title: Effects of CPAP Therapy on Leukocyte Gene Expression

status: Public on Dec 31 2013

first: Sina

last: Gharib

summary: Rationale: Obstructive sleep apnea (OSA) has been associated with a number of chronic disorders that may improve with effective therapy. However, the molecular pathways affected by continuous positive airway pressure (CPAP) treatment are largely unknown.  We sought to assess the system-wide consequences of CPAP therapy by transcriptionally profiling peripheral blood leukocytes (PBLs).  Methods: Subjects diagnosed with severe OSA were treated with CPAP, and whole-genome expression measurement of PBLs was performed at baseline and following therapy. We used Gene Set Enrichment Analysis (GSEA) to identify gene sets that were differentially enriched. Network analysis was then applied to identify key drivers of pathways influenced by CPAP.  Results: 18 subjects with severe OSA (apnea hypopnea index ≥ 30 events/hour) underwent CPAP therapy and microarray analysis of their PBLs.  Treatment with CPAP improved AHI, daytime sleepiness and blood pressure but did not affect anthropometric measures. GSEA revealed a number of enriched gene sets, many of which were involved in neoplastic processes and displayed down-regulated expression patterns in response to CPAP. Network analysis identified several densely connected genes that are important modulators of cancer and tumor growth.     Conclusions: Effective therapy of OSA with CPAP is associated with alterations in circulating leukocyte gene expression. Functional enrichment and network analyses highlighted transcriptional suppression in cancer-related pathways suggesting potentially novel mechanisms linking OSA with neoplastic signatures.

overall_design: Total RNA from peripheral blood leukocytes of 18 subjects with severe sleep apnea at baseline and after effective CPAP therapy was hybridized to 36 Affymetrix Genechip Human Gene 1.0 ST microarrays

first: Ashley

last: Seiger

first: Amanda

middle: L

last: Hayes

first: Reena

middle: M

last: Mehra

first: Sanjay

middle: R

last: Patel


title: High-throughput RNA sequencing of methanosarcina grown on methylated sulfur compounds

status: Public on Feb 18 2015

city: Athens

first: He

last: Fu

state: GA

address: 120 Cedar St

department: Microbiology

country: USA

institute: University of Georgia

type: Expression profiling by high throughput sequencing

summary: Methylated sulfur compounds, including dimethylsulfide (DMS), methylmercaptopropionic acid (MMPA) and methylsulfide (MeSH), are well-documented to play roles in global sulfur cycle and climate homeostasis, yet the molecular mechanisms of how they are metabolized by methanogens remain largely uncharacterized. Here, using high-throughtput sequencing of RNA (RNA-seq), we gained insight into how methanogens respond to methylated sulfur compounds at the transcriptional level.

overall_design: The mRNA from wild-type of Methanosarcina acetivorans C2A grown on methylated sulfur compounds were harvested, sequenced and mapped to the genome. Then, we compared RNA-seq profiles to that grown on MeOH in search of unque genes.

first: Petra

last: Kohler

first: William

middle: W

last: Metcalf


title: Expression data from transgenic ERG, GATA1s KI and ERG/GATA1s fetal livers

city: Shoham

first: jasmine

last: Jacob

state: -Select-

address: haChevel 33

country: Israel

institute: Sheba Medical Center at Tel HaShomer

summary: DS children have a 500-fold increased risk for developing acute megakaryoblastic leukemia (AMKL). Around 10% of DS newborns have a transient myeloproliferative disorder (TMD) that resolves spontaneously. Somatic mutations acquired during fetal hematopoiesis in the GATA1 transcription factor are detected in megakaryoblasts from all the DS TMDs or AMKLs. GATA1 is an X chromosome transcription factor essential for the development of multiple hematopoietic lineages. Loss of GATA1 results in embryonic lethality due to severe anemia. The GATA1 mutations result in the expression of a shorter isoform, GATA1s. Replacement of GATA1 with GATA1s causes transient proliferation of immature fetal megakaryocytic progenitors. The Hsa21 ETS transcription factor, ERG, is expressed in megakaryocytes and erythrocytes and is involved in several types of cancer. Mutation in GATA1 gene leading to expression of the short isoform (GATA1s) that occurs on the background of trisomy 21 is regarded as one of the driving forces for megakaryocytic expansion observed in DS fetal livers. ERG, which is located on chromosome 21, is considered one of the leading candidates to cooperate with GATA1 mutation in the generation of DS AMKL. To study the in vivo cooperation between ERG and GATA1 isoforms, we crossed the ERG transgenic mice with the GATA1s Knock-in mice (GATA null background). We found that males expressing both ERG and the short isoform of GATA1(GATA1s) died in uterus between embryonic days E121/2 and E141/2.We studied erythropoiesis and megakaryopoiesis in fetal livers from the different genotypes generated from our cross.

overall_design: We used expression array to study the specific interaction of ERG with the different GATA1 isoforms in fetal livers from E121/2 and E141/2 and identify ERG, GATA1 and GATA1s target genes by comparing sets of genes that are activated or repressed in the presence of ERG and the two isoforms of GATA1.

first: Yehudit

last: Birger

first: Liat

last: Goldberg

first: Timothy

last: Chlon

first: Benjamin

last: Goldenson

first: Inna

last: Muler

first: Ginette

last: Schiby

first: Jasmin

last: Jacob-Hirsch

first: Gideon

last: Rechavi

first: John

middle: D

last: Crispino

first: Shai


title: Gene expression analysis of airway epithelial cells exposed to flagellin via RNA-seq

status: Public on Dec 01 2014

city: Seattle

first: Sina

last: Gharib

state: WA

address: 850 Republican St.

department: Medicine

institute: University of Washington

summary: Airway epithelial cells (AEC) are critical components of the inflammatory and immune response during exposure to pathogens. AECs in monolayer culture and differentiated epithelial cells in air-liquid interface (ALI) represent two distinct and commonly used in vitro models, yet differences in their response to pathogens have not been investigated. In this study, we compared the transcriptional effects of flagellin on AECs in monolayer culture versus ALI culture using exon microarrays and RNAsequencing. We found that AECs cultured in monolayer and ALI have strikingly different transcriptional states at baseline. When challenged with flagellin, monolayer AEC cultures greatly increased transcription of numerous genes mapping to wounding response, immunity and inflammatory response. In contrast, AECs in ALI culture had an unexpectedly muted response to flagellin, both in number of genes expressed and relative enrichment of inflammatory and immune pathways. In conclusion, In vitro culturing methods have a dramatic effect on the transcriptional profile of AECs at baseline and after stimulation with flagellin. These differences suggest that epithelial responses to pathogen challenges are distinctly different in culture models of intact and injured epithelium.

overall_design: A total of eight independent RNAseq experiments were conducted. Four RNAseq experiments (n = 2 unstimulated, n = 2 stimulated with flagellin) were performed using AECs grown in monolayer. Four RNAseq experiments (n =2 unstimulated, n = 2 stimulated with flagellin) were conducted using AECs grown in ALI cultures

first: Kyong-Hee

last: Kim


title: Expression data of leukemia samples taken from transgenic ERG mice

status: Public on Aug 13 2013

summary: The Ets transcription factor, ERG, plays a central role in definitive hematopoiesis and its overexpression in acute myeloid leukemia is associated with a stem cell signature and bad prognosis. However, little is known about the underlying mechanism by which ERG causes leukemia. Therefore we sought to identify ERG targets that participate in development of leukemia by integration of expression arrays and Chromatin immunoprecipitation.

overall_design: Bone marrow was collected from three transgenic ERG mice harboring a myeloid leukemia and twelve wild type mice. Nine wild type bone marrow samples were lineage depleted and pooled into 3 samples (each one consisting of three lineage negative wild type bone marrows). The resulting 9 samples were used for RNA extraction and hybridization on affymetrix microarrays.

first: Marloes

last: Tijssen

first: Rebecca

last: Hannah

first: Sarah

middle: J

last: Kinston

first: Judith

last: Schütte

first: Dominik

last: Beck

first: Kathy

last: Knezevic

first: Jasmine

first: Anat

last: Biran

first: Yoel

last: Kloog

first: Guido

last: Marcucci

first: Clara

last: Bloomfield

first: Peter

last: Aplan

middle: E

last: Pimanda

first: Berthold

last: Göttgens

last: Izraeli


title: Epigenome analysis of ischemic stroke patients

status: Public on Aug 19 2015

city: Barcelona

first: Carolina

last: Soriano-Tarraga

state: Barcelona

address: Calle Doctor Aiguader 88

department: Department of Neurology

country: Spain

institute: Institut Hospital del Mar d’Investigacions Mèdiques (IMIM).Hospital del Mar

summary:
We performed a genome-wide methylation study in whole-blood DNA from 404 ischemic stroke patient cohort, distributed across 3 ischemic stroke subtypes: Large-artery atherosclerosis (n=132), Small-artery disease (n=141) and Cardio embolic (n=127) . Illumina HumanMethylation450 BeadChip array was used to measure DNA methylation in CpG sites.

We performed a genome-wide methylation study in whole-blood DNA from 185 ischemic stroke patient cohort. Illumina HumanMethylation450 BeadChip array was used to measure DNA methylation in CpG sites.

overall_design:
Bisulphite converted DNA from the 404 samples were hybridised to the Illumina HumanMethylation450 BeadChip array
Bisulphite converted DNA from the additional 185 samples [replication cohort] were hybridised to the Illumina HumanMethylation450 BeadChip array

Please note that, for the replication cohort [GSM3026613-GSM3026797];
The 'Average Beta normalized data' is provided in the betas_normalized_meneas_185.txt & pval_detection_meneas_185.txt
Raw 'unmethylated and methylated signal intensities' data is provided in meth_raw_meneas_185.txt & unmeth_raw_meneas_185.txt, and idat files.

first: Jaume

last: Roquer

first: Jordi

last: Jimenez-Conde


title: Time-dependent toxic effects of dietary TCDD on juvenile zebrafish

city: Clemson

first: Qing

last: Liu

state: SC

address: Jordan Hall

department: Biological Sciences

institute: Clemson University

summary: Juvenile zebrafish were fed Biodiet starter (4% body weight per day) for 42 d with TCDD added at 0 ppb, 0.1 ppb, 1 ppb, 10 ppb or 100 ppb. Fish were collected, sexed, weighed and length measured at 0, 7, 14, 28 or 42 d for TCDD assessment, histopathologic and microarray analysis. Microarray experiments were conducted using 0 and 100 ppb-TCDD treated male and female sexed zebrafish at 7, 14, 28 and 42 d. NimbleGen Gene Expression 12X135K zebrafish microarrays and One-Color DNA labeling Kit (NimbleGen, WI) were used for genome-wide expression analysis of TCDD-treated zebrafish. TCDD accumulated in a dose- and time-dependent manner and 100 ppb TCDD caused TCDD accumulation in female (15.49 ppb) and male (18.04 ppb) fish at 28 d post exposure. TCDD caused multiple lesions in liver, kidney, intestine and ovary of zebrafish and functional dysregulation such as depletion of glycogen in liver, retrobulbar edema, degeneration of neurosensory epithelium, underdevelopment of intestine, and diminution in the fraction of ovarian follicles containing vitellogenic oocytes. At 42d, no mature female fish were observed.

overall_design: Juvenile wild-type zebrafish (stock originally purchased from EkkWill Waterlife Resources, Ruskin, FL) (0.16 g, 2.10 cm) were were reared in 28 °C dechlorinated, filtered municipal water (DFMW) in the NIEHS Children's Environmental Health Sciences Core Center (CEHSC) animal facility.  Zebrafish were fed Biodiet starter (4% body weight per day) for 42 d with TCDD added at 0 ppb, 0.1 ppb, 1 ppb, 10 ppb or 100 ppb (nominal concentration, ethanol used as vehicle). Fish were collected, sexed, weighed and length measured at 0, 7, 14, 28 or 42 d for TCDD assessment and microarray analysis. Microarray experiments were conducted using 0 and 100 ppb-TCDD treated male and female sexed zebrafish at 7, 14, 28 and 42 d. Zebrafish were randomly selected from each group for the microarray experiments. NimbleGen Gene Expression 12X135K zebrafish microarrays and One-Color DNA labeling Kit (NimbleGen, WI) were used for genome-wide expression analysis of TCDD-treated zebrafish. Differential expression analysis was performed with Bayesian Estimation of Temporal Regulation (BETR) method using Multiple Array Viewer (MeV, Dana-Farber Cancer Institute, MA) software, version 4.8.1.

first: Chun-Yuan

last: Huang

last: Jiang

first: Giles

last: Goetz

first: Reinhold

last: Hutz

last: Tonellato

first: Michael

last: Carvan


title: Identification of human nephron progenitors capable of generation of kidney structures and functional repair of chronic renal disease

status: Public on Jul 23 2013

first: jasmine

last: Jacob

summary: NCAM1+ subpopulation of fetal human kidneyl cells are nephron progenitors

overall_design: We used microarrays to detail the global programme of gene expression in the NCAM1+ sub-population in comparison to total culture.

first: Orit

last: Harari-Steinberg

first: Sally

last: Metsuyanim

first: Dorit

last: Omer

first: Yehudit

last: Gnatek

first: Rotem

last: Gershon

first: Sara

last: Pri-Chen

first: Derya

last: Ozdemir

first: Yaniv

last: Lerenthal

first: Herzel

last: Ben-Hur

first: Zvi

last: Vaknin

first: David

middle: F

last: Schneider

first: Bruce

last: Aronow

first: Ronald

middle: S

last: Goldstein

last: Hohenstein

first: Benjamin

last: Dekel


title: Gene expression analysis of airway epithelial cells exposed to flagellin via RNA-seq and microarray

first: Sina

last: Gharib

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

overall_design: Refer to individual Series


title: Characteristic molecular and proteomic signatures of drug-induced liver injury in a rat model

status: Public on Aug 16 2013

city: Suwon, Korea

first: Jung Woo

last: Eun

state: Korea

address: Department of Gastroenterology

country: South Korea

institute: Ajou University of Korea

summary: we assessed characteristic molecular and proteomic signatures in rat liver treated with drugs (pyrazinamide, ranitidine, enalapril, carbamazepine, and chlorpromazine) that are known to cause DILI in humans.

overall_design: In the present study, we assessed the characteristic gene expression signature for DILI in a rat model. Rats were administered representative drugs that are already known to induce DILI in humans and transcriptomic changes in rat liver were analyzed. The representative drugs, which induce three types (hepatocellular, mixed, and cholestatic) of DILI, that were used in this study were pyrazinamide (PZA, 150~1500 mg/kg), ranitidine (RAN, 209.5~2095 mg/kg), enalapril (ENA, 148.65~1486.5 mg/kg), carbamazepine (CBZ, 97.85~978.5 mg/kg), and chlorpromazine (CPZ, 7.1~71 mg/kg).

first: Jung

first: Suk

last: Nam


title: Global regulation of alternative splicing by adenosine deaminase acting on RNA (ADAR) [expression]

status: Public on Jun 15 2013

first: jasmine

last: Jacob

summary: Alternative mRNA splicing is a major mechanism for gene regulation and transcriptome diversity. Despite the extent of the phenomenon, the regulation and specificity of the splicing machinery are only partially understood. Adenosine-to-inosine (A-to-I) RNA editing of pre-mRNA by ADAR enzymes has been linked to splicing regulation in several cases. Here we used bioinformatics approaches, RNA-seq and exon-specific microarray of ADAR knockdown cells to globally examine how ADAR and its A-to-I RNA editing activity influence alternative mRNA splicing. Although A-to-I RNA editing only rarely targets canonical splicing acceptor, donor, and branch sites, it was found to affect splicing regulatory elements (SREs) within exons. Cassette exons were found to be significantly enriched with A-to-I RNA editing sites compared with constitutive exons. RNA-seq and exon-specific microarray revealed that ADAR knockdown in hepatocarcinoma and myelogenous leukemia cell lines leads to global changes in gene expression, with hundreds of genes changing their splicing patterns in both cell lines. This global change in splicing pattern cannot be explained by putative editing sites alone. Genes showing significant changes in their splicing pattern are frequently involved in RNA processing and splicing activity. Analysis of recently published RNA-seq data from glioblastoma cell lines showed similar results. Our global analysis reveals that ADAR plays a major role in splicing regulation. Although direct editing of the splicing motifs does occur, we suggest it is not likely to be the primary mechanism for ADAR-mediated regulation of alternative splicing. Rather, this regulation is achieved by modulating trans-acting factors involved in the splicing machinery.

overall_design: HepG2 and K562 cell lines were stably transfected with plasmids containing siRNA designed to specifically knock down ADAR expression (ADAR KD). This in order to examine how ADAR affects alternative splicing globally.

first: Oz

last: Solomon

first: Shirely

last: Oren

first: Michal

last: Safran

first: Naamit

last: Deshet-Unger

first: Pinchas

last: Akiva

first: Jasmine

last: Jacob-Hirsch

first: Karen

last: Cesarkas

first: Reut

last: Kabesa

first: Ninette

last: Amariglio

first: Ron

last: Unger

first: Gideon

last: Rechavi

first: Eran

last: Eyal


title: Global regulation of alternative splicing by adenosine deaminase acting on RNA (ADAR)

status: Public on Jun 17 2013


title: Differential expression of keratin genes in regenerating digit of C57Bl/6 versus MRL/MpJ mice

status: Public on Jul 01 2013

city: Tampa

first: Chia-Ho

last: Cheng

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

summary: Expression of genes encoding multiple keratin- and keratin-associated proteins varies between C57BL/6 and MRL/MpJ (superhealer) mice following digit amputation.  We characterized changes in gene expression by microarray analysis of regenerating digits in these mice at various timepoints following surgical amputation.  These changes were validated by quantitative rtPCR analyses.

overall_design: In this dataset, we include the expression data obtained from regenerating mouse digits following surgical amputation as well unamputated digits (total 24 samples). These data are used to obtain genes that are differentially expressed between the two groups of digits.

first: John

last: Leferovich

first: Xiang-Ming

last: Zhang

first: Khamilia

last: Bedelbaeva

first: Dmitri

last: Gourevitch

first: Cathy

last: Basson

first: Ellen

last: Heber-Katz

first: Kenneth

middle: A

last: Marx


title: Toxic effects of dietary methylmercury (MeHg) on young adult zebrafish

status: Public on Jun 01 2013

first: Qing

last: Liu

summary: Three-month old zebrafish were fed Biodiet starter (4% body weight per day) with MeHg added at 0, 0.5, 5 and 50 ppm for six weeks. Atomic absorption spectrometry was applied to measure the level of MeHg in the whole fish body. Zebrafish at six weeks were sampled from each group for gene expression analysis by NimbleGen Gene Expression 12X135K zebrafish microarrays. MeHg-exposed trout and zebrafish did not show overt signs of toxicity, nor were significant differences seen in mortality, length, mass, or condition factor. The chronic accumulation of total Hg in zebrafish exhibited dose- and time-dependent patterns. The dysregulated genes in MeHg-treated fish have multiple functional annotations, such as involving metabolism, cellular development, ion binding, stress response, transcriptional regulation, and apoptotic pathways. These results show that numerous molecular pathways involved in the growth and development of multiple organ systems are disrupted by exposure to moderate levels of dietary MeHg.  The dysregulated genes will be selected by further analysis and used as biomarkers for MeHg exposure in aquatic environments. This study will allow us to assess the potential impacts of low-level exposure to environmental MeHg in the food chain and on the health of humans and animals.

overall_design: Three-month old zebrafish (Danio rerio, average body 0.149 g) were fed Biodiet Starter (Bio-Oregon) 4% of body weight per day with MeHg added at 0ppm, 0.5ppm, 5ppm and 50ppm (with ethanol as vehicle). Fish at six weeks were sampled from each group for gene expression analysis. Three fish from each treatment group were used for microarray experiments. Total RNA from individual fish was isolated using Trizol reagent  (Invitrogen) and further purified using the RNeasy MiniElute cleanup kit (Qiagen). Double-strand cDNA was synthesized from 10ug total RNA of individual fish by using Superscript Double-Stranded cDNA synthesis Kit (Invitrogen). ). One ug double strand DNA was labeled with Cy3 using One-Color DNA labeling Kit (NimbleGen), then hybridized to NimbleGen 12X135K array. The arrays were scanned at 2um on a NimbleGen MS200 scanner with auto-gain adjust.  The TIFF images were gridded and extracted using NimbleScan v. 2.6. Expression data were normalized using the Robust Multichip Average (RMA) algorithm.

first: Matthew

last: Rise

first: Giles

last: Goetz

first: Niladri

last: Basu

first: Reinhold

last: Hutz

first: Peter

last: Tonellato

first: Michael

last: Carvan


title: Gene expression analysis of rat glomerular parietal epithelial cells

status: Public on Aug 01 2014

first: Sina

last: Gharib

summary: Very little is known about the function of glomerular parietal epithelial cells  (PECs). In this study, we performed genome-wide expression analysis on PEC-enriched capsulated vs. PEC-deprived decapsulated rat glomeruli to determine the transcriptional state of PECs under normal conditions. We identified hundreds of differentially expressed genes that mapped to distinct biologic modules including development, tight junction, ion transport, and metabolic processes. Since developmental programs were highly enriched in PECs, we characterized several of their candidate members at the protein level. Collectively, our findings confirm that PECs are multifaceted cells and help define their diverse functional repertoire.

overall_design: We developed a sequential sieving methodology to selectively isolate capsulated (PEC-enriched) glomeruli from un-capsulated (PEC-deprived) glomeruli in rats. Three samples were obtained for each preparation. Total RNA was isolated and its integrity confirmed via Bioanalyzer 2100. Each sample (n =6) was hybridized to an Affymetrix Rat GeneChip 1.0ST microarray.

first: Jeffrey

last: Pippin


title: Toxic effects of dietary methylmercury (MeHg) on rainbow trout and zebrafish

sample_organism:
Danio rerio
Oncorhynchus mykiss

platform_organism:
Danio rerio
Osmerus mordax
Oncorhynchus mykiss
Salmo salar
Coregonus clupeaformis
Oncorhynchus tshawytscha


title: Epigenome analysis of alcohol consumption in lymphocyte cell (LC) samples

status: Public on Sep 24 2014

city: Iowa City

first: Robert

middle: Alan

last: Philibert

state: IA

address: 500 Newton Rd

institute: University of Iowa

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profiling of individuals consuming alcohol and controls in LC samples. Individuals consuming alcohol were profiled at time of intake (T1) into treatment facility and four weeks into treatment (T2). Controls were profiled once. The Illumina Infinium 450k Human DNA Methylation BeadChip v1.0 was used to obtain DNA methylation profiles across 485,577 CpGs in LC samples. Samples included 33 case subjects at T1, 26 case subjects at T2 and 33 controls.

overall_design: Bisulfite-converted DNA from 92 samples were hybridized to the Illumina Infinium 450k Human Methylation BeadChip v1.0.


title: IQGAP1 Scaffold-Kinase Interaction Blockade Selectively Targets Ras-MAP Kinase Driven Tumors

status: Public on Apr 01 2013

city: Stanford

first: Douglas

last: Porter

state: CA

address: 269 Campus Drive

department: Dermatology

institute: Stanford

summary: MAPK scaffolds, such as IQGAP1, assemble pathway kinases together to effect signal transmission and disrupting scaffold function therefore offers a potentially orthogonal approach to MAPK cascade inhibition. Consistent with this possibility, we observed an IQGAP1 requirement in Ras-driven tumorigenesis in mouse and human tissue. Delivery of the IQGAP1 WW peptide sequence that mediates Erk1/4 binding, moreover, disrupted IQGAP1-Erk1/2 interactions, abolished Ras/Raf-driven tumorigenesis, bypassed acquired resistance to the B-Raf inhibitor vemurafinib (PLX- 4032), and acts as a systemically deliverable therapeutic to significantly increase lifespan of tumor bearing mice. Scaffold-kinase interaction blockade (SKIB) acts by a mechanism distinct from direct kinase inhibition and represents a strategy to target over-active oncogenic kinase cascades in cancer.

overall_design:
Gene expression profiling: Fragmented cRNA was hybridized to the Mouse Gene 1.0 ST Array (Affymetrix).
Iqgap1 wild-type and Iqgap1 knockout mouse treated with topical 4OHT for 0 days and 6 days days are compared.

first: Katherine

last: Jameson

first: Pawel

middle: K

last: Mazur

first: Ashley

last: Zehnder

first: Jiajing

first: Brian

last: Zarnegar

first: Julien

last: Sage

first: Paul

last: Khavari


title: Activation of a NCAM1 expressing progenitor cell population in adult human kidney epithelia

first: jasmine

last: Jacob

summary: NCAM1+ subpopulation of adult human kidney epithelial cells (hKEpC) can be specifically activated in vitro to stem-like cells that de-differentiate and recapitulate embryogenesis.

overall_design: We used microarrays to detail the global programme of gene expression in the NCAM1+ sub-population in comparison to NCAM1-.

first: Ella

last: Buzhor

first: Orit

last: Harari-Steinberg

first: Dorit

last: Omer

first: Einav

last: Vax

first: Zohar

last: Dotan

first: Tsahi

last: Noiman

first: Ronald

last: Goldstein

first: Benjamin

last: Dekel


title: Toxic effects of dietary methylmercury (MeHg) on juvenile rainbow trout

first: Qing

last: Liu

summary: Juvenile rainbow trout were fed Biodiet starter (4% body weight per day) with MeHg added at 0, 0.5, 5 and 50 ppm for six weeks. Atomic absorption spectrometry was applied to measure the level of MeHg in the whole fish body. Trout at six weeks were sampled from each group for gene expression analysis by cGRASP 16K cDNA microarrays. MeHg-exposed rainbow trout did not show overt signs of toxicity, nor were significant differences seen in mortality, length, mass, or condition factor. The chronic accumulation of total Hg in trout exhibited dose- and time-dependent patterns. The dysregulated genes have multiple functional annotations, such as involving metabolism, cellular development, ion binding and homeostasis, stress response, immune response, transcriptional regulation, hemolytic development, and apoptotic pathways. These results show that numerous molecular pathways involved in the growth and development of multiple organ systems are disrupted by exposure to moderate levels of dietary MeHg.  The dysregulated genes will be selected by further analysis and used as biomarkers for MeHg exposure in aquatic environments.

platform_organism:
Osmerus mordax
Oncorhynchus mykiss
Salmo salar
Coregonus clupeaformis
Oncorhynchus tshawytscha

overall_design: Juvenile rainbow trout (Oncorhynchus mykiss, average body 0.118g) were fed Biodiet Starter (Bio-Oregon) 4% of body weight per day with MeHg added at 0ppm, 0.5ppm, 5ppm and 50ppm (with ethanol as vehicle). Trout at six weeks were sampled from each group for gene expression analysis. Total RNA from individual fish was isolated using Trizol reagent  (Invitrogen) and further purified using the RNeasy MiniElute cleanup kit (Qiagen).RNA of ten fish from control group was pooled as a common reference, and total RNA of five individual fish from control and MeHg-treated groups were randomly selected for microarray experiment.  cDNA was synthesized from 1 μg pooled RNA using SuperScript II Reverse Transcriptase (Invitrogen) according to the manufacturer’s protocol. The common reference cDNA targets were labeled with Cy3 and cDNA of individual fish from each group was labeled with Cy5 using the Array 900 Expression Array Detection kit (Genisphere) according to the manufacturer’s protocol. The labeled cDNA targets were hybridized to cGRASP 16K cDNA microarrays at 50°C for 16 hours. Following the first hybridization, arrays were washed in 2X SSC, 0.2% SDS solution at 50 C 1 x 15 min, 2X SSC 1 x 15 min at room temperature, then 0.2X SSC for 1 x 15 min at room temperature. The fluorescent labeling hybridization (50 C for 4hr) utilized the Genisphere 3DNA Cy3 and Cy5 capture reagents in formamide hybridization buffer. The slides were washed as described above, and the arrays were dried by centrifugation. were scanned using the ScanArray Express (PerkinElmer) at 10 um resolution. The TIFF images of arrays were generated with ScanArray Express software and the intensities of raw data of two-channel arrays were collected by the ImaGene 6.0 (BioDiscovery). Statistical analysis of microarray data was performed using scripts written in R language with LIMMA package.

first: Matthew

last: Rise

first: Giles

last: Goetz

first: Niladri

last: Basu

first: Reinhold

last: Hutz

first: Peter

last: Tonellato

first: Michael

last: Carvan


title: Global regulation of alternative splicing by adenosine deaminase acting on RNA (ADAR) [RNA-seq]

first: Oz

last: Solomon

first: Shirely

last: Oren

first: Michal

last: Safran

first: Naamit

last: Deshet-Unger

first: Pinchas

last: Akiva

first: Jasmine

last: Jacob-Hirsch

first: Karen

last: Cesarkas

first: Reut

last: Kabesa

first: Ninette

last: Amariglio

first: Ron

last: Unger

first: Gideon

last: Rechavi

first: Eran

last: Eyal


title: Global methylation analysis identifies PITX2 as an upstream regulator of the androgen receptor and IGF-I receptor genes in prostate cancer

status: Public on Dec 12 2012

first: jasmine

last: Jacob

summary: The insulin-like growth factor-I (IGF-IR) and androgen (AR) receptors are important players in prostate cancer biology. Functional interactions between the IGF-I and androgen signaling pathways seem to have crucial roles in the progression of prostate cancer from early (benign) to advanced (metastatic) stages. DNA methylation is a major epigenetic alteration affecting gene expression. Hypermethylation of tumor suppressor promoters is a frequent event in human cancer, leading to inactivation and repression of specific genes. The aim of the present study was to identify the entire set of methylated genes (“methylome”) in a cellular model that replicates prostate cancer progression.

overall_design: The methylation profiles of the P69 (early stage, benign) and M12 (advanced stage, metastatic) prostate cancer cell lines were established by treating cells with the demethylating agent 5-Aza-2’-deoxycytidine (5-Aza) followed by DNA microarray analysis. Comparative genome-wide methylation analyses of 5-Aza-treated versus untreated cells identified 297 genes overexpressed in P69 and 191 genes overexpressed in M12 cells. One hundred and two genes were upregulated in both benign and metastatic cell lines. In addition, our analyses identified the PITX2 gene as a master regulator upstream of the AR and IGF-IR genes.

first: Hagit

last: Schayek

first: Itay

last: Bentov

first: Choh

last: Yeung

first: Chand

last: Khanna

first: Lee

middle: H

last: Helman

first: Stephen

last: Plymate

first: Haim

last: Werner


title: Transcriptome sequencing of Prunus mume for different tissues.

status: Public on Dec 27 2012

city: Shenzhen

first: Zhijun

last: Zheng

address: #11 Building 2/F│Beishan Industrial Zone│Yantian District

country: China

institute: BGI

summary: We have sequenced a wild Prunus mume and constructed a reference sequence for this genome. In order to improve quality of gene models, RNA samples of five tissues (bud, leaf, root, stem, fruit) were extracted from the Prunus mume. To investigate tissue specific expression using the reference genome assembly and annotated genes, we extracted RNA samples of different tissues and conducted transcriptome sequencing and DEG analysis.

overall_design: Five RNA pools were created corresponding to different tissues of the Prunus mume.

first: Qixiang

last: Zhang

first: Wenbin

last: Chen

first: Lidan

last: Sun


title: Time-course in rice leaves of the temperature shift experiment

status: Public on Dec 07 2012

city: Tsukuba

first: Takeshi

last: Izawa

state: Ibaraki

address: 2-1-2 Kannondai

country: Japan

institute: National Institute of Agrobiological Sciences

summary: Time-course transcriptional profiling of rice leaf of the temperature shift experiment in a growth chamber. This experiment was performed to validate the results of field transcriptomic modeling.

overall_design: Rice leaves (cv. Norin8) were collected at 2:00 and 14:00 on the day -1, 2, 4 and 6 from the temperature shift (diurnal cycle temperature condition to continuous temperature condition). Two biological replicates for each sampling time point.

first: Atsushi

last: Nagano


title: ACTL6a Enforces the Epidermal Progenitor State by Suppressing SWI/SNF-Dependent Induction of KLF4

status: Public on Nov 30 2012

first: Douglas

last: Porter

summary: Somatic progenitors suppress differentiation to maintain tissue self-renewal. While epigenetic regulators of DNA and histone modifications can support such repression, a role for nuclear actin-like proteins is unclear. In epidermis, ACTL6a/BAF53A was found enriched in progenitors and down-regulated during differentiation. Conditional ACTL6a deletion abolished epidermal self-renewal and induced terminal differentiation, whereas ectopically expressed ACTL6a suppressed differentiation. Among known activators of epidermal differentiation, KLF4 was found to control 227 genes also regulated by ACTL6a. ACTL6a loss upregulated KLF4 and its target genes, effects that were blocked by KLF4 depletion. Among multiple ACTL6a-interacting epigenetic regulators, the SWI/SNF complex was required for KLF4 activation and differentiation. In progenitors, ACTL6a loss led to enhanced SWI/SNF binding to the promoters of KLF4 and other differentiation genes. ACTL6a thus maintains the undifferentiated progenitor state, in part by suppressing SWI/SNF complex-enabled induction of KLF4.

overall_design: Gene expression analysis: To identify the gene set controlled by ACTL6a in human keratinocyte. Total RNA was isolated in biologic duplicate from cells with ACTL6a loss as compared to controls, and hybridized to Affymetrix HG-U133 2.0 Plus arrays.

first: Xiaomin

last: Bao

first: Jiong

last: Tang

first: Vanessa

last: Lopaz-Pajares

first: Shiying

last: Tao

first: Kun

last: Qu

first: Gerald

last: Crabtree

first: Paul

last: Khavari


title: Transcriptional analysis of injured airway epithelial cells in Mmp7-null and wildtype mice

status: Public on Nov 01 2012

first: Sina

last: Gharib

summary: Matrix metalloproteinase 7 (MMP7) is expressed at low levels in intact, normal airways by non-mucous-producing cells, including ciliated cells. In response to injury and infection, MMP7 expression is quickly and markedly upregulated and functions to regulate wound repair and various mucosal immune processes. We evaluated the global transcriptional response of airway epithelial cells from wild type and Mmp7-null mice cultured at an air-liquid interface. A common injury response was seen in both genotypes with up-regulation of genes associated with proliferation and migration. Analysis of differentially expressed genes between genotypes after injury revealed enrichment of functional categories associated with inflammation, cilia and differentiation. Because these analyses suggested MMP7 regulated ciliogenesis, we evaluated the recovery of the airway epithelium in wild type and Mmp7-null mice in vivo after naphthalene injury. These studies identified a new role for MMP7 in attenuating ciliogenesis during wound repair.

overall_design: A total of 16 air-liquid interface cultures of mouse airway epithelial cells were studied under four conditions: 1. Mmp7-null, no injury (n = 4); 2. Mmp7-null, scratch injury (n = 4); 3. Wildtype, no injury (n =4); 4. Wiltype, scratch injury (n = 4).

first: William

last: Altemeier

first: Laura

last: Van Winkle

first: Charles

middle: C

last: Plopper

first: Saundra

middle: Y

last: Schlesinger

first: Catherine

last: Buell

first: Rena

last: Brauer

last: Parks

first: Peter


title: Rice leaves in the field in 2009

first: Takeshi

last: Izawa

summary: Time-course transcriptional profiling of rice leaf in the field in 2009. This experiment was performed to validate the results of field transcriptomic modeling.  Using 461 field transcriptome data obtained in 2008 (GSE36040; GSE36042; GSE36043; GSE36044; GSE18685) and the corresponding meteorologicla dara, we perfomred statistical modeling of transcriptome.

overall_design: Rice leaves (Norin8 vs. osgi) in the paddy field were collected on Aug. 10 - 12, 24 - 25, 31, Oct. 8 - 9 in 2009.

first: Atsushi

last: Nagano


title: Control of Somatic Tissue Differentiation by the Long Non-Coding RNA TINCR

status: Public on Oct 10 2012

first: Douglas

last: Porter

type: Non-coding RNA profiling by high throughput sequencing


title: Visceral fat trancriptome in obstructive sleep apnea

status: Public on Sep 01 2012

summary:
Rationale: Obstructive sleep apnea (OSA) has been associated with metabolic dysregulation and systemic inflammation. This may be due to pathophysiologic effects of OSA on visceral adipose tissue. We sought to assess the transcriptional consequences of OSA on adipocytes by utilizing pathway-focused analyses.
Methods: Patients scheduled to undergo ventral hernia repair surgery were recruited to wear a portable home sleep monitor for two nights prior to surgery. Visceral fat biopsies were obtained intra-operatively. RNA was extracted and whole-genome expression profiling was performed. Gene Set Enrichment Analysis (GSEA) was used to identify curated gene sets that were differentially enriched in OSA subjects. Network analysis was applied to a select set of highly enriched pathways.
Results: 10 patients with OSA and 8 control subjects were recruited. There were no differences in age, gender, body mass index between the two groups, but the OSA subjects had a significantly higher respiratory disturbance index (19.2 vs. 0.6, P-value 0.05) and worse hypoxemia (minimum oxygen saturation 79.7% vs. 87.8%, P-value < 0.001). GSEA identified a number of gene sets up-regulated in adipose tissue of OSA patients including the pro-inflammatory NF-κB pathway and the proteolytic ubiquitin/proteasome module. A critical metabolic pathway, the peroxisome proliferator-activated receptor (PPAR), was down-regulated in subjects with OSA. Network analysis linked members of these modules together and identified regulatory hubs.
Conclusions: OSA is associated with alterations in visceral fat gene expression. Pathway-based network analysis highlighted perturbations in several key pathways whose coordinated interactions may contribute to the metabolic dysregulation observed in this complex disorder.

overall_design: Total RNA from visceral fat of 18 subjects (10 OSA, 8 Control) was hybridized to 18 Affymetrix Genechip Human Gene 1.0 ST microarrays.

first: Amanda

last: Hayes

first: Michael

last: Rosen

first: Sanjay

last: Patel


title: Rice leaves

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

overall_design: Refer to individual Series


title: Identification of Proteins Binding Coding and Non-coding Human RNAs using Protein Microarrays

summary: We describe a refined approach to identify new human RNA-protein interactions. In vitro transcribed labeled RNA is bound to ~9,400 human recombinant proteins spotted on protein microarrays. This approach identified 137 RNA-protein interactions for 10 human coding and non-coding RNAs, including an interaction between Staufen 1 protein and TP53 mRNA that promoted the latter’s stability. RNA hybridization to protein microarrays allows rapid identification of human RNA-protein interactions on a large scale.

overall_design: Sense and antisense strands for 10 RNA transcripts representing protein coding RNAs TP53, HRAS, MYC, BCL2 and non-coding sequences PWRN1, SOX2OT, OCC1, IGF2RNC, lncRBM26 and DLEU1 were in vitro transcribed, labeled with Cy5 and independently hybridized on human protein microarrays. The labeling process was optimized in order to achieve ~ 3 pmol dye per every microgram RNA with average efficacy of 1 dye molecule for approximately every 850 bp RNA to minimally influence RNA native structure and at the same time yield in signal intensities that were readily visualized.

first: Dan

last: Webster


title: Oncogenic Potential of SIRT7 in Human Hepatocellular Carcinoma and its Regulation by the Tumor Suppressors MiR-125a-5p and MiR-125b

status: Public on Sep 30 2012

first: Jung Woo

last: Eun

summary: Sirtuins (SIRT) are NAD-dependent protein deacteylases and function in cellular metabolism, stress resistance, proliferation and disease. For SIRT7, a role in ribosomal gene transcription is proposed, but its function in cancer is currently unknown. In this study, we showed that SIRT7 expression was up-regulated in a large cohort of human hepatocellular carcinoma (HCC) patients, and that high expression of SIRT7 was associated with poor prognosis of HCC patients. Notably, inactivation of SIRT7 by siRNA suppressed tumor cell growth and caused G1/S cell cycle arrest in liver cancer cells. This treatment restored p21WAF1/Cip1 activity, induced Beclin-1 and autophagic gene expression and repressed cyclin D1. To explore mechanisms in SIRT7 regulation, microRNA (miRNA) profiling was carried out. This identified five significantly down-regulated miRNAs in HCC. Bioinformatic analysis of target sites and ectopic expression in HCC cells evidenced miR-125a-5p and miR-125b to suppress SIRT7 and cyclin D1 expression and to induce p21WAF1/Cip1-dependent G1 cell cycle arrest. Furthermore, treatment of HCC cells with 5-aza-2’-deoxycytidine or ectopic expression of wild-type but not mutated p53 restored miR-125a-5p and miR-125b expression and inhibited tumor cell growth to suggest their regulation by promoter methylation and p53 activity. To evidence clinical significance of these findings, mutations in the DNA binding domain of p53 and promoter methylation of miR-125b were investigated. Four out of nine patients with induced SIRT7 carried mutations in p53 gene and one patient showed hypermethylation of miR-125b promoter region. Conclusion: Our findings suggest that oncogenic potential of SIRT in hepatocarcinogenesis and that a regulatory loop is proposed whereby SIRT7 inhibits transcriptional activation of p21WAF1/Cip1 via repression of miR-125a-5p and miR-125b. This makes SIRT7 a promising target in cancer therapy.

overall_design: miRNA expression profiling of 8 normal liver and 16 HCC tissues was performed using GenoExplorer Microarray platform. 10 µg of total RNA was isolated from normal liver and HCC tissues and then labeled and hybridized to a to microRNA chip for analysis under optimized conditions. The arrays with hybridized targets were scanned using an Axon scanner and the scanned images were analyzed using GenePix® Pro 5.0 software (Axon Instruments) and spots of poor quality determined by visual inspection were also removed from further analysis. The resulting data, the average of 3 mean fluorescence signal intensities for each probe, collected from each array was submitted to the GenePlex 3.0 (Istech Inc. Seoul, Korea) database. Data were normalized using the method of quantile normalization and class-specific filtering.

first: JeongKyu

last: Kim

first: JiHeon

last: Noh

first: KwangHwa

last: Jung

first: JungWoo

first: HyunJin

last: Bae

first: MinGyu

first: YoungGyoon

last: Chang

first: Qingyu

last: Shen

first: WonSang

last: Park

first: JungYoung

last: Lee

first: Jürgen

last: Borlak

first: SukWoo

last: Nam


title: ADAR1 regulates melanoma progression via miRNAs biogenesis

status: Public on Aug 31 2012

first: jasmine

last: Jacob

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

summary: Aberrant RNA-editing was observed in several human tumors, but its significance is mostly unknown. Here we show that ADAR1, a ubiquitous RNA-editing enzyme, is commonly lost in metastatic melanoma cells and specimens. Experimental ADAR1 silencing significantly alters melanoma cell morphology, facilitates proliferation and cell-cycle, and increases the tumorigenicity in-vivo. A series of ADAR1 truncation mutants establishes a novel RNA-editing-independent role for ADAR1 in controlling the nuclear and cytoplasmic processing steps of miRNA biogenesis. Altered expression of ADAR1-controled miRNAs accounts for the observed phenotype. We show that the oncogenic miR-17-5p endogenously regulates ADAR1 expression and that its genomic sequence is frequently amplified in melanoma to overexpress the mature miR-17-5p form. ADAR1 and miR-17-5p are ubiquitously expressed, suggesting the generality of this mechanism.

platform_organism:
Homo sapiens
synthetic construct

overall_design: Melanoma cell line expressing low ADAR1 levels (ADAR1-Knockdown) using shRNA technique were selected  for RNA extraction and hybridization on Affymetrix microarrays. We sought to examine the alterations in the genes and microRNA expression profile in the manipulated cell system, due to ADAR1 possible involvement cancer development. To that end, we selected ADAR1-knockdown (ADAR1-KD) cells that demonstrated an enhanced aggressive phenotype both in vivo and in vitro as compared to the control cells (Control).

first: Yael

last: Nemlich

first: Eyal

last: Greenberg

first: Rona

last: Ortenberg

first: Michal

last: Besser

first: Iris

last: Barshack

first: Jasmine

last: Jacob-Hirsch

last: Safran

first: Victor

middle: G

last: Prieto

first: Nitin

last: Chakravarti

first: Lynn

last: Duncan

first: David

last: Kallenberg

first: Dorothy

last: Bennett

first: Ninette

last: Amariglio

first: Menashe

last: Bar-Eli

first: Jacob

last: Schachter

first: Gideon

last: Rechavi

first: Gal

last: Markel


title: Control of Somatic Tissue Differentiation by the Long Non-Coding RNA TINCR (HTS)

first: Douglas

last: Porter

summary: Several of the thousands of human long non-coding RNAs (lncRNAs) have been functionally characterized; however, potential roles for lncRNAs in somatic tissue differentiation remain poorly understood. Here we show that a 3.7kb lncRNA, terminal differentiation-induced ncRNA (TINCR), controls human epidermal differentiation by a post-transcriptional mechanism. TINCR is required for high mRNA abundance of key differentiation genes, many of which are mutated in human skin diseases, including FLG, LOR, ALOXE3, ALOX12B, ABCA12, CASP14 and ELOVL3. TINCR-deficient epidermis lacked terminal differentiation ultrastructure, including keratohyalin granules and intact lamellar bodies. Genome-scale RNA interactome analysis revealed that TINCR interacts with a suite of differentiation mRNAs. TINCR-mRNA interaction occurs through a 25 nucleotide “TINCR box” motif which is strongly enriched in interacting mRNAs and required for TINCR binding. A high-throughput screen to analyze TINCR binding capacity to ~9,400 human recombinant proteins revealed direct binding of TINCR RNA to the Staufen1 (STAU1) protein. STAU1-deficient tissue recapitulated the impaired differentiation seen with TINCR depletion. Loss of UPF1 and UPF2, both of which are required for STAU1-mediated RNA decay (SMD), however, lacked differentiation impacts. Instead, the TINCR/STAU1 complex seems to mediate stabilization of differentiation mRNAs, such as KRT80. These data identify TINCR as a key lncRNA required for somatic tissue differentiation, which occurs through inducible lncRNA binding to differentiation mRNAs to ensure their expression.

overall_design: Examination of TINCR-binding RNAs using two independent pools of TINCR-targeting oligos

first: Chu

last: Ci

first: Kun

last: Qu


title: Control of Somatic Tissue Differentiation by the Long Non-Coding RNA TINCR (array)

summary: Several of the thousands of human long non-coding RNAs (lncRNAs) have been functionally characterized; however, potential roles  for lncRNAs in somatic tissue differentiation remain poorly understood. Here we show that a 3.7kb lncRNA,  terminal differentiation-induced  ncRNA (TINCR), controls human epidermal differentiation by a post-transcriptional mechanism. TINCR is required for high mRNA abundance of key differentiation genes, many of which are mutated in human skin diseases, including  FLG, LOR, ALOXE3, ALOX12B, ABCA12, CASP14 and ELOVL3. TINCR-deficient epidermis lacked terminal differentiation ultrastructure, including keratohyalin granules and intact lamellar bodies. Genome-scale RNA interactome analysis revealed that TINCR interacts with a suite of differentiation mRNAs. TINCR-mRNA interaction occurs through a 25 nucleotide “TINCR box” motif which is strongly enriched in interacting mRNAs \and required for TINCR binding. A high-throughput screen to analyze TINCR binding capacity to ~9,400 human recombinant proteins revealed direct binding of TINCR RNA to the Staufen1 (STAU1) protein. STAU1-deficient tissue recapitulated the impaired differentiation seen with TINCR depletion. Loss of UPF1 and UPF2, both of which are required for STAU1-mediated RNA decay (SMD), however, lacked differentiation impacts. Instead, the TINCR/STAU1 complex seems to mediate stabilization of differentiation mRNAs, such as KRT80. These data identify TINCR as a key lncRNA required for somatic tissue differentiation, which occurs through inducible lncRNA binding to differentiation mRNAs to ensure their expression.

overall_design: Gene expression analysis: To establish a gene expression signature for regenerated human epidermis depleted of TINCR, as well as STAU1, total RNA was isolated in biologic duplicate from organotypic cultures of cells with a non-targeting siRNA, or an siRNA to the gene of interest. This RNA was processed and then hybridized to Affymetrix HG-U133 2.0 Plus arrays.

first: Markus

last: Kretz

first: Dan

last: Webster

first: Ci

last: Chu

first: Zurab

last: Siprashvili

first: Ashley

last: Zehnder

first: Carolyn

last: Lee

first: Ross

last: Flockhart

first: Abigail

last: Groff

first: Jennifer

last: Chow

first: Danielle

last: Johnston

first: Grace

last: Kim

first: Robert

last: Spitale

first: Ryan

last: Flynn

middle: X

last: Zheng

first: Subhadra

last: Aiyer

first: Arjun

last: Raj

first: John

last: Rinn

first: Howard

last: Chang

first: Paul

last: Khavari


title: Disrupted transcripitonal network in ΔNp63 AEC tissue model [gene expression]

status: Public on Jun 18 2012

first: Douglas

last: Porter

summary: The transcriptional basis for disrupted epidermal differentiation arising from TP63 AEC mutations remains to be elucidated.  Here we present an organotypic model of AEC dysfunction that phenocopies differentiation defects observed in AEC patient skin.  Transcriptional analysis of model AEC tissue revealed impaired induction of differentiation regulators, including OVOL1, GRHL3, KLF4, PRDM1 and ZNF750.  Genome wide binding analyses of TP63 during epidermal differentiation showed direct binding of OVOL1, GRHL3, and ZNF750 promoters suggesting AEC mutants prevent normal activation of these targets by direct transcriptional interference.  Remarkably, exogenous ZNF750 restores impaired epidermal differentiation caused by AEC mutation.  Thus, repression of ZNF750 is central to disrupted epidermal differentiation in model AEC tissue.

overall_design: Gene expression analysis: To establish a differentiation signature for primary human keratinocytes, with p63i-depleted, and ΔNp63α AEC mutants overexpressed, total RNA was isolated in biologic duplicate from cells in different conditions and hybridized to Affymetrix HG-U133 2.0 Plus arrays.

first: Brian

last: Zarnegar

first: Dan

last: Webster

first: Brook

middle: V

last: Hunt

first: Karen

last: Yan

first: Kun

last: Qu

first: David

last: Berk

first: George

middle: L

last: Sen


title: Oncogenic BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration [Affymetrix]

status: Public on Apr 28 2012

summary: Most cancer genomics papers to date have focused on aberrations in genomic DNA and protein-coding transcripts. However, around 50% of transcripts have no coding potential and may exist as non-coding RNA. We performed RNA-seq in BRAFv600e melanoma skin cancer and on melanocytes over-expressing oncogenic BRAF to catalog transcriptome remodeling. We discovered that BRAF regulates expression of 1027 protein coding transcripts, 39 annotated lncRNAs and 70 novel transcripts. Many of the novel transcripts are lncRNAs. We used an indepenedent dataset to interrogate our novel transcripts and found that the novel lncRNA BANCR is a BRAF-regulated lncRNA recurrently upregulated in melanoma. Knockdown of BANCR impairs melanoma cell migration.

overall_design: To identify genes regulated by BANCR we perrformed shRNA knockdown experiments using 2 independent shRNA sequences in col829 melanoma cells. RNA was then extracted for microarray analysis.

first: Ross

last: Flockhart

first: Joanna

last: Kovalski

first: Nicholas

last: Mascarenhas

first: Markus

last: Kretz


title: Oncogenic BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration


title: Disrupted transcriptional network in ΔNp63 AEC tissue model [ChIP-Seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ChIP-Seq analysis: Examination of p63 binding in proliferating and differentiating human keratinocytes

middle: R

first: Geoge


title: Disrupted transcripitonal network in ΔNp63 AEC tissue model


title: Oncogenic BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration [HT-seq]

overall_design: Whole transcriptome RNA-seq followed assembly to Refseq/Gencode and de novo transcript assembly. RNA-seq performed on: 2 BRAFv600e melanomas, melanocytes+RFP control and melanocytes + BRAFv600e. We discovered protein-coding transcripts, annotated ncRNAs and novel transcripts (including lncRNAs) regulated by BRAFv600e also coordinately expressed in melanoma.


title: Identification of Oncogenic Potential of SIRT7 and Its Regulatory MicroRNAs in Liver Tumorigenesis

status: Public on Mar 01 2012

first: Jung Woo

last: Eun

summary: To investigate the specific roles of SIRT7 in the development of HCC, we employed large-scale gene expression analysis to identify the molecular signature that may affect enabling characteristics of cancer cells. Differentially expressed genes were analyzed on the Hep3B cells transfected with SIRT7 shRNAs, and recapitulated molecular signatures that related to hallmarks of cancer.

overall_design: For each of the experimental conditions, total RNA was extracted from three independent sets of the corresponding cell lines using TRIzol Reagent (Invitrogen), followed by clean up on Ambion columns (Illumina Total-Prep RNA Amplification Kit, Ambion). For each experimental condition, an RNA pool was then obtained by mixing equal quantities of total RNA from each of the three independent RNA extractions. Biotin-labelled cRNA targets were synthesized starting from 1.5 µg of total RNA. Double stranded cDNA synthesis was performed with Illumina® TotalPrep RNA Amplification Kit (Ambion), and biotin-UTP-labelled antisense RNA was transcribed in vitro using Ambion’s Kit. All steps of the labelling protocol were performed as suggested by Ambion (http://www.ambion.com/techlib/prot/ fm_IL1791.pdf). The size and the accuracy of quantitation of targets were checked by Experion (Bio-rad Laboratories., Hercules, CA) electrophoresis system, prior to and after cRNA purification. After purification, targets were diluted in hybridization buffer at a concentration of 240 ng/µl, and hybridization was allowed to proceed at 58°C for 20 h. For microarray analysis, the Illumina HumanHT-12 v4 Sentrix Expression BeadChip was used (Illumina, San Diego, CA). Hybridization of labelled cRNA to the BeadChip, washing, and scanning were performed according to the Illumina BeadStation 500× manual. The array signal was developed via 10-min incubation with streptavidin-Cy3. The HumanHT-12 v4 Sentrix Expression BeadChip was washed and subsequently dried via centrifugation for 4 min at a setting of 275 xg. The arrays were scanned on the Illumina BeadArray reader, a confocal-type imaging system with 532 (Cy3) nm laser illumination. Data from each sample was extracted with Genome Studio software (Illumina) using default parameters and then analyzed using GenPlex 3.0.

first: Jeong

last: Kim

first: Ji

last: Noh

first: Jung

middle: W

first: Kwang

last: Jung

first: Hyun

last: Bae

first: Hong

last: Xie

first: Min

first: Young

first: Won

last: Park

last: Lee

first: Suk

last: Nam


title: Aberrant Regulation of HDAC2 Mediates Proliferation of Hepatocellular Carcinoma Cells by Deregulating Expression of G1/S Cell Cycle Proteins

summary: To investigate the specific roles of HDAC2 in the development of liver cancer, we employed large-scale gene expression analysis to identify the molecular signature that may affect enabling characteristics of cancer cells. Differentially expressed genes were analyzed on the Hep3B cells transfected with HDAC2 shRNAs, and recapitulated molecular signatures that related to hallmarks of cancer.

overall_design: With the aim of identifying changes in gene expression following gene knockdown of HDAC2, we performed expression profiling in shRNA expression vector-transfected Hep3B cells, and compared the results to those obtained from vector-transfected Hep3B cells.

first: Ji-Heon

first: Kwang-Hwa

first: Jeong-Kyu

first: Jung-Woo

first: Hyun-Jin

first: Hong-Jian

first: Young-Gyoon

last: Chang

first: Min-Gyu

first: Won-Sang

first: Jung-Young

first: Suk-Woo


title: Role of SIRT1 in human hepatocellular carcinoma

first: Jung Woo

summary: To investigate the specific roles of SIRT1 in the development of hepatocellular carcinoma, we employed large-scale gene expression analysis to identify the molecular signature that may affect enabling characteristics of cancer cells. Differentially expressed genes were analyzed on the SNU-182 cells transfected with SIRT1 siRNA and recapitulated molecular signatures that related to hallmarks of cancer.

overall_design: SIRT1 expression in hepatocellular carcinoma was analyzed by RT-PCR and western blot. RNA interference-mediated protein knockdown method was used to investigate oncogenic potential of SIRT1 in hepatocelluar carcinoma


title: Mapping the Transcriptional Landscape of Autoimmune Targeted Tissues: Transient Alterations in the Extracellular Milieu Precede Innate and Delayed Adaptive Immune Responses in Spontaneous Experimental Autoimmunity.

status: Public on Mar 10 2012

city: Gainesville

first: Ammon

middle: B

last: Peck

state: FL

address: 1945 SW 16th Avenue

department: Department of Infectious Diseases & Pathology

institute: University of Florida

summary:
The C57BL/6.NOD-Aec1Aec2 mouse is a model for primary Sjögren’s syndrome and was constructed by introducing two genetic intervals derived from the NOD mouse that confers Sjögren’s syndrome (SjS)-like disease in SjS-non-susceptible C57BL/6 mice.
To define the chronological interrelationships of biological themes associated with progression from pre- to sub-clinical to overt spontaneous experimental SjS-like disease involving the extracellular milieu (EM) of the salivary glands, we carried out a study utilizing microarray technology in which the parental C57BL/6J mouse was used as the healthy control strain. A bioinformatics-based data analysis methodology designed for comprehensive visualization of global datasets between C57BL/6J and C57BL/6.NOD-Aec1Aec2 mice has permitted a definition of the molecular changes that correlate with onset of stomatitis sicca (xerostomia) in the SjS-susceptible mice.  The transcriptome data set of C57BL/6J permitted identification of normal physiological activity.

overall_design: The study was designed to define the changing gene expression profiles within the salivary glands of C57BL/6.NOD-Aec1Aec2 mice at multiple time points representing a pre-disease stage (4 weeks), the early pre-clinical stage (8 weeks), the initial influx of leukocytes into the salivary glands (12 weeks), and the early clinical phase of autoimmunity (16 weeks) to characterize the influence of the extracellular milieu on early development of disease.  Because the C57BL/6.NOD-Aec1Aec2 mouse was derived from the C57BL/6J line, C57BL/6J mice were used as the comparative healthy controls.  This comparison permitted the identification of disease-associated gene expressions by subtracting out normal physiological processes. This present study represents the C57BL/6J healthy control mice. Series GSE15640 includes the data for the C57BL/6.NOD-Aec1Aec2 mice.

first: Nicolas

last: Delaleu

first: Ashok

last: Sharma

first: Cuong

middle: Q

last: Nguyen

first: Richard

last: McIndoe

first: Jin-Xiong

last: She


title: Suppression of Progenitor Differentiation Requires the Long Non-Coding RNA ANCR [lincRNA 391k Tiling Array V2]

status: Public on Jan 01 2012

first: Douglas

last: Porter

type: Non-coding RNA profiling by genome tiling array

summary: Long non-coding RNAs (lncRNAs) regulate diverse processes, yet a potential role for lncRNAs in maintaining the undifferentiated state in somatic tissue progenitor cells remains uncharacterized. We used transcriptome sequencing and tiling arrays to compare lncRNA expression in epidermal progenitor populations versus differentiating cells. We identified ANCR (anti differentiation ncRNA) as an 855 bp lncRNA down-regulated during differentiation. Depleting ANCR in progenitor-containing populations, without any other stimuli, led to rapid differentiation gene induction. In epidermis, ANCR loss abolished the normal exclusion of differentiation from the progenitor-containing compartment. The ANCR lncRNA is thus required to enforce the undifferentiated cell state within epidermis.

overall_design: Custom tiling arrays designed to assay the intergenic space corresponding to regions of H3K4me3-H3K36me3 domains (Khalil et al., 2009) were used to assay changes in RNA expression of putative lncRNAs. RNA from progenitor populations and terminally differentiated populations of human keratinocytes, adipocytes, and osteoblasts were hybridized to these arrays and differential expression was assessed.

first: Dan

middle: E

last: Webster


title: ZNF750 Drives Terminal Epidermal Differentiation via Induction of Klf4

status: Public on Feb 15 2012

summary: Disrupted differentiation is a hallmark of numerous diseases, which in epidermis alone impact >25% of the population. In a search for dominant mediators of differentiation, we defined a requirement for the ZNF750 nuclear protein in terminal epidermal differentiation. ZNF750 controlled genes mutated in numerous human skin diseases, including FLG, LOR, LCE3B, ALOXE3, and SPINK5. ZNF750 potently induced progenitor differentiation via an evolutionarily conserved C2H2 zinc finger motif. The epidermal master regulator, p63, bound the ZNF750 promoter and was necessary for its induction. ZNF750 restored differentiation to p63-deficient tissue, suggesting it acts downstream of p63. A search for functionally important ZNF750 targets via analysis of ZNF750-regulated genes identified KLF4, a transcription factor that activates late epidermal differentiation genes. ZNF750 binds the Klf4 promoter and controls its expression. ZNF750 thus provides a direct link between a tissue-specifying factor, p63, and an effector of terminal differentiation, Klf4, and represents a potential future target for disorders of this process.

overall_design: Gene expression analysis: To establish a differentiation signature for primary human keratinocytes, with ZNF750-depleted, and Klf4-depleted, total RNA was isolated in biologic duplicate from cells in different conditions and hybridized to Affymetrix HG-U133 2.0 Plus arrays.

first: George

last: Sen

first: Lisa

middle: D

last: Boxer

first: Rose

last: Tran

first: Kun

last: Qu

first: Brian

middle: J

last: Zarnegar

first: Danielle

last: Johnston

first: Zurab

last: Siprashvili

first: Paul

last: Khavari


title: Transcriptome profiling of epidermal differentiation

status: Public on Feb 02 2012

summary: The aim of this study was to establish a deeply sequenced transcriptome at multiple timepoints during the differentiation of human epidermal keratinocytes from the progenitor state (d0).  These transcriptomes were then assembled in order to discover novel genes and transcriptional events that are dynamically regulated during terminal differentiation of a human somatic tissue.

overall_design: Paired-end RNA sequencing was performed on primary human keratinocytes at three timepoints during calcium-induced epidermal differentiation.


title: Suppression of Progenitor Differentiation Requires the Long Non-Coding RNA ANCR [HG-U133_Plus_2]

overall_design: Gene expression analysis: To establish the global gene regulatory effects of ANCR depletion, total RNA was isolated in biologic duplicate from cells in different conditions and hybridized to Affymetrix HG-U133 2.0 Plus arrays.


title: Suppression of Progenitor Differentiation Requires the Long Non-Coding RNA ANCR

overall_design: Refer to individual Series


title: The Effect of liver regeneration on hESCs transplanted into SCID mice

status: Public on Dec 31 2011

first: jasmine

last: Jacob

summary: A source of functioning hepatocytes for liver cell transplantation and liver support is in need. hESCs , when transplanted, generally form teratomas. We studied capacity of hESCs to differentiate to hepatocyte like cells under the effect of in vivo liver regeneration. In SCID-Beige mice hepatocyte replication peaked 48 hours after CCl4 injection; 24 hours earlier 106  hESCs or EBs at different stages of differentiation were transplanted into the spleen. Comparisons were made to teratomas formed in the hind limb of untreated animals. RT-PCR and gene microarray were used for liver and human specific markers. Immunohistochemistry to AFP,AAT, ALB, HEP-PAR I AND CK-18,19 were performed. EBs formed a single large teratoma in the spleen and small teratomas in the liver. Expression of PCR- identified liver specific markers was greater in the spleen than in the liver. Adult hepatocyte specific markers were expressed in the hind limb teratoma excised after 7 weeks. When late EBs were transplanted before CCl4 exposure, no teratomas formed. Rather, an abundance of probably undifferentiated ectodermal origin cells presented. In this descriptive study, transplanted early human EBs formed teratomas that differed in size and molecular markers. Within teratomas, the degree of maturation into hepatocytes correlated better with the time duration in vivo than with growth stimulation. Late EBs formed non differentiated ectodermal cells only in a regenerative microenvironment.

overall_design: 4 samples were analyzed. Clean mouse liver used as neg. control. Mouse liver injected with CCl4 and transplanted with late Ebs, tumor was not observed. Two mouse livers injected with CCl4 and transplanted with late Ebs, tumor was observed.

first: Ilanit

last: Boyango

first: Ella

last: Veitsman

first: Vladislav

last: Tsiperson

first: Elene

last: Axelman

first: Sharon

last: Gerecht-Nir

first: Michal

last: Amit

first: Joseph

last: Itskovitz-Eldor

first: Gidon

last: Shoshany

first: Yaacov

last: Baruch


title: HDAC6 functions as a tumor suppressor by activating caspase-independent autophagic cell death in hepatocarcinogenesis

first: Jung Woo

last: Eun

summary: To investigate the specific roles of HDAC6 in the development of liver cancer, we employed large-scale gene expression analysis to identify the molecular signature that may affect enabling characteristics of cancer cells. Differentially expressed genes were analyzed on the Hep3B cells transfected with empty mock or pcDNA_HDAC6, and recapitulated molecular signatures that related to hallmarks of cancer.

overall_design: To characterize the biological effects of HDAC6 on liver cancer, large-scale gene expression analysis to identify molecular signature was performed on the Hep3B cells.

first: Kwang-Hwa

last: Jung

first: Ji-Heon

last: Noh

first: Jeong-Kyu

last: Kim

first: Jung-Woo

first: Hyun-Jin

last: Bae

first: Hong-Jian

last: Xie

first: Young-Gyoon

last: Chang

first: Min-Gyu

first: Won-Sang

last: Park

first: Jung-Young

last: Lee

first: Suk-Woo

last: Nam


title: Gene expression profiles of AML derived stem cells: similarity to hematopoietic stem cells

status: Public on Dec 01 2011

first: jasmine

last: Jacob

summary: Tumors contain a fraction of cancer stem cells that maintain the  propagation of the disease. The CD34CD38_ cells, isolated  from acute myeloid leukemia (AML), were shown to be enriched  leukemic stem cells (LSC). We isolated the CD34CD38_ cell  fraction from AML and compared their gene expression profiles  to the CD34CD38 cell fraction, using microarrays. We  found 409 genes that were at least twofold over- or underexpressed  between the two cell populations. These include  underexpression of DNA repair, signal transduction and cell  cycle genes, consistent with the relative quiescence of stem  cells, and chromosomal aberrations and mutations of leukemic  cells. Comparison of the LSC expression data to that of normal  hematopoietic stem cells (HSC) revealed that 34% of the  modulated genes are shared by both LSC and HSC, supporting  the suggestion that the LSC originated within the HSC progenitors.  We focused on the Notch pathway since Jagged-2, a  Notch ligand was found to be overexpressed in the LSC  samples. We show that DAPT, an inhibitor of gamma-secretase,  a protease that is involved in Jagged and Notch signaling,  inhibits LSC growth in colony formation assays. Identification  of additional genes that regulate LSC self-renewal may provide  new targets for therapy.

overall_design: Microarrays were used to compare the gene expression patterns between AML CD34+CD38- cells and AML CD34+CD38+

first: Hila

last: Gal

first: Ninette

last: Amariglio

first: Luba

last: Trakhtenbrot

first: Jasmine

last: Jacob-Hirsch

first: Ofer

last: Margalit

first: A

last: Avigdor

first: Aharon

last: Nagler

first: Sigal

last: Tavor

first: L

last: Ein-Dor

first: T

last: Lapidot

first: Eitan

last: Domani

first: Gideon

last: Rechavi

first: David

last: Givol


title: A novel way for enriching human melanoma precursor cells to identify cellular targets for antineoplastic therapy

status: Public on Dec 29 2011

summary:
Metastatic melanoma is difficult to treat and is resistant to most current therapies. We hypothesized that stem cell related pathways may play a role in melanoma growth since stem cells and cancer cells share essential properties.  Lately, the ABC transporter, ABCB5, as well as Cripto-1, CD20, CD133 and ABCG2  were used to isolate tumorigenic cells. Melanoma cells expressing MDR1 (ABCB1) were found in our lab to be enriched with ABCB5, Nanog, and Oct3/4 expression and were characterized by increased self-renewal capacity and anchorage independence. Melanoma significant heterogeneity was further demonstrated by Quintana et al. who found high prevalence of melanoma initiating cells when implanted into severely immunocompromised mice. Therefore, we took a more general approach in order to unravel pathways that are important for self-renewal and tumorigenicity of melanoma. We enriched for melanoma precursor cells (MPC) using culture conditions shown to enrich for normal melanocyte precursors. MPCs expressed higher levels of nanog and Oct3/4, as well as ABCB1 (MDR1) and ABCB5. Microarray analysis revealed deregulation of genes related to development, invasion, and cell cycle, in addition to upregulation of genes involved in Wnt signaling such as DVL3, DKK1, ID3, JAG1 and Wnt receptor, FZD7. We focused on Wnt signaling and found enrichment of FZD7+ cells in MPCs. Furthermore, FZD7+ cells co-expressed MDR1 and were enriched in highly tumorigenic xenograft parts when tested in mice. Inhibition of the Wnt pathway using secreted frizzled related protein-1 (sFRP1), resulted in attenuation of melanoma proliferation in a dose dependent manner demonstrating the important role of the Wnt pathway in melanoma growth and suggesting this pathway as a target for rational therapy. The canonical Wnt/beta-catenin pathway was not activated in MPC, as revealed using the Tcf Reporter assay. In contrast, we found increased of phosphorylated CAMKII, suggesting activation of the non-canonical Wnt pathway. Our data indicate that precursors within the melanoma tumor may acquire increased survival abilities that should be therapeutically targeted. In particular, we found that the non canonical wnt pathway and the wnt receptor FZD7 play a role in melanoma proliferation and tumorigenicity.
We used specialized culture conditions that were found to enrich for normal melanoblasts, the precursors of melanocytes [7]. We found previously that these conditions result in a typical dedifferentiated unpigmented phenotype of melanoma cells in addition to enrichment of self-renewing cells [2]. Further characterization of these precursor cultures prepared from 6 human metastatic melanoma lesions revealed increased expression of stemness genes such as nanog and Oct3/4, as well as two recently reported melanoma precursor markers, MDR1 and ABCB5. Consistent with the normal melanoblast cultures we found increased expression of the melanoblast marker POU3F2 (BRN2, DCT). In contrast, the expression of MITF, a melanocyte differentiation marker was reduced by 85% in MPCs when compared with the primary culture (Figure 1a, relative expression of MPC vs. cells obtained from the same patient and cultured in regular conditions). Cell cycle analysis excluded death of differentiated cells as the cause of the precursor enrichment, as no apoptosis was evident (Figure 1b, c). Interestingly, there was an increase in S phase cells, indicating that these cells are undergoing divisions. Similarly, Wang et al. reported that CD133+ glioma cells have higher percentage of S phase cells as compared to CD133- cells [8]. We concluded that these culture conditions cause dedifferentiation of melanocytes in addition to enrichment by increased divisions of melanoma precursor cells. Therefore, we defined these cells as melanoma precursor cells (MPC).

overall_design: To reveal pathways of self-renewal in melanoma we have used two single cell clones that were prepared from primary human melanoma cultures obtained from a primary lesion. These cell clones differed in the self-renewal capacity (in the limiting dilution assay) and in their morphology: high self-renewal/polygonal vs low self-renewal/spindle shaped. We compared the two cell types described above, cultured in either regular RPMI-based media or culture conditions developed to enrich for normal melanocytic precursors (Cook AL, Donatien PD, Smith AG, Murphy M, Jones MK, et al. (2003) Human melanoblasts in culture: expression of BRN2 and synergistic regulation by fibroblast growth factor-2, stem cell factor, and endothelin-3. J Invest Dermatol 121: 1150-1159.), designated MPC (melanoma precursor cells) conditions, for two weeks.

first: Gilmor

middle: I

last: Keshet

first: Liraz

last: Shenhav

first: Karen

last: Cesarkas

first: Itamar

last: Goldstein

first: Orit

last: Itzhaki

first: Noa

last: Stettner

first: Alon

last: Harmelin

first: Avraham

last: Treves

first: Jacob

last: Schachter


title: Deletion of HDAC1 induces caspase-independent autophagic cell death and mitotic defect in Hep3B cells

status: Public on Aug 17 2011

first: Jung Woo

last: Eun

summary: HDAC1 aberrantly over expressed in HCC and it was considered as an oncogene gene in HCC development. So we want to analyze in greater detail of the genes regulated by HDAC1 using microarray assay.

overall_design: Hep3B RNA was extracted after transfected by HDAC1 shRNA or scrambled shRNA (Mock) for 72hr. For microarray analysis of gene expression unpon depletion of HDAC1, 0.5 μg of total RNA was used to make biotin-labeled cRNA using the Ambion Illumina cRNA amplification and labeling kit according to manufacturers’ instructions (Ambion, Austin, TX)

first: Hong-Jian

last: Xie

first: Ji-Heon

last: Noh

first: Jeong-Kyu

last: Kim

first: Kwan-Hwa

last: Jung

first: Jung-Woo

first: Hyun-Jin

last: Bae

first: Jung-Young

last: Lee

first: Won-Sang

last: Park

first: Suk-Woo

last: Nam


title: TMPRSS2:ERG promotes invasiveness and epithelial to mesenchymal transition in prostate cancer model

status: Public on Dec 30 2010

first: jasmine

last: Jacob

summary:
Recently, a frequent chromosomal aberration fusing Androgen regulated TMPRSS2 promoter and the ERG gene (T/ERG) was discovered in prostate cancer. Several studies demonstrated cooperation between the T/ERG and other defective pathways in cancer progression however, the biological mechanism by which the T/ERG operates is yet to be determined. Using immortalized prostate epithelial cells (EP) model we were able to show that EP with the combination of androgen receptor(AR) and T/ERG(EP-AR T/ERG cell line) demonstrate an Epithelial to Mesenchymal Transition (EMT) manifested by a mesenchyme-like morphological appearance and behavior.
To further elucidate the mechanism by which T/ERG executes the EMT program at large, we took a genome-wide approach and conducted micro-array based comparison between EP-AR and EP-AR T/ERG cells

overall_design: Four biological replicate EP-AR and EP-AR T/ERG cell lines were infected in two different infections, two of each were used for expression analysis.

last: Leshem

first: Shalom

last: Madar

first: Ira

last: Kogan-Sakin

first: Iris

last: Kamer

first: Yehudit

last: Cohen

first: Jasmine

last: Jacob-Hirsch

first: Marcelo

last: Ehrlich

first: Shmuel

last: Ben-Sasson

first: Naomi

last: Goldfinger

first: Varda

last: Rotter

first: Raanan

last: Berger


title: HDAC2 Mediates Gene Inactivating of p16INK4a and Promotes Gastric Carcinogenesis by Enhancing Cell Survival and Growth

first: Jung Woo

last: Eun

summary:
To investigate the specific roles of HDAC2 in the development of gastric cancer, we employed large-scale gene expression analysis to identify the molecular signature that may affect enabling characteristics of cancer cells. Differentially expressed genes were analyzed on the MKN-1 cells transfected with HDAC2 shRNAs, and recapitulated molecular signatures that related to hallmarks of cancer.
DNA methylation of p16INK4a promoter region was assessed by methylation specific polymerase chain reaction. Recruiting the HDAC2 at the p16INK4a promoter was identified using chromatin immunoprecipitation assay. RNA interference-mediated protein knockdown method was used to investigate oncogenic potential of HDAC2 in in vitro and in vivo gastrocarcinogenesis of MKN-1 cells.

overall_design: RNA interference-mediated protein knockdown versus mock treatment

first: Jeong-Kyu

last: Kim

first: Ji-Heon

last: Noh

first: Kwang-Hwa

last: Jung

first: Hongjian

last: Xie

first: Min-Gyu

first: Young-Gyoon

last: Chang


title: Alu sequences in undifferentiated human embryonic stem cells display high levels of A-to-I RNA editing

status: Public on Jun 28 2010

first: jasmine

last: Jacob

summary: Adenosine to Inosine (A-to-I) RNA editing is a site-specific modification of RNA transcripts, catalyzed by members of the ADAR (Adenosine Deaminase Acting on RNA) protein family. RNA editing occurs in human RNA in thousands of different sites. Some of the sites are located in protein-coding regions but the majority is found in non-coding regions, such as 3’UTRs, 5’UTRs and introns - mainly in Alu elements. While editing is found in all tissues, the highest levels of editing are found in the brain. It was shown that editing levels within protein-coding regions are increased during embryogenesis and after birth and that RNA editing is crucial for organism viability as well as for normal development. In this study we characterized the A-to-I RNA editing phenomenon during neuronal and spontaneous differentiation of human embryonic stem cells (hESCs). We identified high editing levels of Alu repetitive elements in hESCs and demonstrated a global decrease in editing levels of non-coding Alu sites when hESCs are differentiating, particularly into the neural lineage. Using RNA interference, we showed that the elevated editing levels of Alu elements in undifferentiated hESCs are highly dependent on ADAR1. DNA microarray analysis showed that ADAR1 knockdown has a global effect on gene expression in hESCs and leads to a significant increase in RNA expression levels of genes involved in differentiation and development processes, including neurogenesis. Taken together, our data suggest that A-to-I editing of Alu sequences plays a role in the regulation of hESC early differentiation decisions.

overall_design: Two samples, One control and the second treated

first: Sivan

last: Osenberg

first: Nurit

last: Paz Yaacov

first: Michal

last: Safran

first: Sharon

last: Moshkovitz

first: Ronit

last: Shtrichman

first: Ofra

last: Sherf

first: Gilmor

last: Keshet

first: Ninette

last: Amariglio

first: Joseph

last: Itskovitz-Eldor

first: Gideon

last: Rechavi


title: Gene expression changes in patient-matched gastric normal mucosa, adenomas, and carcinomas

status: Public on Sep 28 2010

first: Jung Woo

last: Eun

summary: sequential changes in gene expression profiles in the gastric adenoma-carcinoma sequence by analyzing eight patient-matched gastric normal mucosa, adenomas and carcinomas.

overall_design: We examined gene expression changes during the gastric adenoma-carcinoma sequence in 26 snap-frozen samples (normal mucosa, adenoma, and carcinoma samples from eight patients and two additional carcinomas) by oligonucleotide microarray

first: Hyunki

first: Hoguen


title: Kidney spheroids generate a functional quiescent niche leading to enhanced tubulogenic potency of human kidney-derived cells

summary: Cell-based approaches utilizing autologous human renal cells require their isolation, expansion in vitro and reintroduction back into the host for renal tissue regeneration. Nevertheless, human kidney epithelial cells (hKEpC) lose their phenotype, dedifferentiate and assume the appearance of fibroblasts after relatively few passages in culture. We hypothesized that growth conditions may influence hKEpC phenotype and function.   hKEpC retrieved from human nephrectomy tissue samples showed the ability to reproducibly form kidney-spheres when grown in suspension culture developed in non-adherent conditions. Genetic labeling and time-lapse microscopy indicated, at least in part, the aggregation of hKEpC into 3D-spheroids rather than formation of pure clonally expanded spheres. Characterization of hKEpC spheroids by real-time PCR and FACS analysis showed up-regulation of some renal developmental and 'stemness' markers compared to monolayer and mostly an EpCAM+CD24+CD133+CD44+ spheroid cell phenotype. Oligonucleotide microarrays which were used to identify global transcriptional changes accompanying spheroid formation, showed predominantly up-regulation of cell matrix/cell contact molecules and cellular biogenesis processes and down-regulation of cell cycle, growth and locomotion. Accordingly, hKEpC spheroids proliferated slowly as indicated by low Ki-67 staining, but when grafted in low cell numbers onto the chorioallantoic membrane (CAM) of the chick embryo, they exclusively reconstituted various renal tubular epithelia. Moreover, efficient generation of kidney spheroids was observed after long-term monolayer culture resulting in re-establishment of tubulogenic capacity upon CAM grafting.  Thus, generation of a specialized quiescent niche in hKEpC spheroids may provide a functional benefit for kidney-derived cells in vivo.

overall_design: 6 samples, 3 adherent and 3 spheroids samples

first: Ella

last: Buzhor

first: Orit

last: Harari-Steinberg

first: Dorit

last: Omer

first: Sally

last: Metsuyanim

first: Jasmin

last: Jacob-Hirsch

first: Tsahi

last: Noiman

first: Zohar

last: Dotan

first: Ronald

middle: S

last: Goldstein

first: Benjamin

last: Dekel


title: Identification of post-generation effect of MDMA on the mouse brain by large-scale gene expression analysis

status: Public on Jan 16 2010

summary: The expression analysis of the brain of F1 pups, after maternal ingestion of 3,4-methylenedioxymethamphetamine (MDMA, 20mg/kg), resulted in significant transcriptional changes in both male and female pups.

overall_design: In this study, in order to investigate whether maternal ingestion of MDMA and prenatal exposure to MDMA affects the transcriptional configuration of the brain of offspring, we assessed large-scale gene expression changes in the mouse brains of mice exposed to long-term ingestion of MDMA in utero.

first: Sukwoo

last: Nam


title: Transcriptional Profiling of Cerebral Malaria

status: Public on Oct 01 2007

first: Sina

last: Gharib

summary:
Cerebral malaria (CM) is a leading cause of death in the world. Better understanding of the pathogenesis of this disease is critical for the development of novel therapies. In this work, we investigated temporal gene expression profiles in the brains of CM-susceptible and CM-resistant mice during infection with P. Berghia ANKA (PbA).
In this model of CM, susceptible mice develop neurological signs by day 6 post infection while resistant mice do not develop neurological manifestations during malarial infection.
Keywords: Time course

overall_design: C57/B6 (CM-susceptible) and Balb/C (CM-resistant) mice were infected with PbA. Gene expression profiles from whole brains were obtained at day 0 (uninfected), day 1, day 3, and day 6.

middle: A

first: Fiona

last: Lovegrove


title: Salivary gland during development and onset of xerostomia in  murine model of Sjögren's syndrome-like disease

status: Public on Apr 11 2009

first: Ammon

last: Peck

summary:
Differential gene expression in the salivary gland during development and onset of xerostomia in Sjögren’s syndrome-like disease of the C57BL/6.NOD-Aec1Aec2 mouse.
Recently, we reported the development of the C57BL/6.NOD-Aec1Aec2 mouse that carries two genetic intervals derived from the NOD mouse capable of conferring Sjögren’s syndrome (SjS)-like disease in SjS-non-susceptible C57BL/6 mice.
In an attempt to define the molecular bases underlying onset of stomatitis sicca (xerostomia) in this C57BL/6.NOD-Aec1Aec2 mouse model, we have carried out a study utilizing  microarray technology.

overall_design: The present study was designed to define the changing gene expression profiles within the salivary glands of C57BL/6.NOD-Aec1Aec2 mice at five time points representing a pre-disease stage (4 weeks), the early pre-clinical stage (8 weeks), the initial influx of leukocytes into the salivary glands (12 weeks), the early clinical phase of autoimmunity (16 weeks), and the early onset of clinical SjSlike disease characterized by secretory dysfunction (20 weeks). The C57BL/6.NOD-Aec1Aec2 mouse is a model of primary SjS in which the Idd3 region of chromosome 3 and the Idd5 region of chromosome 1 derived from the NOD mouse were bred into the non-autoimmune C57BL/6 mouse, resulting in a SjS-like disease susceptibility that mimics both the pathophysiological characteristics and reduced secretory responses observed with NOD mice during development and onset of disease. This SjS-susceptible strain was designated C57BL/6.NOD-Aec1Aec2, where Aec1 corresponds to Idd3 (of chromosome 3) and Aec2 corresponds to Idd5 (of chromosome 1).

first: Cuong

last: Nguyen

first: Ashok

last: Sharma

first: Byung

middle: H

last: Lee

first: Jin-Xiong

last: She

first: Richard

last: McIndoe


title: Mechanical Ventilation Augments LPS-induced Lung Injury

status: Public on Aug 01 2005

summary:
This experiment investigated the role of mechanical ventilation (MV) in modulating lung's transcriptional response to LPS.   Twenty four  C57/B6 male mice were randomized to four groups: 1. Control, 2. MV, 3. LPS and 4. MV+LPS.  Expression profiling of whole lungs revealed a significant augmentation of the transcriptional response in the combined MV+LPS group relative to the other 3 conditions.
Keywords: repeat sample

first: William

last: Altemeier

first: Gustavo

last: Matute-Bello

first: Robb

last: Glenny

first: Thomas

last: Martin

first: W. Conrad

last: Liles


title: Gene expression profiling of parkinsonian substantia nigra

status: Public on Mar 10 2010

first: jasmine

last: Jacob

summary:
Affymetrix HG-Focus array was used to determine a global gene expression profile of clinically and neuropathologically confirmed cases of sporadic Parkinson's disease compared to controls.
Major alterations were detected in signal transduction, protein degradation, dopaminergic transmission/metabolism, energy pathways/glycolysis, cell adhesion/cytoskeleton, extracellular matrix components and cell cycle functional classes.

overall_design: Post-mortem human brains were obtained from moderately to severe parkinsonism individuals based on the Hoehn & Yahr criteria. All the subjects were negative for AD pathology according to Braak & Braak. The average age for PD and control is 76.6 and 77.8 years, respectively. The average postmortem delay for PD and control is 26.2 and 19.8 hours, respectively.

first: Grunblatt

last: Edna

first: Mandel

last: Silvia

first: Jacob-Hirsch

last: Jasmine

first: Zeligson

last: Sharon

first: Amariglo

last: Ninette

first: Rechavi

last: Gideon

first: Li

last: Jie

first: Ravid

last: Rivka

first: Roggendorf

last: Wolfgang

first: Peter

last: Riederer

first: Youdim

last: Moussa


title: Evaluation of HIPK2-modulated genes in cancer cells.

summary: HIPK2, a member of the homeodomain-interacting protein kinase family, is a transcriptional corepressor whose activity inhibits tumor progression and allows tumor cell apoptosis in response to chemotherapy. HIPK2 regulates the function of numerous molecules and its inhibition by siRNA, hypoxia or mutations, strongly favours molecular pathways involved in tumor progression, angiogenesis, invasion and chemoresistance. Hence the identification of novel molecules regulated by HIPK2 may be beneficial for better understanding tumor progression and for evaluating targeted antitumor therapies.

overall_design: By using microarray analysis, derived from HIPK2 overexpression (that mimics HIPK2 activation) in colon cancer RKO cells, we aim at evaluating the HIPK2 modulated gene expression involved in tumor progression.

first: Jasmine

last: Jacob-Hirsch

first: Michal

last: Sheffer

first: Gideon

last: Rechavi

first: David

last: Givol

first: Gabriella

last: D’Orazi.


title: Hypoxic pulmonary hypertension study

status: Public on Mar 16 2005

first: Sina

last: Gharib

summary:
These microarray studies were performed using whole lungs of BALB/C mice during development of hypoxia-induced pulmonary hypertension (days 1-21) and resolution of pulmonary hypertension after return to normoxia (days 22-35) .  Mice were sampled during nine time-points and each time-point was replicated 4 times (with dye swapping).
Keywords = hypoxia
Keywords = pulmonary hypertension
Keywords: other