title: Molecular Analysis of antigen-specific B cell responses

status: Public on Feb 02 2006

city: Stanford

first: Irving

middle: L.

last: Weissman

email: irv@stanford.edu, deepta@stanford.edu

state: CA

address: 279 Campus Dr.

institute: Stanford University

summary:
In order to better understand the factors that regulate B cell differentiation upon exposure to antigen, we compares global gene expression profiles from naive B cells with antigen-specific plasma, germinal center, and memory B cells after immunization with the T-dependent antigen, NP-CGG.  The memory B cell-enriched transcripts were then compared with memory T cell-enriched and hematopoietic stem cell-enriched transcripts in order to generate a transcriptional profile of self-renewal within the hematopoietic system.
Keywords: Cell Type Comparison

overall_design: Naive B cells were FACS sorted from unimmunized mice, while plasma, germinal center, and memory B cells were sorted from NP-CGG-immunized mice at 1, 2, or 10 weeks after immunization, respectively, using a combination of cell surface markers.  RNA was extracted, amplified, and hybridized to Affymetrix microarrays.

first: Deepta

last: Bhattacharya

first: Chance

last: Luckey

first: Christophe

last: Benoist

first: Diane

last: Mathis


title: Inhibition of NOX1 Gene Expression with shRNA in Human Colon Cancer

status: Public on Mar 27 2007

city: Duarte

first: Agnes

last: Juhasz

address: 1500 E. Duarte Rd

department: Medical Oncology

country: USA

institute: City of Hope Compr. Cancer Center

summary:
NOX1 gene is member of the NADPH-dependent superoxide producing enzyme family. It generates reactive oxygen species (ROS) in regulated manner in response to growth factors, cytokines and calcium signal. Low levels of ROS play role in many processes including cell proliferation, inflammatory response and mitogenesis.  NOX1 over-expression in colon cancer cell lines as well as surgical samples suggests a role in colon cancer. We identified unique target sequences of siRNAs for post-transcriptional silencing of NOX1. Gene specific and scrambled (control) sequence carrying U6 promoter/shRNA cassettes were cloned into GFP expression vector. Stable clones were selected based on NOX1 expression after transient transfection of HT-29 cells. Clone 6A and 6C showed 70-80% decrease in NOX1 expression.  The cells were expanded and analyzed further. We measured decreased ROS production, cell proliferation and G1/S block of the cell cycle. HT-29 parental cells, clone SA (scrambled) and clone 6A (gene specific) were utilized to establish xenografts in athymic mice to investigate the effect of NOX1 silencing on tumor growth and gene expression in vivo. Significant decrease was measured in the volume of forming tumors.  The stable clones and corresponding xenografts were analyzed on microarray.  The microarray data was validated with real-time PCR and western-blot analysis demonstrating the inhibition of genes important in cell cycle regulation and angiogenesis.  The results of this study show silencing NOX1 levels of generated ROS decreased, the tumor formation attenuated in vivo suggesting NOX1 may be a therapeutic target for colon cancer.
Keywords: gene silencing with shRNA

overall_design: We have found that NOX1 over-expression in colon cancer cell lines as well as surgical samples suggests a role in colon cancer. We identified unique target sequences of siRNAs for post-transcriptional silencing of NOX1. Gene specific and scrambled (control) sequences carrying the U6 promoter/shRNA cassettes were cloned into a GFP expression vector. Stable clones were selected based on NOX1 expression after transient transfection of HT-29 cells.  HT-29 parental cells, clone SA (scrambled) and clone 6A (gene specific) were utilized to establish xenografts in athymic mice to investigate the effect of NOX1 silencing on tumor growth and gene expression in vivo. A significant decrease was measured in the volume of tumors formed.  The stable clones and corresponding xenografts were analyzed on microarray.  The microarray data was validated with real-time PCR and western-blot analysis demonstrating the inhibition of genes important in cell cycle regulation and angiogenesis.  The results of this study show silencing NOX1 levels of generated ROS decreased, the tumor formation attenuated in vivo suggesting NOX1 may be a therapeutic target for colon cancer.

first: Susan

last: Markel

first: Shikha

last: Gaur

first: Xiwei

last: Wu

first: James

middle: H

last: Doroshow


title: Plane of nutrition prepartum and bovine hepatic gene expression profiles

status: Public on May 23 2006

city: Urbana

first: Juan

middle: J.

last: Loor

state: IL

address: 1207 West Gregory Drive

department: Animal Sciences

institute: University of Illinois

summary:
Cows were selected from two groups of 12 cows enrolled in a large experiment to assess the effects of ad libitum or restricted intake of moderate-energy diets during the entire dry period on pre-partum metabolism and post-partum metabolism and performance.  A corn silage-based diet (26% of diet dry matter) providing 1.59 Mcal/kg during the far-off dry period (first 5 wk of an 8-wk dry period) or providing 1.61 Mcal/kg during the close-up dry period (last 3 wk of the dry period) was fed for ad libitum or restricted intake.  Four multiparous Holstein cows were randomly selected from the ad libitum and restricted intake groups.
Keywords: time course, ad libitum or restricted feeding prepartum

overall_design: A 7,872-element cDNA microarray spotted in duplicate on amino silane-coated glass slides (Everts et al. 2005, Vet. Immunol. Immunopathol. 105:235-245) was used for transcript profiling.  Annotation was based on similarity searches (January, 2005) using sequential BLASTN and TBLASTX against human and mouse UniGene databases and the human genome.  The 7,872-element array represents more than 6,300 unique genes.  Gene Ontology (GO) terms were parsed from LocusLink to functionally annotate cDNA sequences.  RNA (20 ug) from liver tissue and a reference standard derived from a mixture of tissues not including liver were used to make aminoallyl-labeled cDNA followed by incorporation of Cy3-ester and Cy5-ester (Amersham, Piscataway, NJ).  Each experimental sample was co-hybridized with the reference standard, which allowed the treatment of fluorescence ratios as measurements of relative expression across all samples and time points.  Probes were hybridized to the array for 2 days at 42 C.  All samples were hybridized to duplicate slides for a total of 4 spots per cDNA element.  A total of 106 microarrays were run to complete the experiment.  Slides were scanned for both dye channels with a Scanarray 4000 (GSI-Lumonics, Billerica, MA) dual-laser confocal scanner and images were processed using GenePix 4.0 (Axon Instruments, Inc., CA).

middle: J

first: Heather

middle: M

last: Dann

first: Nicole

middle: A

last: Janovick Guretzky

first: Robin

middle: E

last: Everts

first: Rosane

last: Oliveira

first: Cheryl

last: Green

first: Noah

last: Litherland

first: Sandra

middle: L

last: Rodriguez-Zas

first: Harris

last: Lewin

middle: K

last: Drackley


title: BCR-ABL enhances differentiation of long-term repopulating hematopoietic stem cells

status: Public on Jan 01 2010

city: Bronx

first: Ulrich

last: Steidl

state: NY

address: 1300 Morris Park Ave., Chanin #606

department: Department of Cell Biology

institute: Albert Einstein College of Medicine

summary: The biology of chronic myeloid leukemia (CML)-stem cells is still incompletely understood. Therefore, we previously developed an inducible transgenic mouse model in which stem cell targeted induction of BCR-ABL expression leads to chronic phase CML-like disease. Here, we now demonstrate that the disease is transplantable using BCR-ABL positive LSK cells (lin-Sca-1+c-kit+). Interestingly, the phenotype is enhanced when unfractionated bone marrow (BM) cells are transplanted. However, neither progenitor cells (lin-Sca-1-c-kit+) nor mature granulocytes (CD11b+Gr-1+), or potential stem cell niche cells were able to transmit the disease or alter the phenotype. The phenotype was largely independent of BCR ABL priming prior to transplant. However, BCR-ABL abrogated the potential of LSK cells to induce full blown disease in secondary recipients. Subsequently, we found that BCR-ABL increased the fraction of multipotent progenitor cells (MPP) at the expense of long term HSC (LT-HSC) in the BM. Microarray analyses of LSK cells revealed that BCR-ABL alters the expression of genes involved in proliferation, survival, and hematopoietic development. Our results suggest that BCR-ABL induces differentiation of LT-HSC and decreases their self renewal capacity. Furthermore, reversion of BCR-ABL eradicates mature cells while leukemic stem cells persist, giving rise to relapsed CML upon re-induction of BCR-ABL.

overall_design:
Total RNA of LSK cells of control mice or SCLtTAxBCR-ABL double transgenic (dtg) mice (3 pools of 3 animals each) was amplified by 2 rounds of RT and T7 promoter-based in-vitro transcription and the resultant biotinylated cRNA was then hybridized to Affymetrix Mouse Genome 430 2.0 arrays.

CEL files were not provided for this submission.

first: Mirle

last: Schemionek

first: Christian

last: Elling

last: Baeumer

first: Ashley

last: Hamilton

first: Tilmann

last: Spieker

first: Joachim

middle: R

last: Goethert

first: Martin

last: Stehling

first: Amy

last: Wagers

first: Claudia

middle: S

last: Huettner

first: Daniel

middle: G

last: Tenen

first: Lara

last: Tickenbrock

first: Wolfgang

last: Berdel

first: Hubert

last: Serve

first: Tessa

last: Holyoake

first: Carsten

last: Mueller-Tidow

first: Steffen

last: Koschmieder


title: Gene expression data from S. aureus-exposed macrophages

status: Public on Apr 23 2009

city: Hamilton

first: Addie

last: Whitney

state: MT

address: 903 S 4th St

department: LHBP

institute: NIH/NIAID/RML

summary:
It is becoming increasingly apparent that Staphylococcus aureus are able to survive engulfment by macrophages, and that the intracellular environment of these cells, which is essential to innate host defenses against invading microorganisms, may in fact provide a refuge for staphylococcal survival and dissemination.  Based on this, we postulated that S. aureus might induce cytoprotective mechanisms by changing gene expression profiles inside macrophages similar to obligate intracellular pathogens, such as Mycobacterium tuberculosis.
In order to examine the effect of S. aureus on the macrophage transcriptome, we performed microarray expression analysis on human monocyte-derived macrophages treated with S. aureus.

Keywords: time course

overall_design: Human monocyte-derived macrophages (hMDMs) were separated from fractions of peripheral blood mononuclear cells (PBMCs) obtained from the blood of healthy donors. Control and S. aureus-exposed macrophages were incubated at 37C for 8, 24, or 48 hours

first: J

last: Koziel

first: A

last: Maciag-Gudowska

first: T

last: Mikolajczyk

first: M

last: Bzowksa

first: D

last: Sturdevant

first: L

middle: N

last: Shaw

first: F

last: DeLeo

last: Potempa


title: MDM from COPD patients and healthy subjects after treatment with LPS or fine and ultrafine particles

status: Public on Aug 01 2007

city: Munich

first: Thomas

last: Hofer

address: Max-Lebsche-Platz 31

department: Comprehensive Pneumology Center

country: Germany

institute: Helmholtz Zentrum Munich

summary:
In this study gene expression of monocyte-derived macrophages (MDM) from chronic obstructive pulmonary disease (COPD) patients and healthy subjects was investigated. MDM were treated with LPS, a combination of fine TiO2 and ultrafine Printex90 particles, or remained untreated.
Keywords: disease state analysis

overall_design: MDM of 13 COPD patients and 13 healthy subjects were incubated for four hours with LPS (10ng/ml), a combination of fine TiO2 and ultrafine Printex90 (32ug/ml each) or remained untreated. Cells were harvested, counted, and total RNA was isolated (phenol-chloroform extraction) for each subject individually. Total RNA of the 13 individuals from each group (COPD, healthy) and incubation (untreated, LPS, particles) were pooled and hybridized on a seperate array.

middle: P

last: Frankenberger

last: Mages

first: R

last: Lang

first: P

last: Meyer

last: Hoffmann

last: Ziegler-Heitbrock


title: P. vivax: proof-of-principle global transcription analysis from two wild isolates

status: Public on Apr 12 2008

city: Barcelona

first: Hernando

last: del Portillo

state: Barcelona

address: rosello, 132 (4a)

country: Spain

institute: Barcelona Centre for International Health Research

summary:
The complete genome sequence of the P. vivax Sal-1 strain allowed the design of a first version array representing 1 oligo/2 kb of coding sequences (http://zblab.sbs.ntu.edu.sg/vivax/index.html). Here, proof-of-principle experiments using total RNA of parasites obtained from the Sal-1 strain, from P. falciparum and from parasites obtained directly from two human patients are presented.
Keywords: expression profiles

sample_organism:
Plasmodium falciparum
Plasmodium vivax

overall_design: To determine the extent of cross-hybridization of P. falciparum with P. vivax, and to determine overlaps in expression profiles of the P. vivax Sal1 monkey-adapted strain vs wild isolates, single dual hybridization analyses were performed.

first: Ricardo

middle: Z

last: Vêncio

first: Marcio

last: Yamamoto

first: Carmen

last: Fernandez-Becerra


title: Expression profiles of human macrophages

status: Public on Dec 14 2007

city: Göteborg

first: Daniel

last: Hägg

address: Vita Stråket 15

department: Department of Molecular and Clinical Medicine

country: Sweden

institute: Göteborg University

summary:
The project was designed to identify genes with an altered expression in macrophages from subjects with atherosclerosis compared to macrophages from control subjects.
Keywords: Case-control

overall_design: We used monocyte-derived macrophages from peripheral blood cultured in the absence or presence of oxidized LDL, baseline macrophages or foam cells. The macrophages were obtained from 15 subjects with subclinical atherosclerosis and a family history of CHD. Macrophages from 15 age and sexmatched subjects with no atherosclerosis and no family history of CHD were used as control.

first: Per-Arne

last: Svensson

first: Margareta

last: Jernås

first: Olle

last: Wiklund

first: Björn

last: Fagerberg