title: Activated Innate Immunity and Involvement of the CX3CR1-FKN Axis in Promoting Hematuria in IgA Nephropathy Patients

city: Valenzano-Bari

first: Sharon

middle: Natasha

last: Cox

department: Renal Lab

country: Italy

institute: Schena Foundation

summary:
The hallmark of IgA nephropathy (IgAN) is gross hematuria (GH) coinciding with or immediately following an upper respiratory or gastrointestinal tract infection and can represent the disease triggering event. Therefore, a whole genomic screening of IgAN patients during the GH was done to clarify the link between mucosal encountered antigens and the occurrence of glomerular hematuria. The modulated genes during GH show a clear involvement of the interferon signalling, antigen presenting pathway, and the immuno-proteasome. The gene characterizing cytotoxic effector lymphocytes (CX3CR1) implicated in vascular endothelial damage, was found up-regulated at both mRNA and protein level. In vitro antigenic stimulation of PBMCs on an independent set of IgAN patients and healthy blood donors (HBS) demonstrated that patients upregulate specifically CX3CR1 in an enhanced and dose dependant manner, while an expected down-regulation occurred in HBD. This enhanced activation occurred in both patients characterized by recurrent GH and by permanent microscopic hematuria (MH). We then analyzed glomerular fractalkine (FKN) expression, since this ligand is involved in the vascular gateway for CX3CR1+ cells towards the inflamed tissues. A significantly higher FKN expression on the capillary vessels and podocytes was found in recurrent GH patients compared to permanent MH, suggesting a predisposition for cytotoxic cell extravasation in recurrent GH patients.
Taken together, our findings demonstrate, for the first time, a defect in antigen handling in PBMCs of IgAN patients with a specific up-regulation of CX3CR1. Furthermore, the constitutive up regulation of glomerular FKN, suggests an involvement of the CX3CR1-FKN axis in the exacerbation of GH.

overall_design: Gene expression profile comparison 3 IgAN patients at two different clinical time points, the first sample during the gross hematuria episode and the second during the remission phase of the disease characterized by microscopic hematuria

first: SHARON

last: COX

first: FABIO

last: SALLUSTIO

first: GRAZIA

last: SERINO

first: ANTONIA

last: LOVERRE

first: FRANCESCO

last: PESCE

first: GIANLUIGI

last: ZAZA

first: NICOLA

last: ANCONA

first: PATRIZIA

last: STIFANELLI

last: SHENA


title: Genome-wide analysis of gene expression levels in placenta and cord blood samples from newborns babies

status: Public on Mar 29 2012

city: Philadelphia

first: Nahid

last: Turan

state: PA

address: 3307 North Broad Street, AHB

department: Fels Institute

country: USA

institute: Temple University School of Medicine

summary: Genome wide expression profiling of placenta and cord blood samples from 48 newborns.

overall_design: Total RNA obtained from placenta and cord blood samples from 48 newborns.

first: Carmen

last: Sapienza


title: DNA methylation and gene expression differences at growth related genes correlate with birth weight.

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: Depletion of RUNX1/ETO in t(8;21) AML cells leads to genome-wide changes in chromatin structure and transcription factor binding (Illumina expression)

status: Public on Mar 28 2012

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

summary: The t(8;21) translocation fuses the DNA binding domain of the hematopoietic master regulator RUNX1 to the ETO protein. The resultant RUNX1/ETO fusion protein is a leukemia-initiating transcription factor that interferes with RUNX1 function. The result of this interference is a block in differentiation and, finally, the development of acute myeloid leukemia (AML). To obtain insights into RUNX1/ETO-dependant alterations of the epigenetic landscape we measured genome-wide RUNX1- and RUNX1/ETO bound regions in t(8;21) cells and assessed to what extent the effects of RUNX1/ETO on the epigenome depend on its continued expression in established leukemic cells. To this end we determined dynamic alterations of histone acetylation, RNA Polymerase II binding and RUNX1 occupancy in the presence or absence of RUNX1/ETO using a knockdown approach. Combined global assessments of chromatin accessibility and kinetic gene expression data show that RUNX1/ETO controls the expression of important regulators of hematopoietic differentiation and self-renewal. We show that selective removal of RUNX1/ETO leads to a widespread reversal of epigenetic reprogramming and a genome-wide re-distribution of RUNX1 binding, resulting in the inhibition of leukemic proliferation and self-renewal and the induction of differentiation. This demonstrates that RUNX1/ETO represents a pivotal therapeutic target in AML.

overall_design: Total RNA were obtained using 8 samples over a time course of 10 days or using two samples two days after siRNA electroporation (mismatch control siRNA and RUNX1/ETO knock-down)

first: Anetta

last: Ptasinska

middle: A

first: Deepak

last: Mannari

first: Sally

middle: R

last: James

first: Dan

last: Williamson

first: Jenny

last: Dunne

first: Maarten

last: Hoogenkamp

first: Wu

last: Mengchu

first: Matthew

last: Care

first: Hesta

last: McNeill

first: Pierre

last: Cauchy

last: Cullen

first: Reuben

last: Tooze

middle: G

last: Tenen

first: Bryan

last: Young

first: Peter

middle: N

last: Cockerill

first: David

last: Westhead

first: Olaf

last: Heidenreich

first: Constanze

last: Bonifer


title: Depletion of RUNX1/ETO in t(8;21) AML cells leads to genome-wide changes in chromatin structure and transcription factor binding [expression array data]

first: Salam

last: Assi

overall_design: Total RNA were obtained using 8 samples over four time courses (mismatch control and knock-down)

last: Ptasinska

last: Mannari


title: Impact of albino chemical on Arabidopsis seedlings

city: Taipei

first: Kevin Long-Chi

last: WANG

address: 128 Section 2, Academia Road

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

summary: Analysis of wild type genome expression profile altered by albino chemicals. Results uncovered a several groups of genes that were significant responsive to these chemicals which may contribute to the albino phenotype.

overall_design: WT (Col-0) sown on 0.5x MS agar medium and stratified in the dark at 4 °C for 3 days and then germinated in the light condition (16 h light/8 h dark) for 5 days at 22 °C, and then transfer to the 0.5x MS solution one day for adapt the treatment condition. In the DAG 6 (day after germination), final concentration 50 μM chemicals (7606596 and 5929745) were supplemented into the medium for chemical treatment. Approximately 2,000 seedlings were used to collect tissues before the chemicals treatment as the time zero samples. Seedlings were collected after the chemical treatment for 3 hours and 12 hours. Total RNA extracted from the collected samples was applied in each microarray experiment with Arabidopsis ATH1 GeneChip (Affymetrix). Qiagen RNAeasy mini kit (Qiagen) was used for RNA preparation. cDNA labeling, array hybridization, and scanning followed by standard Affymetrix expression array protocol. Two independent sets of microarray analyses were performed in this assay.

first: Lee-Chung

last: Lin

first: Long-Chi

last: Wang


title: miR-34a targets PDGFRA in proneural malignant glioma

status: Public on Mar 27 2012

city: New York

first: Joachim

last: Silber

state: NY

address: 1275 York Ave #20

institute: Memorial Sloan-Kettering Cancer Center

summary: To identify potential targets of miR-34a, we performed transcriptional profiling on proneural TS543 GBM cells, focusing on mRNAs whose levels decreased in response to miR-34a transfection as compared to control oligonucleotide.

overall_design: Proneural TS543 GBM cells were transfected with 100 nM hsa-miR-34a or control oligonucleotide using Hiperfect transfection reagent (Qiagen). After 3 days, RNA was isolated and expression analyses were performed using Illumina HT-12 bead array. The microarray dataset was normalized using a variance stable normalization (VSN) procedure in the ‘lumi’ package from the Bioconductor framework.

first: Anders

last: Jacobsen

first: Tatsuya

last: Ozawa

first: Girish

last: Harinath

first: Alicia

last: Pedraza

first: Chris

last: Sander

first: Eric

middle: C

last: Holland

first: Jason

middle: T

last: Huse


title: Prostaglandin D2 Inhibits Hair Growth and Is Elevated in Bald Scalp of Men with Androgenetic Alopecia

status: Public on Mar 26 2012

city: Baltimore

first: Luis

middle: Andres

last: Garza

state: MD

address: 1550 Orleans St. Suite 204 CRBII Koch

department: Dermatology

institute: Johns Hopkins School of Medicine

summary: Testosterone is necessary for the development of male pattern baldness, known as androgenetic alopecia (AGA); yet the mechanisms for decreased hair growth in this disorder are unclear. Here, we show that prostaglandin D2 synthase (PTGDS) is elevated at the mRNA and protein levels in bald scalp compared to haired scalp of men with AGA. The product of PTGDS enzyme activity, prostaglandin D2 (PGD2), is similarly elevated in bald scalp. During normal follicle cycling in mice Ptgds and PGD2 levels increase immediately preceding the regression phase, suggesting an inhibitory effect on hair growth. We show that PGD2 inhibits hair growth in explanted human hair follicles and when applied topically to mice. Hair growth inhibition requires the PGD2 receptor G protein-coupled receptor 44 (GPR44), but not the prostaglandin D2 receptor 1(PTGDR). Furthermore, we find that a transgenic mouse, K14-Ptgs2, which targets prostaglandin-endoperoxide synthase 2 expression to the skin, demonstrates elevated levels of PGD2 in the skin and develops alopecia, follicular miniaturization and sebaceous gland hyperplasia, which are all hallmarks of human AGA. These results define PGD2 as an inhibitor of hair growth in AGA and suggest the PGD2-GPR44 pathway as a potential target for treatment.

overall_design: 5 individuals with Androgenetic Alopecia were biopsied at both their haired and bald scalp for  mRNA purification and microarray (total 10 arrays)

first: George

last: Cotsarelis


title: Effect of LPS on global gene expression in human skin fibroblasts

status: Public on Mar 22 2012

city: Chicago

first: Swati

last: Bhattacharyya

state: IL

address: 240 E Huron st, McGAW, M230

department: Medicine

institute: Northwestern University

summary: To examine responses induced by TLR4 activation at the genome-wide level, confluent fibroblasts in serum-free media were incubated with or without LPS for 6 h, and RNA was isolated using RNeasy mini kits (Qiagen, Valencia, CA). The integrity of RNA was ascertained using Agilent Bioanalyzer (Santa Clara, CA), cDNA was labeled using an Ambion labeling kit (Ambion), and hybridized to Illumina human HT-12 version 4 Expression Microarray Chips (Illumina, San Diego, CA) as described. Raw signal intensities for each probe were obtained using Illumina Beadstudio data analysis software and imported to the Bioconductor lumi package for data transformation and normalization. Probes with all samples   absent   (near or below background levels) were filtered. To control for multiple testing and reduce the false positive rate (FDR), stringent statistical criteria were used to identify differentially expressed genes with raw p < 0.01 and FDR adjusted p value < 0.05.

overall_design: Confluent human skin fibroblasts in serum-free media were incubated with or without LPS for 6 h, and RNA was isolated using RNeasy mini kits (Qiagen, Valencia, CA).


title: Genes showing differential expression profiles in control and in neoplastic growth using drosophila wing imaginal tissues

city: NICE cedex 2

first: julien

last: colombani

address: Centre de biochimie - Parc Valrose

department: Institut de Biologie Valrose (iBV)

country: France

institute: CNRS UMR7277

summary:
Classical regeneration experiments in insects have demonstrated an important role for imaginal tissues (also called discs, the larval tissues that give rise to the adult appendages) in coupling tissue growth, maturation and patterning during development We used the rotund-Gal4 driver (Rn>) for disc-targeted silencing of the avalanche gene (avl; Rn>avl-RNAi), encoding a syntaxin that functions in the early endocytic machinery (H. Lu, D. Bilder, Nat Cell Biol 7, 1232; Dec, 2005). Rn>avl-RNAi discs reach near to normal size after 5 days of development, and then undergo unrestricted neoplastic growth. We were interested in identifying genes showing differential expression profiles in control and in neoplastic growth. We identified dilp8 as one of the most differentially expressed gene in control and Rn>avl-RNAi discs.
Abstract from the associated publication: Little is known about how organ growth is monitored and coordinated with the developmental timing in complex organisms. In insects, impairment of larval tissue growth delays growth and morphogenesis, revealing a coupling mechanism.  We carried out a genetic screen in Drosophila to identify molecules expressed by growing tissues participating in this coupling and identified dilp8 as a gene whose silencing rescues the developmental delay induced by abnormally growing tissues. dilp8 is highly induced in conditions where growth impairment produces a developmental delay. dilp8 encodes a peptide whose expression and secretion is sufficient to delay metamorphosis without affecting tissue integrity. We propose that dilp8 is a secreted signal that coordinates the growth status of tissues with developmental timing.

overall_design: RNA were extracted from wing discs of either Rn>+ or Rn>Avl RNAi staged third larval instar at 92, 116 or 168 hours AED (After Egg Deposition) using Qiagen RNeasy lipid tissue microkit according to the manufacturer protocol. Three separate samples were collected for each time point.

first: Julien

last: Colombani

first: Ditte

last: Andersen

first: Pierre

last: Leopold


title: Expression data from human vascular smooth muscle cells exposed to minimally oxidized (mox) LDL

status: Public on Mar 16 2012

city: Toronto

first: Jochen

last: Weile

state: ON

address: 160 College Street

department: Department of Molecular Genetics

country: Canada

institute: University of Toronto

summary: Atherosclerosis (AT) is a chronic inflammatory disease characterized by the accumulation of inflammatory cells, lipoproteins and fibrous tissue in the walls of arteries. AT is the primary cause of heart attacks and stroke and the leading cause of death in westernized countries. To date, the pathogenesis of AT is not well-defined. Studies have shown that the dedifferentiation of contractile and quiescent vascular smooth muscle cells (SMC) to the proliferative, migratory and synthetic phenotype in the intima is pivotal for the onset and progression of AT. To further delineate the mechanisms underlying the pathogenesis of AT, we have analyzed the early molecular pathways and networks of SMC phenotype transformation as induced by the presence of minimally-oxidized LDL (moxLDL).

overall_design: 3 pooled samples were analyzed, one untreated control, one 3h after treatment, one 21h after treatment, no replicates

first: Joe

middle: O

last: Minta

first: James

middle: J

last: Yun

first: Rosanne

last: St  Bernard


title: Gene expression in CD4 memory T cell responses with age

status: Public on Mar 14 2012

city: Stanford

first: Mingcan

last: Yu

state: CA

address: CCSR Bldg. Rm. 2215, 269 Campus Drive West

department: Medicine: Immunology and Rheumatology

institute: Stanford University School of Medicine

summary: With increasing age, the ability of the immune system to protect against recurring infections or to control chronic infections erodes. The objective of the current  study was to identify gene expression signatures in elderly CD4 T cell responses

overall_design: Vβ2+ CD4 memory T cells from four 20-35 and four 70-75 year-old individuals were stimulated with toxic shock syndrome toxin (TSST) presented by myeloid dendritic cells (mDC) derived from young adults. Gene expression was examined at 16, 40 and 72 h after stimulation using Affymetrix arrays.

first: Jorg

last: Goronzy


title: Expression data from st 12-13 embryos from 2xbcd and 6xbcd mothers

city: Mishima

first: Kentaro

middle: M

last: Tanaka

country: Japan

institute: NIG

summary: Embryo from 6xbcd mother shows expansion of prospective head region.  In this embryo, excessive cell death can be observed. This array expreriment is for identifying differentially expressed genes in the 2xbcd and 6xbcd conditions at stage 12-13

overall_design: We crossed TT16 males with TT16 females for the 2xbcd condition and bcd+t8 females for 6xbcd.  In both crosses, eggs were collected in 90 minutes and incubated for 8 hours at 25°.  After excluding unfertilized eggs under stereomicroscope, we extracted RNA from more than 100 eggs and hybridized by GeneChip Drosophila Genome 2.0 arrays (Affymetrix) for hybridization.  We carried out paired (2xbcd vs. 6xbcd) microarray experiments in three replicates using independent RNA samples.

first: Aya

last: Takahashi


title: Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context (mRNA)

status: Public on Mar 19 2012

city: Boston

first: Joshua

middle: WK

last: Ho

state: MA

address: 41 Avenue Louis Pasteur

department: Department of Medicine

institute: Brigham and Women's Hospital

summary: The Drosophila MSL complex mediates dosage compensation by increasing transcription of the single X chromosome in males approximately two-fold. This is accomplished through recognition of the X chromosome and subsequent acetylation of histone H4K16 on X-linked genes. Initial binding to the X is thought to occur at a subset of sites. However, the consensus sequence motif of entry sites (“MSL recognition element” or MRE) is only slightly enriched on the X (~2 fold), and only a fraction of them is utilized by the MSL complex. Here we ask whether chromatin context could distinguish between utilized and non-utilized copies of the motif, by comparing their relative enrichment for histone modifications and chromosomal proteins mapped in the NHGRI modENCODE project. Through a comparative analysis of the chromatin features in male S2 cells, which contain MSL complex, and female Kc cells, which lack the complex, we find that the presence of active chromatin modifications, together with an elevated local GC content in surrounding sequence, has strong predictive value for functional MSL entry sites, independent of MSL binding. We tested these sites for function in Kc cells by RNAi knockdown of Sxl, resulting in induction of MSL complex. We show that ectopic MSL expression in Kc cells leads to H4K16 acetylation around these sites, and a relative increase in X chromosome transcription. Collectively, our results support a model in which a pre-existing active chromatin environment, coincident with H3K36me3, contributes to MSL entry site selection. The consequences of MSL targeting of the male X chromosome include increase in nucleosome lability, enrichment for H4K16 acetylation and JIL-1 kinase, and depletion of linker histone H1 on active X-linked genes. Our finding serves as a model to understand how chromatin and local sequence features are involved in the selection of functional protein binding sites in the genome.

overall_design: The key Drosophila female sex determinant protein, SXL, represses dosage compensation by inhibiting MSL2 translation.  Loss of SXL results in the expression, stabilization, and targetting of the MSL complex in female cells.  Therefore, depletion of SXL by RNA interference (RNAi) in female Kc cells will lead to a MSL2-dependent increase in transcription from the female X chromosomes, consistent with the induction of dosage compensation. In this experiment, we generated gene expression profiles of Kc cells of control (GFP), Sxl RNAi and Sxl-Msl2 RNAi experiments.

first: Marnie

last: Gelbart

first: Artyom

last: Alekseyenko

first: Erica

last: Larschan

middle: W

first: Shouyong

last: Peng

first: Peter

last: Park

first: Mitzi

middle: I

last: Kuroda


title: Genes regulated by GRF1 and GRF3 in Arabidopsis roots

status: Public on Mar 13 2012

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

summary: Arabidopsis Affymetrix ATH1 GeneChips were used to compare the mRNA profiles of root tissues of the grf1/grf2/grf3 triple mutant and transgenic plants overexpressing miR396-resistant variants of GRF1 (P35S:rGRF1) or GRF3 (P35S:rGRF3) with those of the corresponding wild-type (Col-0 or WS).   Wild-type (Arabidopsis thaliana ecotypes Col-0 and Ws), the triple mutant grf1/grf2/grf3, and transgenic plants overexpressing rGRF1 or rGRF3 were grown in vertical culture dishes on modified Knop’s medium for 2 weeks and then root tissues were collected for RNA extraction.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Tarek Hewezi.  The equivalent experiment is AT109 at PLEXdb.]

overall_design: genotype: Arabidopsis thaliana ecotypes Col-0(3-replications);  genotype: Arabidopsis thaliana ecotypes WS(3-replications);  genotype: Triple mutant grf1/grf2/grf3(3-replications);  genotype: P35S:rGRF1 overexpression(3-replications);  genotype: P35S:rGRF3 overexpression(3-replications)

first: Tarek

last: Hewezi

first: Thomas

last: Baum


title: Expression data from primary breast tumors (IJB+OXF)

status: Public on Mar 31 2012

city: Auckland

first: Cris

last: Print

address: Grafton Campus, Park Rd

country: New Zealand

institute: Auckland University

summary:
Frozen tissue specimens from primary breast tumors were collected under IRB-approved protocols from 2 medical centers and profiled using Affymetrix U133 series expression microarrays. This cohort comprises of two subcohorts derived from the Institute Jules Bordet (IJB), Brussels (n=41) (2002) and Guys Hospital, London (n=7) (2003). Dr. Christos Sotiriou (Institute Jules Bordet) directed the microarray work in Brussels.
A publication describing the generation of these data is not yet available. However, these data can be used alongside other Affymetrix breast tumour data sets to form large meta-cohorts for breast cancer research, as was done in Lasham et. al. J Natl Cancer Inst. 2012 Jan 18;104(2):133-146.

overall_design:
Frozen tumor tissues comprising of >60% tumor cellularity were extracted for total RNA and hybridized on Affymetrix microarrays.
Clinical data was requested, but not provided by submitter

first: Lance

middle: D

last: Miller

first: Christos

last: Sotiriou


title: Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context

type: Genome binding/occupancy profiling by genome tiling array


title: Effects of the JADE-HBO1 complex on gene expression

status: Public on Mar 15 2012

city: Lausanne

first: Eric

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

country: Switzerland

institute: EPFL

summary: We find that 499 genes are up-regulated and 457 are down-regulated in response to over-expression of JADE1, while 397 genes are up-regulated and 385 are down-regulated after HBO1 knock-down.

overall_design: For each condition - HBO1 siRNA treatment or JADE1 over-expression - two biological replicates were analyzed in duplicate.

first: Nikita

last: Avvakumov

first: Marie-Eve

last: Lalonde

first: Nehmé

last: Saksouk

first: Anne-Julie

last: Landry

first: Karen

last: Glass

first: Yannick

last: Doyon

first: Christelle

last: Cayrou

first: Geneviève

last: Robitaille

first: Darren

last: Richard

first: Xiang-Jiao

last: Yang

first: Tatiana

last: Kutateladze

first: Jacques

last: Côté


title: Effect of a dual specificity PI3K/mTOR inhibitor, NVP-BEZ235, on human ovarian cancer cell lines grown in 3D culture

first: Joan

middle: S.

last: Brugge

address: 240 Longwood Avenue

department: Department of Cell Biology

institute: Harvard Medical School

summary:
Analysis of the effects of a dual specificity PI3K/mTOR inhibitor on two human ovarian cell lines, OV2008 and MCAS.  Results provide insight into the adaptive response to PI3K/mTOR inhibition in matrix attached ovarian cancer cells.
The PI3K/mTOR-pathway is the most commonly deregulated pathway in epithelial cancers and thus represents an important target for cancer therapeutics. Here we show that dual inhibition of PI3K/mTOR in ovarian cancer 3D-spheroids leads to death of the inner matrix-deprived cells, whereas matrix-attached cells are resistant. Resistance is associated with up-regulation of a cellular survival program that involves both FOXO-regulated transcription and a novel translational resistance mechanism resulting in specific up-regulation of IRES-mediated, cap-independent translation. Inhibition of any of several up-regulated proteins, including Bcl-2, EGFR, or IGF1R, abrogates resistance to dual PI3K/mTOR inhibition. These results demonstrate that acute adaptive response to PI3K/mTOR inhibition resembles well-conserved adaptive response to nutrient and growth factor deprivation and how development of rational drug combinations can bypass resistance mechanisms.

overall_design: Total RNA was isolated 6h and 24h after treatment with 1 μM NVP-BEZ235 or DMSO vehicle control from 3D grown structures

first: Taru

last: Muranen

first: Laura

last: Selfors

first: Fabiana

last: Morales

first: Gordon

middle: B

last: Mills

middle: S


title: Inhibition of the LSD1 (KDM1A) demethylase reactivates the all-trans-retinoic acid differentiation pathway in acute myeloid leukemia [Illumina HumanHT-12 gene expression array]

first: Hans-Ulrich

last: Klein

department: Neurology

institute: Columbia University Medical Center

summary: All-trans-retinoic acid (ATRA) has been successfully used in therapy of acute promyelocytic leukemia (APL), a cytogenetically distinct subtype of acute myeloid leukemia (AML) but the response of non-APL AML cases to ATRA-based treatment has been poor. Here we show that, via epigenetic reprogramming, inhibitors of LSD1/KDM1 demethylase including tranylcypromine (TCP) unlocked the ATRA-driven therapeutic response in non-APL AML. LSD1 inhibition did not lead to an increase in genome-wide H3 lysine4 dimethylation (H3K4me2) but did increase H3K4me2 and expression of myeloid differentiation-associated genes. Importantly, treatment with ATRA plus TCP dramatically diminished engraftment of primary human AML cells in vivo in NOD.SCID mice, suggesting that ATRA in combination with TCP may target leukemia-initiating cells. Furthermore, initiation of ATRA plus TCP co-treatment 15 days post-engraftment of human AML cells in NOD.SCID gamma mice also revealed the ATRA plus TCP drug combination to have a potent anti-leukemic effect, which was superior to treatment with either drug alone. These data identify LSD1 as a therapeutic target and strongly suggest that it may contribute to AML pathogenesis by inhibiting the normal pro-differentiative function of ATRA, paving the way for novel combinatorial therapies of AML.

overall_design: Overall, 30 specimens derived from HL-60 or TEX cell line were treated with drugs and hybridized to Illumina HumanHT-12 gene expression arrays.

first: Tino

last: Schenk

first: Weihsu

last: Chen

first: Stefanie

last: Göllner

first: Louise

last: Howell

first: Liqing

last: Jin

first: Katja

last: Hebestreit

first: Andreea

last: Popescu

first: Alan

last: Burnett

first: Ken

first: Robert

last: Casero Jr

first: Laurence

last: Marton

first: Patrick

last: Woster

first: Mark

last: Minden

first: Martin

last: Dugas

first: Jean

last: Wang

first: John

middle: E

last: Dick

first: Carsten

last: Müller-Tidow

first: Kevin

last: Petrie

first: Arthur

last: Zelent


title: Secreted STIP1 stimulates cell proliferation of ovarian cancer through SMAD signaling pathways

status: Public on Mar 03 2012

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

institute: Ming Chuan Univ

summary: Stress-induced phosphoprotein 1 (STIP1) is a co-chaperone that regulates other chaperone proteins that was recently shown to be secreted by ovarian cancer cells to induce cell proliferation. In this study, we found that STIP1 induced the phosphorylation of endogenous SMAD1/5, and knockdown of SMAD1/4/5 blocked STIP1-activated ID3 expression. Inhibition of ALK2, a serine/threonine kinase receptor, with siRNA or the specific inhibitor LDN193189, blocked STIP1-induced phosphorylation of SMAD1/5 and inhibited STIP1-related cell proliferation. The signaling pathway was found to involve binding of secreted STIP1 to ALK2, phosphorylation of SMAD, and activation of ID3 to induce cell proliferation was identified not only by in vitro immunofluorescent microscopy and biochemical identification of complex formation, but also by in vivo immunohistochemical analyses of ovarian cancer tissues.

overall_design:
MDAH2774 cell treated with rhSTIP1
MDAH2774 cell treated without rhSTIP1
MDAH2774 cell treated with rhSTIP1-2
MDAH2774 cell treated without rhSTIP1-2


title: Light- and plastid-regulated transcriptomes in Arabidopsis seedlings

status: Public on Mar 02 2012

city: East Lansing

first: Michael

last: Ruckle

state: MI

address: S-208 Plant Biology, Michigan State University

department: Plant Research Labs

institute: Michigan State University

summary:
Plastids emit signals that broadly affect cellular processes. Based on previous genetic analyses, we propose that plastid signaling regulates the downstream components of a light signaling network and that these interactions coordinate chloroplast biogenesis with both the light environment and development by regulating gene expression.  We tested these ideas by analyzing light-regulated and plastid-regulated transcriptomes.  We found that the plastid is a major regulator of light signaling, attenuating the expression of more than half of all light-regulated genes in our dataset and changing the nature of light regulation for a smaller fraction of these light-regulated genes.
Our analyses provide evidence that light and plastid signaling are interactive processes and are consistent with these interactions serving as major drivers of chloroplast biogenesis and function.

overall_design: Four biological replicates were grown separately under the same conditions.  Arabidopsis seedlings were grown in the presence (+Lin) or absence (-Lin) of lincomycin in 0.5 µmol m-2 s-1 blue plus red (BR) light for 6 days. After 6 days of growth in 0.5 µmol m-2 s-1 of BR light, seedlings were transferred to 60 µmol m-2 s-1 BR light.   50-100 seedlings were collected before (0 h) and 0.5 h, 1 h, 4 h, and 24 h after the 0.5 to 60 µmol m-2 s-1 BR-fluence-rate shift for RNA extraction and hybridization on Affymetrix microarrays.

last: Larkin

first: Lyle

last: Burgoon


title: Microarray analysis of  Arabidopsis Col-0 and catalase 2 mutant define interactions between CO2, daylength and H2O2

status: Public on Mar 07 2012

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: Growth daylength, ambient CO2 level, and intracellular hydrogen peroxide (H2O2) availability all impact plant function by modulating signalling pathways, but interactions between them remain unclear. Using a whole-genome transcriptomics approach, we exploited the conditional photorespiratory nature of the catalase-deficient cat2 mutant to identify gene expression patterns responding to these three factors. Arabidopsis Col-0 and cat2 grown for 5 weeks in high CO2 in short days (SD) were transferred to air in SD or long days (LD), and microarray analysis was performed. Of more than 500 genes differentially expressed in Col-0 between high CO2 and transfer to air in SD, the response of about one-third was attenuated by transfer to air in LD. H2O2-responsive genes in cat2 were highly dependent on daylength. The majority of H2O2-induced genes were more strongly up-regulated after transfer to air in SD than to LD, while a smaller number showed an opposing pattern. Responses of other H2O2-dependent genes indicate redox-modulation of the daylength control of fundamental cell processes. The overall analysis provides evidence that (1) CO2 level modulates stress-associated gene expression; (2) both CO2 and H2O2 interact with daylength and photoreceptor signalling pathways; and (3) cellular signalling pathways may be primed to respond to increased H2O2 in a daylength-determined manner.

overall_design: Two genotypes x five conditions experiment, including Arabidopsis Col0WT and cat2-1 plants grown in soil for 5 weeks in a 8h light/16h dark (short day) regime at high CO2 concentration (3000 ppm CO2) and subsequently transferred to air (400 ppm CO2) in a short day or long day (16h light/8h dark) regime for 2 and 4 days. Three biological replicates were used that consist each of a pool of two leaves from different plants. Each sample was hybridized to one Genechip® Arabidopsis ATH1 Genome Array (Affymetrix).

first: Guillaume

last: Queval

first: Jenny

last: Neukermans

first: Sandy

last: Vanderauwera

first: Frank

last: Van Breusegem

first: Graham

last: Noctor


title: Oncogeneic KRAS Regulates BMP4 Expression in Colon Cancer

status: Public on Mar 01 2012

first: Manish

last: Gala

state: MASSACHUSETTS

address: 55 Fruit Street, GRJ 825

institute: Massachusetts General Hospital

summary: Microarray analysis comparing SW480 cells treated with scramble siRNA control with SW480 cells treated with siRNA against mutant KrasV12.

overall_design: Two biological replicates of each sample were performed.

first: Eva-Maria

last: Duerr

first: Yusuke

last: Mizukami

first: Kentaro

last: Moriichi

first: Won-seok

last: Jo

first: Hirotoshi

last: Kikuchi

first: Daniel

last: Chung


title: Genome wide analysis of long term L1TD1 knockdown effects in NT2D1 cell line with inducible shRNA vectors

status: Public on Feb 28 2012

city: Turku

first: Nelly

last: Rahkonen

address: Tykistökatu 6 A

country: Finland

institute: Turku Centr for Biotechnology

summary: The purpose of this study was to analyze genome wide effects of long term L1TD1 silencing in embryonal carcinoma cell line (NT2D1) and to identify molecular level mechanismis of L1TD1 function and determine its possible role in pluripotency and self-renewal

overall_design: Six clones from NT2D1 cell line stably expressing TetR3 and L1TD1shRNA were analyzed. From each clone two samples were prepared: non-induced cells as control and doxycycline induced cells (+) to knockdown L1TD1, resulting altogether 12 samples. Samples were collected on day 6 after start of dox induction. One sample had to be excluded from the analysis because it did not cluster according to the sample groups.


title: Effect of scarification on gene expression in the skin of C57BL/6 mice

city: Midlothian

first: Neil

middle: A.

last: Mabbott

address: Easter Bush

department: The Roslin Institute & Royal (Dick) School of Veterinary Sciences

institute: University of Edinburgh

summary:
To study the effects of scarification on gene expression in the skin we performed microarray analysis on intact skin (control) and skin collected 2 h after scarification.
Comparison of microarray data between the two groups showed that 451 probe sets (1.0% of a total 45038 probe sets on the arrays) representing 338 known genes were upregulated ≥ 2.0 fold in scarified skin samples when compared to controls.  Further analyses of these genes showed that many were associated with an inflammatory immune response.  Others were associated with wound-repair, response to stress, apoptosis and transcriptional regulation.  The induction of high levels of genes encoding the neutrophil chemoattractants Cxcl1 and Cxcl2, the G-CSF receptor Csf3r, the GM-CSF receptor Csf2rb, the calcium binding proteins S100a8 and a9 (S100a8 and S100a9, respectively) the cytokines Ilb and Il6, and Cd14, Mmp9 and Sell, amongst many others, suggested a significant influx of neutrophillic granulocytes into the skin after scarification.   Indeed, the expression of Cxcl2 and Il1b were up-regulated 50 fold in scarified skin when compared to intact skin.

overall_design: C57BL/6 mice (6-12 weeks old), 2-3 per group used.  Prior to scarification approximately 1 cm2 area of hair covering the site of scarification was trimmed using curved scissors and then removed completely with an electric razor.  Twenty-four hours later a 23-gauge needle was used to create a 5 mm long abrasion in the epidermal layers of the skin at the scarification site.  2 h later, ear skin was collected into RNAlater (Ambion, location) and stored at -80 oC prior to analysis.  The quality of RNA for microarray analysis was first determined on an Agilent BioAnalyzer 2100 (Agilent Technologies).  RNA was reverse transcribed to cDNA, amplified and labelled using the Genechip 3’ IVT Express Labelling Kit (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s instructions.  Samples were hybridized to HT_MG-430_PM Affymetrix chips (Affymetrix), stained and scanned by ARK Genomics (ARK Genomics, Edinburgh, UK).

first: Gwennaelle

last: Wathne

first: Adrien

last: Kissenpfennig

first: Bernard

last: Malissen

first: Chiara

last: Zurzolo

middle: A


title: Expression data from GFAP-negative LC cells exposed to 24 hours of hypoxia

city: Dublin

first: Ruaidhri

middle: Patrick

last: Kirwan

state: Leinster

address: Belfield

department: Conway Institute of Biomolecular and Biomedical Research & School of Medicine and Medical Science

country: Ireland

institute: University College Dublin

summary: Vascular hypoperfusion is a pathological phenomenon in the glaucomatous optic nerve head. We report transcriptional responses in GFAP-negative LC cells exposed to in-vitro hypoxic stress (1%O2).

overall_design:
The study design was as follows:

For GSM659595: "human donor 1" LC cells were passaged into three p100 plates of cells and then exposed to normoxia for 24 hours. The RNA from each of these three plates was then extracted, pooled and hybridised to the microarray "normoxia_1".

For GSM659592: "human donor 1" LC cells were passaged into three p100 plates of cells and then exposed to hypoxia for 24 hours. The RNA from each of these three plates was then extracted, pooled and hybridised to the microarray "hypoxia_1".

"hypoxia_1" and "normoxia_1" microarray data were then compared to calculate differential gene expression in response to hypoxia.

This experiment (same design) was then conducted a second and third time using biologically independent "human donor 2" and "human donor 3" cell lines respectively.

middle: P

first: Luca

last: Felica

first: Abbot

middle: F

last: Clark

first: Colm

last: O'Brien

first: Martin

last: Leonard


title: A mouse model of the most aggressive subgroup of human medulloblastoma [HT_MG-430_PM]

status: Public on Feb 29 2012

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: A series of mouse models designed to mimic pediatric medulloblastoma types in humans were tested by microarray and compared to published human medulloblastoma data

overall_design: Myc-type tumors [dka201-203] were generated by orthotopic injection of Myc-infected cerebellar cells from Cdkn2c-/-, Trp53-/-, Atoh1-GFP mice into the cerebral cortex of immunocompromised nude mice. For Shh-type medulloblastomas [dka204-206], spontaneous medulloblastomas from [Cdkn2c-/-; Trp53Fl/Fl; Nestin-Cre] (Uziel et al.,2005 Genes Dev) were used.  FACS-sorted GFP-positive [dka220-222] and GFP-negative [dka211, 212 and 219] populations were obtained from postnatal day 6 Cdkn2c-/-, Trp53-/-, Atoh1-GFP cerebella.  Myc-type secondary tumors [dka223-225] were generated by orthotopic transplantation of cultured sphere cells from Myc-type primary tumors.

first: Daisuke

last: Kawauchi

first: Giles

last: Robinson

first: Tamar

last: Uziel

first: Paul

last: Gibson

first: Jerold

last: Rehg

first: Cuilan

last: Gao

first: Chunxu

last: Qu

first: Stanley

last: Pounds

last: Ellison

first: Richard

last: Gilbertson

first: Martine

last: Roussel


title: Receptor Tyrosine Kinase Activation in Infantile Fibrosarcoma/Congenital Mesoblastic Nephroma

first: Elizaebth

last: Perlman

address: 2373 North Lincoln Avenue

department: Pathology

institute: Northwestern University

summary: The goal of this study is to identify downstream pathways, diagnostic markers, and potential therapeutic targets for IFS/CMN.

overall_design: Global gene expression of 14 cellular mesoblastic nephromas/infantile fibrosarcoma was compared with 10 RT, 16 clear cell sarcomas of the kidney, and 15 Wilms tumors using  Affymetrix U133A arrays to identify genetic pathways that clarify the pathogenesis of Rhabdoid Tumors and to discover new therapeutic targets for these tumors

first: Samantha

last: Gadd

first: Elizabeth


title: Polycomb repressive complex 2-dependent and –independent functions of Jarid2 in transcriptional regulation in Drosophila [Affymetrix]

status: Public on Feb 23 2012

city: Kansas CIty

first: Alexander

middle: (Garrett)

last: Garruss

state: Missouri

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

summary: Jarid2 was recently identified as an important component of the mammalian Polycomb Repressive Complex 2 (PRC2), where it has a major effect on PRC2 recruitment in mouse embryonic stem cells. Although Jarid2 is conserved in Drosophila, it has not previously been implicated in Polycomb (Pc) regulation. Therefore, we purified Drosophila Jarid2 and its associated proteins and find that Jarid2 associates with all of the known canonical PRC2 components, demonstrating a conserved physical interaction with PRC2 in flies and mammals. Furthermore, in vivo studies with Jarid2 mutants in flies demonstrate that among several histone modifications tested, only H3K27 methylation, the mark implemented by PRC2, was affected. Genome-wide profiling of Jarid2, Su(z)12 and H3K27me3 occupancy by ChIP-seq indicates that Jarid2 and Su(z)12 have a very similar distribution pattern on chromatin. However, Jarid2 and Su(z)12 occupancy levels at some genes are significantly different with Jarid2 being present at relatively low levels at many Pc response elements (PREs) of certain Homeobox (Hox) genes, providing a rationale for why Jarid2 was never identified in Pc screens. Gene expression analyses show that Jarid2 and E(z) (a canonical PRC2 component) are required not only for transcriptional repression but might also function in active transcription. Identification of Jarid2 as a conserved PRC2 interactor in flies provides an opportunity to begin to probe some of its novel functions in Drosophila development.

overall_design: Expression analyses of Jarid2 mutants in larvae and eye imaginal discs.  Expression analyses of E(z) RNAi in larvae.

last: Garrett

first: Hans-Martin

last: Herz

first: Ali

last: Shilatifard


title: Expression data from L3 Drosophila antennal-eyediscs

status: Public on Feb 20 2012

city: San Juan de Alicante

first: andres

last: garelli

address: c/Ramón y Cajal s/n

country: Spain

institute: instituto de neurociencias de alicante

summary: Growth of the drosophila eye imaginal discs is controlled by the activation of Notch in the dorsal-ventral boundary. Overexpression in the eye disc of the Notch ligand Delta together with lola and pipsqueak from the GS(2)88A8 line induces tumoral growth. We used microarray to analyze the expression profile of tumoral discs.

overall_design: Antennal-eye discs of Drosophila L3 larvae were selected for RNA extraction and hybridization on Affymetrix microarrayas. Two genetic conditions were analyzed: tumoral eye discs (ey-Gal4 GS(2)88A8 UAS-Dl) and control eye discs (GS(2)88A8 UAS-Dl). Three different biological replicates of each condition, each one consisting on 300 hundred pairs of eye discs, were analyzed.

first: Maria

last: Dominguez

first: Alisson

last: Gontijo

first: Andrés

last: Garelli

first: Verónica

last: Miguela

first: Esther

last: Caparrós


title: Expression data from normal and MDS erythroids cell cutlures ex vivo

status: Public on Feb 14 2012

city: Paris

first: olivier

last: kosmider

address: 27 Rue du faubourg St Jacques

institute: Hopital Cochin

summary:
CD34 positive cells of bone marrow samples from normal and MDS samples were cultured ex vivo into erythroid conditions.
We used microarrays to detail the gene expression programm of erythroid cells between normal and pathological (MDS) samples

overall_design: Mononuclear cells from bone marrow samples were selected on the expression of the CD34 membran marker. Then, they were cultured ex vivo during 14 days and total RNA samples were analyzed at day 7, 10 and/or 14 then compared between normal and MDS samples.

first: Emmanuel

last: Gyan

first: Michaela

last: Fontenay


title: Comparison of pan-inhibitor of HDACS (TSA) to specific HDAC8 inhibitor (HDAC Inhibitor XIX, Compound 2) in human myometrium

status: Public on Feb 07 2012

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

institute: Newcastle University

summary: To compare gene expression in human myometrium after TSA treatment to gene expression after treatment with a specific HDAC8 inhibitor

overall_design: Four Control, four TSA and four Compound 2 samples (2 patients, replicated) derived from non-pregnant myometrial strips

first: Magda

last: Karolczak-Bayatti

first: Daniel

middle: C

last: Swan


title: The Regulatory Specificity of a Homeodomain Protein is Determined by Unique DNA-Binding Sequences

status: Public on Feb 08 2012

city: Bethesda

first: Brian

last: Busser

state: Md

address: 10 Center Drive

institute: NHLBI/NIH

summary: Homeodomain (HD) proteins comprise a large family of evolutionarily conserved transcription factors (TFs) having diverse developmental functions, yet they paradoxically recognize very similar DNA sequences.  To investigate how HDs control cell-specific gene expression patterns, we determined the DNA binding specificities of a broad range of HDs critical for Drosophila embryonic mesoderm development.  These studies revealed particular sequences that are bound by one HD and not by others.  Such HD-preferred binding sites are overrepresented in the noncoding regions of genes that are regulated by the corresponding HD.  Moreover, we show at single-cell resolution in intact embryos that the HD Slouch (Slou) controls myoblast gene expression through unique DNA sequences that are preferentially bound by Slou.  These findings demonstrate that the sequence of a HD-binding site dictates which HD family member binds to and regulates a particular enhancer.  This represents a novel mechanism for how cell type-specific TFs induce the distinct genetic programs of individual embryonic cells.

overall_design: Mesodermal cells were profiled from wild type, slou gain-of-function and msh gain-of-function backgrounds.

first: B

first: L

last: Shokri

first: S

last: Jaeger

last: Gisselbrecht

first: A

last: Singhania

first: M

last: Berger

last: Zhou

middle: L

last: Bulyk

middle: M

last: Michelson


title: Comparison of low water potential (drought)-regulated gene expression in wild type (Col-0) and the hai1-2 (At5g59220) mutant

status: Public on Feb 03 2012

city: Taipei

first: Verslues

middle: Edwin

last: Paul

address: 128 Sec. 2, Academia Rd, Nankang, Taipei 11529 Taiwan, R.O.C.

department: Institute of Plant and Microbial Biology

institute: Academia Sinica

summary:
The Clade A PP2C Highly ABA-Induced1 (HAI1, At5g59220) is strongly up-regulated by low water potential in an ABA-dependent manner.  Using knockout mutants of hai1, we found that HAI1 functions as a negative regulator of low water potential-induced proline and osmoregulatory solute accumulation.  We also found a relatively weak and limited interaction of HAI1 with the RCAR/PYL family of ABA receptors.  This, plus its induced expression, suggest that HAI1 remains active during stress and attenuates specific aspects of drought response.

Microarray experiments were used to identify genes differentially expressed in hai1-2 (SALK_108282) versus wild type under both unstress control conditions and after low water potential (i.e., drought, water deficit).  A relatively long term (96 h) low water potential treatment was used as phenotypes of hai1-2 were most apparent after this longer term low water potential treatment.

overall_design: Seven-day-old seedlings of wild type (Col-0) or hai1-2 were transferred from agar plates of control media to low water potential stress (PEG-infused agar plates at -1.2 MPa) or to fresh control media (-0.25 Mpa). Samples (whole seedlings) were collected 96 h after transfer. Three independent experiments were conducted with one sample of each treatment (wild type stress and control, hai1-2 stress and control) collected from each experiment.

first: Bhaskara

middle: G

last: Badiger

first: Nguyen

middle: T

last: Thao

first: Paul

last: Verslues


title: Expression data from human with IgA nephropathy (IgAN) [HG-U133A]

status: Public on Feb 02 2012

city: Ann Arbor

first: Celine

last: Berthier

address: 1150 W. Medical Center Dr, MSRB2

institute: University of Michigan

summary:
Proteinuria is the most important predictor of outcome in glomerulonephritis and experimental data suggest that the tubular cell response to proteinuria is an important determinant of progressive fibrosis in the kidney.  However, it is unclear whether proteinuria is a marker of disease severity or has a direct effect on tubular cells in the kidneys of patients with glomerulonephritis.   Accordingly we studied an in vitro model of proteinuria, and identified 231 albumin-regulated genes differentially expressed by primary human kidney tubular epithelial cells exposed to albumin. We translated these findings to human disease by studying mRNA levels of these genes in the tubulo-interstitial compartment of kidney biopsies from patients with IgA nephropathy using microarrays. Biopsies from patients with IgAN (n=25) could be distinguished from those of control subjects (n=6) based solely upon the expression of these 231 albumin-regulated genes.  The expression of an 11-transcript subset related to the degree of proteinuria, and this 11-mRNA subset was also sufficient to distinguish biopsies of subjects with IgAN from control biopsies.  We tested if these findings could be extrapolated to other proteinuric diseases beyond IgAN and found that the all forms of primary glomerulonephritis (n=33) can be distinguished from controls (n=21) based solely on the expression levels of these 11 genes derived from our in vitro proteinuria model.  Pathway analysis suggests common regulatory elements shared by these 11 transcripts.  In conclusion, we have identified an albumin-regulated 11-gene signature shared between all forms of primary glomerulonephritis.  Our findings support the hypothesis that albuminuria may directly promote injury in the tubulo-interstitial compartment of the kidney in patients with glomerulonephritis.
We used microarrays to analyze the transcriptome of microdissected renal biopsies from patients with IgA nephropathy (IgAN)

overall_design: RNA from tubulointerstitial compartments was extracted and processed for hybridization on Affymetrix HG-U133A microarrays.

first: Heather

middle: N

last: Reich

first: David

last: Tritchler

last: Cattran

first: Andrew

last: Herzenberg

first: Felix

last: Eichinger

first: Anissa

last: Boucherot

first: Anna

last: Henger

first: Viji

last: Nair

first: Clemens

middle: D

last: Cohen

first: James

middle: W

last: Scholey

first: Matthias

last: Kretzler


title: The response of human primary airway epithelial cells to Influenza or RSV infection [hAECs_Illumina]

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: To investigate how human airway epithelial cells respond to Influenza or RSV infection, we harvested airway epithelial cells from the mainstream bronchi of human donors and cultured them as previously described (Pickles et al,1998) in a polarized system  that resembles the in vivo mucociliary pseudostratified epithelium. Quadruplicate hAEC cultures were infected with 2X105 PFUs Influenza A (Udorn) or with 1x106 PFUs RSV for 2h or mock inoculated and harvested 24h after Influenza infection and 48h after RSV infection.

overall_design: Quadruplicate  polarized airway epithelial cell cultures were infected with 2x10^5 PFUs of Influenza A (Udorn) for 2h  or  infected with 1x10^6 PFUs RSV and harvested 24 h post infection for Influenza or 48h post infection for RSV.Duplicate cultures were used as controls for each condition (Two cultures were mock treated mor 2h and harvested after 24h for the Influenza infection and 2 cultures were mock treated for 2h and harvested after 48 hours for the RSV infection.Total RNA was harvested and gene expression was studied using Genespring GX v7.3.1.

first: Ioannis

last: Ioannidis

first: Beth

last: McNally

first: Meredith

last: Willette

first: Emilio

last: Flano


title: Expression data from human with IgA nephropathy (IgAN)

last: Berthier

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

overall_design: Refer to individual Series

first: Daniel


title: Microarray analysis of the migrating human CD4+ T cell population from the spleen of humanized mice in response to treatment with Teplizumab or hIg

status: Public on Feb 27 2012

city: New Haven

first: Frank

last: Waldron-Lynch

state: CT

address: 300 George Street

department: Human Translational Immunology

institute: Yale University Medical School

summary: In order to identify genes expressed by cells that leave the spleen, the spleens were harvested from untreated reconstituted humanized mice (N=4) and a single cell suspension was prepared . The cultures were treated with either teplizumab (anti human CD3 hOKT3g1(Ala-Ala))  or hIg for 18 hrs in vitro. Splenocytes were also harvested 18 hrs after reconstituted mice (N=4) were treated with teplizumab in vivo. The humanized mice used where NOD/SCID IL2gc-/- (NSG) reconstituted with human CD34+ at birth.

overall_design: Total RNA was obtained form sorted human CD4 splenocytes 18 hours post treatment. Comparsons were made between the treatment groups.

first: Kevan

last: Herold


title: Differences in gene expression of Mustard and Kenny mutants relative to control w1118 flies 24 hours after access to food contaminated with Vibrio cholerae

status: Public on Feb 01 2012

city: Boston

first: Paula

last: Watnick

address: 300 Longwood Avenue

department: Infectious Diseases

institute: Children's Hospital, Boston

summary: Mustard and Kenny mutants are resistant to oral infection with V.cholerae. We used microarrays to determine whether Key and Mtd have overlapping regulons.

overall_design: Key1 and Mtd mutant and CTL flies were given access to Vibrio cholerae in LB.  After 24 hours, whole flies were homogenized and RNA was isolated.

first: Cristin

last: Berkey


title: Identification of the differences between expression patterns of kinin-dependent genes in endometrial cancer

status: Public on Mar 10 2012

city: Sosnowiec

first: Urszula

last: Mazurek

address: Jedności 8

department: Department of Molecular Biology

country: Poland

institute: Medical University of Silesia

summary: The present study has focused on the identification of the differences between expression patterns of kinin-dependent genes in endometrial cancer

overall_design: For microarray analysis  20 samples were used: 7 control samples, 3 - G1 samples, 8 - G2 samples and 2 - G3 samples.


title: Genome features of “Dark-fly”, a Drosophila line reared long-term in a dark environment

status: Public on Jan 31 2012

city: Cambridge

first: Jun

last: Zhou

address: 16 Divinity Ave. Rm2112

department: Organismic and Evolutionary Biology

institute: Harvard University

summary: To address the molecular mechanisms underlying environmental adaptation, we studied a Drosophila melanogaster line, termed Dark-fly, which has been maintained in constant dark conditions for 57 years (1400 generations).The structural gene copy number changes between the dark fly and its control were assessed by aCGH array. The comparison showed that hundreds of genes in the dark fly bear duplications or deletions relative to the control line.

overall_design: The copy number increase and decrease in the dark flies were determined by two-channel array hybridization with the control line. In addition to biological replicates, a Cy5-Cy3 dye swap was performed.Self-hybridization was also conducted to serve as a quality control.

first: Naoyuki

last: Fuse


title: The Combination of a Genome-Wide Association Study of Lymphocyte Count and Analysis of Gene Expression Data Reveals Novel Asthma Candidate Genes

city: Tucson

first: Darren

last: Cusanovich

state: AZ

address: 1230 N Cherry Avenue, BSRL 421

department: Cellular and Molecular Medicine

institute: University of Arizona

summary: Recent genome-wide association studies (GWAS) have identified a number of novel genetic associations with complex human diseases. In spite of these successes, results from GWAS generally explain only a small proportion of disease heritability, an observation termed the “missing heritability problem.” Several sources for the missing heritability have been proposed, including the contribution of many common variants with small individual effect sizes, which cannot be reliably found using the standard GWAS approach. The goal of our study was to explore a complementary approach, which combines GWAS results with functional data in order to identify novel genetic associations with small effect sizes. To do so, we conducted a GWAS for lymphocyte count, a physiologic quantitative trait associated with asthma, in 462 Hutterites. In parallel, we performed a genome-wide gene expression study in lymphoblastoid cell lines (LCLs) from 96 Hutterites. We found significant support for genetic associations using the GWAS data when we considered variants near the 193 genes whose expression levels across individuals were most correlated with lymphocyte counts. Interestingly, these variants are also enriched with signatures of an association with asthma susceptibility, an observation we were able to replicate. The associated loci include genes previously implicated in asthma susceptibility, as well as novel candidate genes enriched for functions related to T cell receptor signaling and ATP synthesis. Our results, therefore, establish a new set of asthma susceptibility candidate genes. More generally, our observations support the notion that many loci of small effects influence variation in lymphocyte count and asthma susceptibility.

overall_design: 96 RNA samples were collected (1 subsequently excluded) from lymphoblastoid cell lines derived from Hutterite subjects chosen to represent the extremes of absolute lymphocyte count. The high and low absolute lymphocyte count groups were balanced with respect to age, gender, and relatedness.

first: Christine

last: Billstrand

first: Xiang

first: Claudia

last: Chavarria

first: Sherryl

last: De Leon

first: Katelyn

last: Michelini

first: Athma

last: Pai

first: Carole

last: Ober

first: Yoav

last: Gilad


title: Dramatic effects of social behavior on gene regulation in rhesus macaques [Individual_expression]

city: Durham

first: Jenny

last: Tung

state: NC

address: 125 Science Drive

institute: Duke University

summary: Analysis of gene expression differences in relationship to dominance rank in female rhesus macaques.

overall_design: RNA obtained from isolated peripheral blood mononuclear cells from 49 adult female rhesus macaques of dominance ranks 1 (high) to 5 (low) across 10 social groups. Total 100 samples = (47 individuals X 2 replicates) + (2 individuals X 3 replicates)


title: Dramatic effects of social behavior on gene regulation in rhesus macaques [Cell type_expression]

overall_design: RNA obtained from 4 cell populations (helper T cells, cytotoxic T cells, monocytes, and B cells) from isolated peripheral blood mononuclear cells sampled from 5 adult female rhesus macaques across 5 different social groups and 5 different dominance ranks [dominance ranks : 1 = high, 5 = low]


title: Gene Expression Profiles of Adult Human Olfactory Bulb and Embryonic Neural Stem Cells

status: Public on Jan 30 2012

city: Mansoura

first: Hany

middle: El Sayed

last: Marei

state: Dakahlaya

address: Gomhoraya

department: Histology

country: Egypt

institute: Fac. Vet Med

summary: Global gene expression profiling was performed using RNA from human embryonic neural stem cells (hENSCs) and adult human olfactory bulb-derived neural stem cells (OBNSCs) to define a gene expression pattern and signaling pathways that are specific for each cell lineage. Subtractive gene expression profiling between both cell lineages provides a list of potential genes that are related to their multipotentiality, proliferation, migration, and alternative signaling pathways. To confirm the validity of our DNA microarray data, our results were compared with data from various databases.

overall_design: The gene expression profile of adult olfactory bulb neural stem cells (n=6) was compared with that of human embryonic neural stem cells (n=3).


title: Gene expression profiling of asbestos-related lung squamous cell carcinoma

city: Concord

first: Casey

last: Wright

state: NSW

address: Gate 3, Hospital Road

country: Australia

institute: ADRI

summary: To identify gene expression biomarkers associate with asbestos-related lung squamous cell carcinoma, we analyzed gene expression profiles for a total of 56 lung squamous cell carcinomas using 44K Illumina Gene Expression microarrays. Twenty-six cases had lung asbestos body counts above levels associated with urban dwelling (ARLC-SCC: asbestos-related lung cancer-squamous cell carcinoma) and 30 cases had no lung asbestos bodies (NARLC-SCC: non-asbestos related lung cancer- squamous cell carcinoma). Genes differentially expressed between ARLC-SCC and NARLC-SCC were identified on fold change and P-value, and then prioritised using gene ontology.

overall_design: Total RNA was obtained from fresh frozen lung tumour tissue and stratified by asbestos phenotype. Gene expression profiling was performed to identify differences in the gene profiles of asbestos-related and non-asbestos related lung squamous cell carcinomas.

first: C

first: S

last: Savarimuthu-Francis

first: M

middle: E

last: Tan

first: N

middle: K

last: Hayward

middle: U

last: Martins

first: I

last: Yang

first: R

middle: V

last: Bowman

first: K

last: Fong


title: Inter-ethnic differences in lymphocyte  sensitivity to glucocorticoids reflect variation in transcriptional response

city: Chicago

first: Joseph

last: Maranville

state: IL

address: 920 E. 58th Street

institute: 920 E. 58th Street

summary: Glucocorticoids (GCs) are steroid hormones widely  used as pharmaceutical interventions, which act mainly by regulating gene expression levels. A large fraction of patients (~30%), especially those of African descent, show a weak response to treatment. To interrogate the contribution of variable transcriptional response to inter-ethnic differences, we measured  in vitro lymphocyte GC sensitivity (LGS) and transcriptome-wide response to GCs in peripheral blood mononuclear cells (PBMCs) from African-American and European-American healthy donors. We found that transcriptional response after 8hrs treatment was significantly correlated with variation in LGS within and  between populations. We found that NFKB1, a gene previously found to predict LGS within populations, was more strongly downregulated in European-Americans on average.  NFKB1 could not completely explain population differences, however, and we found an additional 177 genes with population differences in the average log2 fold change (FDR<0.05), most of which also showed a weaker transcriptional response in AfricanAmericans. These results suggest that inter-ethnic  differences in GC sensitivity reflect variation in transcriptional response at many genes, including regulators with large effects (e.g.  NFKB1) and numerous other genes with smaller effects.

overall_design: Total RNA was obtained from paired aliquots of peripheral blood mononuclear cells treated with dexamethasone or vehicle (EtOH) for 8 and 24 hours.

first: Shaneen

middle: S

last: Baxter

first: Jason

last: Torres

first: Anna

last: Di Rienzo


title: Volatiles of two growth-inhibiting rhizobacteria commonly enroll AtWRKY18 function

status: Public on Jan 25 2012

city: Tuebingen

first: Joachim

last: Kilian

address: Auf der Morgenstelle 1

department: ZMBP Plant Physiology

country: Germany

institute: University of Tuebingen

summary:
Volatiles of certain rhizobacteria can cause growth inhibitory effects on plants/ Arabidopsis thaliana. How these effects are initiated and which mechanisms are enrolled is not yet understood. Obviously the plant can survive/live with the bacteria in the soil, which suggest the existance of a regulatory mechanism/network that provide the possibility for coexistance with the bacteria. To shed light on this regulatory mechanism/network we performed a microarray anlaysis of Arabidopsis thaliana co-cultivated with two different rhizobacteria strains.
In this study we used the ATH1 GeneChip microarray to investigate the  transcriptional response of 4 to 5 days old Arabidopsis thaliana seedlings at 6 h, 12 h and 24 h exposure to volatiles of the rhizobacteria Serratia plymuthica HRO-C48 or Stenotrophomonas maltophilia R3089.

overall_design: Seedlings from Arabidopsis thaliana were harvested at different time points at exposure to volatiles of two different strains of bacteria. Samples were taken at the start of the experiment (T0) and after 6, 12 and 24 hours (T6, T12, T24 respectively). Two biological replicates from pooled seedlings (from 5 plates, from the respective time points) were used for RNA extraction and hybridization on Affymetrix microarrays (ATH1 GeneChip; GEO accsession GPL198).

first: Katrin

last: Wenke

first: Dierk

last: Wanke

first: Kenneth

last: Berendzen

first: Klaus

last: Harter

first: Birgit

last: Piechulla


title: Co-targeting of the PI3K pathway improves the response of BRCA1 deficient breast cancer cells to PARP1 inhibition

status: Public on Jan 19 2012

city: Lund

first: Ida

last: Johansson

address: Department of Oncology Clinical Sciences Lund University BMC C13

department: Oncology

country: Sweden

institute: Lund University

summary: Although pre-clinical and clinical studies on PARP1 inhibitors, alone and in combination with DNA-damaging agents, show promising results, further ways to improve and broaden the scope of application of this therapeutic approach are warranted. To this end, we have investigated the possibility of improving the response of BRCA1 mutant breast cancer cells to PARP1 inhibition by co-targeting the PI3K pathway. The human breast cancer cell line MDA-MB-436, which lacks the expression of both BRCA1 and PTEN, was treated with the PARP1 inhibitor AG014699 as a single agent or in combination with the PI3K inhibitor LY294002 for 7 days.

overall_design: The human breast cancer cell line MDA-MB-436 was treated with the PARP1 inhibitor AG014699 as a single agent or in combination with the PI3K inhibitor LY294002 for 7 days. All treatments were performed in triplicates. Total RNA was extracted hybridized onto the Illumina HumanHT-12 v4.0 microarray platform.

first: Siker

last: Kimbung

first: Ewa

last: Biskup

first: Kristina

last: Aaltonen

first: Astrid

last: Ottosson-Wadlund

first: Sofia

last: Gruvberger-Saal

first: Heather

last: Cunliffe

first: Bengt

last: Fadeel

first: Niklas

last: Loman

first: Pontus

last: Berglund

first: Ingrid

last: Hedenfalk


title: TAK1-dependent checkpoint in dendritic cell survival regulates immune homeostasis and function

status: Public on Jan 23 2012

city: Memphis

first: Geoffrey

last: Neale

address: 262 Danny Thomas Place

department: Hartwell Center

country: USA

institute: St Jude Childrens Research Hospital

summary: Homeostatic control of dendritic cell (DC) survival is crucial for a productive adaptive immune response, but the molecular mechanism is not well defined. Moreover, how DCs influence homeostasis of the immune system under steady state remains unclear. Combining DC-specific and inducible deletion systems, we report here that the kinase TAK1 is an essential regulator of DC survival and immune system homeostasis and function. Deficiency of TAK1 in CD11c+ cells diminished DC populations, especially the CD8+ and CD103+ DC subsets in the lymphoid and non-lymphoid organs, respectively. This was associated with increased apoptosis of DCs, whereas DC proliferation and differentiation from precursors appeared largely normal. In addition, acute deletion of TAK1 caused DC apoptosis, indicating a direct role of TAK1 in actively maintaining DC survival. TAK1 deficiency impaired activities of the pro-survival NF-kB and AKT pathways but upregulated expression of the pro-apoptotic molecule Bim. Under steady state, loss of TAK1 in DCs resulted in a myeloid proliferative disorder, and altered homeostasis of T cells. In response to antigen stimulation, TAK1-deficient DCs were impaired for T cell priming and regulatory T cell generation. Therefore, TAK1 orchestrates a pro-survival checkpoint in DCs that affects the homeostasis and function of the immune system

overall_design: RNA extracted from three replicate samples of wild-type and Map3k7 (TAK1) knockout dendritic cells was analyzed on Affymetrix gene expression arrays

first: Yanyan

last: Wang

middle: A

first: Hongbo

last: Chi


title: Genome-wide analysis of gene expression and nuclear/cytoplasmic distribution by compound 1 treatment [293T_NS1-2]

status: Public on Jan 17 2012

city: Dallas

first: liang

last: zhang

state: Texas

address: 5323 harry hines blvd k2.202

institute: utsw

summary:
Analysis of cellular response to DHODH inhibition at gene expression and nuclear/cytoplasmic distribution level.
The NS1 protein of influenza virus is a major virulence factor essential for virus replication as it re-directs the host cell to promote viral protein expression. NS1 inhibits cellular mRNA processing and export, down-regulating host gene expression and enhancing viral gene expression. We report here the identification of a non-toxic quinoline carboxylic acid that reverts the inhibition of mRNA nuclear export by NS1, in the absence or presence of virus. This quinoline carboxylic acid directly inhibited dihydroorotate dehydrogenase (DHODH), a host enzyme required for *de novo* pyrimidine biosynthesis, and partially reduced pyrimidine levels. This effect induced NXF1 expression, which promoted mRNA nuclear export in the presence of NS1. The release of NS1-mediated mRNA export block by DHODH inhibition also occurred in the presence of VSV M protein, another viral inhibitor of mRNA export. This reversal of mRNA export block allowed expression of antiviral factors. Thus, pyrimidines play a necessary role in the inhibition of mRNA nuclear export by virulence factors.

overall_design: Five million 293T cells were non-transfected or transfected with 6ug of pCAGGS-NS1 for 16h. Then, cells were untreated or treated with compound 1(5uM) for 24h. RNA from total cell extracts or from nuclear or cytoplasmic fractions were obtained

first: Liang

last: Zhang

first: Beatriz

last: Fontoura


title: Sox18 regulated genes

city: Vienna

first: Rainer

last: de Martin

address: Schwarzspanierstr. 17

department: Vascular Biology

country: Austria

institute: Medical University of Vienna

summary: Study of Sox18 regulated genes: Human umbilical vein endothelial cells (HUVEC) were either transduced with adenoviral vectors expressing SOX18 from an IRES-EGFP casette, or IRES-EGFP alone, or left untreated. After 16 hours, mRNA was isolated and analyzed by hybridization to Affymetrix HG-U133A arrays.

first: Martina

last: Hoeth


title: Genome-wide analysis of gene expression by compound 1 treatment [HBEC_6_12hr]

summary:
Analysis of cellular response to DHODH inhibition at gene expression level.
The NS1 protein of influenza virus is a major virulence factor essential for virus replication as it re-directs the host cell to promote viral protein expression. NS1 inhibits cellular mRNA processing and export, down-regulating host gene expression and enhancing viral gene expression. We report here the identification of a non-toxic quinoline carboxylic acid that reverts the inhibition of mRNA nuclear export by NS1, in the absence or presence of virus. This quinoline carboxylic acid directly inhibited dihydroorotate dehydrogenase (DHODH), a host enzyme required for *de novo* pyrimidine biosynthesis, and partially reduced pyrimidine levels. This effect induced NXF1 expression, which promoted mRNA nuclear export in the presence of NS1. The release of NS1-mediated mRNA export block by DHODH inhibition also occurred in the presence of VSV M protein, another viral inhibitor of mRNA export. This reversal of mRNA export block allowed expression of antiviral factors. Thus, pyrimidines play a necessary role in the inhibition of mRNA nuclear export by virulence factors.

overall_design: Total RNA obtained from HBEC cells subjected to compound 1/compound 1-14 treatment compared to DMSO treatment.


title: Pax versus tempus expression profile differences

status: Public on Jan 15 2012

city: Munich

first: Divya

last: Mehta

institute: MPI

summary:
The main aim of the study was to compare genome-wide gene expression profiles obtained from the two widely used commercially available whole blood RNA collection systems - PAXgeneTM and TempusTM tubes. Comparisons of present call rates, variances, correlations and influence of globin reduction across the two collection systems was performed using in vivo glucocorticoid stimulation in 24 peripheral blood samples from three individuals.
Three healthy male volunteers aged 30-35 years with body mass index of 20-25 were enrolled in the study.1.5 mg dexamethasone stimulated peripheral blood samples were drawn 3 hours later. For each sample, duplicate measures of 2.5 ml and 3ml blood was collected in PAXgeneTM tubes (PreAnalytiX GmbH, Hombrechtikon, Switzerland) and TempusTM tubes (Applied Biosystems, Foster City, CA, USA) respectively. The PAXgeneTM and TempusTM tubes were stored for 2.5 hours at room temperature and then transferred to -20°C. Due to the lower RNA yield from the PAXgeneTM tubes, RNA from two PAXgeneTM tubes was pooled together for the experiment . Total RNA was isolated from whole blood stored in PAXgeneTM and TempusTM tubes according to the respective manufacturer's instructions. The PAXgeneTM samples were processed using the PAXgeneTM Blood RNA Kit based on the Quiagen method for column purification of nucleic acids (PreAnalytiX GmbH, Hombrechtikon, Switzerland, catalogue number 762174). The TempusTM samples were isolated using the TempusTM Spin RNA Isolation Kit (Applied Biosystems, Foster City, CA, USA, catalogue number 4380204). RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). The concentration and purity of total RNA was independently assessed by 260/280 UV absorption ratios, respectively (Nanophotometer, Implen, Munich, Germany). RNA samples were divided into non-globin reduced and globin reduced groups. The GLOBINclearTM-Human Kit (Ambion, Inc., Texas, USA, catalogue number #AM1980) was used to remove globin mRNA. Sample amplification and labeling for both globin-reduced and non-reduced samples was performed using the IlluminaR TotalPrep RNA Amplification Kit (Ambion, Inc., Texas, USA, catalogue number AMIL1791).

overall_design: RNA quality, yield and numbers of detected transcripts from the two RNA collection systems was comparable, with no significant differences between the tube types. Globin reduction resulted in a significant increase in present call rates in PAXgeneTM and TempusTM tubes and significant decrease in gene expression variance in both RNA collection tubes . Comparisons of glucocorticoid receptor-stimulated gene expression profiles between the two collection tube systems revealed an overlap of only 17 to 54%, depending on the stringency level of the statistical thresholds. This overlap increased by 1-8% when the RNA samples were processed to remove the globin mRNA. These results indicate that gene expression profiles obtained from PAXgeneTM and TempusTM differ drastically and should not be analyzed together. These data suggest that researchers must exert caution while interpreting expression profiles obtained through different RNA collection tubes.

first: D


title: Atherosclerosis study using female peripheral blood samples

first: Chiang-Ching

last: Huang

address: 680 N. Lake Shore Dr., Suite 1400

institute: Northwestern University

summary: This study is to compare the mRNA expression differences between atherosclerosis and non-atherosclerosis samples from female peripheral blood. The possible effects of races are also considered.

overall_design:
Two phenotypes: 1: atherosclerosis; 0: non-atherosclerosis
Four races: 1: non-Hispanic white; 2: Chinese; 3: African American; 4: Hispanic

first: Spencer


title: Expression data from breast cancer FNA and surgical specimens from patients

city: Houston

first: TAKAYUKI

last: IWAMOTO

state: TX

address: 1515 Holcombe Blvd

department: Breast medical Oncology

institute: UT MD Anderson

summary:
The behavior of breast cancers and their response to neoadjuvant systemic therapy depend on their phenotype which is to a large extent determined by gene expression programs within the cancer cell.
The purpose of the analysis was to compare matched gene expression profiles of pretreatment cancer with post-neoadjuvant systemic therapy, residual cancer.

overall_design: Pre-treatment FNA from primary tumors or post-treatment surgical specimens were obtained and RNA extracted and hybridized to afymetrix microarrays according to manufacturer protocol.

first: Ana

last: Gonzalez-Angulo

first: Takayuki

last: Iwamoto

first: Huiqin

last: Chen


title: MOLECULAR CHARACTERIZATION OF LIVER ALLOGRAFTS FROM OPERATIONALLY TOLERANT TRANSPLANT RECIPIENTS (Illumina)

status: Public on Jan 09 2012

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

summary: In clinical organ transplantation complete cessation of immunosuppressive therapy can be successfully accomplished in selected recipients providing a proof-of-principle that allograft tolerance is attainable in humans. The intra-graft molecular pathways associated with human allograft tolerance, however, have not been comprehensively studied before. In this study we analyzed sequential liver tissue samples collected from liver recipients enrolled in a prospective multicenter immunosuppressive withdrawal clinical trial. Tolerant and non-tolerant recipients differed in the intra-graft expression of genes involved in the regulation of iron homeostasis.These results point to a critical role of iron homeostasis in the regulation of intra-graft alloimmune responses in humans and provide a set of novel biomarkers to conduct drug-weaning trials in liver transplantation.

overall_design: The complete database comprised the expression measurements of 48766 probes in liver biopsies. The liver biopsy specimens available for the study were obtained: a) before immunosuppressive drugs were discontinued from tolerant (TOL, n=24) and non-tolerant (Non-TOL, n=29) recipients; b) at the time of rejection from non-tolerant recipients (Non TOL REJ, n=18); In addition, liver tissue samples were also collected from the following control patient groups: a) liver transplant recipients with chronic hepatitis due to recurrent hepatitis C virus infection (HEPC, n=12); b) liver transplant recipients with typical acute cellular rejection taking place during the immediate post-transplant period (REJ, n=9); c) liver transplant recipients under maintenance immunosuppression with normal liver function and normal liver histology 1 year after transplantation (CONT-Tx, n=8); and d) non-transplanted patients undergoing surgery for colorectal liver metastases (CONT, n=10).

first: F

last: Bohne

first: M

last: Martínez-Llordella

first: J

middle: J

first: R

last: Miquel

first: C

last: Benítez

last: Londoño

first: T

last: Manzia

last: Swinkels

first: H

last: Tjalsma

last: López

last: Abraldes

first: E

last: Riani

last: Pirenne

first: A

last: Rimola

first: G

last: Tisone

last: Sánchez-Fueyo


title: Probing sporadic and familial Alzheimer?s disease using induced pluripotent stem cells.

status: Public on Jan 06 2012

city: La Jolla

first: Kristopher

middle: L.

last: Nazor

state: CA

address: 10550 North Torrey Pines Road

department: Regenerative Medicine

institute: The Scripps Research Institute

summary: Our understanding of Alzheimer’s disease (AD) pathogenesis is currently limited by difficulties in obtaining live neurons from patients and the inability to model the sporadic form of AD. It may be possible to overcome these challenges by reprogramming primary cells from patients into induced pluripotent stem cells (iPSCs). We reprogrammed primary fibroblasts from two patients with familial AD (both caused by a duplication of APP1, APPDp), two with sporadic AD (sAD1, 2) and two non-demented control individuals (NDCs) into iPSC lines. Neurons from differentiated cultures were FACS-purified and characterized. Purified cultures contained >90% neurons, clustered with fetal brain mRNA samples by microarray criteria, and could form functional synaptic contacts. Virtually all cells exhibited normal electrophysiological activity. Relative to controls, iPSC-derived, purified neurons from the two APPDp patients and patient sAD2 exhibited significantly higher levels of secreted Aβ1-40, phospho-tauThr231 (pTau) and active GSK3β (aGSK3β). Neurons from APPDp and sAD2 patients also accumulated large Rab5-positive early endosomes compared to controls. Treatment of purified neurons with β-secretase inhibitors, but not g-secretase inhibitors, caused significant reductions in pTau and aGSK3β levels. These results suggest a direct relationship between APP proteolytic processing, but not Aβ, in GSK3β activation and tau phosphorylation in human neurons. Additionally, we observed that neurons with the genome of one sAD patient exhibited the phenotypes seen in familial AD samples. More generally, we demonstrate that iPSC technology can be used to observe phenotypes relevant to AD, even though it can take decades for overt disease to manifest in patients.

overall_design: Total RNA extracted from normal hIPSCs, Alzheimer's patient derived hIPSCs, neurons differentiated from hIPSCs, fetal brain, fetal heart, fetal liver and fetal lung

first: Mason

last: Israel

first: Shauna

middle: H

last: Yuan

first: Cedric

last: Bardy

first: Sol

last: Reyna

first: Yangling

last: Mu

first: Cheryl

last: Herrera

first: Michael

middle: P

last: Hefferan

first: Sebastiaan

last: Van Gorp

first: Francesca

last: Boscolo

first: Christian

last: Carson

first: Louise

middle: C

last: Laurent

first: Martin

last: Marsala

first: Fred

last: Gage

first: Anne

last: Remes

first: Edward

last: Koo

first: Lawrence

last: Goldstein


title: Anti-Inflammatory Effects of Epidermal Growth Factor on the Immature Human Intestine

status: Public on Jan 11 2012

city: Sherbrooke

first: Jean-François

last: Beaulieu

state: Québec

address: 3001, 12ème avenue nord

department: Anatomie & biologie cellulaire

institute: Université de Sherbrooke

summary: The inflammatory response of preterm infants' intestine underlines its inability to respond to hemodynamic stress, microbes and nutrients.  Recent evidence suggests that exogenous epidermal growth factor (EGF) exerts a therapeutic influence on neonatal enteropathies. However, the molecular mechanisms underlying the beneficial effects of EGF remain to be clarified. The purpose of this study was to evaluate the impact of EGF on the gene expression profiles of the developing human small and large intestine at mid-gestation in serum-free organ cultures using Illumina microarrays.

overall_design:
Differential functional effects of EGF along the human fetal intestine [Illumina]
Transcriptional profiling of small and large intestinal explants cultured in the absence (control) or in the presence of EGF (50 ng/mL).

first: Daniel

last: Ménard

first: Eric

last: Tremblay

first: Emanuela

last: Ferretti

first: Babakissa

last: Corentin

first: Ernest

last: Seidman


title: The transcription factor nurr1 exerts concentration-dependent effects on target genes mediating distinct biological processes

status: Public on Jan 01 2012

city: Detroit

first: Magen

middle: Marie

last: Johnson

state: MI

address: 540 E Canfield

department: Pharmacology

institute: Wayne State University

summary: The transcription factor nurr1 plays a pivotal role in the development and maintenance of neurotransmitter phenotype in midbrain dopamine neurons. Conversely, decreased nurr1 expression is associated with a number of dopamine-related CNS disorders, including Parkinson’s disease and drug addiction. In order to better understand the nature of nurr1-responsive genes and their potential roles in dopamine neuron differentiation and survival, we used a neural cellular background in which to generate a number of stable clonal lines with graded nurr1 gene expression that approximated that seen in DA cell-rich human substantia nigra. Gene expression profiling data from these nurr1-expressing clonal lines were validated by quantitative RT-PCR and subjected to bioinformatic analyses. The present study identified a large number of nurr1-responsive genes and demonstrated the potential importance of concentration-dependent nurr1 effects in the differential regulation of distinct nurr1 target genes and biological pathways. These data support the promise of nurr1-based CNS therapeutics for the neuroprotection and/or functional restoration of DA neurons.

overall_design: Total RNA obtained from nurr1-overexpressing SKNAS neuroblastoma clonal cell lines (SKNAS_E & SKNAS_G) compared to empty vector transfected control (SKNAS_C)

middle: M

first: Sharon

last: Michelhaugh

first: Mohamad

last: Bouhamdan

first: Carl

last: Schmidt

last: Bannon


title: Gene expression in pif3 mutant under dark and in wt under Red 1h and Red 18h

status: Public on Jan 03 2012

city: Bellaterra- Cerdanyola del Valles

first: Elena

last: Monte

state: Barcelona

address: Campus UAB-Edifici CRAG

institute: CRAG

summary: PIF3 plays a role as repressor of photomorphogenesis in darkness. To identify PIF3-regulated genes that might be implementing this action, we have performed whole-genome expression analysis in the pif3 mutant.

overall_design: Seeds were surface-sterilized and plated on GM medium without sucrose, stratified at 4ºC in the dark for 4 days, exposed to white light for 3 hours to induce germination, and placed in a growth chamber at 21ºC in darkness for 4 days (D0h) and 4 days and 1 hour (D1h). For Rc treatments seedlings were moved to Rc growth chambers at 21ºC  for 1 (R1h) and 18 (R18h) hours.

first: M

last: Sentandreu

first: J

last: Tepperman

first: P

last: Quail

first: E


title: Routine use of microarray-based gene expression profiling to identify patients with low cytogenetic risk acute myeloid leukemia: accurate results can be obtained even with suboptimal samples

status: Public on Jan 04 2012

city: Angers

first: Philippe

last: Guardiola

state: Maine et Loire

address: 4 rue Larrey

institute: Angers University Hospital

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

overall_design: Refer to individual Series


title: Evidence for the importance of OxPAPC interaction with cysteines in regulating endothelial cell function

status: Public on Feb 14 2012

city: Los Angeles

first: James

middle: Robert

last: Springstead

address: 3210 MRL, 10833 Le Conte Ave

department: Medicine-Cardiology

institute: UCLA

summary: Oxidation products of 1-palmitoyl-2-arachidonoyl-sn-glycerol-2-phosphatidylcholine (PAPC), referred to as OxPAPC, accumulate in atherosclerotic lesions and regulate over 1000 genes in human aortic endothelial cells (HAEC).  We previously demonstrated that OxPAPC covalently binds to a number of proteins in HAEC. The goal of these studies was to gain insight into the binding mechanism and determine if binding regulates activity.  In whole cells N-acetylcysteine inhibited gene regulation by OxPAPC, and blocking cell cysteines with N-ethylmaleimide strongly inhibited OxPAPC binding.  Using MS, we demonstrate that most of the binding of OxPAPC to cysteine is mediated by PEIPC.  We also show that OxPAPC binds to a model protein, H-Ras, at cysteines previously shown to regulate activity in response to 15dPGJ2.  This binding was observed with recombinant protein and in cells overexpressing H-Ras.  15dPGJ2 and OxPAPC increased H-Ras activity at comparable concentrations.  Using microarray analysis, we demonstrate a considerable overlap of gene regulation by OxPAPC and 15dPGJ2 in HAEC, suggesting that some effects attributed to 15dPGJ2 may also be regulated by OxPAPC since OxPAPC lipids and 15dPGJ2 both accumulate in inflammatory sites.   Overall, we provide evidence for the importance of OxPAPC-cysteine interactions in regulating HAEC function.

overall_design:
Control, OxPAPC, and 15dPGJ2-treated HAECs Samples.
'Control' is media (1%FBS, 99%M199)-only treated HAECs.  15dPGJ2 and OxPAPC are treated with those respective compounds in media.

middle: R

first: Sangderk

last: Lee


title: Molecular signatures of peripheral blood mononuclear cells following chronic IFN-alpha: Relationship of OAS2 with Depression and Fatigue

city: Atlanta

first: Gregory

last: Doho

state: GA

address: 1365B Clifton Rd NE

institute: Emory University

summary: Interferon (IFN)-alpha causes high rates of depression and fatigue, and is used to investigate the impact of innate immune cytokines on brain and behavior. However, little is known about transcriptional profiles of circulating immune cells during chronic IFN-alpha administration. Accordingly, genome-wide transcriptional profiling was performed on peripheral blood mononuclear cells from 21 patients with chronic hepatitis C virus either awaiting IFN-alpha therapy (n=10) or after 12 weeks of IFN-alpha treatment (n=11). Significance analysis of microarray data identified 252 up-regulated gene transcripts, the majority of which were related to IFN-alpha/antiviral or innate-immune/inflammatory signaling. Of these upregulated genes, 2'-5'-oligoadenylate synthetase 2 (OAS2) was the only gene that was differentially expressed in patients that developed IFN-alpha-induced depression/fatigue, and correlated with depression and fatigue scores at 12 weeks of IFN-alpha administration. Promoter-based bioinformatic and cellular origin analyses revealed IFN-alpha-induced increases in genes bearing transcription factor binding motifs (TFBMs) related to myeloid differentiation, IFN-alpha signaling, API and CREB/ATF family of transcription pathways, with changes derived primarily from monocytes and plasmacytoid dendritic cells. Patients with high depression/fatigue scores demonstrated up-regulation of genes bearing TFBMs for myeloid differentiation, IFN-alpha and AP1 signaling, and down regulation of TFBMs for CREB/ATF-related transcription factors. Cellular origin analyses indicated a shift toward genes derived from CD8+T and NK cells in subjects with high depression/fatigue scores. These results reveal an antiviral and inflammatory transcriptional profile after 12 weeks IFN-alpha, accompanied by increased OAS2 expression, decreased CREB/ATF transcriptional control, and a shift from monocyte-derived genes to those of cytotoxic lymphocytes in IFN-alpha-induced depression/fatigue.

overall_design: Total RNA was isolated from the peripheral blood mononuclear cells (PBMC) obtained at 12 weeks from HCV patients treated with IFN-alpha plus ribavirin (n=11) and untreated HCV patients awaiting IFN-alpha/ribavirin therapy (control subjects, n=10).

first: Jennifer

last: Felger

first: Steve

middle: W

last: Cole

first: Thaddeus

last: Pace

first: Fang

last: Hu

first: Bobbi

last: Woolwine

first: Charles

middle: L

last: Raison

first: Andrew

last: Miller


title: Zfx controls self-renewal of human embryonic stem cells

city: New York

first: Stuart

last: Chambers

state: NY

address: 1270 York Ave

institute: Sloan-Kettering Institute

summary: Previously, we identified the transcription factor Zfx as a key regulator of self-renewal in murine ESCs. Here we extend those findings to human ESCs. Zfx knockdown in hESCs hindered clonal growth and decreased colony size after serial replating. Zfx overexpression enhanced clone formation, increased colony size and decreased expression of differentiation-related genes in human ESCs. Zfx-overexpressing hESCs resisted spontaneous differentiation but could be directed to differentiate into endodermal and neural cell fates when provided with the appropriate cues. Thus, Zfx acts as a molecular rheostat regulating the balance between self-renewal and differentiation in hESCs, revealing the close evolutionary conservation of the self-renewal mechanisms in murine and human ESCs.

overall_design: Human embryonic stem cells with over expression of ZFX were compared to the original cell line (H9) and a clonally derived wild-type cell line (clone 3)

first: Mark

last: Tomishima

first: Boris

last: Reizis


title: Human lymphocyte activation during the G0 to G1 transition

city: London

first: Eric

last: Blanc

address: New Hunt's House

department: MRC Centre for Developmental Neurobiology

country: United Kingdom

institute: King's College London

summary:
Regulating the transition of T lymphocytes from quiescence into an activated, proliferating state involves initiation of programmes that result in cell cycle entry (proliferation) and the growth cycle (blastogenesis). This study analyses the expression of mRNA regulsted during the transition from quiescence into the cell cycle.
We used micro-arrays to monitor the dynamical behaviour of expression of genes expressed in primary human T cells stimulated with CD3/CD28

overall_design: T cells were collected for RNA extraction in quiescence (G0), and at 1, 2, 3, 4, 8, 16, 24 & 48 hours post-activation with CD3/CD28 beads. Differential expression was computed between 0 and 4 hours, 4 and 8 hours, and 8 and 24 hours. In particular, in our study we have made use of data for mRNA which change in expression between 0 and 24h post CD3/CD28 stimulation.

first: Nicholas

last: Lea

first: N

last: Thomas


title: Expression data in single and double knockouts of AtNHX5 and AtNHX6 in Arabidopsis

city: davis

first: elias

last: bassil

address: 1 shields ave

department: plant sciences

institute: university of california

summary: We generated single and double knockouts of AtNHX5 and AtNHX6 in order to invesigate possible functions in Arabidopsis. nhx5/nhx6 exhibited severe growth retardation related to cell size and proliferation, as well as endosomal trafficking perutrbations. The results implicate endosomal NHX antiporters in novel cellular functions. In order to investigate further the possible functions of AtNHX5 and AtNHX6, we compared the transcrptional profiles of single and double AtNHX5 and AtNHX6 knockouts. We looked for changes in gene expression might help us to elucidate the molecular events associated with the apparent requirement of AtNHX5 and AtNHX6 for normal growth and development.

overall_design: Rosette leaves from 4 weeks old plants grown on soil under normal conditons and 8h L / 16 D were collected for RNA extraction and hybridization on Affymetrix microarray chips.

first: Eduardo

last: Blumwald

first: Elias

last: Bassil


title: Whole-transcript expression data for uveal melanoma

status: Public on Dec 31 2011

first: Brian

last: Denton

address: 307 E. 63rd Street

department: Epidemiology and Biostatistics

institute: Memorial Sloan-Kettering Cancer Center

summary: G protein alpha q and 11 are mutated in 90% of uveal melanoma and they activate the MAPK pathway. Using expression microarray analysis, we identified a unique MEK dependent transcriptional signature with genes that are involved in proliferation and tumor cell invasion.

overall_design: Uveal melanoma cells were profiled on Illumina Human HT-12 arrays per manufacturer's instructions


title: Gene expression profiles of Hodgkin’s lymphoma cells after treatment with vorinostat

city: Halle (Saale)

first: Martin

middle: Sebastian

last: Staege

state: Sachsen-Anhalt

address: Ernst-Grube-Str. 40

department: Universitätsklinik u. Poliklinik für Kinder- u. Jugendmedizin

summary:
By using high-density DNA microarrays, we analyzed the gene-expression profile of Hodgkin's lymphoma cell line L-540 after tretament with the histone deactelyse inhibitor vorinostat.
Kewitz et al., submitted

overall_design: RNA was extracted from established Hodgkin's lymphoma cell line L-540 and hybridized with Affymetrix HG_U133A microarrays.

first: Stefanie

last: Kewitz

first: Toralf

last: Bernig