title: miRNA Expression in 4 prostate cell types from human tumor biopsies

first: John

last: Krill-Burger

summary: Prostate primary epithelial and stromal cells were isolated from normal donorhuman prostate tissue and patient prostate tumors (>Gleason 8) using in vitroselective media conditions and differential substrate adhesion properties.Tumor cells specific to the prostate epithelial cell component attached tomatrigel while epithelial cells from donors preferentially attached to gelatinsubstrate. The prostate tumor cells did not proliferate over time in culturebut cells of normal epithelial phenotype in comparison to the donor tissueeventually emerged from this cell compartment. The epithelial componentof both donor and tumor specimens produced stem cell colonies thatexpressed OCT4 in growth factor reduced media but subsequently formedembryoid bodies in hanging drop cultures which differentiated into multiplegerm line lineages under the influence of growth factors. To determineif prostate tumor-derived stem cells were capable of forming tumors invivo, we compared the behavior of the donor and tumor stem cells aftertransplantation as tissue recombinants under the renal capsule of SCID micein the presence of rat urogenital mesenchyme (rUGM). Stem cells from bothdonor and tumor sources produced glandular structures that secreted prostatespecific antigen (PSA) while no glandular structures were formed from tissuerecombinants of normal epithelial or tumor epithelial cells plus rUGM or fromrUGM alone. Serial transplantation of the stem cell recombinants from tumorspecimens yielded subrenal structures reflecting an abundance of glands with morphological features typical of Prostatic Intraepithelial Neoplasia(PIN). In order to determine whether intrinsic differences existed amongthe donor-derived and tumor-derived stem cells, array based microRNAexpression profiling was performed on all cell types obtained after in vitro isolation.

first: William

middle: A

last: LaFramboise

first: Dean

last: Bacich

first: Patricia

last: Petrosko

middle: M

first: Christin

last: Sciulli

first: Rajiv

last: Dhir


title: Plasmodium knowlesi gene expression differs in ex vivo compared to in vitro blood-stage cultures

status: Public on Jun 08 2015

city: Singapore

first: Zbynek

last: Bozdech

state: Select if applicable

department: Molecular Genetics&Cell Biology

country: Singapore

institute: Nanyang Technological University

summary: The purpose of this reasearch is to identify and evaluate the global gene expression of Plasmodium knowlesi blood-stage parasites and specifically compare the gene expression profiles of samples derived from ex vivo versus long-term in vitro cultures.

overall_design:
For ex vivo samples, a rhesus monkey was infected with P. knowlesi to obtain ring iRBCs to establish a short-term culture to immediately collect ex vivo derived time points every 4 hours in the course of the parasite’s 24-hour life cycle.
For in vivo samples, they were generated from the same clone in the ex vivo culture adapted to long-term in vitro culture and were collected every 4 hours in the course of the parasite's 24-hour life cycle. Two replicate experiments(Aa and Ha) were developed from in vitro cultures.
Samples labeled with Cy5 were hybridized against a reference RNA pool labeled with Cy3, consisting of equal amounts of P. knowlesi RNA from each time point.

first: Stacey

last: Lapp

first: Sachel

last: Mok

first: Zhu

last: Lei

first: Hao

last: Wu

first: Peter

last: Preiser

first: Z

middle: B

first: Mary

middle: R

last: Galinski


title: Gene expression analysis of mesenchymal stromal cells obtained from healthy donors and osteosarcoma patients

status: Public on Jun 30 2015

city: Oslo

first: Marieke

middle: Lydia

last: Kuijjer

address: Gaustadalléen 21

country: Norway

institute: Centre for Molecular Medicine Norway

summary: Gene expression profiles of cultured mesenchymal stromal cells obtained from osteosarcoma patients at diagnosis and healthy donors were compared.

overall_design: Mesenchymal stromal cells were harvested from the iliac crest of 5 healthy donors and 7 osteosarcoma patients at diagnosis and cultured until passage 2-5, after which cells were harvested and total RNA was isolated. Gene expression profiles osteosarcoma patient derived MSCs were compared with healthy donor derived MSCs.

first: Emilie

middle: P

last: Buddingh


title: T47D cell line transfected with various ESR1 fusion genes (or with estrogen treatment), vs. YFP transfection alone

status: Public on Jun 12 2015

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

country: USA

institute: University of North Carolina at Chapel Hill

summary: Gene expression profiling of the downstream transcriptional changes induced by ESR1 fusion genes observed in human breast tumors resistant to hormone therapy

overall_design: Experimental T47D cells stably expressing ESR1 fusion genes (or T47D cells treated with estradiol) vs. T47D cells expressing YFP

first: Xiaping

last: He

first: Jieya

last: Shao

first: Jeremy

last: Hoog


title: Sex-related changes in gene expression patterns of adults exposed to arsenic contaminated drinking water

status: Public on Jun 01 2015

city: Tuxedo

first: Alexandra

middle: Brooke

last: Munoz

state: New York

address: 57 Old Forge Road

department: Environmental Medicine

institute: NYU Medical Center

summary: Arsenic contamination of drinking water occurs globally and is associated with numerous diseases including skin, lung, and bladder cancers, and cardiovascular disease.  The mechanisms behind arsenic's effects remain unclear, but recent research indicates that aresnic acts along sex-specific lines and may be an endocrine disruptor. The objective of this study was to evaluate the nature of gene expression chagnes among males and females exposed to arsenic contaminated water in Bangladesh at high and low dose exposures.The median wAs concentration for the low exposure group was 103 µg/L for males and 117 µg/L for females (range 50–200 µg/L). For the high exposure group, the median wAs concentration was 355 µg /L for males (range 250-500 µg /L) and 434 µg/L for females (range 232–1000 µg /L). The PBMCs of males with high exposure compared to those with low exposure there were 534 differentially expressed genes (p <0.05); and for females with high exposure relative to low exposure there were 645 differentially expressed genes (p <0.05) in PBMCs of females.

overall_design: We obtained peripheral blood mononuclear cell (PBMC) RNA from 29 human subjects exposed to arsenic contaminated drinking water in Bangladesh. PBMC RNA was labelled and hybridized to Affymetrix 1.0 ST arrays.  We compared the gene expression profiles of 9 males with relatively low exposure versus the 6 males with relatively high exposure; and the  6 females with relatively low exposure versus 7 females with relatively high exposure. humans exposed to arsenic contaminated drinking water at high and low doses

first: Yana

last: Chervona

first: Megan

last: Hall

first: Thomas

last: Kluz

last: Gamble

first: Max

last: Costa


title: Prokaryotic expression profiling analysis for single or combined chaperones deletion

status: Public on Jun 18 2015

city: Beijing

first: Dongjie

last: Fan

address: Changbai Road NO 155,

country: China

institute: National institute for communicable disease control and prevention,Chinese center for disease control and prevention

summary:
Chaperones have essential role in assist nascent peptides folding, prevent proteins aggregation and maintain cellular protein homeostasis. Considering spatial and temporal features of chaperones regulating in vivo, changes in single or combined chaperone-depleted E.coli strain is needed to be put into understand at transcriptional level. Here, we utilized expression microarrays to investigate global transcriptional response upon deletion of single or multiple chaperones in E. coli for understanding the transcriptional network affected by chaperones.
To identify prokaryotic expression profiles in deletion of chaperones, several E.coli mutants were constructed in the following: Z116 (△tig 37℃), Z125(△dnaK37℃), Z625(△tig△dnaK 37℃ or 30℃), Z629(△tig△dnaK 30℃), NM (C-domain of tig was deleted 37℃), MC (N-domain of tig was deleted 37℃), NC (M-domain of tig was deleted 37℃). Two types of cDNA mixtures containing Cy3-labeled (or Cy5-labeled) control DNA (from BW25113) and Cy5-labeled (or Cy3-labeled) DNA targets (from mutant strain) were hybridized with E.coli microarrays in a dye-swap strategy.

overall_design: E.coli gene expression data of the deletants compared control WT (BW25113). Please note that other mutant microarray data will be added in the future.


title: Gene network analysis in Arabidopsis thaliana flower development through dynamic gene perturbations

city: Dublin

first: Pat

last: Ryan

address: College Green

country: Ireland

institute: TCD

summary: Microarray experiments conducted using artifical microRNA knockdowns from multiple induction systems

overall_design: Multiple replicates for each artifical microRNA/inducible system combination were conducted on two channel microarrays against uninduced samples using a dye swap

first: Diarmuid

last: Ó’Maoiléidigh

first: Kamilla

last: Kwasnieska

first: Patrick

first: Bennet

last: Thompson

first: Katarzyna

last: Hanczaryk

first: Samuel

last: Wuest

first: Cristel

middle: C

last: Carles

first: Emmanuelle

last: Graciet

first: Frank

last: Wellmer


title: SaOS-2 transfected with CD99 in differentiation medium for 14 days [miRNA]

city: Bologna

first: Andrea

last: Grilli

state: Italy

address: v. di Barbiano 1/10

department: Laboratory of Experimental Oncology

country: Italy

institute: Rizzoli Orthopaedic Institute

summary: We explored the transcriptional modification induced by CD99 transfection in the osteosarcoma cell lines SaOS-2 after 0, 7 and 14 days in differentiation medium.

overall_design: SaOS-2 cell lines transfected with CD99 molecule (Sa/CD99) were compared with parental SaOS-2. Cell lines were maintained in differentiation medium for 14 days. RNA was extracted at days 0, 7 and 14.

first: Marika

last: Sciandra

first: Katia

last: Scotlandi


title: Exacerbated oxidative stress in the fasting liver according to fuel partitioning

status: Public on Jun 03 2015

city: Strasbourg

first: Fabrice

last: Bertile

address: 25 rue Becquerel

department: Analytical Sciences

country: France

institute: CNRS, IPHC

summary: Complete starvation may prove lethal due to excessive loss of body proteins. However, it is still not completely understood whether responses to food deprivation are time-dependently induced or triggered in relation with the successive phases of protein sparing and wasting that characterize prolonged fasting. As the liver has a wide range of vital functions, we examined the hepatic regulatory mechanisms elicited during prolonged fasting. We showed that fasting-induced transcriptome/proteome changes occur in close relation with fuel partitioning, independently of ATP levels. Omics data suggesting a worsening of oxidative stress during the proteolytic stage of fasting, this was further validated using biochemical assays. Low levels of antioxidant factors were indeed paralleled by their decreased activity, which could be impaired by low NADPH levels. Oxidative damages on lipids and proteins were accordingly increased only during late fasting. At this stage, the gene/protein expression of several chaperones was also repressed. Together with the impairment of metabolic achievements, a vicious cycle involving protein misfolding and oxidative stress could jeopardize liver functions when the proteolytic stage of fasting is reached. Thus, monitoring of liver impairments should help to better manage or treat catabolic and/or oxidative stress conditions, such as ageing and degeneration.

overall_design: Liver impairments during prolonged fasting. We analyzed liver from 16 male Sprague Dawley rats randomly divided into 4 groups (4 fed, 4 fasted until phase 2 of fasting [P2], 4 fasted until phase 3 of fasting [P3], 4 fasted until phase 3 and then re-fed for two days [P3r2]) using the Affymetrix Rat Exon 1.0 ST platform. Array data was processed by Affymetrix GCOS v1.4 and Expression Console v1.1. No technical replicates were performed.

first: Thierry

last: Wasselin

first: Sandrine

last: Zahn

first: Yvon

last: Le Maho

first: Alain

last: Van Dorsselaer

last: Raclot


title: Transcriptom analysis of differentially regulated genes in metastasis associated macrophages(MAM) compared with lung and spleen resident macrophages

status: Public on May 15 2015

city: Edinburgh

first: Bin-Zhi

last: Qian

address: 47 Little France Crescent

department: MRC Centre for Reproductive Health

country: United Kingdom

institute: University of Edinburgh

summary: Gene expression changes in metastasis associated macrophage (MAM) FACS sorted cells from mice bearing pulmonary metastasis of breast tumor cells  were compared with  lung and spleen resident macrophages sorted from healthy mice using same sorting protocol.

overall_design: A six chip study using total RNA recovered from metastasis associated macrophages from three individual mice and lungs and spleens all from three individual mice.  Each chip measures the expression level of 42586 genes.

first: Jeffrey

middle: W

last: Pollard


title: Synthetic mRNA switches for detection and purification of cardiomyocytes and endothelial cells derived from human pluripotent stem cells [miRNA]

status: Public on May 20 2015

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Kyoto University

summary: We designed microRNA-responsive, modified mRNA switches (miR-switches) that quantitatively control their own translation level by determining the miRNA activities. We found that the three miR-switches (i.e., miR-1-, miR-208-, and miR-499-switches) enable to purify cardiomyocytes differentiated from hPSCs with high efficiency, accuracy, and safety. The purified cardiomyocytes were engrafted in mouse heart and did not form tumor. Simultaneous purification of two different cell types, cardiomyocytes and endothelial cells, was also performed by transfecting the mRNA responding to the both miR-208 and miR-126, into heterogeneous cell population derived from hPSCs. In addition, selective induction of apoptosis in noncardiomyocytes triggered by miR-1/208-Bim switch enriched cardiomyocytes without cell sorting. The mRNA switch could purify desired cell types and control cell death pathways by monitoring the miRNA expression dynamics during cell fate conversion.

overall_design:
MYH6-EIP4 day8 differentiated cells (EGFP+) for miRNA, N=1
MYH6-EIP4 day8 differentiated cells (EGFP-) for miRNA, N=1
MYH6-EIP4 day20 differentiated cells (EGFP+) for miRNA, N=1
MYH6-EIP4 day20 differentiated cells (EGFP-) for miRNA, N=1
HUVEC for miRNA, N=2
AoSMC for miRNA, N=2
Hepatocytes for miRNA, N=2
NHDF for miRNA, N=2

first: K

last: Miki

first: M

last: Narita

first: H

last: Saito

first: Y


title: Distribution of H3K27me3, H3K27ac, and H3K4me1 in E(z) temperature sensitive cells

status: Public on May 14 2015

city: Boston

first: Hun-Goo

last: Lee

state: MA

address: 185 Cambridge St

department: Molecular Biology

institute: Mass General Hospital

type: Genome binding/occupancy profiling by genome tiling array

summary: PcG protein complex PRC2 is a methyltransferase specific for histone H3 lysine27, and H3K27me3 is essential for stable transcription silencing. Here we have determined genomic distributions of H3K27me3, H3K27ac, and H3K4me1 in cultured Drosophila E(z) temperature sensitive cells at 25°C and 31°C where E(z) is largely inactivated by hybridization of ChIP products with tiling microarrays.

overall_design: Genomic distributions of H3K27me3, H3K27ac, and H3K4me1 in cultured Drosophila E(z) temperature sensitive cells (EZ2-2) at 25°C and 31°C where E(z) is largely inactivated by hybridization of ChIP products with tiling microarrays

middle: G

first: Amanda

last: Simcox

first: Yuri

last: Schwartz

first: Vincenzo

last: Pirrotta


title: Distribution of H3K27me2, dUTX, and histone H3 in Sg4 cells

summary: PcG protein complex PRC2 is a methyltransferase specific for histone H3 lysine27, and H3K27me3 is essential for stable transcription silencing. Less well known but quantitatively much more important is the genome-wide role of PRC2 that dimethylates more than half of total H3K27. Here we have determined genomic distributions of H3K27me2, dUTX, and histone H3 in cultured Drosophila Sg4 cells by hybridization of ChIP products with tiling microarrays.

overall_design: Genomic distributions of H3K27me2, dUTX, and histone H3 in cultured Drosophila Sg4 cells by hybridization of ChIP products with tiling microarrays

first: Tatyana

last: Kahn


title: Efficacy of carboplatin alone and in combination with ABT888 in intracranial murine models of BRCA-mutated and BRCA-wild-type triple negative breast cancer

status: Public on May 12 2015

first: Charles

last: Perou

summary: Purpose:Triple negative breast cancer (TNBC) commonly metastasizes to the brain and predicts poor prognosis with limited therapeutic options. TNBC frequently harbors BRCA mutations translating to platinum sensitivity; platinum response may be augmented by additional suppression of DNA repair mechanisms through poly(ADP-ribose)polymerase (PARP) inhibition. We evaluated brain penetrance and efficacy of Carboplatin +/- the PARP inhibitor ABT888, and investigated gene expression changes in murine intracranial (IC) TNBC models stratified by BRCA and molecular subtype status. Experimental design:Athymic mice were inoculated intra-cerebrally with BRCA-mutant: SUM149 (basal), MDA-MB-436 (claudin-low), or BRCA-wild-type: MDA-MB-468 (basal), MDA-MB-231BR (claudin-low) TNBC cells and treated with PBS control (IP, weekly), Carboplatin (50mg/kg/week, IP), ABT888 (25mg/kg/day, OG), or their combination. DNA-damage (?-H2AX) and apoptosis (cleaved-Caspase-3(cC3)) were assessed via IHC of IC tumors. Gene expression of BRCA-mutant IC tumors was measured. Results: Carboplatin+/-ABT888 significantly improved survival in BRCA-mutant IC models compared to control, but did not improve survival in BRCA-wild-type IC models. Carboplatin+ABT888 revealed a modest survival advantage versus Carboplatin in BRCA-mutant models. ABT888 yielded a marginal survival benefit in the MDA-MB-436 but not in the SUM149 model. BRCA-mutant SUM149 expression of ?-H2AX and cC3 proteins was elevated in all treatment groups compared to Control, while BRCA-wild-type MDA-MB-468 cC3 expression did not increase with treatment.  Carboplatin treatment induced common gene expression changes in BRCA-mutant models.Conclusions: Carboplatin+/-ABT888 improves survival in BRCA-mutant IC TNBC models with corresponding DNA damage and gene expression changes. Combination therapy represents a promising treatment strategy for patients with TNBC brain metastases warranting further clinical investigation.

overall_design: reference x sample

first: Olga

last: Karginova

first: Marni

last: Siegel

first: Carey

middle: K

last: Anders


title: Molecular signatures for chronic lymphocytic leukemia

status: Public on Apr 30 2015

city: Geneva

first: Thomas

last: Matthes

address: Rue Gabrielle Perret-Gentil

department: Hematology

country: Switzerland

institute: Geneva University Hospital

summary:
Analysis of the expression profile of 290 mRNA's, measured with the nCounter (Nanostring Technologies platform),  in 30 samples from the peripheral blood of CLL patients
Chronic lymphocytic leukemia (CLL) is a clonal malignancy of mature B cells that displays a great clinical heterogeneity, with many patients having an indolent disease that will not require intervention for many years, while others present an aggressive and symptomatic leukemia requiring immediate treatment. Although there is no cure for CLL, the disease is treatable and current standard chemotherapy regimens have been shown to prolong survival.  Recent advances in our understanding of the biology of CLL have led to the identification of numerous cellular and molecular markers with potential diagnostic, prognostic and therapeutic significance. We have used the recently developed digital multiplexed gene-expression technique (DMGE) to analyze a cohort of 30 CLL patients for the presence of specific genes with known diagnostic and prognostic potential. Starting from a set of 290 genes we were able to develop a molecular signature, based on the analysis of 13 genes, which allows distinguishing unambiguously CLL from normal peripheral blood and from normal B cells, and a second signature based on 24 genes, which distinguishes mutated from unmutated cases (LymphCLL Mut). A third classifier (LymphCLL Diag), based on a 44-gene signature, distinguished CLL cases from a series of other B-cell chronic lymphoproliferative disorders (n=51). This analysis is easy to perform, ideal for clinical trials and normal routine diagnosis even in small hospitals.

overall_design: 39 samples from peripheral blood: 30 CLL samples; 5 samples from normal blood donors; 4 samples from purified B lymphocytes

first: Agathe

last: Debliquis

first: Edouard

last: Cornet

first: Valérie

last: Rimelen

first: Xavier

last: Troussard

first: Bernard

last: Drénou


title: A genomic algorithm for the molecular classification of renal cortical neoplasms: Development and Validation

status: Public on Apr 29 2015

city: Rutherford

first: Jane

last: Houldsworth

state: NJ

address: 201 Route 17 North

institute: Cancer Genetics, Inc.

summary: Accurate diagnostic discrimination of benign renal oncocytoma (OC) and malignant renal cell carcinomas (RCC) is not only useful for planning appropriate treatment strategies of patients with renal masses but also for estimating prognosis. Classification of renal neoplasms solely by histopathology can often be challenging for a variety of reasons. The aim of this study was to develop and validate a genomic algorithm for molecular classification of renal cortical neoplasms that could be implemented in a routine clinical diagnostic setting. Using TCGA (The Cancer Genome Atlas) copy number profiles of over 600 RCC specimens, prior FISH studies and published literature, a classification algorithm was developed consisting of 15 genomic markers: loss of VHL, 3p21, 8p, and chromosomes 1, 2, 6, 10 and 17, and gain of 5qter, 16p, 17q, 20q, and chromosomes 3, 7, and 12. Criteria for scoring specimens for the presence of each genomic marker were established. As validation, 191 surgically resected formalin-fixed paraffin-embedded renal neoplasms were blindly submitted to targeted array-CGH and were classified according to the algorithm. Upon histologic re-review leading to exclusion of three specimens and using histology as the gold standard, the algorithm correctly classified 58 of 62 (93%) clear cell renal cell carcinoma, 51 of 56 (91%) papillary RCC, and 33 of 34 (97%) chromophobe RCC. Of the 36 OC specimens, 17 were classified as OC, two as a malignant subtype, 14 as benign, and three exhibited alterations not associated with a specific subtype. In ten of the latter two groups, CCND1-rearrangement was detected by fluorescence in situ hybridization, affording a classification as OC. Together, 33 of 36 (92%) OC were classified as OC or benign. For the entire validation cohort, an overall diagnostic sensitivity of 93% and above 97% specificity was achieved, suggesting that the implementation of genome-based molecular classification in a clinical diagnostic setting could impact the overall management and outcome of patients with renal tumors.

overall_design: A total of 191 RCC FFPE samples are analyzed including 63 clear cell RCC (ccRCC), 57 papillary RCC (pRCC), 35 chromophobe RCC (chrRCC) and 36 oncocytoma (OC). Two-color array-comparative genomic hybdrization on custom designed using RCC DNA as test and normal sex-matched DNA as reference.

first: Banumathy

last: Gowrishankar


title: Gene expression of paired samples of hepatic stellate cells (HSC) and hepatocyte cell culture (HCC) treated with conditioned media of HSC cells

status: Public on Apr 24 2015

city: Regensburg

first: Julia

last: Engelmann

address: Josef-Engert-Str. 9

department: Statistical Bioinformatics

country: Germany

institute: University of Regensburg

summary:
All living cells rely on the communication with other cells to ensure their function and survival. Molecular signals are sent among cells of the same cell type and from cells of one cell type to another. In cancer, not only the cancer cells themselves are responsible for the malignancy, but also stromal (non-cancerous) cells and the molecular signals they send to cancer cells are important factors that determine the severity and outcome of the disease. Therefore, the identification of stromal signals and their influence on cancer cells is important when looking for novel treatment strategies.
We have generated gene expression profiles of both stromal (HSC), and liver cancer (HCC) cells treated with HSC conditioned medium to elucidate cell communication from HSC to HCC cells.

overall_design: 15 HSC samples, 15 HCC samples treated with conditioned medium of the HSC samples, 4 control hep samples without treatment

first: Claus

last: Hellerbrand


title: Expression data from mouse brain

status: Public on Apr 23 2015

city: Valladolid

first: Diego

last: Sanchez

state: Valladolid

address: C/ Sanz y Forés 3

department: IBGM

country: Spain

institute: Universidad de Valladolid

summary: A detailed knowledge of the mechanisms underlying brain aging is fundamental to understand its functional decline and the baseline upon which brain pathologies superimpose. Endogenous protective mechanisms must contribute to the adaptability and plasticity still present in the healthy aged brain. Apolipoprotein D (ApoD) is one of the few genes with a consistent and evolutionarily conserved up-regulation in the aged brain. ApoD protecting roles upon stress or injury are well known, but a study of the effects of ApoD expression in the normal aging process is still missing. Using an ApoD-knockout mouse we analyze the effects of ApoD on factors contributing to the functional maintenance of the aged brain. We focused our cellular and molecular analyses in cortex and hippocampus at an age representing the onset of senescence where mortality risks are below 25%, avoiding bias towards long-lived animals. Lack of ApoD causes a prematurely aged brain without altering lifespan. Age-dependent hyperkinesia and memory deficits are accompanied by differential molecular effects in cortex and hippocampus. Transcriptome analyses reveal distinct effects of ApoD loss on the molecular age-dependent patterns of cortex and hippocampus, with different cell-type contributions to age-regulated gene expression. Markers of glial reactivity, proteostasis, and oxidative and inflammatory damage reveal early signs of aging and enhanced brain deterioration in the ApoD-knockout brain. The lack of ApoD results in an age-enhanced significant reduction in neuronal calcium-dependent functionality markers and signs of early reduction of neuronal numbers in the cortex, thus impinging upon parameters clearly differentiating neurodegenerative conditions from healthy brain aging. Our data support the hypothesis that the physiological increased brain expression of ApoD represents a homeostatic anti-aging mechanism.

overall_design: The brain cortex and hippocampus of young and aged mice of wild-type and ApoD-KO genotypes were used for RNA extraction and hybridization on Affymetrix microarrays. We aim at identifying distinct effects of ApoD loss on the molecular age-dependent patterns of cortex and hippocampus.

first: Maria

middle: D

last: Ganfornina


title: Plasma autoantibody associated with basal-like breast cancer-FLAG Array

status: Public on Apr 22 2015

city: Tempe

first: Jie

last: Wang

state: Arizona

address: 1001 S. McAllister Ave.

department: Center for Personalized Diagnostics

institute: Arizona State University

summary: Background: Basal-like breast cancer (BLBC) is a rare aggressive subtype that is less likely to be detected through mammographic screening. Identification of circulating markers associated with BLBC could have promise in detection and management of this deadly disease.  Methods: Using samples from the Polish Breast Cancer study, a high-quality population-based case-control study of breast cancer, we screened 10,000 antigens on protein arrays using 45 BLBC patients and 45 controls, and identified 748 promising plasma autoantibodies (AAbs) associated with BLBC. ELISA assays of promising markers were performed on a total of 145 BLBC cases and 145 age-matched controls. Sensitivities at 98% specificity were calculated and a BLBC classifier was constructed.   Results: We identified a 13-AAbs (CTAG1B, CTAG2, TP53, RNF216, PPHLN1, PIP4K2C, ZBTB16, TAS2R8, WBP2NL, DOK2, PSRC1, MN1, TRIM21) that distinguished BLBC from controls with 33% sensitivity and 98% specificity. We also discovered a strong association of TP53 AAb with its protein expression (p=0.009) in BLBC patients.   Conclusions: These AAbs warrant further investigation in clinical studies to determine their value for further understanding the biology of BLBC and possible detection.

overall_design: The immunoreactivity was compared between 45 BLBC cases and 45 controls against 10,000 human proteins that printed on microscopic slides

first: Jonine

last: Figueroa


title: Plasma autoantibody associated with basal-like breast cancer-GST4 Array

summary: Background: Basal-like breast cancer (BLBC) is a rare aggressive subtype that is less likely to be detected through mammographic screening. Identification of circulating markers associated with BLBC could have promise in detection and management of this deadly disease.  Methods: Using samples from the Polish Breast Cancer study, a high-quality population-based case-control study of breast cancer, we screened 10,000 antigens on protein arrays using 45 BLBC patients and 45 controls, and identified 748 promising plasma autoantibodies (AAbs) associated with BLBC. ELISA assays of promising markers were performed on a total of 145 BLBC cases and 145 age-matched controls. Sensitivities at 98% specificity were calculated and a BLBC classifier was constructed.   Results: We identified a 13-AAbs (CTAG1B, CTAG2, TP53, RNF216, PPHLN1, PIP4K2C, ZBTB16, TAS2R8, WBP2NL, DOK2, PSRC1, MN1, TRIM21) that distinguished BLBC from controls with 33% sensitivity and 98% specificity. We also discovered a strong association of TP53 AAb with its protein expression (p=0.009) in BLBC patients.  Conclusions: These AAbs warrant further investigation in clinical studies to determine their value for further understanding the biology of BLBC and possible detection.


title: Plasma autoantibody associated with basal-like breast cancer-GST3 Array

summary: Background: Basal-like breast cancer (BLBC) is a rare aggressive subtype that is less likely to be detected through mammographic screening. Identification of circulating markers associated with BLBC could have promise in detection and management of this deadly disease.  Methods: Using samples from the Polish Breast Cancer study, a high-quality population-based case-control study of breast cancer, we screened 10,000 antigens on protein arrays using 45 BLBC patients and 45 controls, and identified 748 promising plasma autoantibodies (AAbs) associated with BLBC. ELISA assays of promising markers were performed on a total of 145 BLBC cases and 145 age-matched controls. Sensitivities at 98% specificity were calculated and a BLBC classifier was constructed.   Results: We identified a 13-AAbs (CTAG1B, CTAG2, TP53, RNF216, PPHLN1, PIP4K2C, ZBTB16, TAS2R8, WBP2NL, DOK2, PSRC1, MN1, TRIM21) that distinguished BLBC from controls with 33% sensitivity and 98% specificity. We also discovered a strong association of TP53 AAb with its protein expression (p=0.009) in BLBC patients. Conclusions: These AAbs warrant further investigation in clinical studies to determine their value for further understanding the biology of BLBC and possible detection.


title: Plasma autoantibody associated with basal-like breast cancer-GST2 Array


title: Plasma autoantibody associated with basal-like breast cancer-GST1 Array


title: A Molecular Portrait of Potentially Curable Prostate Cancer

status: Public on Apr 20 2015

city: Toronto

first: Yu-Jia

last: Shiah

state: Ontario

address: MaRS Centre 661 University Avenue Suite 510

department: Informatics and Bio-computing

country: Canada

institute: Ontario Institute for Cancer Research

summary: Herein we describe a molecular portrait of potentially curable, Gleason 7 and intermediate risk prostate cancer based on genome-wide CNV profiles of 96 patients, and subsequent whole-genome sequencing of 28 tumours from 10 patients, using DNA quantities that are achievable in diagnostic biopsies (50 ng). We show that Gleason 7 cancer is highly heterogeneous at the SNV, CNV, and intra-chromosomal translocation levels, and is characterized by a very low number of recurrent SNVs but significant structural variation. We identified a novel recurrent MYCL1 amplification, which was strongly associated with TP53 deletion and prognostic for biochemical recurrence in this cohort. Moreover, we identified clear evidence of divergent tumour evolution in multi focal cancer and, in 2/5 cases evaluated, multiple tumours of independent clonal origin. Taken together, these data represent the first systematic evaluation of the differential genomics of potentially curable prostate cancer, and strongly suggest that a more robust understanding of the relationship between genetic heterogeneity and clinical outcomes is required to effectively develop biomarkers of prognosis based on tumour genomics.

overall_design: Six samples were analyzed in duplicate. Samples included untreated cells, cells transfected with vector only, and cells transfected with 4 different MYCL transcript variants. Expression constructs and vector were purchased from GeneCopoeia

first: Paul

last: Boutros


title: SUV420H2 over-expression affects on gene expression in human breast cancer MDA-MB-231 cells

status: Public on Apr 15 2015

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Analysis of breast cancer MDA-MB-231 cells stably over-expressing SUV420H2, a histone H4K20 methyltransferase. Several genes were significantly up- or down-regulated. Results provide insight into the molecular mechanism by which H4K20me3 contributes to gene expression.

overall_design: SUV420H2 stably over-expressing MDA-MB-231 cells were cloned. Then total RNA was extracted from the SUV420H2 over-expressing cells and the parental MDA-MB-231 cells.

first: Yoshimi

last: Shinchi

first: Miki

last: Hieda


title: Effects of 2'-deoxymugineic acid application on the rice seedling under different pH conditions

status: Public on Apr 10 2015

city: Mishima, Osaka

first: Jun

last: Murata

address: 1-1-1 Wakayamadai, Shimamoto

department: Bioorganic Research Institute

institute: Suntory Foundation for Life Sciences

summary: We revealed that an enhancement of rice growth by 2'-deoxymugineic acid (DMA) application was observed not only under high pH conditions where iron availability for plant uptake was reduced but also under normal pH conditions. This result indicates that DMA application improves not only Fe availability for plants but also plant productivity. To explain a mechanism caused by the DMA application, molecular regulation in rice treated with or without DMA was analyzed using microarray analysis and qRT-PCR. Results provide insight into advantages of DMA application in rice seedlings.

overall_design: Gene expression patterns induced by DMA and EDTA in root and shoot were analyzed with control experiment (no chelator). One independent experiment was performed at each pH (pH 5.8 or pH 8.0).

first: Ryoichi

last: Araki


title: Transcriptomic landscape of lncRNAs in Inflammatory Bowel Disease

city: Copenhagen

first: Aashiq

middle: H.

last: Mirza

state: Herlev

address: Herlev Ringvej 75

department: University of Copenhagen, Herlev Hospital

country: Denmark

institute: Center for non-coding RNA in Technology and Health

summary:
Inflammatory bowel disease (IBD) is a complex multi-factorial inflammatory disease with Crohn’s disease (CD) and ulcerative colitis (UC) being the two most common forms. A number of transcriptional profiling studies have provided compelling evidence that describe the role of protein-coding genes and microRNAs in modulating the immune responses in IBD. In the present study, we performed a genome-wide transcriptome profiling of lncRNAs and protein-coding genes in inflamed and non-inflamed colon pinch biopsies from the IBD patients using expression microarrays platform.
In this study, we identified widespread dysregulation of lncRNAs and protein-coding genes in both inflamed and non-inflamed CD and UC  compared to the healthy controls. In case of inflamed CD and UC (iCD and iUC), we identified 438 and 745 differentially expressed lncRNAs, respectively, while in case of the non-inflamed CD and UC (niCD and niUC), we identified 12 and 19 differentially expressed lncRNAs, respectively. We also observed significant enrichment (p-value < 0.001, Pearson’s Chi-squared test) for 96 differentially expressed lncRNAs and 154 protein-coding genes within the IBD susceptibility loci. Furthermore, we found strong positive expression correlations for the intersecting and cis-neighboring differentially expressed IBD loci-associated lncRNA-protein-coding gene pairs. The functional annotation analysis of differentially expressed genes revealed that they are involved in immune response, pro-inflammatory cytokine activity and MHC protein complex. The lncRNA expression profiling in both inflamed and non-inflamed CD and UC, successfully stratified IBD patients from the healthy controls. Taken together, the identified lncRNA transcriptional signature along with clinically relevant parameters suggests their potential as biomarkers in IBD.

overall_design: A total of 96 biopsy samples (including 6 samples used as technical replicates) extracted from different colonic locations from 45 patients (CD=13, UC=20, Controls=12) were profiled using Agilent Custom 8x60K format lncRNA expression microarray. In Gencode v15 lncRNA microarray design, each lncRNA transcript is targeted by two probes covering 22,001 lncRNA transcripts corresponding to 12,963 lncRNA genes. In addition, each array contains 17,535 randomly-selected protein-coding targets, of which 15,182 (unique 12,787) correspond to protein-coding genes.

middle: H

last: Bang-Berthelsen

first: Stefan

middle: E

last: Seemann

first: Xiaoyong

last: Pan

first: Klaus

middle: S

last: Frederiksen

first: Mogens

last: Vilien

first: Jan

last: Gorodkin

first: Flemming

last: Pociot


title: Colorectal cancer cell lines are representative models of the main molecular subtypes of primary cancer

status: Public on Apr 09 2015

city: Melbourne

first: Oliver

last: Sieber

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Human colorectal cancer (CRC) cell lines are a used widely-used to model system for investigation investigate of tumour biology, experimental therapytherapeutic and biomarkers discovery. However, to what extent these established CRC cell lines represent and maintain the genetic diversity of primary cancers is uncertain. In this study, we analyzed 70 CRC cell lines were analysed for mutations using whole exome sequencing and DNA copy-number using by whole-exome sequencing and SNP microarray profilings, respectively. Presence of gGene expression was defined using RNA-Seq. Data from cellCell line datas were was compared to those that published from for primary CRCs published by in The the Cancer Genome Atlas Network. Notably, we found that The spectrum of exome mutations and DNA copy-number aberrations spectra in 70 CRC cell lines closely resembled those seen inat of primary colorectal tumours. Similarities included the presence of at least two hypermutation phenotypes, as defined by signatures of for defective DNA mismatch repair and DNA polymerase ε (POLE) proof-reading deficiency, and along with concordant mutation profiles in the broadly altered WNT, MAPK, PI3K, TGFβ and p53 pathways. In additionFurther, we documented mutations were enriched in genes involved in chromatin remodelling (ARID1A, CHD6, SRCAP) and histone methylation or acetylation (ASH1L, EP300, EP400, MLL2, MLL3, PRDM2, TRRAP). Chromosomal instability was prevalent in non-hypermutated cases, with similar patterns of whole, partial and focal chromosomal aberrations and overlapping significant minimal regions ofchromosomal gains and losses. While paired cell lines derived from the same tumour were found to exhibited considerable mutation and DNA copy-number differences, in silico simulations suggest that these differenceslargely mainly reflected a pre-existing heterogeneity in the tumour cells heterogeneity. In conclusion, our results establish that human CRC lines are representative of the main subtypes of primary tumours at the genomic level, further validating underscoring their utility as tools for to investigating investigate CRC biology and drug responses.

overall_design: 69 colorectal cancer cell lines were analysed for DNA copy number profiles.

first: Dmitri

last: Mouradov

first: Clare

last: Sloggett

first: Robert

middle: N

last: Jorissen

first: Christopher

last: Love

first: Shan

last: Li

first: Antony

last: Burgess

first: Diego

last: Arango

middle: L

last: Strausberg

first: Daniel

last: Buchanan

first: Samuel

last: Wormald

first: Liam

last: O'Connor

first: Jennifer

last: Wilding

first: David

last: Bicknell

first: Ian

last: Tomlinson

first: Walter

last: Bodmer

first: John

last: Mariadason


title: 1000 Genomes Phase 3 aCGH samples

status: Public on Jul 01 2015

city: Farmington

first: Charles

last: Lee

state: CT

address: 10 Discovery Dr.

institute: Jackson Laboratory for Genomic Medicine

type: Genome variation profiling by genome tiling array

summary: Copy number profiling of 1000 Genomes Phase 3 inidividuals using the Agilent 1M aCGH arrays

overall_design: Two color experiment. NA10851 used as reference against 2534 other individuals from the phase 3 of the 1000 Genomes project


title: Expression of genes involved in the T cell pathway in circulating immune cells of cattle orally challenged with BASE

status: Public on Apr 04 2015

city: Lodi

first: Andrea

last: Trovato

address: Via Einstein

institute: Parco Tecnologico Padano

summary: Bovine Amyloidotic Spongiform Encephalopathy (BASE) is a variant of classical BSE that affects cows and can be transmitted to primates and mice.The present work examined the effects of BASE on gene expression in circulating immune cells. Ontology analysis of genes differentially expressed between cattle orally challenged with brain homogenate from cattle confirmed as BASE and control cattle identified three main pathway which were affected. Within the immune function pathway, the most affected genes were related to the T Cell Receptor-mediated T Cell activation pathways. The differential expression of these genes in BASE challenged animals at 10,12 and 24 months following challenge vs controls, was investigated. The results of this study show that the effects of prion diseases are not limited to the CNS, but involve the immune system and particularly T cell signalling during the early stage following challenge before the appearance of signs if infection or clinical symptoms.

overall_design: In the present work we analysed 5 sample from cows orally challenged with BASE and  5 negative samples for the microarray analysis. Probes,  negative and quality controls of the microarray  were synthesized in duplicate. Samples from four orally challenged cattle and four different negative control Holstein cows were used for the confirmation and time-course studies with real time PCR. Each qRT-PCR reaction was performed in triplicate


title: Microarray analysis of large caged once mated females mortality study

status: Public on Apr 03 2015

city: Kearney

first: Kimberly

middle: Ann

last: Carlson

state: NE

department: Biology

institute: University of Nebraska at Kearney

summary: Two cages of 12,000 once mated females were used.  Samples were collected starting on Day 2 in the box, followed by days 9, 16, 23, 30, 37, 44, 51, 58, 65, 72, and 79 in the boxes.  The gene-expression profiles were computed over the lifespan of these females.

overall_design: Each time point was compared to the control time point of 2 days in the corresponding box.  There were two boxes A & B, with three replicates from each (Box A replicates = A, B, & C; Box B replicates = B, C, & D).

middle: A

first: Kylee

last: Gardner

first: Anjeza

last: Pashaj

first: Darby

middle: J

first: Fang

last: Yu

first: James

last: Eudy

first: Chi

last: Zhang

first: Lawrence

last: Harshman


title: Genomewide measurements of neural-specific mRNA decay in Drosophila embryos

status: Public on Apr 02 2015

city: Merced

first: Michael

last: Cleary

state: CA

address: 5200 N. Lake Rd.

department: School of Natural Sciences

institute: University of California, Merced

summary: Neural-specific mRNA decay measurements by TU-Decay technique in control and Pumilio knockdown embryos

overall_design: These TU-Decay microarrays analyze mRNA levels at three timepoints: a one hour pulse, one hour chase, and three hour chase.  Neural-specific RNA purification was achieved using prospero-GAL4 driving UAS-T.g.UPRT.  Pumilio knockdown in the nervous system was acheived using UAS-Pum(RNAi) driven by prospero-Gal4.

first: Mike

first: Dana

last: Burow


title: Plasma autoantibody associated with basal-like breast cancer

first: Jie

last: Wang

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

overall_design: Refer to individual Series


title: HUES cells: control and overexpressing OCT4

city: Marseille

first: michel

last: PUCEAT

address: 27 bd Jean moulin

department: University aix marseille

institute: INSERM

summary:
HUES24 cell line was nucleofected with POU5f1 cDNA to overexpress OCT4; This leads to the formation of mesendodermal cells
Short- and Long-scales intra- and inter-chromosomal interactions are linked to gene transcription, but the molecular event underlying these structures and how it affects cell fate decision during embryonic development are poorly understood. One of the first embryonic cell fate decisions (i.e mesendoderm determination) is driven by the POU factor OCT4, acting in concert with the high mobility group genes SOX-2 and SOX-17. Here, we identify novel chromatin remodelling mechanism and enhancer function driven by both OCT4 and SALL4 that mediate cell fate switching. We found that OCT4 alters the higher-order chromatin structure at both Sox-2 and Sox-17 loci. OCT4 titrates out cohesin and switches the Sox-17 enhancer from a locked (within an inter-chromosomal Sox-2 enhancer/CTCF/cohesin loop) to an active (within an intra-chromosomal Sox-17 promoter/enhancer/cohesin loop) state. SALL4 concomitantly mobilizes the polycomb complexes at the Soxs loci. Thus, OCT4/SALL4-driven cohesin-and polycombs-mediated changes in higher order chromatin structure mediate instruction of early cell fate in embryonic cells.

overall_design:
ChIP anti-OCT4 on chip.
results_v2.xls file description: Enriched binding sites. Mutant means oct4 overexpressing cells , wt GFP nucleofected cells.

first: Michel

last: Puceat


title: Comparison of gene expression in rice leaves inoculated with a virulent strain of Xanthomonas oryzae and its mutant deficient in typeIII secretion system.

status: Public on Apr 01 2015

city: Tsukuba

first: Eiichi

last: Minami

address: 2-1-2 Kannondai

institute: National Institute of Agrobiological Sciences

summary: Gene expression profiles in rice leaves near the inoculated site of Xanthomonas oryzae and its typeIII secretion mutant were examined.

overall_design: Rice plants (cv Nippnbare, 42 days old) were clip-inoculated with a virulent strain of Xanthomonas oryzae and its △hrcV mutant.  At each time points, leaf segments were excised below the clipped site (3 to 5 mm in length) and gene expression profiles were analyzed by microarray.

first: Shigeru

last: Tanabe

first: Hirokazu

last: Ochiai


title: Gene expression in rice roots in response to inoculation with rice blast fungus

summary: Rice roots grown in hydroponic culture were inoculated with rice blast fungus and gene expression profiles were analyzed by microarray

overall_design: Roots of two isogenic lines of rice cv Nipponbare (blast-resistance gene: Pia or pia) were inoculated with rice blast fungus, P91-15B, carrying avirulence gene, AvrPia.  Total RNA was isolated from crown roots, labeled with cy3, and probed with agilent rice oligoarray (4x44).

first: Tanabe

last: Shigeru


title: Gene expression in rice leaves (Pia) in response to inoculation with rice blast fungus

summary: Fourth leaves of rice seedlings (4.5 leaf stage) grown in hydroponic culture were inoculated with rice blast fungus and gene expression profiles were analyzed by microarray.

overall_design: Fourth leaves of the two isogenic lines of rice cv Nipponbare (blast-resistance gene: Pia or its mutant, pia) were inoculated with rice blast fungus, P91-15B, carrying avirulence gene, AvrPia.  Total RNA was isolated, labeled with cy3, and probed with agilent rice oligoarray (4x44).


title: Gene expression in rice leaves (Pish) in response to inoculation with rice blast fungus

overall_design: Fourth leaves of the two isogenic lines of rice cv Nipponbare (blast-resistance gene: Pish or its mutant, pish) were inoculated with rice blast fungus, Kyu77-07A, carrying avirulence gene, AvrPish.  Total RNA was isolated, labeled with cy3, and probed with agilent rice oligoarray (4x44).


title: Intra-tumor genetic heterogeneity in breast cancers with heterogeneous HER2 gene amplification

status: Public on Apr 16 2015

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

state: MI

address: Via Rita Montalcini 4

department: Biomedical Sciences

institute: Humanitas University

summary: We separately analyzed the HER2-negative and HER2-positive components of 12 HER2 heterogeneous breast cancers using gene copy number profiling and massively parallel sequencing, and identified potential driver genetic alterations restricted to the HER2-negative cells in each case. Our results indicate that even driver genetic alterations, such as HER2, can be heterogeneously distributed in a cancer, and that the HER2-negative components are likely driven by genetic alterations not present in the HER2-positive components, including BRF2 and DSN1 amplification.

overall_design: 13 breast cancers with heterogeneous HER2 protein overexpression and HER2 gene amplification by central immunohistochemistry and CISH were amenable to microdissection, as HER2-positive and HER2-negative areas were sufficiently discrete. The HER2-positive and HER2-negative components were microdissected either on a PixCell II laser capture microdissector (Arcturus) into separate tubes from 8um-thick representative tissue sections stained with HercepTest for guidance, or using a sterile needle under a stereomicroscope in selected cases.

first: Arnaud

last: Gauthier

first: Anne

last: Vincent-Salomon

first: Jorge

last: Reis-Filho


title: Effects of hnRNP A1 on gene expression in oral squamous cell carcinoma

status: Public on Mar 31 2015

city: Wuhan

first: Rong

last: Jia

address: 237 Luoyu Rd

institute: Wuhan University

summary: To find the discover target genes regulated by hnRNP A1 in oral squamous cell carcinoma, NimbleGen 12x135K microarrays were used to find the gene expression changes between hnRNP A1 or non-specific (NS) siRNA treated oral cancer cells.

overall_design: Cal27 cells were treated with hnRNP A1 or non-specific (NS) siRNA twice in a 48-hour interval. After 96 hours, total RNAs were collected for microarray assay.  Total RNAs from hnRNP A1 knockdown (3 samples) or NS siRNA treated cells (3 samples) were used for chip experiment (6 chips). Each chip measures the expression levels of human 45,033 genes. NimbleGen One-Color DNA Labeling Kit was used for sample labeling. Hybridization was performed in NimbleGen Hybridization System. After washing, slides were scanned with Axon GenePix 4000B scanner. Data was extracted and normalized using NimbleScan v2.5 Software.

first: Jihua

last: Guo


title: Identification of genes activated in cancer cells cultured under hypoxia and serum-free condition

city: Yokohama

first: Shiro

last: Koizume

state: Please Select

address: 2-3-2 Nakao Asahi-ku

institute: Kanagawa Cancer Center Research Institute

summary: To identify genes activated under hypoxia (1%O2) and serum-free treatment of a cancer cell line, we performed cDNA microarray analysis with an ovarian cancer cell line, OVSAYO.

overall_design: Cells were cultured under normoxia /hypoxia (1%O2) and serum-plus/serum-minus conditions for 16 hours. Total RNA was isolated for cDNA microarray analysis.


title: Arabidopsis thaliana: wild type vs. scl15 mutant

status: Public on Mar 30 2015

city: Saskatoon

first: Dwayne

last: Hegedus

address: 107 Science Place

institute: Agriculture Canada

summary:
Epigenetic regulation of gene expression is critical for controlling embryonic properties during the embryo-to-seedling phase transition. Here we report that a HISTONE DEACETYLASE19 (HDA19)-associated regulator, SCARECROW LIKE15 (SCL15), is essential for repressing the seed maturation program in vegetative tissues.
SCL15 is expressed and GFP-tagged SCL15 predominantly localizes to the vascular bundles, particularly in the phloem companion cells and neighbouring specialized cells. Mutation of SCL15 leads to a global shift in gene expression in seedlings to a profile resembling late embryogenesis in seeds.
In scl15 seedlings, many genes involved in seed maturation are markedly derepressed and 12S globulin accumulates; this is correlated with elevated levels of histone acetylation at a subset of seed-specific loci.
SCL15 physically interacts with HDA19 and direct targets of HDA19-SCL15 association are identified. These studies revealed that SCL15 acts as an HDA19-associated regulator to repress embryonic traits in seedlings.

overall_design: Two-condition experiment: wild type vs. scl15 mutant seedlings. Biological replicates: 3 wild type and 3 mutant, independently grown and harvested. One replicate per array. Dye-swaps were performed.

first: Ming

last: Gao


title: Physiological and genomic analysis of Saccharomyces cerevisiae artificial hybrids with improved fermentation performance and mannoprotein release capacity

city: Paterna (Valencia)

first: Laura

last: Pérez Través

address: Avda Catedrático Agustín Escardino

institute: IATA

summary:
Yeast mannoproteins contribute to several aspects of wine quality by protecting wine against protein haze, reducing astringency, retaining aroma compounds and stimulating growth of lactic-acid bacteria. The selection of a yeast strain simultaneously overproducing mannoproteins and showing good fermentative characteristics is a difficult task. In this work, a Saccharomyces cerevisiae x Saccharomyces cerevisiae hybrid bearing the two oenologically relevant features was constructed and a reduction in the amount of bentonite necessary for wine stabilization was observed for wines fermented with the generated strain. Additionally, different copy numbers of some genes probably related with these physiological features were detected in this hybrid. Hybrid share with parental Sc1 similar copy number of genes SPR1, SWP1, MNN10 and YPS7 related to cell wall integrity and with parental Sc2 similar copy number of some glycolytic genes as GPM1 and HXK1 as well as genes involved in hexose transport as HXT9, HXT11 and HXT12. This work demonstrates that artificial hybridization and stabilization in winemaking conditions constitute an effective approach to obtain yeast strains with desirable physiological features as mannoprotein overproducing capacity and improved fermentation performance, characteristics genetically depending on the coordinated expression of a multitude of different genes.
In this work, genetically stable mannoprotein overproducing Saccharomyces cerevisiae strains simultaneously showing excellent fermentation capacities were obtained by hybridization methods giving rise to non-GMO strains. The potential relationship between the copy number of specific genes and the improved features was also evaluated by means of aCGH analysis of parental and hybrid strains.

last: Pérez-Través

first: Christian

last: Lopes

first: Ramón

last: González

first: Eladio

last: Barrio

first: Amparo

last: Querol


title: Genome-wide analysis of mRNA expression in brat mutant versus w1118 early Drosophila embryos

status: Public on Mar 28 2015

first: Howard

last: Lipshitz

state: ON

address: 1 King's College Circle

department: Molecular Genetics

institute: University of Toronto

summary: mRNA expression was assessed genome-wide in brat mutant and w1118 early Drosophila embryos, to elucidate the role of BRAT in regulating mRNA stability. Four different time-points were analyzed for each genotype: 0-to-1.5 hours post-egglaying, 1.5-to-3.0 hours post-egglaying, 3.0-to-4.5 hours post-egglaying, and 4.5-to-6.0 hours post-egglaying.

overall_design: There are a total of 24 samples. This includes 3 biological replicates for each of the following: 1) 0-to-1.5 hour brat mutant embryos, 2) 1.5-to-3.0 hour brat mutant embryos, 3) 3.0-to-4.5 hour brat mutant embryos, 4) 4.5-to-6.0 hour brat mutant embryos, 5) 0-to-1.5 hour w1118 embryos, 6) 1.5-to-3.0 hour w1118 embryos, 7) 3.0-to-4.5 hour w1118 embryos, and 8) 4.5-to-6.0 hour w1118 embryos.

first: John

last: Laver

first: Xiao

last: Li

first: Debashish

last: Ray

first: Kate

middle: B

last: Cook

first: Noah

last: Hahn

first: Syed

last: Nabeel-Shah

first: Mariana

last: Kekis

first: Hua

last: Luo

first: Alexander

last: Marsolais

first: Karen

last: Fung

first: Timothy

middle: R

last: Hughes

first: J

middle: T

last: Westwood

first: Sachdev

last: Sidhu

first: Quaid

last: Morris

first: Craig

last: Smibert


title: Transcriptomic profiling of gametogenesis in triploid oysters

status: Public on Mar 26 2015

city: Caen

first: Nolwenn

middle: Marie

last: Dheilly

address: Esplanade de la Paix

department: Biological sciences

institute: Universite de caen

summary:
Background  Triploidy can occur in all species but is often lethal in birds and mammals. In amphibian, invertebrates and numerous species of fishes, triploid animals are viable and undistinguishable from diploid individuals. Gametogenesis is often affected and most animals are sterile for at least one sex, and gametes for the other sex are often unfertile. Although the majority of triploid oysters are sterile (beta individuals, 3nb), a low but persistent proportion of male and female animals produce gametes (alpha individuals, 3na). Thus, oysters constitute a unique model to study the effect of triploidy on germ cells development of both male and females. In this study, we used microarray to study the consequences of polyploidy on triploid oyster germ cells mitosis and meiosis.

Results  We compared the transcriptome of gonads of 3na and 3nb oyster gonads over the course of gametogenesis to the transcriptome of diploid (2n) oyster gonads. This study allowed us to reveal an increase in DNA repair and apoptosis through the NF-kappaB pathway, and a decrease in actin remodeling and chromatin remodeling in all 3n oysters. The comparison of 3na and 3nb individuals with 2n revealed that a pachytene checkpoints may be responsible for the success in gametogenesis of 3na individuals and for the observed delay in gametogenesis. However, the sterility of 3nb individuals can be explained by a disruption of sex determinism mechanisms. Indeed 3nb females express male-specific genes including enkurin and an Elav-like gene, and 3nb males express female-specific genes including Forkhead box L2 and beta-catenin.

Conclusions  Our results bring back to the front of the research field the questions of genetic sex determinism, mitosis/meiosis control, pachytene checkpoint, and cell type specific DNA damage pathways. Furthermore, this study identifies numerous new candidate genes which function should now be studied in details in oysters and in other triploid animals in order to elucidate the complex mechanisms involved in the regulation of triploid cells division.

overall_design: Triploid spats were obtained by crossing tetraploid males and diploid females in the ifremer experimental hatchery (La tremblade, Charente Maritime, France). We performed microarray analysis on a total of 35 individual triploid gonads that can be grouped as follow: 3n stage 0 (4 individuals), 3n alpha Stage 1 (8 individuals), 3n beta Stage 1 (8 individuals), 3n alpha Stage 3 male (4 individuals), 3n beta Stage 3 male (3 individuals), 3n alpha Stage 3 female (4 individuals), and 3n beta stage 3 female (4 individuals).

middle: M

first: Christophe

last: Lelong

first: Pascal

last: Favrel

first: Jouaux

last: Aude


title: RIP-Chip of BRAT and PUM from 0-3 hour Drosophila melanogaster embryos

city: Toronto

first: Howard

last: Lipshitz

summary: BRAT-associated mRNAs and PUM-associated mRNAs were identified in early Drosophila embryos by RNA co-immunoprecipitation of the endogenous proteins using synthetic antibodies, followed by microarray analysis (RIP-Chip).

overall_design: Nine RNA co-immunoprecipitations were performed. This includes 3 biological replicates each of 1) anti-BRAT RNA co-immunoprecipitations from wild-type 0-3 hour embryos, 2) anti-PUM RNA co-immunoprecipitations from wild-type 0-3 hour embryos, and 3) control antibody RNA co-immunoprecipitations from wild-type 0-3 hour embryos. BRAT samples and PUM samples were each normalized separately with the control samples, for a total of 12 processed samples (3 BRAT with 3 control normalized together, and 3 PUM with 3 control normalized together) from the 9 RNA co-immunoprecipitations.

first: John

last: Laver

first: Xiao

last: Li

first: Debashish

last: Ray


title: Genomewide measurements of whole embryo mRNA decay in Drosophila

first: Michael

last: Cleary

summary: whole embryo (all tissues) measurement of mRNA decay by 4-thiouridine pulse-chase

overall_design: These TU-Decay microarrays analyze mRNA levels at three timepoints: a one hour pulse, one hour chase, and three hour chase.  Measurements with or without transcription inhibition by actinomycin D (ActD) were compared.

first: Mike

first: Dana

last: Burow


title: NanoString nCounter GX Cancer Reference Kit and the custom made ITESM (14 genes associated with prostate cancer)

status: Public on Mar 25 2015

city: Monterrey

first: Roberto

last: Portillo Lara

state: Nuevo León

address: Ave. Eugenio Garza Sada 2501 Sur Col. Tecnológico

department: División de Biotecnología y Alimentos

country: Mexico

institute: Tecnológico de monterrey

summary: Cancer stem cells (CSC) drive prostate cancer tumor survival and metastasis. Nevertheless, the development of specific therapies against CSCs is hindered by the scarcity of these cells in prostate tissues. Suspension culture systems have been reported to enrich CSCs in primary cultures and cell lines. However, the molecular mechanisms underlying this phenomenon have not been fully explored. We describe a prostasphere assay for the enrichment of CD133+ CSCs in four commercial PCa cell lines: 22Rv1, DU145, LNCaP, and PC3. Overexpression of CD133, as determined by flow cytometric analysis, correlated with an increased clonogenic, chemoresistant, and invasive potential in vitro. This phenotype is concordant to that of CSCs in vivo. Gene expression profiling was then carried out using the Cancer Reference kit and the custom made ITESM CodeSets with the nCounter system from NanoString Technologies. This analysis revealed several upregulated transcripts that can be further explored as potential diagnostic markers or therapeutic targets. Furthermore, functional annotation analysis suggests that ΔNp63α modulates the activation of developmental pathways responsible for the increased stem identity of cells growing in suspension cultures. We conclude that profiling the genetic mechanisms involved in CSC enrichment will help us to better understand the molecular pathways that underlie CSC pathophysiology. This platform can be readily adapted to enrich and assay actual patient samples, in order to design patient-specific therapies that are aimed particularly against CSCs.

overall_design: PC3 prostasphere cultures were sampled on day 0 (Parental monolayers) (EPI_1), day 4 (EPI_2), day 8 (EPI_3), and day 12 (EPI_4) of culture. Day 12 prostaspheres were also enzymatically dissociated and sorted via MACS using the Anti-CD133/2 (293C3)-PE Antibody (Miltenyi) into CD133+ (EPI_P) and CD133- (EPI_N) fractions. Total RNA was extracted from these fractions and analyzed using the nCounter GX Cancer Reference kit and the custom made ITESM CodeSet from NanoString Technologies. Three independent experiments were carried out in parallel.

first: Mario

last: Moisés Alvarez


title: Chromosomal meiotic segregation, embryonic developmental kinetics and DNA (hydroxy)methylation analysis reassure the safety of human oocyte vitrification in a high security closed system

status: Public on Mar 24 2015

city: Brussels

first: Kurt

last: Jacobs

address: Laarbeeklaan 103

department: Faculty of Medicine and Pharmacy

country: Belgium

institute: Vrije Universiteit Brussel (VUB)

summary: Oocyte vitrification has been introduced into clinical settings without pre-clinical safety testing. In this study, we analyzed the safety of human oocyte

overall_design: Biopsied PBs were collected into sterile PCR tubes. The samples and positive/negative control samples were lysed, fragmented and amplified using the SurePlex whole genome amplification kit (BlueGnome, Cambridge, UK) according to the manufacturer’s instructions (www.illumina.com). Sample and reference DNA (male and female) were labelled with Cy3 and Cy5 following the manufacturer’s instructions. Labelling mixes were combined and hybridized on 24sure Cytochip (V3, BlueGnome, Cambridge, UK) for about 12 hours. Fluorescence intensity was detected using a laser scanner (Agilent scanner G2565BA), and BlueFuse Multi software was used for data processing (BlueGnome, Cambridge, UK). Each sample is compared with both a male and a female reference. Once a specific amplification was observed, autosomal profiles were analysed for gain or loss of whole or partial chromosomal ratios using a 3SD assessment, ⩾0.3log2 ratio call or both. To pass hybridization quality controls, sex-mismatched female samples had to show a consistent gain on chromosome X and a consistent loss of chromosome Y. Sex-matched female samples had to consistently show no change on either chromosome X or Y.

first: Neelke

last: De Munck

first: Laetitia

last: Petrussa

first: Greta

last: Verheyen

first: Catherine

last: Staessen

first: Yves

last: Vandeskelde

first: Johan

last: Sterckx

first: Geertrui

last: Bocken

first: Dominic

last: Stoop

first: Martine

last: De Rycke

first: Hilde

last: Van de Velde


title: Human melanoma transcriptom is modulated by cold plasma treatment

status: Public on Feb 18 2015

city: Greifswald

first: Anke

last: Schmidt

state: MV

address: Felix-Hausdorff-Str. 2

department: Plasma Life Science

institute: INP Greifswald

summary:
Treatment of tumor progression and metastasis continues to be of major importance in the field of cancer. It is reported that cancer cells often show a pronounced sensitivity towards oxidative stress. Cold plasma offers the ability to deliver a delicate mix of reactive oxygen and nitrogen species directly into cells or tissues. Using a well-described argon plasma jet, we investigated the biological responses of plasma on tumor cell death, cell migration, and expression of adhesion-associated genes as well as cytoskeletal modifications. Using the human melanoma cancer cell line SK-Mel-147 we were able to show that plasma induced only little apoptosis but had profound effects on tumor cell motility. Plasma treatment of cells was associated with an inhibition of migration and disorganization of the actin cytoskeleton which were mediated through multiple signaling pathways, as transcriptome-wide gene analysis suggested. Specifically, changes in cell adhesion were regulated by differential expression of cell junction and cell-matrix proteins. These results provide evidence that plasma may be able to disturb the migration and adhesion in metastatic SK-Mel-147 cells.
Microarrays were used to analyze and investigate the biological effects of cold plasma on human melanoma cell line SK-Mel-147. Using an argon plasma jet kinpen, regulated transcripts were analyzed and further described in Schmidt et al. (2015): “Human melanoma cell migration and adhesion is decreased by cold plasma treatment”.

overall_design: A study using total RNA recovered from human SK-Mel-147, treated with cold plasma as well as H2O2-treated and untreated SK-Mel-147 controls.

first: Thomas

last: von Woedtke


title: Gene expression of Vibrio parahaemolyticus in the early stationary phase

status: Public on Jan 31 2015

city: Berlin

first: Stephan

last: Huehn

address: Koenigsweg 69

institute: Freie Universität Berlin

summary: Naturally bacteria are commonly forced to remain in stationary phase. There is no increase in cell mass, however, cell division keep on. Vibrio (V.) parahaemolyticus is an aquatic bacterium capable of causing foodborne gastroenteritis outbreaks all over the world. So far, little is known about whole genomic expression of V. parahaemolyticus in the early stationary phase compared with the phase of exponential growth. Since under starvation cell sizes decrease and endogenous metabolism reduces, genes are considered to be highly repressed in the stationary phase. However, our data shows in total 172 induced genes, while 61 genes were repressed in the early stationary phase compared with exponential phase. In fatty acid and phospholipid metabolism functional category only induced genes were found, whereas in three other metabolic functional groups appeared no significant up-regulated genes (adjusted P-value<0.05). Genes in two metabolic functional categories remained stable in the early stationary phase. DAVID analyses were carried out exploring the gene regulation. In total, ten functional categories showed a total up-regulation in early stationary phase, while only three metabolic functional categories showed a down-regulation and four categories showed stably in early stationary phase.

overall_design: Early stationary phase gene expression was detected in total bacterial RNA of V. parahaemolyticus. Two phases (exponential phase and early stationary phase) were used in 8 biological replicates. Gene expression  in exponential phase was used for normalization.

first: Lu

last: Meng

last: Alter

first: Tommi

last: Aho


title: Radiation-Induced T Cell Lymphoma: Carbon ion- vs. Gamma Ray-Induced

status: Public on Mar 03 2015

city: Inage-ku

first: Benjamin

middle: John

last: Blyth

state: Chiba

address: 4-9-1 Anagawa

department: Centre for Radiation Protection

institute: National Institute of Radiological Sciences

summary: Here, male and female B6C3F1 mice were given single or fractionated whole-body exposure(s) to a monoenergetic carbon ion radiotherapy beam at the Heavy Ion Medical Accelerator in Chiba, Japan, matching the radiation quality delivered to the normal tissue ahead of the tumour volume. These mice were then monitored for the remainder of their lifespan and a large number of T cell lymphomas were analysed, alongside those arising in mice exposed to equivalent doses of standard Cs137 gamma ray-irradiation. Using genome-wide DNA copy number analysis to identify genomic loci involved in radiation-induced lymphomagenesis and subsequent detailed analysis of Notch1, Ikaros, Pten, Trp53 and Bcl11b genes we compared the genetic profile of the carbon ion- and gamma ray-induced tumours. The canonical set of genes previously associated with radiation-induced T cell lymphoma was identified in both radiation groups. While the pattern of disruption of the various pathways was somewhat different between the radiation types, most notably Pten mutation frequency and loss of heterozygosity flanking Bcl11b, the most striking finding was the observation of large interstitial deletions at various sites across the genome in carbon ion-induced tumours, which were only seen infrequently in the gamma ray-induced tumours analysed.

overall_design: 32 unique tumours (12 gamma ray-induced, 20 carbon ion-induced) each with sex-matched reference DNA

first: Yoshiya

last: Shimada


title: Expression analysis of Pseudomonas aeruginosa PAO1 fatty acid synthesase II (FASII) deletions complemented by excess or limited expression of FASII genes accD, fabG, and fabF1

status: Public on Mar 09 2015

city: Worcester

first: Donald

last: Moir

state: Massachusetts

address: 1 Innovation Dr.

department: Anti-infectives

institute: Microbiotix, Inc.

summary:
Investigation of whole genome gene expression level changes in Pseudomonas aeruginosa PAO1 regulated complemented FASII deletions, compared under conditions of excess and limited expression of the complementing copies.  The mutations engineered into this strain render it dependent on lac-regulated expression of the complementing gene copies on the extrachromosomal plasmid pUCP24.
The mutants analyzed in this study are further described in Wallace et al., Antimicrobial Agents and Chemotherapy, vol 9, 2015

overall_design: A twelve chip study using total RNA recovered from three separate cultures of Pseudomonas aeruginosa regualted complemented FASII gene deletions under excess IPTG (high level expression of complementing gene copy) and three separate cultures under limited IPTG (low level expression of complementing gene copy).  Each chip measures the expression level of 5,553 genes from Pseudomonas aeruginosa PAO1-LAC (ATCC47085)  with fourteen 24-mer probe pairs (PM/MM) per gene, with probes on the array five times.  Two biological replicates were done for each sample for a total of 12 chips.

first: Joselynn

last: Wallace


title: A Nested Parallel Experiment Demonstrates Differences in Intensity-Dependence Between RNA-Seq and Microarrays

city: Princeton

first: David

middle: Garrett

last: Robinson

state: New Jersey

address: Washington Road

department: Lewis-Sigler Institute

institute: Princeton University

summary: We carried out a parallel nested experiment performed simultaneously on RNA-Seq and microarrays that systematically split variation into four stages (treatment, biological variation, library preparation, and chip/lane noise), allowing a separation and comparison of the sources of variation in a well-controlled cellular system, Saccharomyces cerevisiae.

overall_design:
Nested design. Two conditions (E for ethanol and G for glucose as sole carbon source), each grown on two biological replicates (1 and 2), prepared in two technical preparations (A and B), then hybridized to two chips (1 and 2)

This submission represents microarray component of study.

middle: G

first: Jean

middle: Y

last: Wang


title: Association of egg mass and egg sex in chicken

status: Public on Jan 29 2015

city: Wageningen

first: Dirkjan

last: Schokker

address: Droevendaalsesteeg 1

department: Wageningen Livestock Research

country: Netherlands

institute: Wageningen UR

summary: Association of egg mass and egg sex: gene expression analysis from maternal RNA in the germinal disc region of layer hens (Gallus gallus)

overall_design: Maternal RNA in the germinal disc region of layer hens (Gallus gallus) was taken from multiple hens, of which half showed female bias ratio and half showed male biased ratio.

first: Aamir

last: Aslam


title: Radiation induced gene signature predicts pathologic complete response to neoadjuvant chemotherapy in breast cancer patients

status: Public on Jan 21 2015

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: Purpose:The identification of biomarkers predictive of neoadjuvant chemotherapy response in breast cancer patients would be an important advancement in personalized cancer therapy. We hypothesized that due to similarities between radiation and chemotherapy induced cellular response mechanisms, radiation responsive genes may be useful in predicting response to neoadjuvant chemotherapy. Materials and Methods: Murine p53 null breast cancer cell lines representative of the luminal, basal-like and claudin-low human breast cancer subtypes were irradiated to identify radiation responsive genes. These murine radiation induced genes were then converted to their human orthologs. These genes were then used to develop a predictor of pathologic complete response (pCR) that was validated on two independent published neoadjuvant chemotherapy data sets of genomic data with response. Results: A radiation induced gene signature consisting of 30 genes was identified on a training set of 337 human primary breast cancer tumor samples that was prognostic for survival. Mean expression of this signature was calculated for individual samples in two independent published datasets and was found to be significantly predictive of pathologic complete response. Multivariate logistic regression analysis in both independent datasets showed that this 30 gene signature added significant predictive information independent of that provided by standard clinical predictors and other gene expression based predictors of pathologic complete response. Conclusion: This study provides new biologic information regarding response to neoadjuvant chemotherapy and a means of possibly improving the prediction of pathologic complete response.

overall_design: reference x sample

first: Daniel

last: Oh

first: Maggie

last: Cheang


title: Loss of malignancy of the spontaneous pulmonary metastasis in a human-in-mouse breast cancer model

status: Public on Dec 31 2014

summary: Patient-derived human-in-mouse breast tumor xenograft models with spontaneous lung metastases1 have emerged as a powerful system to characterize and target cancer metastasis. To evaluate the malignancy of metastatic lesions in the mouse lungs, we implanted the pulmonary metastatic cells into the mouse mammary fat pads. Surprisingly, compared to the parental tumor model, the lung met-derived model showed a slower growth rate and a reduced metastatic potential with a more differentiated epithelial status. Then we characterized the genetic and epigenetic features acquired by the lung met-derived breast tumor model, combining microRNA/gene array analyses with RNA-sequencing. The lung met-derived model displayed differential expression profiles of a few hundred genes and many microRNAs, whereas the RNA sequencing data identified an overall increase of single nucleotide alternations in the 3’UTRs of genes, possibly subject to microRNA regulations. Subsequently, we identified microRNA-138 as a regulator of invasion and epithelial-mesenchymal transition (EMT) by directly targeting EZH2, a polycomb epigenetic regulator. Our results highlight the importance of epigenetic regulation by microRNAs and genes in regulating breast cancer invasion and EMT.

first: Jessica

last: Bockhorn

first: Aleix

middle: P

last: Aparicio

first: Huiping

last: Liu


title: Profiling of long noncoding RNAs and mRNAs in neonatal and adult mouse testis

status: Public on Jan 01 2015

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

summary: Todate, the investigation into the molecular mechanisms of testis development and spermatogenesis has largely focused on the role of protein-coding genes and small noncoding RNA including microRNAs and piRNAs. In recent years, long noncoding RNAs (lncRNAs) have been shown to play critical regulatory roles in mammalian development. To understand the role of lncRNAs in development of the mammalian testis and spermatogenesis, we firstly utilized commercial microarray to systematically investigate lncRNAs expression profiles of neonatal (6-day-old) and adult (8-week-old) mouse testis. By comparison the lncRNAs expression profiles of two developmental stage of testes, we obtained the differentially expressed lncRNAs and examined their genomic context, promoter characteristics, neighbored protein-coding genes, provide an important foundation for future research on molecular mechanisms of lncRNAs in mammalian testis development and spermatogenesis.

overall_design: LncRNAs expression profiles were measured using neonatal (6-day-old) and adult (8-week-old) C57/BL6 mouse testis. Each of two age groups have three biological replicates.

first: Jin

last: Sun


title: Microarray Analysis for the Screening of Genes Inducible by Light or Low Temperature in Post-veraison Grape Berries

status: Public on Dec 16 2014

city: Shizuoka

first: Hiroshi

last: Fujii

state: Shizuoka

address: 485-6 Okitsunakacho, Shimizu

department: Division of Citrus Research

institute: Institute of Fruit Tree Science, NARO

summary:
Flavonoid biosynthesis in grape berry skin is affected by environmental factors such as light and temperature. However, the components of the light-signaling and low-temperature-induced ABA signaling networks related to flavonoid accumulation in grape berry skin have not been fully elucidated.
To clarify details of the possible light- and ABA-related signal transduction networks, we performed comprehensive transcriptome analysis using grape berries cultured under different light and temperature conditions. We identified 40 light-inducible genes, 55 low-temperature-inducible genes, and 34 genes induced by light plus low temperature.

overall_design: 12 samples were analysed. The experiment had 4 conditions and  included 3 repetition.

first: Akifumi

last: Azuma

first: Takehiko


title: TBCRC 018:  Phase II study of iniparib in combination with irinotecan to treat progressive triple negative breast cancer brain metastases

summary: Approximately half of women diagnosed with advanced triple negative breast cancer (TNBC) will develop brain metastases, of which the majority will have uncontrolled extracranial disease. While local therapies to treat brain metastases are standardly prescribed, survival remains less than 6 months.  This phase II, multi-center trial evaluated efficacy of irinotecan and iniparib, anti-cancer agents with activity in TNBC and known to cross the blood brain barrier, among 34 patients with new or progressive TNBC brain metastases.  While time to progression was short (2.1 months), 27% of patients experienced intracranial clinical benefit and therapy was well-tolerated. Correlative studies illustrate partial response was associated with germline BRCA mutation status and high tumor expression of proliferation genes and signatures. To our knowledge, this is the first study showing feasibility of enrolling patients with progressive TNBC brain metastases to a systemic therapy and lays the groundwork for future studies to treat this devastating disease.

overall_design: 24 tumor FFPE samples of this trial, representing 21 individual patients, were gene expression profiled. Expression of 128 selected genes was evaluated, including 5 HK genes.

last: Prat

first: Carey

last: Anders


title: Detection of potential microRNA biomarker for postmenopausal osteoporosis

status: Public on Dec 23 2014

city: Harbin

first: Wenliang

last: Zhu

address: 246 Xuefu Road

institute: the Second Affiliated Hospital of Harbin Medical University

summary: Recent studies have shown that microRNAs (miRNAs) are implicated in the development of postmenopausal osteoporosis, implying potential biomarkers. We performed a microarray-based expression scanning to search for potential circulating miRNA biomarkers for postmenopausal osteoporosis as whole blood obtianed from patients was used.

overall_design: MiRNA expression in the whole blood of 23 Chinese postmenopausal women with osteopenia and that of 25 Chinese postmenopausal women with osteoporosis. After total RNA was extracted, all of the RNA extraction samples were seperately pooled into six subgroups according to the T-score measurement.


title: Gene expression in post cardiac surgery acute kidney injury

status: Public on Sep 29 2014

city: Bristol

first: Mohamed

middle: T.

last: Ghorbel

address: Level 7, BRI, Marlborough street

department: Bristol Heart Institute

institute: University of Bristol

summary:
To determine the changes in intra-renal gene expression in a novel large animal model of post Cardiopulmonary Bypass (CPB) acute kidney injury, we collected renal medulla samples obtained 24hours post intervention.
The transcriptional profile of the mRNA in these samples was measured with gene array technology.

overall_design: Pigs were subjected to 2.5 hours of general anaesthesia or 2.5 hours of CPB under general anaesthesia. Renal medulla samples were collected 24 hours post intervention.


title: Whole blood gene expression profiling of rheumatoid arthritis patients

status: Public on Sep 01 2014

city: Boston

first: Kenzie

last: MacIsaac

state: MA

address: 33 Avenue Louis Pasteur

department: Genetics and Pharmacogenomics

institute: Merck Research Labs

summary: Approximately 30% of rheumatoid arthritis patients achieve inadequate response to anti-TNF biologics. In this study, we sought to identify a blood gene expression biomarker correlating with 12-week response to infliximab in patients with moderate to severe disease. Response was assessed using dynamic contrast-enhanced MRI imaging of the wrist.

overall_design:
Baseline whole blood samples from 59 patients were collected as part of a placebo-controlled clinical study of infliximab in rheumatoid arthritis. Samples were profiled by Affymetrix microarray and correlation between gene expression and 12-week response was assessed.
DAS28 (Disease Activity Score including a 28-joint count)

middle: D


title: MicroRNA expression profile in TRAIL-sensitive and -resistant H460 cells

city: Columbus

first: Alessandra

last: Drusco

state: Ohio

address: 460 W 12th Ave

institute: The Ohio State University

summary: We generated H460 cells with acquired TRAIL resistance by exposing the parental  sentisitve cells to subtoxic concentrations of TRAIL for 6 months. Then we compared the microRNA expression profile in the sensitive versus  resistant cells.

overall_design: H460 cells were treated with subtoxic concentrations of TRAIL for 6 month. After confirmation of the resistance, the RNA was extracted and the microRNA expression profile was analyzed using the NanoString technology.

first: M

last: Garofalo

first: Young-Jun

last: Jeon


title: Cell state transitions regulated by Slug are critical for tissue regeneration and tumor initiation

status: Public on Jun 23 2014

first: Charles

last: Perou

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

overall_design: Refer to individual Series


title: Transcriptome analysis along berry development of 'Syrah' x 'Pinot Noir' offspring extreme for flavonoid content

status: Public on Aug 13 2014

city: S. Michele a/Adige

first: Giulia

last: Malacarne

state: Trento

address: Via Edmund Mach,1

department: Genomics and Biology of Fruit Crops Department

institute: Edmund Mach Foundation

summary:
Anthocyanins and flavonols are natural compounds that accumulate preferentially in grapevine flowers and fruits. They are among the most abundant flavonoids and play a very important role in grape and wine quality. In particular, they confer and stabilize colour and contribute to other organoleptic characteristics of the final product. Their complex profile in terms of concentration and relative abundance varies among cultivars and makes wine typicity. The synthesis of these compounds is mainly regulated at transcriptional level. Flavonoids accumulate at specific stages and in specific tissues during flower and berry development, as a consequence of the timely expression of the genes necessary for their synthesis. Although the general flavonoid pathway has been genetically and biochemically elucidated and the main determinants of colour have been identified, the molecular reasons of the fine variation among grape cultivars are still not completely understood.
To shed light on this issue, extreme genotypes of a segregating population  derived from the cross Syrah x Pinot Noir were characterized at transcriptional level. The transcriptome analysis along three berry developmental stages of these genotypes has allowed the identification of a large set of transcripts differentially modulated between the two groups.

overall_design: A population derived from ‘Syrah’ x ‘Pinot Noir’ consisting of 170 F1 individuals plus the parental lines was characterized for the content of flavonols and anthocyanins in the skins of mature berries (38E-L; 18°Brix). Based on the biochemical data, two groups of 4 high- and 4 low-flavonol producers each (HFPs and LFPs: F1 16, F1 56, F1 63, F1 223 and F1 64, F1 256, F1 260, PN), three of which having also either very high or very low anthocyanin content (HAPs and LAPs: F1 16, F1 56, F1 63 and F1 256, F1 260, PN), were selected for gene expression analysis. A representative sample of 50 berry skins was collected from each of the eight F1 individuals at three berry developmental stages  (hard green berry (33E-L, PV), veraison (35E-L, 50% coloured berries, VER) and maturity (38E-L, 18°Brix, MAT)) during the 2007 season.

first: Emanuela

last: Coller

first: Juri

last: Battilana

first: Claudio

last: Moser


title: Study of miRNAs function in basal progenitors during cortical neurogenesis

status: Public on May 01 2014

city: Paris

first: Matthias

last: Groszer

address: 17, rue du Fer à Moulin

department: Developmental Neuroscience

institute: INSERM U839

summary: During cortical development neurons are generated sequentially from basal progenitors (BPs) which specifically express the transcription factor Tbr2. We used fluorescent-activaed cell sorting (FACS) to isolate BPs from Tbr2GFP knockin reporter mice (Arnold SJ et al. Genesis, 2009) at early (embryonic day, E13) and late (embryonic day, E16) stages of cortical neurogenesis and determined miRNA expression profiles using mouse miRNA microarray (Agilent).Comparison of E13 and E16 microRNA expression profiles allowed us to identify regulatory mechanisms for maintaining stage specific homeostasis of BPs.

overall_design: FACS isolated BPs at E13 and E16 mouse brain cortex were used for miRNA microarray analyses.  Four biological replicates (embryonic cortex from three different litters) for each group (E13 or E16) were analysed.

first: Tanay

last: Ghosh


title: Cell state transitions regulated by Slug are critical for tissue regeneration and tumor initiation [Nanostring nCounter samples]

summary: Gene expression data of MCF10A cell subpopulations: luminal, basal and luminal.

overall_design: Three samples were analized. Expression of 105 selected genes was evaluated, including 5 HK genes.

first: Aleix


title: Primary breast tumor-derived cellular models: characterization of tumorigenic, metastatic, and cancer-associated fibroblasts in dissociated tumor (DT) cultures

status: Public on Aug 22 2014

summary: The study of breast cancer pathogenesis relies heavily on the use of established cell lines often derived from metastatic lesions, which while having significantly contributed to the knowledge of breast cancer biology may inadvertently limit the understanding of the mechanisms governing the metastatic process. Our goal was to establish primary cultures from dissociation of breast tumors in order to provide cellular models that may better recapitulate breast cancer pathogenesis and the metastatic process. These cellular models differ from recently developed patient derived xenograft models (PDX) in that they can be used for both in vitro and in vivo studies. Here we report the characterization of six cellular models derived from the dissociation of primary breast tumor specimens, referred to as “dissociated tumor (DT) cells”. Among the DT cells are those that are tumorigenic and metastatic in immunosuppressed mice, and a group of cancer-associated fibroblasts (CAFs). In vitro, DT cells were characterized by proliferation assays, colony formation assays, protein and gene expression profiling, including PAM50 predictor analysis. The latter showed DT cultures similar to their paired primary tumor and as belonging to the basal and Her2-enriched subtypes, offering novel cellular models of these ER-negative breast cancer subtypes. In vivo, three DT cultures are tumorigenic in NOD/SCID and NSG mice, and one of these is metastatic to lymph nodes and lung after orthotopic inoculation into the mammary fat pad, without excision of the primary tumor. DT cultures comprised of CAFs were isolated from luminal-A, Her2-enriched and basal primary tumors, providing subtype-specific components of the tumor microenvironment. Altogether, these DT cultures provide closer-to-primary cellular models for the study of breast cancer pathogenesis, metastasis and tumor microenvironment.

first: Dorraya

last: El-Ashry


title: Identification of a stable molecular signature in breast tumor endothelial cells that persists ex vivo

status: Public on Mar 21 2014

summary: Long-term, in vitro propagation of tumor-specific endothelial cells (TEC) allows for ex vivo functional studies and gene expression profiling of clonally-derived, well-characterized subpopulations. Using a genetically-engineered mouse model (GEMM) of mammary adenocarcinoma (C3-TAg), we have optimized an isolation procedure and defined growth conditions for long-term propagation of breast TEC. Based on expression of EC-selective markers, the isolated TEC maintain their endothelial specification and phenotype in culture. Furthermore, gene expression profiling of multiple TEC subpopulations revealed striking, persistent overexpression of several candidate genes including Irx2 and Zfp503 (transcription factors), Cd166 and Cd133 (cell-surface markers), Ccl12 and neurotensin (angiocrine factors), and Gpr182 and Cnr2 (G protein-coupled receptors). Taken together, we have described an effective method for isolating and culture-expanding breast TEC from a GEMM and we have uncovered several new TEC-selective genes whose overexpression persists even after long-term in vitro culture. These results suggest that stable changes may be induced in vascular endothelial cells in the tumor microenvironment in vivo that are transmittable ex vivo.

first: Lin

last: Xiao

first: Chuck

last: Harrell

first: Andrew

middle: C

last: Dudley


title: MicroRNA transciptional profiling in murine abdominal aortic aneurysm (AAA), porcine pancreatic elastase (PPE) model - Day 7

status: Public on Aug 31 2014

city: Stanford

first: Joshua

last: Spin

address: 300 Pasteur Drive

institute: Stanford University

summary: We sought to identify differentially regulated microRNAs in infrarenal mouse aortic tissue after AAA-induction with PPE, compared with sham-operated mice. This treatment leads to rapid development of infrarenal aortic aneurysms with significant diameter differences observed by Day 7. We found 41 miRNAs were up-regulated with aneurysm and 37 down-regulated at p<0.05, which were also altered by >1.5-fold.

overall_design: Utilizing the PPE infusion model, we induced AAA in Male 10-week-old C57/Bl6 mice, 7 days after AAA-induction with PPE. One array per mouse, 5 mice per group, two groups (PPE and sham).


title: Cell state transitions regulated by Slug are critical for tissue regeneration and tumor initiation [Agilent microarray samples]

summary: Alterations that perturb differentiation and cell state transitions can lead to defects in development, function and the genesis of cancer. Studying cellular plasticity at high resolution and in real time has proven difficult using existing methods. Here, we use a quantitative approach to gain insights into cell state dynamics of normal mammary epithelial cells (MECs) and validate the model's predictions in vivo. In the absence of Slug/SNAI2, basal mammary progenitor cells transition into a luminal differentiation state, while luminal progenitor cells proliferate and expand; these changes result in abnormal mammary architecture and defects in tissue function. Loss of Slug also disrupts cellular plasticity leading to defects in tissue regeneration and the initiation of cancer. Mechanistically, Slug promotes cellular plasticity by recruiting the chromatin modifier, LSD1 (lysine specific demethylase 1), to promoters of lineage specific genes to represses transcription. Together, these finding demonstrate that Slug is necessary for cellular adaptation during tissue development and regeneration, and that transitioning back into a more primitive stem-like state is a prerequisite for tumor initiation.

last: Prat