS) in young children; however, many febrile children are treated with antibiotics despite the absence of bacterial infection.  Adenovirus, human herpesvirus 6 (HHV-6) and enterovirus are detected in children with FWS more often than other viral species.  Virus and bacteria interact with pattern recognition receptors in circulating blood leukocytes and trigger specific host transcriptional programs that mediate immune response, and unique transcriptional signatures may be ascertained to discriminate between viral and bacterial causes for children with FWS.  Microarray analyses were conducted on peripheral blood samples obtained from 51 pediatric patients with confirmed adenovirus, human herpesvirus 6 (HHV-6), enterovirus or bacterial infection.  Whole blood transcriptional profiles could clearly distinguish febrile children from healthy controls, and febrile children with viral infections from afebrile children carrying the same virus.  Molecular pathways regulating host immune response were the most affected in febrile children with infection.  Pattern recognition programs were prominently activated in all febrile children with infection, while differential activation of transcriptional programs was observed among viral species.  Interferon signaling pathway was uniquely activated in children with febrile viral infection, while a different set of pathways was uniquely activated in children with bacterial infection.  Transcriptional signatures were identified and classified febrile children with viral or bacterial infection with 87% overall accuracy, an improvement from the current clinical practice of deducing from white blood cell (WBC) count status.  Similar degree of accuracy was observed when we validated the signature probes on data sets from an independent study with different microarray platforms.  The current study confirms the clinical utility of blood transcriptional analysis, suggests the composition of transcriptional signatures which can be used to ascertain the infectious etiology of febrile young children without an apparent source, thus limit the overuse of antibiotics on febrile children presenting with this common clinical complaint.

overall_design: Total RNA samples extracted from whole blood of young children were processed for hybridization onto Illumina Human-HT12 version 4 beadchips, and differential expression of the transcripts was analyzed between sick children with either viral or bacterial infection and healthy children.

first: Richard

last: Hu

first: Seth

last: Crosby

first: Gregory

last: Storch


title: Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes

status: Public on Sep 21 2012

city: Berkeley

first: Toshiro

state: CA

address: 211 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

summary: The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes DNA demethylation prior to fertilization, but the targeting preferences and biological significance of this process remain unclear. Here, we show that active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for all of the demethylation in the central cell, and preferentially targets small, AT-rich and nucleosome-depleted transposable elements. The vegetative cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation of similar sequences, and lack of DEMETER in vegetative cells causes reduced small RNA-directed DNA methylation of transposons in sperm. Our results demonstrate that demethylation in companion cells reinforces transposon methylation in plant gametes, thereby assuring stable silencing of transposable elements across generations

overall_design: Examination of DNA methylation in Arabidopsis endosperm, embryo, and pollen

first: Daniel

last: Zilberman


title: Gene expression of samples derived from normal lung and patients with small cell lung cancer (SCLC) or non-small cell lung cancer (NSCLC)

status: Public on Aug 25 2012

city: Vienna

first: Stefan

last: Kastner

address: Dr. Boehringer-Gasse 5-11

country: Austria

institute: Boehringer Ingelheim RCV

summary: Differences in gene expression profiles regarding the expression of genes encoding for proteins with G protein-coupled receptor (GPCR) activity between SCLC and NSCLC and normal lung samples was successfully examined.

overall_design: In the present study, 8 SCLC, 16 NSCLC and 14 normal lung RNA samples (human) had been purchased from OriGene Technologies. Gene expression analysis was performed using Affymetrix microarrays (Human Exon 1.0 ST Array).

first: Tilman

last: Voss

first: Simon

last: Keuerleber

first: Christina

last: Glöckel

first: Michael

last: Freissmuth

first: Wolfgang

last: Sommergruber


title: Tracing pluripotency of human early embryos and embryonic stem cells by single cell RNA-seq

status: Public on Aug 10 2013

first: Mingyu

last: Yang

address: 5 Yiheyuan Road

institute: Peking University

summary: Find the casual relationship between gene expression network and cellular phenotype at single cell resolution. We collected donated human pre-implatation embryos, and the embryonic stem cells derived from them, isolate individual cells, prepared single cell cDNAs, and sequenced them by HiSeq2000. Then we analyzed the expression of known RefSeq genes.

overall_design:
We get transcriptome of 124 individual cells from human pre-implantation embryos and human embryonic stem cells by applying single cell RNA-seq technique we recently developed[1][2][3][4]. We did in-depth bioinformatic analysis to these data and found very dynamic expression of protein-coding genes.
[1] Tang, F. et al. (2010a) Tracing the Derivation of Embryonic Stem Cells from the Inner Cell Mass by Single-Cell RNA-Seq Analysis. Cell Stem Cell 6, 468-478.
[2] Tang, F. et al. (2010b) RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat Protocols 5, 516-535.
[3] Tang, F. et al. (2009) mRNA-Seq whole-transcriptome analysis of a single cell. Nat Meth 6, 377-382.
[4] Tang, F. et al. (2011) Development and applications of single-cell transcriptome analysis. Nat Meth 8, S6-S11.

first: Fuchou

last: Tang

first: Jie

last: Qiao

first: Ruiqiang

last: Li


title: Development and Validation of a Novel Molecular Biomarker Diagnostic Test for the Early Detection of Sepsis

status: Public on Nov 01 2011

city: Brisbane

first: Gareth

last: Price

state: Queensland

address: Carmody Road

country: Australia

institute: Queensland Facility for Advanced Bioinformatics

summary:
Introduction: Sepsis is a complex immunological response to infection characterized by early hyperinflammation followed by severe and protracted immunosuppression, suggesting that a multi-marker approach has the greatest clinical utility for early detection, within a clinical environment focused on SIRS differentiation. Pre-clinical research using an equine sepsis model identified a panel of gene expression biomarkers that define the early aberrant immune activation. Thus, the primary objective was to apply these gene expression biomarkers to distinguish patients with sepsis from those who had undergone major open surgery and had clinical outcomes consistent with systemic inflammation due to physical trauma and wound healing.
Methods: This was a multi-centre, prospective clinical trial conducted across 4 tertiary critical care settings in Australia. Sepsis patients were recruited if they met the 1992 Consensus Statement criteria and had clinical evidence of systemic infection based on microbiology diagnoses (n=27). Participants in the post-surgical (PS) group were recruited pre-operatively and blood samples collected within 24 hours following surgery (n=38).  Healthy controls (HC) included hospital staff with no known concurrent illnesses (n=20). Each participant had minimally 5ml of PAXgene blood collected for leucocyte RNA isolation and gene expression analyses. Affymetrix array and multiplex tandem (MT)-PCR studies were conducted to evaluate transcriptional profiles in circulating white blood cells applying a set of 42 molecular markers that had been identified a priori. A LogitBoost algorithm was used to create a machine learning diagnostic rule to predict sepsis outcomes.
Results: Based on preliminary microarray analyses comparing HC and sepsis groups. A panel of 42-gene expression markers were identified that represented  key innate and adaptive immune function, cell cycling, WBC differentiation, extracellular remodelling and immune modulation pathways. Comparisons against GEO data confirmed the definitive separation of the sepsis cohort. Quantitative PCR results suggest the capacity for this test to differentiate severe systemic inflammation from HC is 92%. AUC ROC curve findings demonstrated sepsis prediction within a mixed inflammatory population, was between 86 - 92%.
Conclusions: This novel molecular biomarker test has a clinically relevant sensitivity and specificity profile, and has the capacity for early detection of sepsis via the monitoring of critical care patients.
GEO Note: Data made available represents the preliminary microarray investigation performed on Human U133 Plus 2.0 GeneChips (Affymetrix), assaying 41 patient samples (Sepsis n=10, Post-Surgical n=11, Control n=20).

overall_design: This was a multi-centre, prospective clinical trial conducted across 4 tertiary critical care settings in Australia. Sepsis patients were recruited if they met the 1992 Consensus Statement criteria and had clinical evidence of systemic infection based on microbiology diagnoses (n=27). Participants in the post-surgical (PS) group were recruited pre-operatively and blood samples collected within 24 hours following surgery (n=38).  Healthy controls (HC) included hospital staff with no known concurrent illnesses (n=20). Each participant had minimally 5ml of PAXgene blood collected for leucocyte RNA isolation and gene expression analyses. The GEO data represents the preliminary microarray investigation performed on Human U133 Plus 2.0 GeneChips (Affymetrix), assaying 41 patient samples (Sepsis n=10, Post-Surgical n=11, Control n=20).

first: Allison

last: Sutherland

first: Mervyn

last: Thomas

first: Roslyn

last: Brandon

first: Jeffrey

last: Lipman

first: Benjamin

first: Anthony

last: McLean

first: Ranald

last: Pascoe

first: Thu

last: Nguyen

first: Glenn

last: Stone

first: Deon

last: Venter


title: Genome-wide transcriptional profiling of HIV positive and negative adults with active tuberculosis, latent TB infection and other diseases

status: Public on Oct 23 2013

first: Michael

last: Levin

address: South Kensington Campus

department: Paediatrics

institute: Imperial College London

summary:
The study aimed to define transcriptional signatures for detection of active TB (TB) compared to latent TB infection (LTBI) as well as to other diseases (OD) with similar clinical phenotypes in patients with and without HIV in two African adult populations.
Transcriptional signatures were identified that distinguished active TB from LTBI, active TB from other diseases, and active TB from both LTBI and other diseases in HIV+/- patients.

overall_design: Adults were recruited from Cape Town, South Africa (n=300) and Karonga, Malawi (n=237) who were either HIV+  or HIV - with either active TB, LTBI or OD. Blood was collected into PAX gene tubes (PreAnalytiX). Total RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). Labeled cRNA was hybridized to Illumina Human HT-12 Beadchips. Data were analysed in R.

first: Suzanne

middle: T

last: Anderson

first: Lachlan

last: Coin

first: Amelia

middle: C

last: Crampin

first: Hazel

last: Dockrell

first: Brian

last: Eley

first: Neil

last: French

first: Robert

last: Heyderman

first: Martin

last: Hibberd

first: Myrsini

last: Kaforou

first: Florian

last: Kern

first: Paul

last: Langford

first: Ling

last: Ling

last: Wilkinson

first: Victoria

last: Wright


title: Host gene expression signatures of influenza A H1N1 and H3N2 virus infection in adults

status: Public on Nov 16 2013

city: Durham

first: Geoffrey

last: Ginsburg

state: NC

address: 101 Science Dr, CIEMAS 2111, Box 3382

department: Genomic Medicine

institute: Duke University Medical Center

summary:
Diagnosis of influenza A infection is currently based on clinical symptoms and pathogen detection.  Use of host peripheral blood gene expression data to classify individuals with influenza A virus infection represents a novel approach to infection diagnosis
We used microarrays to assay peripheral blood gene expression at baseline and every 8 hours for 7 days following intranasal influenza A H1N1 or H3N2 inoculation in healthy volunteers.  We determined groups of coexpressed genes that classified symptomatic influenza infection.  We then tested this gene expression classifier in patients with naturally acquired respiratory illness.

overall_design: We experimentally inoculated healthy volunteers with intranasal influenza A H1N1 and H3N2.  Symptoms were documented and peripheral blood samples drawn into PAXgene RNA tubes for RNA isolation.  We further enrolled patients presenting to the Emergency Department with naturally acquired respiratory illness, and documented symptoms and collected PAXgene RNA samples for RNA isolation.

first: C

middle: W

last: Woods

first: G


title: Campylobacter jejuni Cas9 is necessary for efficient infection of Caco-2 cells and cell stress induction

status: Public on Sep 30 2018

city: Wageningen

first: Peter

last: van Baarlen

address: De Elst 1

department: Animal Sciences

country: Netherlands

institute: Wageningen University

summary:
Objective: We previously showed that Campylobacter jejuni Cas9 was necessary for full virulence and efficient induction of human cell stress followed by cell death, but no virulence mechanism could be unravelled then. Therefore, we carried out global genome-wide transcriptomics, using RNA samples extracted from cells infected by a wild-type C. jejuni strain and the corresponding cas9 deletion strain.

Methods: Caco-2 epithelial cells were infected with C. jejuni wild-type or cas9 deletion strains and RNA was extracted at 5 timepoints post-infection.

Results: Wild-type C. jejuni induced cellular stress, DNA damage and cell death pathways in Caco-2 cells continuously from 30 min up to 4 hours after infection, eventually followed by visual cell death induction after 24 hours; the corresponding cas9 deletion strain did also induce cell stress pathways within the first two hours of infection but at later timepoints, stress pathway induction had dropped and after 4 hours of infection, expression of the corresponding stress genes had normalised to near-t=0 (uninfected) expression values; the cas9 deletion strain did not lead to visual cell death induction after 24 hours.

Conclusions: Campylobacter jejuni Cas9 is necessary for full virulence of C. jejuni and is involved in the efficient induction of cellular stress pathways and eventually, cell death.

overall_design: This study was set up according to a time series, one-treatment, one-control design; treatments were inoculation with either wild-type Campylobacter jejuni strain 11168 or its isogenic cas9 gene deletion strain (delta-Cj1523). The study results contain transcriptional profiles from Caco-2 cells at 5 different timepoints (30, 60, 120, 180 and 240 minutes) post-infection, and one control (t=0, or prior to infection) Caco-2 cells. In total, this study includes data from 5 different timepoints post-infection and 1 control (t=0) timepoint. For each timepoint, 3 replicates were used. In total, n=33 arrays were used.

first: Rogier

last: Louwen

first: John

last: van der Oost


title: The response of PBMCs and primary airway epithelial cells to Influenza and RSV virus

status: Public on Mar 12 2012

city: COLUMBUS

first: IOANNIS

last: IOANNIDIS

state: OH

address: 700 CHILDRENS DRIVE

department: VACCINES AND IMMUNITY

institute: NATIONWIDE CHILDRENS HOSPITAL

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series

first: Ioannis

last: Ioannidis

first: Beth

last: McNally

first: Meredith

last: Willette

first: Emilio

last: Flano


title: RNA sequencing of sheep infraspinatus muscle after tendon release and repair under concomitant nandrolone administration

status: Public on Dec 31 2016

city: Zurich

first: Martin

last: Flück

address: Lengghalde 5

department: Balgrist Campus

country: Switzerland

institute: University of Zurich

summary: Transcripts were measured in infraspinatus muscle before (PRE) and after 16 weeks of tendon release (TR) and 6 weeks of subsequent repair (END) in the operated and contralateral (END-CC) muscle. A group of animals received intramuscular injections of nandrolone starting with the surgery (N22W). In another group injection of nandrolone was started at the time of tendon repair (N6W). The CONTROL group received no nandrolone.

overall_design: Eighteen two-year-old female Swiss Alpine sheep were subjected to release of the infraspinatus tendon in three interventional groups of six animals each (CONTROL, N22W, N6W). After 16 weeks, repair was performed in all groups by reattaching the tendon to the greater tuberosity. N22W received weekly injections of 150mg nandrolone decanoate starting immediately after tendon release. N6W received weekly intramuscular injections of 150mg nandrolone decanoate starting at the time of tendon repair. Prior to tendon release (PRE), 16 weeks after tendon release at tendon repair (TR), 6 weeks after repair (END) and in contralateral control muscle at the end of the experiment (END-CC), biopsies were collected from the operated infraspinatus muscle. Biopsies were subjected to the characterization of muscle composition and transcript expression.

first: Christoph

last: Möhl

first: Severin

last: Ruoss

first: Karl

last: Wieser


title: Expression data for normal flow sorted hematopietic cell subpopulations

status: Public on Feb 21 2010

city: Lund

first: Thoas

middle: Anna

address: Lund University Hospital

country: Sweden

institute: Dept of Clinical Genetics

summary:
Gene expression profiling of normal hematopoietic cell subpopulations

RNA extracted from flow sorted normal hematopietic cells were hybridized onto Affymetrix U133 Plus 2.0 arrays.

overall_design: Eight different flow sorted hematopoietic cell subpopulations were profiled. Two individual samples were obtained for each population.

first: Anna

last: Andersson

last: Fioretos


title: Effect of Lactobacillus plantarum MB452 on the gene expression of the intestinal epithelial cell line Caco-2

status: Public on Oct 07 2009

city: Puddle Alley

first: Alan

middle: Francis

last: McCulloch

state: Mosgiel

address: Invermay

institute: AgResearch NZ

summary: The hypothesis of this research was that probiotic bacteria that increase intestinal barrier function achieve this, partly, by increasing the expression of the genes involved in tight junction signalling in healthy intestinal epithelial cells. L. plantarum MB452 isolated from the probiotic product VSL#3 was chosen as the test bacterium because it has a robust, repeatable, positive effect tight junction integrity, as measured by the trans-epithelial electrical resistance (TEER) in vitro.

overall_design: Gene expression was compared in Caco-2 cells untreated or treated with L. plantarum MB452 for 10 hours. An equal amount of Caco-2 cell RNA from three wells of the same treatment was pooled together to yield enough RNA for the gene expression analysis; two control pools and two pools treated with L. plantarum MB452. Caco-2 cell RNA was hybridised to human oligonucleotide arrays (Agilent). Data was analysed using linear models (Limma package in Bioconductor) and differently expressed genes were examined using pathway analysis tools (Gene Ontology categories, KEGG pathways using EASE and Ingenuity Pathway Analysis).

first: Rachel

last: Anderson

first: Zaneta

last: Park-Ng


title: Gene expression analysis in children with complex seizures by influenza A (H1N1)pdm09 or rotavirus gastroenteritis

status: Public on Sep 05 2013

city: Okayama

first: Mitsuru

last: Tsuge

address: 2-5-1, Shikata-cho

department: Pediatrics

institute: Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences

summary:
The differences of clinical characteristics in complex seizures induced by influenza A(H1N1)pdm09 and rotavirus gastroenteritis are well known, but the pathogenic mechanisms remain unclear. We analyzed the gene expression profiles in the peripheral whole blood cells isolated from pediatric patients using an Affymetrix oligonucleotide microarray.
Results provide insights into the difference of the pathogenesis in the patients with complex seizures induced by influenza A(H1N1)pdm09 and rotavirus infections.

overall_design: The gene expression profiles in the peripheral whole blood of ten patients (n=5; complex seizures, n=5; control) with influenza A(H1N1)pdm09 and six patients (n=3; complex seizures, n=3; control) with rotavirus gastroenteritis were examined. Whole blood samples were collected from patients in the acute phase of the disease and in the recovery phase.

first: Takashi

last: Oka


title: Temporal expression data from 17 health human subjects before and after they were challenged with live influenza (H3N2/Wisconsin) viruses

status: Public on Jul 12 2011

city: Ann Arbor

first: Yongsheng

last: Huang

state: MI

address: 100 Washtenaw Ave

department: Bioinformatics

institute: University of Michigan

summary: The transcriptional responses of human hosts towards influenza viral pathogens are important for understanding virus-mediated immunopathology.  Despite great advances gained through studies using model organisms, the complete temporal host transcriptional responses in a natural human system are poorly understood.  In a human challenge study using live influenza (H3N2/Wisconsin) viruses, we conducted a clinically uninformed (unsupervised) factor analysis on gene expression profiles and established an ab initio molecular signature that strongly correlates to symptomatic clinical disease. This is followed by the identification of 42 biomarkers whose expression patterns best differentiate early from late phases of infection. In parallel, a clinically informed (supervised) analysis revealed over-stimulation of multiple viral sensing pathways in symptomatic hosts and linked their temporal trajectory with development of diverse clinical signs and symptoms.  The resultant inflammatory cytokine profiles were shown to contribute to the pathogenesis because their significant increase preceded disease manifestation by 36 hours.  In subclinical asymptomatic hosts, we discovered strong transcriptional regulation of genes involved in inflammasome activation, genes encoding virus interacting proteins, and evidence of active anti-oxidant and cell-mediated innate immune response. Taken together, our findings offer insights into influenza virus-induced pathogenesis and provide a valuable tool for disease monitoring and management in natural environments.

overall_design: During the challenge study, subjects had  peripheral blood taken 24 hours prior to inoculation with virus (baseline), immediately prior to inoculation (pre-challenge) and at set intervals (8 hour intervals) following challenge. RNA was extracted at Expression Analysis (Durham, NC) from whole blood using the PAXgene™ 96 Blood RNA Kit (PreAnalytiX, Valencia, CA) employing the manufacturer's recommended protocol. While whole blood RNA is initially extracted, a secondary procedure (B-globin reduction) was then employed to remove the contribution of red blood cell (RBC) RNA to the total RNA. A set of four peptide nucleic acid (PNA) oligomers whose sequences are complementary to the 3’ portions of the alpha and beta hemoglobin RNA transcripts were added to reduce globin RNA transcription due to RBC. The inhibition of globin cDNA synthesis dramatically reduces the relative amount of anti-sense, biotin-labeled cRNA corresponding to the hemoglobin transcripts. Hybridization and microarray data collection was performed using the Human Genome U133A 2.0 Array (Affymetrix, Santa Clara, CA) and expression profiles were pre-processed using robust multi-array (RMA) method

first: Geoffrey

last: Ginsburg

first: Alfred

middle: O

last: Hero III


title: CD44+ or CD44– tumor cells isolated from K19-Wnt1/C2mE mice

status: Public on Mar 17 2010

first: Osamu

last: Nagano

state: DDS PhD

address: ３５　Shinanomachi

department: Institute for Advanced Medical Research

institute: Keio University School of Medicine

summary: We hypothesized that CD44+ tumor cells might have an increased capacity for reactive oxygen species (ROS) defense in the gastric tumors of K19-Wnt1/C2mE mice. To address this possibility, we examined the expression of antioxidant genes in tumor cells isolated from K19-Wnt1/C2mE mice by fluorescence-activated cell sorting (FACS). Lineage marker (Lin)–negative cells that were CD44+ or CD44– were thus isolated from the gastric tumors of 30-week-old K19-Wnt1/C2mE mice and subjected to cDNA microarray analysis. The expression of several key antioxidant genes, including those for glutathione peroxidase (GPX) and peroxiredoxin (PRDX) isoforms, was found to be increased in CD44+ tumor cells compared with that in CD44– cells.

overall_design: Lineage marker (Lin)–negative cells that were CD44+ or CD44– were isolated from the gastric tumors of 30-week-old K19-Wnt1/C2mE mice. Total RNA was isolated and subjected to cDNA microarray analysis. Two CD44+ replicates and two CD44- replicates were examined.

first: T

last: Ishimoto

first: O

first: H

last: Saya


title: Gene expression signatures of symptomatic respiratory viral infection in adults

status: Public on Aug 06 2009

address: 470 Research Drive, Room 254, box 90141

department: Center for Genomic Medicine

institute: Duke Institute for Genome Sciences & Policy

summary:
Diagnosis of acute respiratory viral infection is currentlybased on clinical symptoms and pathogen detection.  Use of host peripheral blood gene expression data to classify individuals with viral respiratory infection represents a novel means of infection diagnosis.
We used microarrays to capture peripheral blood gene expression at baseline and time of peak symptoms in healthy volunteers infected intranasally with influenza A H3N2, respiratory syncytial virus or rhinovirus. We determined groups of coexpressed genes that accurately classified symptomatic versus asymptomatic individuals.

overall_design: We experimentally inoculated healthy volunteers with intranasal influenza, respiratory syncytial virus or rhinovirus.  Symptoms were documented and peripheral blood samples drawn into PAXgene tubes for RNA isolation.

first: Lawrence

last: Carin


title: Expression analysis of Saos-2 cells expressing p53-His273

status: Public on Apr 15 2009

city: Stockholm

first: Jeremy

last: Lambert

institute: Karolinska Institutet

summary: Our compound (PRIMA) selectively kills tumor cells expressing mutant p53. Here in our study we decided to investigate the impact of our compound on the transcriptome of p53 mutant-expressing cells, Saos2-His273.

overall_design: We plated Saos-2-His273 cells and treated them with our compound for 6h or 12h. We then harvested the cells, extracted the RNA, and followed the protocol to run affymetrix array to analyse the impact of our drug on the whole transcriptome of cells expressing mutant p53.

first: Ali

last: Moshfegh

first: Klas

last: Wiman

first: Pierre

last: Hainaut

first: Vladimir

last: Bykov


title: Regulation of intestinal epithelial cells transcriptome by enteric glial cells

status: Public on Jul 10 2009

city: Nantes

first: Raluca

last: TEUSAN

address: 1, rue gaston veil

institute: INSERM U915

summary:
Identification of cellular functions and signalling pathways of intestinal epithelial cells modulated by enteric glial cells

Keywords: Transcriptome regulation

overall_design: Two-condition experiment (intestinal epithelial cells cultured in absence or in presence of enteric glial cells) with 3 time points (t=0, 8 and 24h). 4 Biological replicates/condition. Every replicate was hybridized against a reference pool composed by a mix of the 4 replicates of t=0 condition in equal quantity.

first: Laurianne

last: Van Landeghem

first: Maxime

last: Mahé

first: Jean

last: Léger

first: Isabelle

last: Guisle

last: Teusan

first: Rémi

last: Houlgatte

first: Michel

last: Neunlist


title: Identification of target genes of cancer-related microRNAs in human cancer

status: Public on Nov 12 2012

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1 Inohana,Chuo-ku

department: School of Medicine

institute: Chiba University

summary: To identify target genes of cancer-related microRNAs in human cancer, several cell lines (bladder cancer, prostate cancer, renal cell carcinoma, esophageal squamous cell carcinoma, and head and neck squamous cell carcinoma) were subjected to Agilent whole genome microarrays.

overall_design: Human cancer cell lines (BOY, T24, A498, 786-O, caki-1, LNCap, PC3, TE2, T.Tn, FaDu, SAS, HSC3, and IMC-3) were transfected with miRNAs (miR-375, miR-145, miR-200a, miR-200b, miR-200c, miR-141, miR-429, miR-138, miR-218, miR-874, miR-31, miR-222, miR-1285, and miR-206) or siRNAs (si-FOXA1_1, si-FOXA1_3, and si-TAGLN2). The miRNA-transfected human cancer cell lines were compared to control cell lines.


title: Gene Expression Profiling During Early Acute Febrile Stage of Dengue Infection Can Predict The Disease Outcome

status: Public on Sep 01 2010

city: Pittsburgh

first: Ernesto

last: Marques

state: PA

address: 9022 BST3 3501 Fifth Avenue

department: Infectious Diseases and Microbiology

institute: University of Pittsburgh

summary: Background: We report the detailed development of biomarkers to predict the clinical outcome under dengue infection. Transcriptional signatures from purified peripheral blood mononuclear cells were derived from whole-genome gene-expression microarray data and validated by quantitative PCR and tested in independent samples.   Methodology/Principal Findings: The study was performed on patients of a well-characterized dengue cohort from Recife, Brazil. The samples analyzed were collected prospectively from acute febrile dengue patients who evolved with different degrees of disease severity, classic dengue fever or dengue hemorrhagic fever (DHF) and compared with similar samples from other non-dengue febrile illnesses. The DHF samples were collected 2-3 days before the presentation of the plasma leakage symptoms. Differentially-expressed genes were selected by univariate statistical tests as well as multivariate classification techniques. The results showed that at early stages of dengue infection, the genes involved in effector mechanisms of innate immune response presented a weaker activation on patients who later developed hemorrhagic fever, whereas the genes involved in apoptosis were expressed in higher levels.   Conclusions/Significance: Some of the gene expression signatures displayed estimated accuracy rates of more than 95%, indicating that expression profiling with these signatures may provide a useful means of DHF prognosis at early stages of infection

overall_design: The samples correspond to blood samples from 26 patients from a cohort in Brazil, divided into three classes, DHF, DF, ND, as follows: 18 were confirmed dengue 3, genotype III cases, among which 10 were diagnosed as dengue hemorrhagic fever (DHF) and 8 as classical dengue fever (DF),  and 8 control samples (ND) from febrile patients confirmed to be not infected with dengue. None of the DHF patients presented vasculopathy signs and symptoms at the time the samples used in the functional genomic characterization were collected.  At the time of collection the patients referred approximately 5 days of disease and the absence of fever was reported two to three days after enrollment. The samples from the DF, DHF and ND patients were matched to avoid significant differences regarding patient age, gender, dengue infection history and days of symptoms among the groups.

first: Eduardo

last: Nascimento

first: Ulisses

last: Braga-Neto

first: Carlos

middle: E

last: Calzavara-Silva

first: Ana

last: Gomes

first: Frederico

last: Abath

middle: A

last: Brito

first: Marli

last: Cordeiro

last: Silva

first: Cecilia

last: Magalhães

first: Raoni

last: Andrade

first: Laura

last: Gil

last: Marques Jr


title: Transcriptional profile of PBMCs in patients with acute RSV or Influenza infection

city: Dallas

first: Damien

last: Chaussabel

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

summary: To study the transcriptional profile of patients with acute RSV or Influenza infection,children of median age 2.4 months (range 1.5-8.6) hospitalized with acute RSV and influenza virus infection were offered study enrollment after microbiologic confirmation of the diagnosis.  Blood samples were collected from them within 42-72 hours of hospitalization. We excluded children with suspected or proven polymicrobial infections, with underlying chronic medical conditions (i.e congenital heart disease, renal insufficiency), with immunodeficiency, or those who received systemic steroids or other immunomodulatory therapies.  The RSV cohort consisted of 51 patients with median age of 2 months (range 1.5-3.9) and the influenza cohort had 28 patients with median age of  5.5 months (range 1.4-21).  Control samples were obtained from healthy children undergoing elective surgical procedures or at outpatient clinic visits.  To exclude viral co-infections we performed nasopharyngeal viral cultures of all subjects. We recruited 10 control patients for the RSV cohort with median age of 6.7 months (range 5-10), and 12 control patients for the influenza cohort with median age of18.5 months (range 10.5-26).

overall_design: We used microarrays to obtain the transcriptional profile of PBMCs from patients with acute RSV or Influenza infection and compared these signatures with the transcriptional profile of primary airway epithelial cells infected with RSV or Influenza.

first: Asuncion

last: Mejias

first: Ioannidis

last: Ioannis

first: Emilio

last: Flano


title: IPH-926 human lobular breast cancer cells

status: Public on Dec 21 2011

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

summary: IPH-926 is an anticancer drug-resistant tumor cell line derived from a chemo-refractory human infiltrating lobular breast cancer (ILBC). IPH-926 ILBC cells were subjected to gene expression profiling using an Affymetrix HG U133 Plus 2.0 array.

overall_design: To characterize the global gene expression of IPH-926, cells were subjected to transcriptional profiling using the Affymetrix HG U133 Plus 2.0 technology. The correct identity of the IPH-926 cells subjected to gene expression profiling was authenticated by short tandem repeat (STR) profiling.

first: R

first: M

last: Christgen

first: U

last: Lehmann


title: Gene expression patterns in blood leukocytes discriminate patients with acute infections

status: Public on Mar 16 2007

summary:
Each infectious agent represents a unique combination of pathogen-associated molecular patterns that interact with specific pattern-recognition receptors expressed on immune cells. Therefore, we surmised that the blood immune cells of individuals with different infections might bear discriminative transcriptional signatures. Gene expression profiles were obtained for 131 peripheral blood samples from pediatric patients with acute infections caused by influenza A virus, Gram-negative (Escherichia coli) or Gram-positive (Staphylococcus aureus and Streptococcus pneumoniae) bacteria. Thirty-five genes were identified that best discriminate patients with influenza A virus infection from patients with either E coli or S pneumoniae infection. These genes classified with 95% accuracy (35 of 37 samples) an independent set of patients with either influenza A, E coli, or S pneumoniae infection. A different signature discriminated patients with E coli versus S aureus infections with 85% accuracy (34 of 40). Furthermore, distinctive gene expression patterns were observed in patients presenting with respiratory infections of different etiologies. Thus, microarray analyses of patient peripheral blood leukocytes might assist in the differential diagnosis of infectious diseases.
Keywords: expression analysis

overall_design: Entire study included 144 samples. Only 143 are included in this series because the CHP/CEL file was not available for sample PBMC_Healthy_INF295.


title: Effect of interferon-gamma on macrophage differentiation and response to Toll-like receptor ligands

status: Public on Dec 31 2008

city: New York

first: Janice

last: Chen

state: NY

address: 535 East 70th St, 4th floor Research

department: Research

institute: Hospital for Special Surgery

summary: Gene expression analysis of freshly isolated CD14+ human monocytes and monocytes cultured in the presence or absence of interferon (IFN) -gamma for 24 h and then stimulated with Pam3Cys, a Toll-like receptor (TLR) 2 ligand, for 6 h. Results provide insight into mechanisms by which IFN-gamma reprograms early macrophage differentiation and subsequent response to TLR ligands.

overall_design: Peripheral blood mononuclear cells were isolated from the blood of two independent healthy human donors by centrifugation on a Ficoll density gradient, and monocytes were positively selected using anti-CD14 magnetic beads. Monocytes were cultured in RPMI 1640 supplemented with 10% fetal bovine serum and 10 ng/mL M-CSF in the presence or absence of 100 U/mL IFN-gamma for 24 h, and then stimulated with 10 ng/mL Pam3Cys for 6 h. Where indicated, RNA was extracted from fresh monocytes immediately upon isolation. Total RNA extraction was performed using TRIzol reagent (Invitrogen) and RNeasy mini kit (Qiagen). Labeled cRNA was prepared with the Affymetrix GeneChip IVT Labeling Kit, and samples were hybridized to Affymetrix HG U133 Plus 2.0 microarrays. Data was processed using Affymetrix protocols and further analyzed using GeneSpring software.

first: Lionel

last: Ivashkiv


title: Gene profile of breast cancers with immunohistochemical phenotypes of ER+/- and/or HER2+/-

status: Public on Mar 14 2009

city: Itabashi

first: shinobu

last: Masuda

state: Tokyo

address: 30-1 Ohyaguchikami-cho

department: pathology

institute: Nihon Univeristy School of Medicine

summary:
Hormones and growth factors accelerate cell proliferation of breast cancer cells, and these molecules are well investigated targets for drug development and application.  The mechanisms of cell proliferation of breast cancers lacking estrogen receptor (ER) and HER2 have not been fully understood.  The purpose of the present study is to find genes that are differentially expressed in breast cancers and that might significantly contribute to cell proliferation in these cancers.  Forty tumor samples, consisting of ten each of immunohistochemically ER(+)/HER2(-), ER(+)/HER2(+), ER(-)/HER2(+), and ER(-)/HER2(-) cancer were analyzed using oligonucleotide microarrays.  Both genes and tumor samples were subjected to hierarchical clustering.  ER(+)/HER2(-) breast cancers and ER(-)/HER2(-) cancers tended to form a tumor cluster, but HER2 positive breast cancers were split into different tumor clusters.
Significant differential expression between IHC-ER(-)/HER2(-) and other tumors was defined as having an expression level at least 2-fold higher or 2-fold lower, and analyzed by multi-step two-way ANOVA.  Genes overexpressed differently in IHC-ER(-)/HER2(-) breast cancers compared to other all three types were 8 genes (FABP7, GABRP, GAL, CXCL13, CDC42EP4, C2F, FOXM1, CSDA), and underexpressed genes were nine including ITGB5, KIAA0310, MAGED2, PRSS11, SORL1, TGFB3, KRT18, CPE, BCAS1.  No gene was directly related to cell proliferation such as cyclins, cyclin-dependent kinase, p53, p16, and the pRb and p21 families.  We had a particular focus on a transcriptional factor E2F-5 from a list of genes overexpressed in ER negative breast cancers compared to ER positive breast cancers, and further examined.
Gene amplification of E2F-5 was detected in 5/57 (8.8%) in breast cancers by FISH.  No point mutation was found at the binding domain with DNA or dimerization partner of E2F-5.  Immunohistochemically E2F-5 positive cancers were more frequent in ER(-)/HER2(-) cancer (14/27, 51.9%) than in other types of cancer (5/30, 16.7%) (p=0.05).  E2F-5 positive cancers had higher Ki-67 labeling index (59.5%) than E2F-5 negative cancers (36.3%).  E2F-5 positive cancers showed higher histological grade including metaplastic carcinoma, and worse clinical outcome with shorter disease free survival in node negative patients.  In conclusion, we demonstrated that there is a population of breast cancer with overexpression of a cell cycle related transcriptional factor E2F-5.  E2F-5 positive breast cancers were frequent in ER(-)/HER2(-) group with high Ki-67 labeling index, high histological grade and worse clinical outcome.
Keywords: immunohistochemical phenotype

overall_design: 40 breast cancer consisted of ten each of immunohistochemically ER(+)/HER2(-), ER(+)/HER2(+), ER(-)/HER2(+), and ER(-)/HER2(-) cancers are compared.

first: Masatomo

last: Shirane

first: Susumu

last: Takekoshi

first: Yutaka

last: Tokuda

first: Kazushige

last: Mori

first: Yoshiyuki

last: Osamura


title: The humoral immune system has a key prognostic impact in node-negative breast cancer

status: Public on Jul 01 2008

city: Leverkusen

first: Mathias

last: Gehrmann

address: Kaiser-Wilhelm-Allee

department: BTS-PT-AS-AT

institute: Bayer Technology Services GmbH

summary:
Estrogen receptor (ER) expression and proliferative activity are established prognostic factors in breast cancer. In a search for additional prognostic motives we analyzed the gene expression patterns of 200 tumors of patients who were not treated by systemic therapy after surgery using a discovery approach. After performing hierarchical cluster analysis, we identified co-regulated genes related to the biological process of proliferation, steroid hormone receptor expression, as well as B cell and T cell infiltration. We calculated metagenes as surrogate for all genes contained within a particular cluster and visualized the relative expression in relation to time to metastasis with principal component analysis. Distinct patterns led to the hypothesis of a prognostic role of the immune system in tumors with high expression of proliferation associated genes. In multivariate Cox regression analysis the proliferation metagene showed a significant association with metastasis-free survival of the whole discovery cohort (Hazard Ratio (HR) 2.20, 95% confidence interval (CI) 1.40-3.46). The B cell metagene showed additional independent prognostic information in carcinomas with high proliferative activity (HR 0.66, 95% CI 0.46 - 0.97). A prognostic influence of the B-cell metagene was independently confirmed by multivariate analysis in a first validation cohort enriched for high grade tumors (n=286, HR 0.78, 95% CI 0.62-0.98), and a second validation cohort enriched for younger patients (n=302, HR 0.83, 95% CI 0.7-0.97). Thus, we could demonstrate in three cohorts of untreated node-negative breast cancer patients, that the humoral immune system plays a pivotal role for metastasis-free survival of carcinomas of the breast.
Keywords: disease state analysis

overall_design: Population based N0 untreated breast cancer cohort study including 200 samples

first: Marcus

last: Schmidt

first: Daniel

last: Böhm

first: Christian

last: von Törne

first: Eric

last: Steiner

first: Alexander

last: Puhl

first: Henryk

last: Pilch

first: Hans-Anton

last: Lehr

first: Jan

last: Hengstler

first: Heinz

last: Kölbl


title: Affymetrix data for training of Endopredict algorithm

status: Public on Oct 11 2011

city: Köln

first: Karsten

middle: Ernst

last: Weber

address: Nattermannallee 1

institute: Sividon Diagnostics GmbH

type:
Expression profiling by array
Third-party reanalysis

summary: These data, combined with other cohorts (GSE6532, GSE12093, and qRT-PCR based cohorts), was used to construct the EP algorithm, which predicts the likelihood of developing of a distant recurrence of early stage breast cancer under endocrine treatment. In addition, EPclin, a combination of the EP score, the nodal status and the tumor size, was constructed.

overall_design:
All samples used for the development of the EP algorithm were taken from patients who received adjuvant tamoxifen only. Fresh-frozen tumours obtained from three centers were profiled on HG-U133A arrays. In brief, starting from 5 µg total RNA, labeled cRNA was prepared using the Roche Microarray cDNA Synthesis, Microarray RNA Target Synthesis (T7) and Microarray Target Purification Kit (Roche Applied Science, Mannheim, Germany), according to the manufacturer’s instructions. Raw .cel file data were processed by MAS 5.0 software (AFFYMETRIX, Santa Clara, CA). In the analysis settings, the global scaling procedure was chosen which multiplied the output signal intensities of each array to a mean target intensity of 500.

We selected those samples from the GSE6532 and GSE12093 cohorts that we considered appropriate for our analyses (n=130 and n=130) and calculated MAS5 expression values from the corresponding .CEL-Files. One of the selection criteria was the GPL96 platform we also used for our measurements. GSE26971_GSE12093_dataset.txt.gz and GSE26971_GSE6532_dataset.txt.gz files contain data for both cohorts including the GSM numbers in row A and MAS5 expression data in the remaining rows. Processing of .CEL-files of these samples was exactly the same as the processing of the .CEL-files of our own samples: GPL96, MAS5, TGT 500.

first: Volkmar

last: Müller

first: Fritz

last: Jänicke

first: Achim

last: Rody

first: Manfred

last: Kaufmann

first: Tanja

last: Ropers

first: Inke

last: Feder

first: Ralf

last: Kronenwett