title: Direct genesis of functional rodent and human Schwann cells from skin mesenchymal precursors (human)

first: Freda

last: Miller

summary: Recent reports of directed reprogramming have raised questions about the stability of cell lineages.  Here, we have addressed this issue, focusing upon skin-derived precursors (SKPs), a dermally-derived precursor cell.  We show by lineage tracing that murine SKPs from dorsal skin originate from mesenchymal and not neural crest-derived cells.  These mesenchymally-derived SKPs can, without genetic manipulation, generate functional Schwann cells, a neural crest cell type, and are highly similar at the transcriptional level to Schwann cells isolated from the peripheral nerve.  This is not a mouse-specific phenomenon, since human SKPs that are highly similar at the transcriptome level can be made from facial (neural crest-derived) and foreskin (mesodermally-derived) dermis, and the mesodermally-derived SKPs can make myelinating Schwann cells.  Thus, non-neural crest-derived mesenchymal precursors can differentiate into bona fide peripheral glia in the absence of genetic manipulation, suggesting that developmentally-defined lineage boundaries are more flexible than widely thought.

overall_design: We obtained 4 independent samples of neonatal human foreskin and 4 independent samples of discarded facial skin tissue from children less than two years old.  Primary cells were isolated and cultured as SKPs and RNA was collected from those cultured samples.  RNA samples deriving from these cells were analyzed on the Affymetrix Human Gene 2.0 ST Array.

first: Matthew

middle: P

last: Krause

first: Shaalee

last: Dworski

first: Konstantin

last: Feinberg

first: Karen

last: Jones

first: Adam

last: Johnston

first: Smitha

last: Paul

first: Maryline

last: Paris

first: Elior

last: Peles

first: Darius

last: Bagli

first: Christopher

middle: R

last: Forrest

first: David

last: Kaplan


title: Expression data from esophageal squamous cell carcinomas and normal esophageal epithelia

status: Public on Aug 01 2014

city: Guangzhou

first: Jing

last: Wen

address: 651 Dongfeng East Road

country: China

institute: Sun Yat-sen University Cancer Center

summary:
Preoperative chemoradiotherapy (CRT)  followed by surgery has been proved to improve esophageal squamous cell carcinoma (ESCC) patients’ survival in comparison with surgery alone. However, the outcomes of CRT are heterogeneous, and no clinical or pathological method could predict CRT response.
We aim to identify mRNA markers for ESCC CRT-response prediction through gene expression analyses.

overall_design: Gene expression analyses were performed on pretreatment cancer biopsies from 28 ESCCs who received neoadjuvant CRT and surgery and 10 normal esophageal epithelia using Affymetrix U133 Plus 2.0 arrays.

first: Hong

last: Yang

first: Jianhua

last: Fu


title: Promoter methylation data from genomic DNA in patient with rectal cancer

city: daejeon

first: Jonglyul

last: Park

address: 52, Eoeun-dong, Yuseong-gu

department: Medical genomics

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

type: Methylation profiling by genome tiling array

summary:
The identification of surrogate methylation markers that can predict responses to preoperative chemoradiotherapy (CRT) in rectal cancer patients. Genome-wide association studies in clinical populations are theoretically capable of identifying markers that are capable of tumor regression after CRT. We used Infinium® Methylation Assay to detail methylation status of patient’s group showing differential responsiveness to preoperative CRT and profiled SNP biomarkers.
The chemoradiosensitivity of tumor tissue from the initial cohort of 45 patients was assessed using clinical responses of tumor regression grade (TRG). TRG was clinically categorized as complete response (CR) as TRG 1, dominant response (ER or finally as DR) as TRG 1 and 2, and efficient response (RYN or finally as ER) as TRG 1, 2, and 3 (TRG grade from Mandard et al, 1994).

overall_design:
Examination of genome-wide DNA methylation in 45 colon cancer tissues.
We separated patients into TRG1,2,3,4 and 5 group after chemoradiotherapy(CRT). As proposed by Mandard et al. TRG 1, complete tumor response; TRG2, residual cancer cells scattered through fibrosis; TRG 3, an increased number of residual cancer cells, with predominant fibrosis; TRG 4, residual cancer outgrowing fibrosis; and TRG 5, no regressive changes within the tumor: Responders (TRG 1 and 2) and nonresponders (TRG 3?5). Mandard et al. Cancer 1994
Group 1 and Group 2 in ER, CR and RYN was divided by TRG classification.
CR: group 1 - TRG 2,3,4 and 5; group 2 - TRG 1
ER: group 1 - TRG 3,4,5; group 2 - TRG 1 and 2
RYN: group 1 - TRG 4 and 5; group 2 - TRG 1,2 and 3

first: Jin

middle: C

last: Kim

first: Seon-Young

first: Yong

middle: S


title: Expression data from 24 hours of Sox17 overexpression in pancreatic islets of a 16-week old mice

status: Public on Jul 31 2014

city: Cincinnati

first: James

last: Wells

state: OH

address: 3333 Burnet Ave

country: USA

institute: Cincinnati Childrens Hospital Medical Center

summary:
Secretion of insulin by pancreatic β cells in response to glucose is central for glucose homeostasis, and dysregulation of this process is a hallmark of the early stages of diabetes. We utilized a tetracycline-inducible approach to investigate the immediate impact of a pulse of Sox17 expression on the insulin secretory pathway. Sox17 gain-of-function animals (Sox17-GOF) were generated using an Ins2-rtTA mouse line and a line in which Sox17 expression is regulated by the tetracycline transactivator (tetO-Sox17).  Administering doxycycline to 16-week old mice resulted in Sox17 overexpression in mature β cells in the islets.
In order to identify the molecular basis by which Sox17 regulates the secretory pathway in β cells, we performed microarray analysis on isolated islets following a 24-hour pulse of Sox17 overexpression.

overall_design: We chose to analyze a 24 hour pulse of Sox17  for islet pancreas RNA extraction and hybridization on Affymetrix microarrays since it was sufficient to stimulate the insulin secretory pathway without causing changes in islet architecture.

first: Jim


title: Genome-wide profiling and validation for forensic tissue-specific DNA methylation markers

summary:
Forensic body fluid identification is important for crime scene reconstruction.
We used Illumina HumanMethylation 450K bead array containing over the 450,000 CpG sites in 16 body fluid samples to find novel DNA methylation marker for forensic body fluid identification.

overall_design: Examination of genome-wide DNA methylation profiling in 16 body fluid samples

first: Jong-Lyul


title: Differential methylation in CN-AML preferentially targets non-CGI regions and is dictated by DNMT3A mutational status and associated with predominant hypomethylation of HOX genes

city: Stockholm

first: Ying

last: Qu

state: Stockholm

address: Hälsovagen 7

department: Department of Medicine, Huddinge

country: Sweden

institute: Karolinska Institute

summary: The study investigated the abberrent DNA methylation in correlation with gene expression in cytogenetic normal acute myeloid leukemia. CN-AML blasts isolated from patient bone marrow aspriation were compared to CD34+ cell population from healthy donors by DNA methylation array and affymetrix gene expression microarray.

overall_design: Bisulfited genomic DNA from patients and normal materials were hybirdized to Illumia Infinium Human Methylation 450K Beadchip. Gene expression profiling on selected patient cohort are publish aviable.

first: Andreas

last: Lennartsson

first: Verena

first: Stefan

last: Deneberg

first: Mohsen

last: Karimi

first: Sofia

last: Bengtzén

first: Martin

last: Höglund

first: Lars

last: Bullinger

first: Konstanze

last: Döhner

first: Sören

last: Lehmann


title: Expression data from breast cancer cell line MCF-7 with ectopic expression of the transcription factor Snail

status: Public on Jul 29 2014

city: Atlanta

first: Roman

middle: F. N.

last: Mezencev

state: GA

address: 310 Ferst Dr

department: School of Biology

institute: Georgia Institute of Technology

summary:
The transcription factor Snail has been proposed to mediate epithelial-to-mesenchymal transition (EMT) and confer mesenchymal invasive phenotype to epithelial cancer cells
To analyze the molecular effects of ectopic Snail expression on an epithelial breast cancer cell line, gene expression profiles of MCF-7 cells transfected to overexpress Snail-6SA variant (MCF-7-Snail) and MCF-7 cells transfected with control plasmid (MCF-7-control) were compared. Development of the cell lines has been previously reported by Zhou et al. (PMID: 15448698).

overall_design: Dataset includes 3 replicate cultures of MCF-7-Snail cells and 3 replicate cultures of MCF-7-control cells

first: John

middle: F

last: McDonald


title: Gene expression analysis in the spleen of wild type, Sle1.3 (lupus mice) and Sle1.3 mice haplodeficient for E2-2 (exhibiting non functional pDCs)

status: Public on Jul 30 2014

city: New York City

first: Vanjs

last: Sisirak

state: NY

address: 701 west 168th street

department: Microbiology and Immunology

institute: Columbia University

summary: Systemic lupus erythematosus (SLE) is an autoimmune disorder characterized by the production of antibodies to self-nucleic acids, immune complex deposition and tissue inflammation such as glomerulonephritis. Innate recognition of molecular complexes containing self-DNA and RNA and the ensuing production of type I interferons (IFN) contribute to SLE development. Plasmacytoid dendritic cells (pDCs) have been proposed as a relevant source of pathogenic IFN in SLE; however, their net contribution to the disease remains unclear. We addressed this question using haplodeficiency of the pDC-specific transcription factor E2-2 (Tcf4), which causes a specific impairment of pDC function in otherwise normal animals. We report that Tcf4+/- animals were significantly protected from SLE-like disease caused by the overexpression of the endosomal RNA sensor Tlr7. The protection was also observed after the monoallelic deletion of Tcf4 specifically in the dendritic cell lineage. Furthermore, Tcf4 haplodeficiency in the B6.Sle1.Sle3 multigenic model of SLE ameliorated key disease manifestations including anti-DNA antibody production, immune activation and glomerulonephritis. These results provide genetic evidence that pDCs are critically involved in SLE pathogenesis, confirming their potential utility as therapeutic targets in the disease.

overall_design: Cellluar suspension were obtained from the spleen of wild type, Sle1.3 and Sle1.3/E2-2het mice. 10 million of cells were used to isolate RNA from each sample.  After RNA isolation a microarray analysis using the Ambion WT labeling kit was done. Expression was analyzed using Affymetrix Mouse Gene 1.0 ST.  2 Wild type mice, 3 Sle1.3 and 3 Sle1.3/E2-2 het mice were used for the analysis.

first: Vanja

first: Boris

middle: V

last: Reizis

first: Dipyaman

last: Ganguly


title: Expression data from breast tumors  in different age-specific cohorts  and for different sequentional disease stages

city: Riyadh

first: Dilek

last: Colak

address: MBC03, PO Box 3354

department: Biostatistics, Epidemiology and Scientific Computing

country: Saudi Arabia

institute: KFSHRC

summary:
Compared transccriptome of breast cancer in young women to those arising in two mature groups to characterize the underlying biological mechanisms of the breast cancer in Middle Eastern young women.
Also, compared the gene expression profile characteristic of the sequential disease stages (ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC)) of breast cancer to elucidate the molecular mechanisms of breast cancer progression in young women.

overall_design: Analyzed the whole-genome mRNA expression profile from tumor (n=73) and adjacent disease free tissues (n=36) using Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays.

first: Suad

middle: M

last: Bin Amer


title: KAP1(TRIM28/TIF1beta) represses differentiation-inducible genes in  embryonic stem cells through cooperative binding with PRC1(Ring1b/Rnf2) and derepresses pluripotency-associated genes (ChIP-seq)

city: Ann Arbor

first: Tom

middle: Klaus

last: Kerppola

state: Michigan

address: 1150 West Medical Center Drive

department: Biological Chemistry

institute: University of Michigan

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Embryonic stem (ES) cells express pluripotency-associated genes and repress differentiation-inducible genes.  The activities of these genes are coordinately reversed during differentiation.  The changes in the transcriptome upon conditional KAP1 knockout in ES cells overlapped with the changes during embryoid body formation.  KAP1 repressed differentiation-inducible genes and derepressed pluripotency-associated genes in ES cells.  KAP1 formed complexes with polycomb repressive complexes 1 (PRC1) through an interaction that was mediated by the KAP1 coiled-coil region.  KAP1 and PRC1 bound cooperatively at the promoters of differentiation-inducible genes and repressed their transcription.  In contrast, KAP1 bound the transcribed and flanking sequences of pluripotency-associated genes, did not enhance PRC1 binding, and derepressed their transcription.  KAP1 had opposite effects on differentiation-inducible and pluripotency-associated gene transcription both in ES cells and in differentiating embryoid bodies.  The region of KAP1 that mediated the interaction with PRC1 was required for KAP1 enhancement of PRC1 binding and for KAP1 repression of transcription at differentiation-inducible promoters. This region of KAP1 was not required for KAP1 suppression of PRC1 binding or for KAP1 derepression of transcription at pluripotency-associated promoters.  The opposite effects of KAP1 on transcription of differentiation-inducible versus pluripotency-associated genes contributed to the reciprocal changes in their transcription during differentiation.

overall_design: Analysis of the regions occupied by KAP1(TRIM28/TIF1beta) and by Ring1b(Rnf2) in mouse embryonic stem cells before and after conditional KAP fl/fl and Ring1b fl/fl knockout

middle: K

first: Bo

last: Cheng

first: Xiaojun

last: Ren


title: Transcriptome-Methylome study of blood samples from flavanol diet intervention Paper title: Dietary flavanols modulate the transcription of genes associated with cardiovascular pathology and induces complex changes of their DNA methylation state.

city: Saint Genes Champanelle

first: Celine

last: BOBY

address: Centre INRA Auvergne-Rhône-Alpes

country: France

institute: INRA

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

overall_design: Refer to individual Series


title: Expression data from human Dupuytren's disease cells

status: Public on Jul 25 2014

city: GRANADA

first: MIGUEL

last: ALAMINOS

address: AV. INVESTIGACION 11, FAC. MEDICINA PTS

department: HISTOLOGY

country: Spain

institute: UNIVERSITY OF GRANADA

summary:
The objective of this study was to analyze gene expression associated to extracellular matrix components of normal palmar fascia and tissues affected by Dupuytren's disease.
We used microarrays to detail the global programme of gene expression associated to Dupuytren's disease.

overall_design: Total RNA was isolated from three different samples corresponding to two different individuals with Dupuytren's disease: Dupuytren's diseased contracture cords (DDC), palmar fascia clinically unaffected by Dupuytren's disease contracture (NPF), and normal forehand fascia (NFF).

first: Camilo-Andrés

last: Alfonso-Rodríguez

first: Ingrid

last: Garzón

first: Juan

last: Garrido-Gómez

first: Ana-Celeste-Ximenes

last: Oliveira

first: Miguel-Ángel

last: Martín-Piedra

first: Giuseppe

last: Scionti

first: Víctor

last: Carriel

first: Pedro

last: Hernández-Cortés

first: Antonio

last: Campos

first: Miguel

last: Alaminos


title: Effect of experimental stroke on meningeal gene expression and the influence of mast cells on these gene changes

city: Palo Alto

first: Ulrich

last: Schlecht

address: 3165 Porter Drive

department: Biochemistry

institute: Stanford University

summary: Stroke is a leading cause of adult disability and death. Inflammation plays an important role in stroke pathology, but the factors which promote brain inflammation in this setting remain to be fully defined. Here we investigate the meninges, the membranes that envelop the brain, for a potential role in modulating immune cell trafficking to the brain. We also investigate the potential of mast cells (MCs) to modulate this response as MCs are often considered as 'first responders' playing a critical role in the initiation and development of inflammation in many disease settings. We find that stroke increases expression of inflammatory and immune response genes in the meninges in mice consistent with a potential role in modulating immune cell trafficking. Moreover, genetic and cell transfer approaches identify MCs as important modulators of this response.

overall_design: Three categories of male mice were used: wild-type (WT) mice, mast cell-deficient (KO) mice, and mast cell-engrafted mice (EN), which are mast cell-deficient mice repaired of their mast cell deficiency by engraftment of mast cells i.v. 8-10 weeks prior to experimentation. The mouse strain was WBB6F1-Kit+/+ (wild-type ) and WBB6F1-KitW/W-v (mast cell-deficient ). Each mouse category was subdivided into two groups, naïve (N) and stroke (S), with n=3 per group. The stroke model was 30 minute filament occlusion of the middle cerebral artery. The dura were removed from the mouse brains at 2d post-stroke and from aged-matched naïve mice for microarray analysis. Dura were not pooled but run on separate arrays.

first: Ahmet

last: Arac

first: Michele

middle: A

last: Grimbaldeston

first: Anna

last: Tsykin

first: Gregory

middle: J

last: Goodall

first: Stephen

last: Galli

first: Tonya

last: Bliss

first: Gary

last: Steinberg


title: Expression data from the lungs of Scnn1b-Transgenic and wild-type mice

status: Public on Jul 24 2014

city: Heidelberg

first: Raman

last: Agrawal

state: BW

address: Im Neuenheimer Feld 350

department: Translational Lung Research Center

country: Germany

institute: Heidelberg University

summary: Airway mucus obstruction triggers macrophage activation and MMP12-dependent emphysema

overall_design: microarray expression profiling of lungs from Scnn1b-Tg mice to search for emphysema candidate genes


title: Comparison of gene expression from thymocyte populations and equivalent OP9-DL1 cultured cells

status: Public on Jul 19 2014

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: Comparison between ex vivo immature, mature and stimulated T cells and in vitro generated counterparts. The T cells generated in vitro were cultured on OP9-DL1 stroma supplied with growth factors.

overall_design: Three in vivo (Thymus DPCD3+, Thymus SP8, PBMC CD8 POST) and three in vitro (CCd14 DPCD3+, CCd20 SP8, CCd27 Post) samples were collected.  T-cells were sorted to high purity, RNA was extracted and hybridized on Affymetrix microarrays. No technical replicates were used. The expression profiles of in vivo samples were then compared to the ones of in vitro samples.

first: Bart

last: Vandekerckhove

first: Sylvia

last: Snauwaert


title: Effect of L. rhamnosus GR-1 and L. reuteri RC-14 on host responses in a trial of post-menopausal women

status: Public on Jul 20 2014

city: London

first: Jordan

middle: Eduard

last: Bisanz

state: Ontario

address: 268 Grosvenor Street, Room F2-116

country: Canada

institute: Lawson Health Research Institute

summary: A lactobacilli dominated microbiota in most pre and post-menopausal women is an indicator of vaginal health. A Nugent scoring system serves as a proxy for determining the ratio of lactobacilli to other vaginal inhabitants where a high score usually represents a diseased state, whilst an intermediate score represents a warning zone. The objective of this double blinded, placebo-controlled crossover study was to evaluate in 14 post-menopausal women with an intermediate score, the effect of vaginal administration of probiotic L. rhamnosus GR-1 and L. reuteri RC-14 on the microbiota and host response. The probiotic treatment did not result in changes to clinical parameters such as dryness, irritation and comfort, compared to when placebo was applied. Analysis using 16S rRNA sequencing and metabolomics profiling revealed that the proportional abundance of Lactobacillus was increased following probiotic administration as compared to placebo, which was weakly associated with an increase in lactate levels. Analysis of host responses by microarray showed the probiotics had an immune-modulatory response and multiplex cytokine analysis showed up-regulation of IL-5. This is the first study to use an interactomic approach for the study of vaginal probiotic administration in post-menopausal women. It shows that in some cases multifaceted approaches are required to detect the subtle trigger molecular changes induced by the host to instillation of probiotic strains.

overall_design: A total of 35 total RNA samples extracted from vaginal brushes were analyzed on Affymetrix Gene 2.0 ST arrays from 14 Participants collected over multiple visits including administration of either a probiotic supplement or placebo control.

middle: E

first: Gregor

last: Reid


title: Using a rhabdomyosarcoma patient-derived xenograft to examine precision medicine approaches and model acquired resistance

status: Public on Jul 22 2014

city: Grand Rapids

first: David

last: Cherba

state: MI

address: 333 Bostwick Ave

department: Bioinformatics and Biostatistic Core

institute: Van Andel Institute

summary:
Original patient tumor is directly implanted in mice xenografts. Tumor is propagated to multiple mice for conduct of 6 arm treatment trials and control. Therapies are selected based on T0 and F0 genomic profiles.
ICE-T refractory tumor are implanted and additional 6 arm treatment trial and control conducted based on genomic profiles of F2 generation mice to suggested therapies

overall_design: Original patient tumor expanded in F0 mouse generation to F1 generation for multiple arm therapy trial and then refractory tumors implanted for additional multiple arm therapy trial

first: Noel

last: Monks


title: Expression data of human lung adenocarcinoma cell line H441 treated with TTF-1/NKX2-1 siRNA and TGF-beta

status: Public on Jul 27 2014

city: Tokyo

first: Daizo

last: Koinuma

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

department: Pathology

country: Japan

institute: University of Tokyo

summary:
We determined and analyzed the effect of TTF-1/NKX2-1 on Smad3/Smad4 binding sites by ChIP-sequencing.
We used expression microarrays to evaluate the effect of TTF-1/NKX2-1 siRNA on TGF-beta-induced gene expressions.

overall_design:
H441 cells were transfected with siRNAs and treated with TGF-beta for RNA extraction and hybridization on Affymetrix microarrays.

This submission represents transcriptome component of study.

first: Kazunobu

last: Isogaya

first: Shuichi

last: Tsutsumi

first: Akira

last: Saito

first: Keiji

last: Miyazawa

first: Hiroyuki

last: Aburatani

first: Kohei

last: Miyazono


title: Dietary flavanols modulate the transcription of genes involved in cardiovascular pathology with complex changes of their DNA methylation state

first: Celine

last: BOBY

summary: Background: In a recent intervention study, the daily supplementation with 200 mg monomeric and oligomeric flavanols (MOF) from grape seeds for 8 weeks revealed a vascular health benefit in male smokers. The objective of the present study was to determine the impact of MOF consumption on the gene expression profile of leukocytes and to assess changes in DNA methylation. Methodology/Principal Findings: Gene expression profiles were determined using whole genome microarrays (Agilent) and DNA methylation was assessed using HumanMethylation450 BeadChips (Illumina). MOF significantly modulated the expression of 864 genes. The majority of the affected genes are involved in chemotaxis, cell adhesion, cell infiltration or cytoskeleton organisation, suggesting lower immune cell adhesion to endothelial cells. This was corroborated by in vitro experiments showing that MOF exposure of monocytes attenuates their adhesion to TNF-α-stimulated endothelial cells. Nuclear factor-kappa B (NF-κB) reporter gene assays confirmed that MOF decrease the activity of NF-κB. Strong inter-individual variability in the leukocytes’ DNA methylation was observed. As a consequence, on group level, changes due to MOF supplementation could not be found. However, in individuals, significant changes in DNA methylation of genes involved in leukocyte rolling, adhesion and cytoskeleton remodelling were seen. Conclusion: Our study revealed that regular consumption of MOF modulates the expression of genes in immune cells which, however, cannot be correlated to alterations in the DNA methylome. Remarkably, at the individual level, genes related to leukocyte adhesion pathways present complex variation in DNA methylation. As such, the individual transcriptional and epigenetic modulation of genes involved in early manifestation of cardiovascular diseases constitutes important subcellular mechanisms by which MOF promote vascular health in humans.

overall_design: DNA methylation levels of blood samples from 10 subjects were assessed using HumanMethylation450 BeadChips (Illumina), both before and after a diet intervention with MOF.

first: Dragan

last: Milenkovic

first: Wim

last: Vanden Berghe

first: Céline

last: Boby

first: Christine

last: Leroux

first: Ken

last: Declerck

first: Katarzyna

last: Szarc vel Szic

first: Karen

last: Heyninck

first: Kris

last: Laukens

first: Francois

last: Fuks

first: Guy

last: Haegeman

first: Guido

last: Haenen

first: Aalt

last: Bast

first: Antje

last: Weseler


title: Glutamine deprivation in U2OS cells

city: Pearl River

first: Naval

last: Shanware

address: 401 North Middle Town Road

institute: Pfizer

summary:
To understand the effects of glutamine deprivation on cell physiology we performed global analysis of gene expression in response to glutamine deprivation.
U2OS cells were subjected to glutamine deprivation for 24h followed by RNA extraction and microarray analysis.

overall_design: U2OS cells were plated overnight followed by treatment for 24h with glutamine-containing and glutamine-depleted media. Three biological replicates were assayed for each condition.

first: Kevin

last: Bray

first: Christina

middle: H

last: Eng

first: Fang

last: Wang

first: Maximillian

last: Follettie

first: Jeremy

last: Myers

first: Valeria

last: Fantin

first: Robert

middle: T

last: Abraham


title: Human rhinovirus infection causes different DNA methylation changes in nasal epithelial cells from healthy and asthmatic subjects

status: Public on Jul 28 2014

city: Chicago

first: Peter

last: McErlean

state: Illinois

address: 240 E. Huron, McGaw M-530h

department: Allergy Immunology

institute: Northwestern University

summary: Background: Mechanisms underlying the development of virus-induced asthma exacerbations remain unclear. Objective: To investigate if epigenetic mechanisms could be involved in virus-induced asthma exacerbations, we undertook DNA methylation profiling in asthmatic and healthy nasal epithelial cells (NECs) during Human Rhinovirus (HRV) infection in vitro. Methods: Global and loci-specific methylation profiles were determined via Alu element and Infinium Human Methylation 450K microarray respectively. Principal components analysis identified the genomic loci influenced the most by disease-status and infection. Real-time PCR and pyrosequencing was used to confirm gene expression and DNA methylation respectively. Results: Global methylation was increased in Asthmatics during infection. Disease status and virus infection influenced the methylation of 389 loci. Healthy and asthmatic NECs were characterized predominately by methylation profiles and patterns in loci that were not influenced by virus infection. However, both groups also exhibited distinct DNA methylation profiles in response to infection. Despite these differences, we found that the methylation of small nucleolar RNA, H/ACA box 12 (SNORA12) was common during infection. Further analysis indicated a relationship existed between SNORA12 DNA methylation and gene expression in response to infection. Conclusions:  Findings from our study indicate that in addition to the well described phenotypic and genomic differences, the airway epithelium of asthmatics is characterized by a distinct methylome and that epigenetic mechanism may contribute to the development of virus-induced asthma exacerbations.

overall_design: Bisulphite converted DNA from matched mock and human rhinovirus-16 infected nasal epithelial cells from Healthy (n=3) and Asthmatics (n=6) adults were hybridized to the Illumina DNA methylation 450K Bead Array.

first: Silvio

last: Favoreto Jr

first: Fabricio

last: Costa

first: Junqing

last: Shen

first: Jihan

last: Quarishi

first: Assel

last: Biyasheva

first: Jocelyn

last: Cooper

first: Denise

last: Scholtens

first: Elio

last: Vanin

first: Maria

last: de Bonaldo

first: Hehuang

last: Xie

first: Marcelo

middle: B

last: Soares

first: Pedro

last: Avila


title: Stability of the CpG island methylator phenotype during glioblastoma progression.

status: Public on Jul 18 2014

city: Birmingham

first: Farida

last: Latif

address: College of Medical and Dental Sciences

country: United Kingdom

institute: University of Birmingham

summary: The Illumina HumanMethylation 450 BeadChip was used on 20 matched pairs of early and late secondary gliomas to assess the changes in DNA methylation during progression.

overall_design: Bisulphite converted DNA from the 40 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip.

first: Victoria

last: Hill


title: Temporal Endogenous Gene Expression Profiles in Response to Polymer-Mediated Transfection and Profile Comparison to Lipid-Mediated Transfection

status: Public on Jul 23 2014

city: Lincoln

first: Timothy

last: Martin

state: NE

address: 32 Chase Hall

department: Biological Systems Engineering

institute: University of Nebraska-Lincoln

summary: The current understanding of the molecular factors underlying polyethylenimine(PEI)-mediated transfection is largely unknown.  Cationic PEI  was used to transfer GFP transgene to HEK293T cells.  FACS separation of transfected (GFP positive), untransfected (GFP negative), and untreated cells enabled gene expression profiles to be obtained using Affymetrix® HG-U133A 2.0 microarrays for each cell population.  Gene profiles were differentially compared for each population combination.

overall_design: Control (untreated),  transfected (GFP positive), and untransfected (GFP negative) RNA samples were purified from HEK293T cells after FACS isolation.  Treated experiments were repeated on triplicate days to run 3 microarrays for each cell population. Controls were run on duplicate to give 2 microarrays for each population.

first: Sarah

last: Plautz

first: Angela

last: Pannier


title: Matrix Elasticity Does Not Affect Replicative Senescence or DNA Methylation Patterns of Mesenchymal Stem Cells

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

type:
Expression profiling by array
Methylation profiling by array


title: Expression Data from PECAM1+ and PECAM1- B16F10 Clones

city: Chapel Hill

first: James

last: Dunleavey

state: NC

address: 111 Mason Farm Road

institute: University of North Carolina- Chapel Hill

summary:
We have isolated cells from the B16F10 melanoma cell line which express the vascular-selective marker PECAM1
Here we used microarrays to determine expression profile differences across the mouse genome to determine whether these cells display additional endothelial characteristics

overall_design: PECAM1+ and PECAM1- B16F10 clones, along with mouse endothelial cells were cultured and harvested for RNA, which was then used in an Affymetrix Mouse Gene 1.0 ST array to determine expression signatures

first: Andrew

last: Dudley


title: Molecular profiling of three tumor subtypes in Ptch medulloblastomas

city: Bar Harbor

first: Vivek

last: Philip

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary:
we discovered that medulloblastomas that form in Ptch mice are composed of three different sibtypes depending on the cell of origin and tumor progression.
The goal was to identify gene signature that can distinguish the three subtypes

overall_design: RNA from tumor tissues from the three subtypes were extracted by Trizol and hybridized on Affy St1.0 chips for analysis

first: Kyuson

last: Yun


title: Whole Genome Expression Profiling shows that BRG1 Transcriptionally Regulates UV Inducible Genes and other Novel Targets in Human Cells

status: Public on Jul 21 2014

city: Miami

first: Feng

last: Gong

state: FL

address: 1011 NW 15th ST

department: Biochemistry and Molecular Biology

institute: University of Miami

summary: BRG1, an ATPase catalytic subunit of the SWI/SNF chromatin remodeling complex, has been identified as a tumor suppressor protein, as it has been shown to play a role in Nucleotide Excision Repair (NER) of CPDs, suppress apoptosis, and restore checkpoint deficiency, in response to UV exposure.   Although BRG1 has been shown to regulate transcription of some genes that are instrumental in proper DNA damage repair and cell cycle maintenance in response to UV, its role in transcriptional regulation of the whole genome in response to UV has not yet been elucidated.  With whole genome expression profiling in SW13 cells, we show that upon UV induction, BRG1 regulates transcriptional expression of many genes involved in cell stress response.  Additionally, our results also highlight BRG1’s general role as a master regulator of the genome, as it transcriptionally regulates approximately 4.8% of the human genome, including expression of genes involved in many pathways.

overall_design: SW13 cells without or with BRG1 protein exrpession were treated with UV-C (10 J/m2) or mock treated. Cells were incubated for 6 hrs after UV or mock treaments, total RNA was prepared using TRIZOL reagent (Invitrogen, Carlsbad, CA), followed by the RNeasy kit (Qiagen, Valencia, CA), according to the manufacturer’s instructions. Three independent biological replicates of SW13+pREP7 and SW13+pREP7+BRG1 were subjected to microarray analysis using Affymetrix U133 plus 2.0 gene chip. Target synthesis and GeneChip hybridization, washing, staining, and scanning were performed at the Molecular Biology Core at Washington State University. Microarray output was examined visually for excessive background noise and physical anomalies. The default MAS statistical values were used for all analyses. All probe sets on each array were scaled to a mean target signal intensity of 125, with the signal correlating to the amount of transcript in the sample. An absolute analysis using MAS was performed to assess the relative abundance of the 47,000 represented transcripts and variants, including 38,500 human genes, based on signal and detection

first: Ling

last: Zhang

first: Leah

last: Nemzow


title: Telomere length effect on genes near the telomere in myoblasts

status: Public on Jul 17 2014

city: Dallas

first: Kimberly

last: Batten

state: TX

address: 5323 Harry Hines Blvd

department: Cell biology

institute: UT Southwestern Medical Center

summary:
We examined differential expression of genes within 10MBs of telomeres in myoblasts with long or short telomeres
We offer telomere looping with telomere length as a partial mechanistic explanation for the changes gene expression that is observed.

overall_design: Compare expression of genes within 10MB of the telomere in  normal myoblasts with long (15 kb) and short (6 kb) telomeres.

first: Jerome

middle: D

last: Robin

first: Jerry

middle: W

last: Shay

first: Woodring

last: Wright


title: The effect of YAP/TAZ knockdown on the intestinal epithelium

city: Kyoto

first: Masamichi

last: Imajo

address: Yoshidakonoe-cho, Sakyo-ku,

institute: Kyoto University

summary: The Hippo pathway plays a crucial in organ size control during development and tissue homeostasis in adult life. To examine a role for Hippo signaling in the intestinal epithelium, we analyzed gene expression patterns in the mouse intestinal epithelilum transfected with siRNAs or expression plasmids for shRNAs targeting the Hippo pathway effectors, YAP and TAZ.

overall_design: We performed two independent series of experiments (siGFP (n=3) vs siYAP/siTAZ (n=3), and shLacZ (n=1) vs shYAP/shTAZ (n=1)). Control siRNA (siGFP), YAP/TAZ siRNAs, or expression plasmids for control shRNA (shLacZ) or YAP/TAZ shRNAs were introduced into the mouse intestinal epithelium by the newly-developed in vivo transfection method. Four days after transfection, intestinal epithelial cells were isolated from the tissues and total RNA was extracted.

first: Miki

last: Ebisuya

first: Eisuke

last: Nishida


title: MMSET regulates transcription factors critical for survival of t(4;14) myeloma myeloma cells

status: Public on Jul 16 2014

city: Singapore

first: Zhigang

last: Xie

address: 14 Medical Drive, CeLS Building #02-07

department: CSI Singapore

country: Singapore

institute: National University of Singapore

summary: Multiple myeloma (MM) is characterized by recurrent chromosomal translocations. The multiple myeloma SET domain (MMSET), identified by its fusion to the IgH locus in t(4;14) MM, is universally overexpressed and has been suggested to play an important role in tumorigenicity in t(4;14) MM. In order to identify downstream functional targets of MMSET, we knocked down MMSET expression with shRNAs in KMS11, a t(4;14) MM cell line, and identified differentially expressed genes by gene expression microarray analysis.

overall_design: KMS11 cells were treated with shRNAs for 48 h. Total RNA was extracted by using the Qiagen RNeasy Mini kit (Germany). Gene expression was performed using the GeneChip Human Genome U133A Array (Affymetrix) following the manufacturer’s instructions. Data analysis was performed using GeneSpring software from Agilent Technologies.

first: Chonglei

last: Bi

first: Wee

last: Chng


title: Temporal Endogenous Gene Expression Profiles in Response to Lipid-Mediated Transfection

first: Timothy

last: Martin

summary: The current understanding of the molecular factors underlying LF2000-mediated transfection is largely unknown.  Cationic LF2000 gene delivery system was used to transfer GFP transgene to HEK293T cells.  FACS separation of transfected (GFP positive), untransfected (GFP negative), and untreated cells enabled gene expression profiles to be obtained using Affymetrix® HG-U133A 2.0 microarrays for each cell population.  Gene profiles were differentially compared for each population combination.

first: Sarah

last: Plautz

first: Angela

last: Pannier


title: Matrix Elasticity Does Not Affect Replicative Senescence or DNA Methylation Patterns of Mesenchymal Stem Cells [DNAm profiling]

first: Wolfgang

last: Wagner

summary: Matrix elasticity influences differentiation of mesenchymal stem cells (MSCs) but it is unclear if these effects are only transient - while the cells reside on the substrate - or if they reflect persistent lineage commitment. In this study, MSCs were continuously culture-expanded in parallel either on polydimethylsiloxane (PDMS) gels of different elasticity or on tissue culture plastic (TCP) to compare impact on replicative senescence, in vitro differentiation, gene expression, and DNA methylation (DNAm) profiles. The maximal number of cumulative population doublings was not affected by matrix elasticity. Differentiation towards adipogenic and osteogenic lineage was increased on soft and rigid biomaterials, respectively - but this propensity was no more evident if cells were transferred to TCP. Global gene expression profiles and DNAm profiles revealed relatively few differences in MSCs cultured on soft or rigid matrices. Furthermore, only moderate DNAm changes were observed upon culture on very soft hydrogels of human platelet lysate (hPL-gel). Our results support the notion that matrix elasticity influences cellular differentiation while the cells are organized on the substrate, but it does not have major impact on cell-intrinsic lineage determination, replicative senescence or DNAm patterns.

overall_design: 20 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip

first: Anne

last: Schellenberg

first: Sylvia

last: Joussen

first: Kristin

last: Moser

first: Nico

last: Hampe

first: Niels

last: Hersch

first: Hatim

last: Hemeda

first: Bernd

last: Denecke

first: Qiong

last: Lin

first: Norbert

last: Pallua

first: Martin

last: Zenke

first: Rudolf

last: Merkel

last: Hoffmann


title: Whole brain expression data from postnatal day 7-aged mice exposed to ethanol at postnatal day 7

first: Morgan

middle: L

last: Kleiber

address: Biological and Geological Sciences Building

department: Biology

institute: University of Western Ontario

summary:
The developing brain is particularly sensitive to ethanol during the brain growth spurt or synaptogenesis (third human trimester equivalent).  This has been shown to lead to abnormal brain development and behavioural changes in the adult mouse that are relevant to those seen in humans with fetal alcohol spectrum disorders (FASD).  We evaluated the acute (4h post-treatment) gene expression changes that occur in the brain due to ethanol exposure during synaptogenesis (postnatal day 7).
We used microarray analyses to evaluate the changes in brain gene expression at postnatal day 7 that occur due to ethanol treatment at postnatal day 7 (synaptogenesis).

overall_design: To generate samples, C57BL/6J pups were injected with ethanol (experimental) or saline (control) at postnatal day 7 (2 x 2.5 g/kg at 0h and 2h).   Pups were sacrificed 4 hours following the initial injection.  Total RNA was extracted from whole brain tissue and RNA from three male mice from three different litters were pooled as one biological replicate.  Each male ethanol-treated mouse represented in a sample was matched by a control littermate present in a control sample.  This study consists of two experimental (ethanol-treated) biological replicates and four control (saline vehicle-treated) replicates (total mice used was n=18).


title: Molecular-guided therapy predictions reveal drug resistance phenotypes and treatment alternatives in malignant peripheral nerve sheath tumors

first: David

last: Cherba

summary: Use existing public data, cell lines and patient tumors with a personalized medicine approach to predict effective therapies for treatment of Neurofibroma tumors.

overall_design: Compare expression profile to reference set to identify over expressed genes that are drugable targets.

first: Jacqueline

last: Peacock

first: Matt

last: Steensma


title: A Systems Biology Approach identified different regulatory networks targeted by KSHV miR-K12-11 in B cells and endothelial cells

status: Public on Jul 15 2014

city: Gainesville

first: Lauren

last: McIntyre

address: 2033 Mowry Rd

institute: University of Florida

summary: Background: Kaposi’s sarcoma associated herpes virus (KSHV) is associated with tumors of endothelial and lymphoid origin. During latent infection, KSHV expresses miR-K12-11, an ortholog of the human tumor gene hsa-miR-155. Both gene products are microRNAs (miRNAs), which are important post-transcriptional regulators that contribute to tissue specific gene expression. Advances in target identification technologies and molecular interaction databases have allowed a systems biology approach to unravel the gene regulatory networks (GRNs) triggered by miR-K12-11 in endothelial and lymphoid cells. Understanding the tissue specific function of miR-K12-11 will help to elucidate underlying mechanisms of KSHV pathogenesis.  Results: Ectopic expression of miR-K12-11 differentially affected gene expression in BJAB cells of lymphoid origin and TIVE cells of endothelial origin. Direct miRNA targeting accounted for a small fraction of the observed transcriptome changes: only 29 common genes were identified as putative direct targets of miR-K12-11 in both cell types. However, a number of commonly affected biological pathways, such as carbohydrate metabolism and interferon response related signaling, were revealed by gene ontology analysis. Integration of transcriptome profiling, bioinformatic algorithms, and databases of protein-protein interactome from the ENCODE project identified different nodes of GRNs utilized by miR-K12-11 in a tissue-specific fashion. These effector genes, including cancer associated transcription factors (TFs) and signaling proteins, amplified the regulatory potential of a single miRNA, from a small set of putative direct targets to a larger set of genes.   Conclusions: This is the first comparative analysis of miRNA-K12-11’s effects in endothelial and B cells, from tissues infected with KSHV in vivo. MiR-K12-11 was able to broadly modulate gene expression in both cell types. Using a systems biology approach, we inferred that miR-K12-11 establishes its GRN by both repressing master TFs and influencing signaling pathways, to counter the host anti-viral response and to promote proliferation and survival of infected cells. The targeted GRNs are more reproducible and informative than target gene identification, and our approach can be applied to other regulatory factors of interest.

overall_design: The experiment was designed for the comparison of miR-155 transduced cells, miR-K12-11 treated cells, and mock transduced cells. The experiment was conducted in four subsequent time periods such that all the experimental conditions were independently repeated. TIVE and BJAB cells were retrovirally transduced at two levels of Multiplicity of Infection (MOI): 1 and 10. 72hr post transduction, positive cells were sorted according to their GFP signal. RNA was extracted using the RNA-Bee reagent according to the manufacturer’s instructions. For each HG-133 plus 2.0 chip, 200ng RNA was used as the starting material. RNA was synthesized and labeled using GeneChip® 3’ IVT Express Kit and chips were hybridized according to manufacturer instructions (Affymetrix). Raw data were summarized using Affymetrix Expression Console software (v1.1).

first: Yajie

last: Yang

first: Isaac

last: Boss

first: Rolf

last: Renne


title: Expression data from AsPC1 cells treated with ICG-001

city: Los Angeles

last: Dawson

state: CA

address: 10833 LeConte Avenue

department: Pathology and Laboratory Medicine

institute: University of California Los Angeles

summary:
The CREB binding protein inhibitor ICG-001 suppresses pancreatic cancer growth
We used microarrays to detail global gene expression changes in the pancreatic cancer cell line AsPC1 following treatment with ICG-001 or siRNA-mediated knockdown of CTNNB1 (beta-catenin)

overall_design: AsPC1 cells were treated with 10uM ICG-001 or vehicle control (DMSO) for either 6 hours or 24 hours.  AsPC-1 cells were also separately transfected with 20nM control siRNA or CTNNB1 siRNA for 48 hours.  RNA was extracted at these time points for hybridization to Affymetrix microarrays


title: Effect of Hypertension of Dendritic Cell Gene Expression

city: Nashville

first: Annet

last: Kirabo

address: 2220 Pierce Avenue

institute: Vanderbilt

summary:
Oxidative injury and inflammation have been implicated in the genesis of hypertension but the mechanisms involved are not fully understood. We describe a new pathway in which angiotensin II promotes dendritic cell (DC) activation of T cells and ultimately hypertension.  NADPH oxidase-dependent superoxide production is increased 5-fold in DCs isolated from hypertensive mice as compared to sham-treated mice.  This is associated with DC accumulation of protein-isoketal adducts and production of IL-6, IL-1β and IL-23.  DCs from hypertensive mice but not sham mice promote survival and proliferation of CD8+ T cells in culture.  Chemically diverse isoketal scavengers not only prevent activation and immunogenicity of DCs, but also attenuate angiotensin II-induced hypertension.  Moreover, adaptive transfer of DCs from hypertensive mice prime development of hypertension in response to a subpressor dose of angiotensin II.  Exposure of DCs to tert butyl hypdroperoxide promoted isoketal formation, DC stimulation of CD8+ T cell proliferation and primed hypertension in response to low dose angiotensin II.  Serum isoprostanes, precursors to isoketals, were found to be elevated in humans with treated hypertension and were markedly elevated in patients with resistant hypertension.  These studies show that angiotensin II-induced hypertension activates DCs, in large part by causing superoxide production and formation of isoketals. They define a new mechanism of hypertension and identify a potential new therapeutic approach for this disease.
We used microarrays to detail the expression differences in dendritic cells under hypertensive conditions.

overall_design: Dendritic cells were isolated from mosue spleen and subsequently treated with Angiotensin II with or without co-treatment with 2-hydroxybenzylamine (2-HOBA) for RNA extraction and hybridization on Affymetrix microarrays. We sought to determine the effect of oxidative stress on dendritic cell expression profiles.

last: Harrison


title: Adaptation of breast cancer cells to brain, bone marrow, and lung tissue

status: Public on Jul 14 2014

city: San Diego

first: John

last: Welsh

state: California

address: 3030 Bunker Hill Street

institute: Vaccine Research Institute of San Diego

summary: The Her-2/Neu-positive mouse breast cancer cell line was serially co-cultured with minced brain, bone marrow, and lung tissue in an intravital microscopy chamber mounted on the dorsal skinfold of nude mice, alternating with growth in vitro. Gene expression analysis was performed on the cells grown in culture after sorting and further growth in vitro. Gene expression under these growth conditions differed in time and according to the co-cultivated organ tissue. This study reveals genes that are expressed by cells as they adapt differentially to various foreign tissue microenvironments, and may represent a paradigm to discover gene expression changes that occur immediately upon extravasation when cancer metastasizes.

overall_design: Gene expression analysis was performed for four time points and three tissues, brain, bone marrow, and lung, using Affymetrix microarrays. Technical replicates of the array analysis were performed for the brain samples. Biological replicates were performed for the first two brain time points, and one passage of N202 cells on breast tissue was analyzed.

first: Gaelle

last: Rondeau

first: Parisa

last: Abedinpour

first: Prerak

last: Desai

first: Veronique

last: Baron

first: Per

last: Borgstrom


title: Replication Stress is a Potent Driver of Functional Decline in Aging in Hematopoietic Stem Cells

city: San Francisco

first: Sietske

middle: Tet

last: Bakker

address: 35 Medical Center Way

department: Department of Medicine

institute: University of California San Francisco

summary: To understand at the molecular level the differences between old HSCs and young HSCs we have performed genome-wide analyses using Affymetrix Gene ST 1.0 microarrays with FACS purified cell populations. In contrast to other datasets comparing young and old HSCs, we compared both young and old HSCs and GMPs, and subtracted for genes that were also differentially expressed between young and old GMPs using a zero-intercept linear model. This allowed us to identify 913 significantly differentially expressed genes that were specific to old HSCs and segregated into different clusters.

overall_design: Hematopoietic Stem Cells (HSC) (Lin-/cKit+/Sca1+/Flk2-/CD48-/CD150+) and Granulocyte/Macrophage progenitors (GMP) (Lin-/cKit+/Sca1-/FcyR+/CD34+) were isolated from young (6-12 weeks) and old (22-30 months) C57Bl/6 mice and subjected to microarray analysis  wild type C57Bl/6 mice

first: Emmanuelle

last: Passegué

first: Johanna

last: Flach


title: Monocytic cell differentiation from band-stage neutrophils under inflammatory conditions

status: Public on Jul 11 2014

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

summary: During inflammation, neutrophils are rapidly mobilized from the bone marrow storage pool into peripheral blood to subsequently enter lesional sites where most of them rapidly undergo apoptosis. Monocytes constitute a second wave of inflammatory immigrates giving rise to long-lived macrophages and dendritic cell subsets. According to descriptive immunophenotypic and cell culture studies, neutrophils may directly “transdifferentiate” into monocytes/macrophages. We here provide mechanistic data in human supporting the existence of this cellular pathway. Global transcriptional profiling of  neutrophil-dervived monocytic cells revealed close resemblance of gene expression with monocytes and a clear separation of these cells from neutrophils.

overall_design: G-CSF mobilized neutrophils from peripheral blood were isolated and in vitro stimulated with GM-CSF, TNFa, and Il-1b for 5 days to generate monocytic cells. RNA were isolated from these cells and freshly isolated blood neutrophils and monocytes.

first: René

last: Köffel

first: Herbert

last: Strobl


title: Gene expression analysis of cMyc-deficient CD8 T cells retrovirally overexpressing cMyc or AP4

status: Public on Jul 13 2014

city: Saint Louis

first: Takeshi

last: Egawa

state: MO

address: 660 South Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

summary: To determine functional overlap between cMyc and AP4 in CD8+ T cell priming, we retrovirally expressed cMyc or AP4 in cMyc-deficient CD8+ T cells and examined gene expression after activation.

overall_design: Naive CD8+ T cells from Myc conditional knockout mice with a tamoxifen inducible Cre transgene were retrovirally transduced with Myc or AP4 followed by a treatment with 4-hydroxytamoxifen in the presence of IL-7 for 2 days. RNA was harvested 48 hours after restimulation of transduced cells with anti-CD3 antibody and gene expression was compared by microarray. CD8+ T cells from littermate wildtype mice that were transduced with an empty retrovirus were used as control.

first: Chun

last: Chou


title: Microarray analysis of the effects of IL-2 signaling on in vitro activated WT CD8 T cells

summary: Interleukin 2 (IL-2) promotes proliferation and differentiation of CD8+ T cells in vitro and in vivo. To define gene expression regulated by IL-2, we purified naive CD8+ T cells,  activated them for 2 days followed by treatment with recombinant IL-2 or with neutralizing antibody against IL-2 and compared gene expression between the two treatments.

overall_design: Total RNA was extracted using the NucleoSpin RNA XS kit (Macherey-Nagel), amplified using a PicoSL RNA amplification kit (Nugen) and biotinylated with Encore biotin module (Nugen). Labeled RNA was hybridized to Mouse Gene 1.0ST microarrays (Affymetrix) according to the manufacturer’s instruction.


title: Microarray analysis of WT and Tfap4-KO CD8 T cells during early activation

summary: Gene expression of Tfap4–/– and WT CD8+ T cells were compared after activation with anti-CD3 and anti-CD28 antibodies in vitro or with Listeria monocytogenes infection in vivo

overall_design: For in vitro activation, naive CD8+ T cells were purified from WT and Tfap4–/– mice and activated with anti-CD3 and anti-CD28 antibodies for 72 hours. For in vivo activation, naive CD8+ T cells from Tfap4–/– OT-I or control WT OT-I TCR transgenice mice were adoptively transferred to congenic host mice that were subsequently infected with Listeria mnocytogenes expression ovalbumin. Activated OT-I cells were harvested 48 hours after infection.


title: The expression profiling comparison of mice with Scap and Insig deletion from perinatal lung (E17.5-PN1)

status: Public on Jul 10 2014

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary:
In this study, we studied the genomic responses of  the Insig and Scap deletion from perinatal lung.
Through comprehensive data analysis and integration, time dependent effects of epithelial SCAP/INSIG/SREBP deletion and defined SCAP/INSIG/SREBP-associated genes, bioprocesses and downstream pathways were identified.

overall_design: Total lung RNA was isolated from ScapΔ/Δ, Insig1/2Δ/Δ, and respective control littermates at E17.5, E18.5 and PN1 were used for mRNA expression profiling analysis (n=3 for each condition)

first: James

middle: P

last: Bridges

first: Angelica

last: Schehr

first: Yanhua

last: Wang

first: Liya

last: Huo

first: Valerie

last: Besnard

first: Machiko

last: Ikegami

first: Jeffrey

last: Whitsett


title: Escalating-dose peptide immunotherapy induces progressive immunoregulatory changes in self-reactive T cells

city: Bristol

first: Hai

last: Fang

address: Woodland Road

department: Department of Computer Science

institute: University of Bristol

summary: Peptide immunotherapy aims to specifically restore tolerance to the administered self-antigen and prevent autoimmunity without the perturbation of normal immune function. We have developed a dose escalation protocol for subcutaneous delivery of the MHC II-restricted myelin basic protein peptide analogue Ac1-9[4Y] to T cell receptor transgenic (Tg4) mice. Dose escalation allows safe administration of high doses of peptide, which effectively induces antigen-specific tolerance and suppresses the development of experimental autoimmune encephalomyelitis, a model for the human condition multiple sclerosis. CD4+ T cells isolated from treated mice are anergic and suppressive in vitro and respond to stimulation by secretion of the immunoregulatory cytokine IL-10. To understand the molecular changes occurring throughout the course of dose-escalation immunotherapy, we undertook microarray analysis of CD4+ T cells at different the stages of treatment, using Tg4 Rag-1 deficient mice, which lack naturally occurring regulatory T cells and have a monoclonal CD4+ T cell population

overall_design: CD4+ T cells were collected from Tg4 Rag1 deficient TCR-transgenic mice at six sequential stages of EDI plus a PBS-treated control, RNA extracted and then subjected to microarray hybridization using Affymetrix Mouse Gene 1.0 ST array

first: Bronwen

middle: R

last: Burton

first: Graham

last: Britton

first: Julian

last: Gough

first: David

middle: C

last: Wraith


title: Expression data from FIT-039 or Flavopiridol compound treated HeLa cells

status: Public on Jul 08 2014

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

institute: Kindai University

summary:
FIT-039 is a novel antiviral compound. Antiviral mechanism of FIT-039 is the inhibition of the viral transcription through suppression of the CTD phosphorylation of RNA polymerase II.
We used microarrays to evaluated the effect of FIT-039 on host cellular transcriptome, compared with Flavopiridol which is an existing pan-specific CDK9 inhibitor.

overall_design: HeLa cells were incubated with FIT-039 or flavopiridol at the concentration of IC80 for 24 hr, and cellular RNAs were collected and subjected to microarray analysis. The solvent DMSO was used as a negative control.

last: Iida

first: Makoto

last: Yamamoto


title: Frequent Loss-of-Function Mutations in MLK4 Suppresses Signaling in the JNK-cJUN-p21/p15 Pathway to Promote Growth of Colon Cancer Cells

status: Public on Jul 09 2014

city: Manchester

first: Anna

last: Marusiak

address: Wilmslow Road

institute: CRUK Manchester Institute

summary:
The goal of the study was to evaluate the influence of mutations in MLK4 on the protein function and the process of tumorigenesis in colorectal cancers. Biochemical data imply that a majority of MLK4 mutations in colon cancer are loss-of-function, including, E314K and Y330H mutations.
Two colorectal cell lines, HCT15 and HT115, harboring MLK4 loss-of-function mutations, Y330H and E314K respectively, were used in the study.
To evaluate the consequences of loss-of-function MLK4 mutations in those colon cancer cell lines, HCT15 and HT115 cell lines were generated where expression of MLK4-WT (in HCT15 and HT115 cell lines) or MLK4-Y330H (in HCT15 cells) or MLK4-E314K (in HT115 cells) can be induced by tetracycline.
The reconstitution of MLK4-WT in colon cancer cells reduced viability, proliferation and ability to form colonies as well as significantly slowed down the tumor growth in mouse xenografts.
To investigate the downstream effectors of MLK4 that mediate the above effects, we transcriptionally profiled colon cancer cell lines after MLK4-WT reconstitution. The data indicates that re-expression of functional MLK4 leads to reduction in cell proliferation, likely due to increased expression of cJUN and cdk inhibitors (p15 or p21).

overall_design:
HCT15 and HT115 were treated with tetracycline for 24 hours to induce expression of MLK4. Cells were harvested and mRNA was isolated using Qiagen RNeasy Plus Mini Kit. Samples were hybridized to Affymetrix Human U133 Plus 2.0 array.
Experiments were performed in triplicates for every sample. Induction of Y330H in HCT15 cells and MLK4-E314K in HT115 cells was used as a control.

first: Yaoyong

last: Li

first: John

last: Brognard


title: Study of stem cells and progenitor cells in K14 Snail mice

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

institute: VIB

summary: Expression of the EMT-inducing transcription factor Snail is enhanced in different human cancers. To investigate the in vivo role of Snail during progression of epithelial cancer, we used a mouse model with skin-specific overexpression of Snail. Snail transgenic mice spontaneously developed distinct histological subtypes of skin cancer, such as basal cell carcinoma, squamous cell carcinoma and sebaceous gland carcinoma. Development of sebaceous gland carcinomas strongly correlated with the direct and complete repression of Blimp-1, a central regulator of sebocyte homeostasis. Snail expression in keratinocyte stem cells significantly promotes their proliferation associated with an activated FoxM1 gene expression signature, resulting in a larger pool of Mts24-marked progenitor cells. Furthermore, primary keratinocytes expressing Snail showed increased survival and strong resistance to genotoxic stress. Snail expression in a skin-specific p53-null background resulted in accelerated formation of spontaneous tumours and enhanced metastasis. Our data demonstrate that in vivo expression of Snail results in de novo epithelial carcinogenesis by allowing enhanced survival, expansion of the cancer stem cell pool with accumulated DNA damage, a block in terminal differentiation and increased proliferation rates of tumour-initiating cells.

overall_design: A total of 8 samples were analysed. CD34 samples contain sorted pooled keratinocytes from 11 different mice, and Mts24 samples contain sorted pooled keratinocytes from 9 different mice. Samples with negative fractions are considered to be the control samples to samples with positive fractions.

first: Bram

last: De Craene

first: Geert

last: Berx


title: Epigenetic and transcriptional aberrations in human pluripotent stem cells reflect differences in reprogramming mechanisms [methylation array]

city: La Jolla

first: Robert

last: Morey

address: 2880 Torrey Pines Scenic Dr

institute: UCSD

summary: Human pluripotent stem cells hold great potential for regenerative medicine, but existing cell types have imitations. Human embryonic stem cells derived from fertilized embryos (IVF-ESCs) are considered the “gold standard”, but are allogeneic to potential recipients. Autologous induced pluripotent stem cells (iPSCs) can be produced from somatic cells by forced expression of pluripotency-associated factors, but are prone to genetic and epigenetic aberrations. To determine whether accumulation of such aberrations is intrinsic to somatic cell reprogramming, or secondary to the reprogramming method, we employed an alternative approach by somatic cell nuclear transfer (SCNT). SCNT-based reprogramming to NT-ESCs is mediated by factors present in oocyte’s cytoplasm, thus mimicking early embryogenesis. We generated genetically matched pluripotent stem cells and conducted genome-wide genetic, epigenetic and transcriptional analyses. We discovered that unlike iPSCs, NT-ESCs have a low burden of de novo copy number variations (CNVs), reflecting superior maintenance of genetic stability. Moreover, DNA methylation and transcriptome profiles of NT-ESCs corresponded closely to those of IVF-ESCs. In contrast, iPSCs harbored methylation abnormalities including residual CpG methylation typical of parental fibroblasts, suggesting incomplete reprogramming. We conclude that human somatic cells can be faithfully reprogrammed to pluripotency by SCNT with the potential to satisfy the clinical requirements for cell replacement therapies.

overall_design: Bisulphite converted DNAs of two IVF-ESCs, two sendai produced iPSC lines, two retro-virus produced iPSC lines, four NT-ESCs, and the parental fibroblast were  hybridized to the Illumina Infinium HumanMethylation 450K Beadchip


title: Genome-wide analysis in human colorectal cancer cells reveals ischemia-mediated  expression of motility genes via DNA hypomethylation (expression)

status: Public on Jul 07 2014

city: Guelph

first: Brenda

last: Coomber

address: 50 Stone Road

department: Department of Biomedical Sciences

institute: University of Guelph

summary: DNA hypomethylation is an important epigenetic modification found to occur in many  different cancer types, leading to the upregulation of previously silenced genes and  loss of genomic stability. We previously demonstrated that hypoxia and  hypoglycaemia (ischemia), two common micro-environmental changes in solid tumors,  decrease DNA methylation through the downregulation of DNMTs in human colorectal  cancer cells. Here, we utilized a genome-wide cross-platform approach to identify  genes hypomethylated and upregulated by ischemia. Following exposure to hypoxia or  hypoglycaemia, methylated DNA from human colorectal cancer cells (HCT116) was  immunoprecipitated and analysed with an Affymetrix promoter array. Additionally, RNA  was isolated and analysed in parallel with an Affymetrix expression array. Ingenuity  pathway analysis software revealed that a significant proportion of the genes  hypomethylated and upregulated were involved in cellular movement, including PLAUR  and CYR61. A Matrigel invasion assay revealed that indeed HCT116 cells grown in  hypoxic or hypoglycaemic conditions have increased mobility capabilities. Confirmation  of upregulated expression of cellular movement genes was performed with qPCR. The  correlation between ischemia and metastasis is well established in cancer progression,  but the molecular mechanisms responsible for this common observation have not been  clearly identified. Our novel results suggest that hypoxia and hypoglycaemia may be  driving changes in DNA methylation through downregulation of DNMTs. This is the first  report to our knowledge that provides an explanation for the increased metastatic  potential seen in ischemic cells; i.e. that ischemia could be driving DNA  hypomethylation and increasing expression of cellular movement genes.

overall_design: HCT116 cells were grown in either Hypoxic or Hypoglycaemic conditions, and compared to cells grown under normal conditions

first: Karolina

last: Skowronski

first: Joseph

last: Andrews

last: Rodenhiser


title: Genome-wide analysis in Human Colorectal Cells reveals Ischaemia-mediated expression of motility genes via DNA hypomethylation

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

overall_design: Refer to individual Series


title: Methylome analysis of normal kidney, nephrogenic rest and Wilms tumor

city: London

first: Jocelyn

last: Charlton

address: 30 Guilford Street

department: Institute of Child Health

institute: University College London

summary: Genome wide DNA methylation profiling of normal kidney (n=36), nephrogenic rest (n=22) and Wilms tumour (n=37) was performed using the Illumina 450k array. Two papers were composed after analysis of this data (1) describes comparative analysis of 22 matched normal kidney-Wilms tumour pairs which identified biomarker differentially methylated regions (DMRs) that could be detected in patient blood; (2) describes comparative analysis of 20 matched trios which identified changes in methylation associated with progression from the precursor lesion towards tumourigenesis.

overall_design: Bisulfte converted DNA from 95 samples of normal kidney, nephrogenic rest and Wilms tumour was hybridised to Illumina HumanMethylation450 bead chips.

first: Richard

last: Williams

first: Mark

last: Weeks

first: Neil

last: Sebire

first: Sergey

last: Popov

first: Gordan

last: Vujanic

first: William

last: Mifsud

first: Tasnim

last: Chagtai

first: Mariana

last: Maschietto

first: Marisa

last: Alcaide-German

first: Tiffany

last: Morris

first: Lee

middle: M

last: Butcher

first: Paul

last: Guilhamon

first: Stephan

last: Beck

first: Kathy

last: Pritchard-Jones


title: Systemic inflammatory response to smoking in chronic obstructive pulmonary disease: evidence of a gender effect

status: Public on Jul 02 2014

city: Barcelona

first: Susana

last: Kalko

state: BARCELONA

address: c/Rosello 153

department: Bioinformatics Platform

institute: IDIBAPS

summary: We analyzed total leukocyte gene expression using Affymetrix microarrays from healthy smokers, COPD patients and non-smoking control subjects before and after exposure to acute cigarette smoke (smoking two cigarettes in 30 minutes).

overall_design: We analysed the gene expression profile of total leukocytes obtained from healthy control and copd subjects (106 in total). RNA was extracted and processed for further hybridization on Affymetrix microarrays (Affymetrix® Human Genome U219 Array Plate)

first: Rosa

last: Faner


title: Expression data from primary human leukocytes (peropheral blood mononuclear cells, PBMC) cultured in vitro with HIV-1MN, HIV-2NIH-Z, CpG-A ODN or media alone

first: Adriano

last: Boasso

address: 369 Fulham road

department: Immunology at Chelsea and Westminster Hospital

institute: Imperial College London

summary:
HIV-1 and HIV-2 can both infect humans, but HIV-2 causes a slow progressing disease and is well controlled by the immune system for prolonged period of times.
Here we tested acute response aainst HIV-1 and HIV-2 exposure in peripheral blood mononuclear cells (PBMC) from three indepednent donors.

overall_design: A total of 24 samples were analyzed. PBMC from three donors were cultured with Media alone, HIV-1MN, HIV-2NIH-Z or the TLR9 agonist CpG-A (4 conditions), and cells were harvested at 6h and 12h (2time points) for RNA extraction.

first: C

last: Royle

first: D

last: Graham

first: S

last: Sharma

last: Fuchs

first: A


title: Gene expression analysis of crypt base epithelial cells from WT and Nod2-/- mice

status: Public on Jul 01 2014

city: New York

first: Deepshika

last: Ramanan

state: New York

address: 550 First Ave

department: Immunology

institute: New York University

summary:
Nod2 has been extensively characterized as a bacterial sensor that induces an antimicrobial and inflammatory gene expression program. Therefore, it is unclear why Nod2 mutations that disrupt bacterial recognition are paradoxically among the highest risk factors for Crohn’s disease, which involves an exaggerated immune response directed at intestinal bacteria. Previous studies from our lab have shown that mice deficient in Atg16L1, another Crohns disease susceptibility gene, develop abnormalities in Paneth cells, specialized epithelial cells in the small intestine involved in antimicrobial responses.
The goal of our study is to determine whether Nod2 deficiency leads to differences in the transcriptional profile of Paneth cells, ultimately leading to small intestinal inflammation.

overall_design: Small intestinal sections (ileum) of 8 week old WT and Nod2-/- mice were fixed in methacarn and embedded in paraffin. The Leica LMD6000 Laser Microdissection system was used to capture crypt base epithelial cells to enrich for Paneth cells. RNA was extracted from these cells, followed by cDNA synthesis and qPCR to confirm enrichment of Paneth cells using unique markers (a-defensins).

first: Ken

last: Cadwell


title: Role and function of Sox4 in BCR-ABL1 driven pre-B cells

status: Public on Jul 04 2014

first: Markus

last: Müschen

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

institute: University of Southern California

summary: In order to investigate the function of Sox4 in ALL, we isolated bone marrow cells from Sox4 fl/fl mice and transformed them with BCR-ABL1. In a second transduction the BCR-ABL1 driven pre-B cells were transformed either with CRE-ERT2 or empty vector control (ERT2) and subjected to gene expression analysis.

overall_design: 24h after induction of deletion with 4OHT, total RNA of cells was extracted and subjected to gene expression analysis.

first: Parham

last: Ramezani-Rad


title: DNA methylation sensitivity at detecting cancer in prostate core biopsies [DNA Methylation Profiles]

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

summary: The aim of this study was to analyze critically the potential usefulness of selected DNA methylation biomarkers in supporting conventional histological diagnostic tests for PCa. The selection of potential biomarkers was conducted by microarray profiling of DNA methylation on prostate tissues extracted from the gland after total radical prostatectomy.

overall_design: DNA methylation profiles of 16 prostate samples without carcinoma and 16 matched pairs of samples with and without cancer cells isolated from prostates containing prostate carcinoma

first: Agnieszka

last: Paziewska

first: Michalina

last: Dabrowska

first: Artur

last: Antoniewicz

first: Jakub

last: Dobruch

first: Michal

last: Mikula

first: Dorota

last: Jarosz

first: Lukasz

last: Zapala

first: Andrzej

last: Borowka

first: Jerzy

last: Ostrowski


title: Gene expression Profiling in Follicular Lymphomas

city: omaha

first: Javeed

last: Iqbal

address: 40th street

department: Pathology and Microbiology

institute: University of Nebraska Medical Center

summary:
Follicular lymphoma (FL) is an indolent, but incurable subtype of non-Hodgkin lymphoma. These tumor harbor t (14;18) translocation in at least 90% of patients. Recently, activating EZH2 mutations have been Follicular lymphoma (FL) is an indolent, but incurable subtype of non-Hodgkin lymphoma. These tumor harbor t (14;18) translocation in at least 90% of patients. Recently, activating EZH2 mutations have been found in a significant number of patients with FL.
Gene expression profiling (GEP) was performed to determine differential gene-expression between the EZH2 mutated vs unmutated subgroups in FL.

overall_design: Total RNA extracted from fresh frozen specimens with FL diagnosis were processed for hybridization to Affymetrix HG-U133 plus 2 arrays. To enhance the identification of differential gene expression in FL tumor cells only, FL cases with a high B-cell content (enriched B-cell signature of >2-fold above the mean of the B-cell signature (pan B-cell markers) in the entire FL data set) were chosen for analysis.

first: Shuangping

last: Guo


title: DNA methylation status is more sensitive than gene expression at detecting cancer in prostate core biopsies


title: Transcriptomics of vitamin D treatment effects in Mycobacterium tuberculosis-infected THP-1 cells

city: Berkeley

first: Hugh

last: Salamon

address: 725 Folger Avenue

institute: Knowledge Synthesis Inc.

summary: Previous reports have shown low vitamin D serum levels and polymorphisms in the vitamin D receptor (VDR) to be associated with increased risk for TB. Given that 1α,25-dihydroxyvitamin D3 has a role in lipid metabolism control, we tested whether the link between 1α,25-dihydroxyvitamin D3 and tuberculosis involves macrophage lipid metabolism. Since formation of lipid droplets (LD) is a hallmark of lipid dysregulation in M. tuberculosis-infected macrophages, we measured LD content as a readout of altered lipid metabolism in infected THP-1 cells.  Induction of LD, which peaked by 24 hours post-infection was prevented by addition of 1α,25-dihydroxyvitamin D3 at the time of infection. To investigate the mechanism of  1α,25-dihydroxyvitamin D3  modulation of LD formation, we analyzed the transcriptome of M. tuberculosis-infected THP-1 cells with and without 1α,25-dihydroxyvitamin D3 treatment.

overall_design: THP-1 cells were cultured in 24-well flat bottom plates, pre-treated with 20ng/ml PMA for 24 h, and incubated with M. tuberculosis H37Rv. After 4 hours of infection, cells were washed to remove extracellular bacteria and treated with 100 nM of 1α,25-dihydroxyvitamin D3. THP-1 cells were collected and analyzed at 24h. 3 biological replicates in each of the 4 groups were prepared: Infected, Infected plus 1α,25-dihydroxyvitamin D3, Non-infected, Non-infected plus 1α,25-dihydroxyvitamin D3.

first: Maria

last: Gennaro

first: Karim

last: Lakehal

first: Richard

last: Pine

first: Patricia

last: Soteropoulos

last: Yamaguchi


title: Genome-wide DNA methylation patterns in pancreatic ductal adenocarcinoma (PDAC)

city: Brisbane

first: Katia

last: Nones

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer MEdical Research Institute

summary: Determine methylation pattern in PDAC a genome-wide analysis was performed in a cohort of 167 PDAC and 29 adjacent pancreatic tissues samples using the Infinium 450k methylation arrays (Illumina).

overall_design: 167 pancreatic tumors (PDAC) x 29 adjacent -non tumor samples.

first: Nic

last: Waddell

first: Sarah

last: Song

first: Ann-Marie

last: Patch

first: Karin

last: Kassahn

first: Amber

last: Johns

first: Jianmin

last: Wu

first: David

last: Wood

first: Peter

last: Bailey

last: Miller

first: Suzanne

last: Manning

first: Angelika

last: Christ

first: Craig

last: Nourse

first: Michelle

last: Thomas

first: Clare

last: Watson

first: Mark

last: Pinese

last: Cowley

first: Aldo

last: Scarpa

first: Rita

last: Lawlor

first: John

middle: V

last: Pearson

first: Andrew

last: Biankin

first: Sean

last: Grimmond


title: DNA Methylation Analysis of Systemic Lupus Erythematosus

city: Huntsville

first: Devin

last: Absher

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

summary: This study performed Illumina Methylation450 analysis of CD4+ T-cells, CD19+ B-cells and CD14+ Monocytes from lupus patients and controls.  A validation cohort was further analyzed with the same platform using CD4+ T-cells, CD45RO-CD45RA+ naive T-cells, CD45RO+CD45RA- memory T-cells, and CD25+CD127- regulatory T-cells.

overall_design: SLE v Control comparisions were made within each cell type.  The SLE patient samples are labeled SLEnnnn and the controls Xnnnn.  The cell type CD4, CD14, CD19, Tmem, Treg, Tnaive is appended to each sample ID.


title: Gene expression data from 1833 cells expressing RKIP vs control

city: Chicago

first: Miao

last: Sun

institute: University of Chicago

summary: RKIP regulates human breast tumor metastasis. We use gene expression array analysis to identify genes regulated by RKIP in human breast cancer cells.

overall_design: Total RNAs were extracted from 1833 cells expressing mutant RKIP (S153E-RKIP, a more potent Raf-1 inhibitor) and vector control. Affymetrix GeneChip hgu133plus2.0 Arrays were performed to detail the gene expression and identify the genes regulated by RKIP in human breast cancer cells.

first: Marsha

last: Rosner


title: Differentiation of human limbal-derived induced pluripotent stem cells into limbal-like epithelium

status: Public on Jun 30 2014

city: Los Angeles

first: Jie

last: Tang

address: 8700 Beverly Blvd

institute: Cedars Sinai Medical Center

summary: Limbal epithelial stem cell (LESC) deficiency represents a significant clinical problem especially in bilateral cases. Induced pluripotent stem cells (iPSC) may be a promising source of LESC, allowing standardized and continual propagation and banking. The objective of this study was to generate iPSC from human limbal epithelial cultures and differentiate them back into limbal epithelial cells using substrata mimicking the natural LESC niche. Using Yamanaka’s episomal vectors limbal-derived iPSC were reprogrammed from LESC cultured from donor corneoscleral rims and from human skin fibroblasts. A clone from limbal-derived iPSC expressed stemness markers, had a diploid karyotype, and produced teratomas in nude mice representing three germ layers. Compared to parental LESC, this clone had fewer specific gene methylation changes revealed using the Illumina Infinium Methylation 450k Beadchips than compared to skin fibroblasts. The expression of putative LESC markers was examined by quantitative RT-PCR and immunostaining in limbal-derived and fibroblast-derived iPSC cultured on denuded human amniotic membrane or denuded cornea. Limbal-derived iPSC had markedly stronger expression of PAX6, ABCG2, Np63, keratins 14, 15, 17, and N-cadherin than fibroblast-derived iPSC. On denuded corneas, limbal-derived iPSC showed the expression of differentiated corneal keratins 3 and 12. The data suggest that iPSC differentiation to a desired lineage may be facilitated by their generation from the same tissue. This may be related to preservation of parental tissue epigenetic methylation signatures in iPSC and use of biological substrata similar to the natural niche of parental cells. The data pave the way for generating transplantable LESC from limbal-derived iPSC.

overall_design: Bisulphite converted DNA from the 12 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Dhruv

last: Sareen

first: Mehrnoosh

last: Saghizadeh

first: Vincent

last: Funari

first: Vasu

last: Punj

first: Clive

middle: N

last: Svendsen

first: Alexander

last: Ljubimov


title: Targeted correction of RUNX1 mutation in FPD patient-specific induced pluripotent stem cells rescues megakaryopoietic defects

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

summary: Familial platelet disorder with predisposition to acute myeloid leukemia (FPD/AML) is an autosomal dominant disease of the hematopoietic system, which is caused by heterozygous mutations in RUNX1.  FPD/AML patients have a bleeding disorder characterized by thrombocytopenia with reduced platelet numbers and functions, and a tendency to develop AML. Currently no suitable animal models exist for FPD/AML as Runx1+/- mice and zebrafish do not develop bleeding disorders or leukemia. Here we derived induced pluripotent stem cells (iPSCs) from two patients in a family with FPD/AML, and found that the FPD iPSCs display defects in megakaryocytic differentiation in vitro.  We corrected the RUNX1 mutation in one FPD iPSC line through gene targeting, which led to normalization of megakaryopoiesis of the iPSCs in culture.  Our results demonstrate successful in vitro modeling of FPD with patient-specific iPSCs and confirm that RUNX1 mutations are responsible for megakaryopoietic defects in FPD patients.

overall_design: Here, we derived iPSCs from two FPD/AML patients and demonstrated that these iPSCs have a megakaryopoietic defect in culture.  Importantly we were able to rescue the megakaryopoietic defect by correcting the RUNX1 mutation with a gene targeting strategy enhanced by zinc finger nucleases (ZFNs).  Three independent samples were obtained for each time point.

first: Erika

last: Kwon

first: Abdel

first: P

last: Liu

first: Weiwei

last: Wu


title: 1833 cells expressing RKIP vs control

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


title: Expression data from MTT murine pheochromocytoma tumor sample

city: Bethesda

first: Uma

last: Shankavaram

state: MD

address: 9000 Rockville Pike

department: NCI

institute: NIH

summary:
Genotype specific differences in expression profiles have been evaluated using Gene Chips.
Viable MTT cells were collected at 80% confluence and snap frozen

overall_design: Microarray analysis was performed on MTT tumor cells

first: Alessio

last: Giubellino

first: Karel

last: Pacak


title: Cognitive dysfunction and amyloid beta accumulation are ameliorated by the ingestion of green soybean extract in aged mice

status: Public on Jun 26 2014

city: Akita

first: Tomokazu

last: Konishi

state: Akita

address: Shimoshinjyo Nishi

department: Bioresource Sciences

institute: Akita Prefectural University

summary: The prevention or delay of brain senescence would enhance the quality of life for older persons. We investigated the effects of soybean extracts in senescence-accelerated (SAMP10) mice. This mouse is a model of brain senescence with a short life span, cerebral atrophy and cognitive dysfunction. Mice were fed a diet containing soybean extracts from 1 to 12 months of age. The effects of green and yellow soybean extracts were compared with a control diet without soybean extracts. Cognitive functions were higher in aged mice fed green soybean than age-matched control mice and mice fed yellow soybean. We further investigated transcriptome of the SAMP10 hippocampus indicated that expression levels of 36 genes were significantly higher and 19 genes were lower in mice that ingested green soybean than in mice that ingested yellow soybean. Some of the evidences were reconfirmed by real time PCR analysis; the levels of Cdh1 and Ptgds mRNA were significantly higher and that the level of Aplp1 was significantly lower in aged SAMP10 mice fed green soybean than mice ingested yellow soybean and control mice. Additionally, the amount of amyloid beta 40 and 42 was lower in the insoluble fraction of aged SAMP10 mice fed green soybean than control mice and mice fed yellow soybean, although the levels of amyloid beta 40 and 42 in the soluble fraction were not different. Lipocalin-type prostaglandin D2 synthase (L-PGDS) has been proposed as the endogenous amyloid beta - chaperone, suggesting that amyloid aggregation was lower in mice fed green soybean than control mice and mice fed yellow soybean. These results indicate that the intake of green soybean improved cognitive function in aged mice, and suppressed amyloid beta accumulation. Green soybean might help healthy aging of the brain in older persons.

overall_design: The effect of green and yellow soybean extracts on cognitive function in aged SAMP10 mice. Mice were fed a CE-2 diet containing 3.0% soybean extracts taken from both yellow and green soybean species, from 1 to 12 months of age. Total RNA was extracted from the stored hippocampus for DNA microarray analysis.

first: Keiko

last: Unno


title: ZFX silencing introduced differential gene expression in leukemia cells

city: Jiangsu

first: Yun

last: Zhao

address: No. 1, Shizi Street

institute: Cyrus Tang Hematology Center, Soochow University

summary: Zinc finger protein, X-linked (ZFX) is deregulated in various human leukemia patients. The silence of ZFX leads to the inhibited growth and enhance drug sensitivity of both K562 cells and Jurkat cells. To obtain molecular insights of how ZFX controls the proliferation and drug sensitivity of these cells, we generate the microarray data comparing control and ZFX silenced K562 and Jurkat cells.

overall_design: 3 independent biological replicates of control (shNC) and ZFX silenced (shZFX#1 and shZFX#2) K562 and Jurkat cells have been used for RNA extraction, and equal amount of RNA extracts are pooled together to perform microarray analysis with Affymetrix platform.


title: Gene expression correlated with inattention and hyperactivity/impulsivity rating scales in Tourette syndrome

city: Sacramento

first: Yingfang

last: Tian

institute: University of California at Davis

summary:
Inattention, impulsivity and hyperactivity are the primary behaviors associated with Attention Deficit / Hyperactivity Disorder (ADHD). Previous studies proved that peripheral blood gene expression signature could mirror central nervous system disease.
This study determined if gene expression in blood correlated with inattention, hyperactivity/impulsivity rating scales and/or both in subjects with Tourette syndrome (TS).

overall_design: Whole blood was collected from each subject, and RNA was isolated from the blood of 21 un-medicated TS subjects, gene expression measured on Affymetrix human U133 Plus 2.0 arrays

first: Joan

last: Gunther

first: Lisa

last: Lit

first: Boryana

last: Stamova

first: Xinhua

last: Zhan

first: Dazhi

first: Bradley

last: Ander

first: Glen

last: Jickling

first: Blythe

middle: A

last: Corbett

first: Netty

last: Bos-Veneman

first: Pieter

middle: J

last: Hoekstra

first: Julie

last: Schweitzer

first: Frank

last: Sharp


title: Effects of soy supplementation on gene expression in breast cancer

first: Ashley

middle: Stephen

last: Doane

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: Background   There are conflicting reports on the impact of soy on breast carcinogenesis. This study examines the effects of soy supplementation on breast cancer-related genes and pathways.  Methods   Women (n = 140) with early-stage breast cancer were randomized to soy protein supplementation (n = 70) or  placebo (n = 70) for 7 to 30 days, from diagnosis until surgery. Adherence was determined by plasma isoflavones:  genistein and daidzein. Gene expression changes were evaluated by NanoString inin pre- and post-treatment  tumor tissue. Genome-wide expression analysis was performed on post-treatment tissue. Proliferation (Ki67) and  apoptosis (Cas3) were assessed by immunohistochemistry.  Results   Plasma isoflavones rose in the soy group (two-sided Wilcoxon rank-sum test, P < .001) and did not change in  the placebo group. In paired analysis of pre- and post-treatment samples, 21 genes (out of 202) showed altered  expression (two-sided Student’s t-test, P < .05). Several genes including FANCC and UGT2A1 revealed different  magnitude and direction of expression changes between the two groups (two-sided Student’s t-test, P < .05).  A high-genistein signature consisting of 126 differentially expressed genes was identified from microarray analysis  of tumors. This signature was characterized by overexpression (>2 fold) of cell cycle transcripts, including  those which promote cell proliferation, such as FGFR2, E2F5, BUB1, CCNB2, MYBL2, CDK1, and CDC20 (P < .01).  Soy intake did not result in statistically significant changes in Ki67 or Cas3.  Conclusions   Gene expression associated with soy intake and high plasma genistein define a signature characterized by overexpression  of FGFR2 and genes that drive cell cycle and proliferation pathways. These findings raise the concerns  that in a subset of women soy could adversely affect gene expression in breast cancer.

overall_design: Genome-wide expression analysis was performed on breast cancer tissue from women following treatment with soy (n=28) or placebo (n=23).

first: Moshe

last: Shike

middle: S

first: Raya

last: Khanin

first: Jacqueline

last: Bromberg

first: William

last: Gerald

first: Larry

last: Norton


title: Geminin represses mesendoderm cell fate acquisition in embryoid bodies

city: Saint Louis

first: Kristen

last: Kroll

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

summary: Geminin is a small nucleoprotein that neuralizes ectoderm in the Xenopus embryo. Geminin promotes neural fate acquisition of mouse embryonic stem cells: Geminin knockdown during neural fate acquisition decreased expression of neural precursor cell markers (Pax6, Sox1), while increasing expression of Pitx2, Lefty1 and Cited2, genes involved in formation of the mouse node. Here we differentiated mouse embryonic stem cells into embryoid bodies to study Geminin's ability to repress primitive streak mesendoderm fate acquisition. We used microarrays to define the sets of genes that are regulated by Geminin during cell fate acquisition in embryoid bodies, using Dox-inducible Geminin knockdown or overexpression mouse embryonic stem cell lines.

overall_design: ES cell lines for Geminin over-expression (GemOE) were treated without or with Dox from day 3 to day 5 of EB differentiation and were collected on days 4 or 5 for microarray analysis. Gem knockdown (KD) ES cell lines were treated without or with Dox from day 0 to day 4 of EB differentiation and were collected on day 4 for microarray analysis.

first: Elizabeth

last: Caronna


title: Defining key signaling nodes and therapeutic biomarkers in NF1-mutant cancers

city: Boston

first: Clare

last: Malone

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School -  Brigham Women's Hospital

summary: The NF1 tumor suppressor encodes a RAS GTPase-Activating Protein (RasGAP).  Accordingly, deregulated RAS signaling underlies the pathogenesis of NF1-mutant cancers. However, while various RAS effector pathways have been shown to function in these tumors, it is currently unclear which specific proteins within these broad signaling pathways represent optimal therapeutic targets. Here we identify mTORC1 as the key PI3K pathway component in NF1-mutant nervous system malignancies and conversely show that mTORC2 and AKT are dispensable. We also report that combined mTORC1/MEK inhibition is required to promote tumor regression in animal models, but only when the inhibition of both pathways is sustained. Transcriptional profiling studies were also used to establish a predictive signature of effective mTORC1/MEK inhibition in vivo. Within this signature, we unexpectedly found that the glucose transporter gene, GLUT1, was potently suppressed but only when both pathways were effectively inhibited. Moreover, unlike VHL and LKB1 mutant cancers, reduction of 18F-FDG uptake measured by FDG-PET required the effective suppression of both mTORC1 and MEK. Together these studies identify optimal and sub-optimal therapeutic targets in NF1-mutant malignancies and define a non-invasive means of measuring combined mTORC1/MEK inhibition in vivo, which can be readily incorporated into clinical trials.

overall_design: 8 samples, in duplicate, 2X vehicle, 2X Rapamycin, 2X PD-0325901, 2X Rapamycin/PD-0325901

first: Karen

last: Cichowski


title: The role of PKCtheta in Epithelial to Mesenchymal Transistion

status: Public on Jun 22 2014

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

institute: University of Canberra

summary: Epithelial to mesenchymal transition (EMT) is activated during cancer invasion and metastasis, enriches for cancer stem cells (CSCs), and contributes to therapeutic resistance and disease recurrence. Signal transduction kinases play a pivotal role as chromatin-anchored proteins in eukaryotes. Here we report for the first time that protein kinase C-theta (PKC-θ) regulates EMT by acting as a critical chromatin-anchored switch for inducible genes. Genome-wide transcriptome analysis identifies a unique cohort of inducible PKC-θ-sensitive genes in MCF7 cells stimulated with phorbol ester.

overall_design: MCF7 Cells treated with mock or siRNA against PKCtheta were left unstimulated or stimulated with PMA. No replicates.

first: Anjum

last: Zafar

first: Fan

last: Wu

first: Sudha

last: Rao


title: Expression data from conditional Klf5 knockout Pten-null mouse prostates

status: Public on Jun 21 2014

city: Atlanta

first: Jin-Tang

last: Dong

state: GA

address: 1365C Clifton Rd

department: Department of Hematology & Medical Oncology

institute: Emory University

summary:
KLF5 is a basic transcription factor that regulates multiple biological processes, but its function in tumorigenesis appears contradictory in the current literature, with some studies showing tumor suppressor activity and others showing tumor promoting activity. In this study, we examined the function of Klf5 in prostatic tumorigenesis using mice with prostate specific deletion of Klf5 and Pten, both of which are frequently deleted in human prostate cancer. Histological and molecular analyses demonstrated that when one Pten allele was deleted, which causes mouse intraepithelial neoplasia (mPIN), Klf5 deletion accelerated the emergence and progression of mPIN. When both Pten alleles were deleted, which causes prostate cancer, Klf5 deletion promoted tumor growth and caused more severe morphological and molecular alterations, and homozygous deletion of Klf5 was more effective than hemizygous deletion. Unexpectedly, while Klf5 deletion clearly promoted tumorigenesis in luminal cells, it actually diminished the numbers of Ck5-positive basal cells in the Pten-null tumors. Klf5 deletion also increased the cell proliferation rate in tumors with Pten deletion, which involved extensive activation of the PI3K/AKT and MAPK mitogenic signaling pathways and inactivation of the p15 cell cycle inhibitor. Global gene expression and pathway analyses demonstrated that multiple mechanisms could be responsible for the tumor promoting effect of Klf5 deletion,
We used microarrays to detail the global programme of gene expression of Klf5-wildtype and Klf5-null mouse dorsal prostates under Pten-null context to figure out the differential expression profiling underlying tumorigenesis

overall_design: 4 Klf5-wildtype and 4 Klf5-null mouse (6 months age) dorsal prostates under Pten-null context were used for RNA extraction and hybridization on Affymetrix mouse st 1.0 array

first: Changsheng

last: Xing

first: Xinpei

last: Ci