title: Aberrant BAF57 Signaling Facilitates Pro-metastatic Phenotypes

status: Public on Jun 04 2013

city: PHILADELPHIA

first: Adam

last: Ertel

address: 233 S 10TH ST

department: Cancer Biology

institute: Thomas Jefferson University

summary:
BAF57, a component of the SWI/SNF chromatin remodeling complex conglomerate,modulates  androgen receptor activity to promote prostate cancer. However the molecular consequences of tumor associated BAF57 elevation have remianed undefined in advanced disease such as castration resistant prostate cancer and/or metastasis
Global gene expression analyses were performed in models mimicking tumor-associated BAF57 expression. These analyses demonstrated that BAF57 deregulation circumvented androgen mediated signaling and elicited upregulation of α2 integrin and other migration and metastasis related gene signatures.

overall_design: LNCaP cells were transfected to overexpress BAF57 and validated for BAF57 transcript induction. Appropriate vector control transfected cells were also used. Vector and BAF57 transfected samples were treated with 0.1% vehicle with a 1nM DHT vector control. Gene expression analyses were performed on biological duplicates.

first: Sucharitha

last: Balasubramaniam

first: Sankar

last: Addya

first: Karen

last: Knudsen


title: Induced pluripotent stem cells can be generated in bulk culture

status: Public on Jun 03 2013

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

summary: Induced pluripotent stem cells (iPSCs) are usually clonally derived. The selection of fully reprogrammed cells generally involves picking of individual colonies with morphology similar to embryonic stem cells (ESCs). However, successfully reprogrammed cells are highly proliferative and escape from cellular senescence - it is therefore conceivable that they outgrow non-pluripotent and partially reprogrammed cells during culture expansion without the need of clonal selection. In this study, we have reprogrammed human dermal fibroblasts (HDFs) with episomal plasmid vectors. Colony frequency and size was higher when using murine embryonic fibroblasts (MEFs) as stromal support instead of HDFs or human mesenchymal stromal cells (MSCs). We have then compared iPSCs which were either clonally derived by manual selection of a single colony, or derived from bulk-cultures of all initial colonies. After few passages their morphology, expression of pluripotency markers, and gene expression profiles did not reveal any significant differences. Furthermore, clonally-derived and bulk-cultured iPSCs had indistinguishable in vitro differentiation potential towards the three germ layers. Therefore, manual selection of individual colonies does not appear to be necessary for the generation of iPSCs – this is of relevance for standardization and automation of cell culture procedures

overall_design: Gene expression profiles of induced fibroblasts (“iF”) from three different donors which were either clonally derived (“C”) or bulk-cultured (“B”) were compared

first: Charlotte

middle: A

last: Willmann

first: Harim

last: Hemada

first: Michael

last: Lenz

first: Jie

last: Qin

first: Stephanie

last: Sonntag

first: Paul

last: Wanek

first: Bernd

last: Denecke

first: Martin

last: Zenke


title: Expression data from mock- or LMO3-silenced human preadipocytes isolated from SAT or VAT

status: Public on Jun 12 2013

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

summary:
In this study, we aimed to gain further insight on the role of glucocorticoids (GCs) in adipocyte differentiation. For the future drugability of candidate targets, it is of utmost importance to find factors relevant to human biology. Thus, we analyzed the transcriptome of GC-induced primary human adipose stem cells (hASCs) isolated from paired subcutaneous adipose tissue (SAT) and visceral adipose tissue (VAT) to identify novel factors downstream of GC action.
We used microarrays to detail the global program of gene expression following GC treatment and identified distinct classes of up- and down-regulated genes during this process.

overall_design: Human preadipocytes (human adipose stem cells) were obtained from lipoaspirates or visceral fat biopsies by enzymatic digestions, followed by several steps of centrifugations (Mikkelsen et. al Cell. 2010 Oct 1;143(1):156-69.). Following isolation, human adipose stem cells were transfected with either siCtrl or siLMO3 oligonucleotides, followed by treatment with hydrocortisone.

last: Bilban


title: HMGA2/TET1/HOXA9 pathway regulates breast cancer growth and metastasis.

city: Chicago

first: Miao

last: Sun

country: USA

institute: University of Chicago

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

summary: HMGA2, Tet1 and HOXA9 are all regulated human breast tumorigenesis. We use gene expression array analysis to identify and compare the genes regulated by HMGA2, Tet1 and/or HOXA9 in human breast cancer cells.

overall_design: Total RNAs were extracted from 1833 cells with HMGA2-depletion, Tet1-expression or HOXA9-expression. Affymetrix GeneChip Human Gene 1.0 ST Arrays were performed to detail the gene expression and identify the genes regulated by HMGA2, Tet1 and HOXA9 in human breast cancer cells.

first: Marsha

last: Rosner


title: DEG in human gastric carcinoma formed in stomach wall and metastasized to ovary in mice system

status: Public on Jun 01 2013

city: Seoul

first: Myung-Soo

last: Kang

address: 50 Irwon-dong

department: SAIHST

country: South Korea

institute: Samsung Medical Center

summary: Spontaneous metastasis of gastric carcinoma to secondary organs is seldom reproduced in the mice. In this study, we established highly reproducible, experimental mice model in which gastric carcinoma progressively grows in the site of gastric walls and metastasize to secondary sites. A highly tumorigenic GC cells were engineered to express type 2 luciferase and injected via orthotopic route into BALB/c nude mice. The mice developed highly progressive GC tumors in the gastric wall where implanted and slow metastases to liver, spleen, lung, kidney and ovary, with rate of metastases to ovary being 63.6% of implanted mice. The tumors colonized in the ovary expressed a GI marker MUC5A, suggestive of typical human Krukenberg tumor. Immuno-histochemical stainings revealed that many mesenchymal markers were strongly positive in motile tumor cells in the vein of ovary and became gradually weak during extravasations to colonize in the ovary. When routes of metastasis were further investigated, the mesenchymal marker SMA stained low in the tumor cells of the primary site of stomach wall, became high in intravasating vein in the stomach wall, remained high in extravasating veins in the liver and ovary and finally returned low in the colonized tumor in the liver and ovary. However, expression of an epithelial marker Claudin did not show in the opposite profile to SMA, indicating that acquisition of mesenchymal phenotypes rather than loss of epithelial characteristics may more give rise to metastatic potential. Dissociated cells derived from tumors in the implanted mouse stomach or metastasized to ovaries retain their tumorigenicity and metastatic potentials. The mRNA microarray and Western blot analyses showed that metastatic tumor-derived cells showed significantly higher expression of GAGE12 gene family than orthotopic tumors-derived cells. The shRNA-mediated knock-down of the GAGE12 family in the metastatic tumors-derived cells abolished the tumor formation in gastric wall and metastasis as well. In conclusion, we established an in vivo orthotopic gastric cancer mouse model spontaneously metastasizing to secondary organs including ovary, which exhibits typical characteristics of a Krukenberg tumor. Expression of mesenchymal markers should be functionally associated with the gain of metastatic ability in this study.

overall_design: A hightly tumorigenic gastric carcinoma SNU-16 cells were orthotpically injected into stomach wall. Tumors formed in the stomach wall (16S) and mestasized to ovary (16O) were dissociated and cultured for 7 day. These cells were re-injected orthotopically and tumors formed in the stomach from 16S (16SS) and ovary from 16O injection (16OO) were dissociated. Total RNAs were isolated from 16S, 16SS, 16O and 16OO2 and subjected to mRNA microarrays

first: Eun-Kyung

last: Lee


title: A systematic evaluation of miRNA:mRNA interactions involved in the migration and invasion of breast cancer cells [HuGene-1_0-st]

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

summary: In this study we performed a systematic evaluation of functional miRNA-mRNA interactions associated with the aggressiveness of breast cancer cells using a combination of integrated miRNA and mRNA expression profiling, bioinformatics prediction, and functional assays. Analysis of the miRNA expression identified 11 miRNAs that were differentially expressed, including 7 down-regulated (miR-200c, miR-205, miR-203, miR-141, miR-34a, miR-183, and miR-375) and 4 up-regulated miRNAs (miR-146a, miR-138, miR-125b1 and miR-100), in aggressive cell lines when compared to normal and less aggressive cell lines. Transient overexpression of miR-200c, miR-205, and miR-375 in MDA-MB-231 cells led to the inhibition of cell migration and invasion. The integrated analysis of miRNA and mRNA expression identified 35 known and novel target genes of miR-200c, miR-205, and mir-375, including CFL2, LAMC1, TIMP2, ZEB1, CDH11, PRKCA, PTPRJ, PTPRM, LDHB, and SEC23A. Surprisingly, the majority of these genes (27 genes) were target genes of miR-200c, suggesting that it plays a more important role in regulating the aggressiveness of breast cancer cells. We characterized one of the target genes of miR-200c, CFL2, and demonstrated that CFL2 is overexpressed in aggressive breast cancer cell lines and can be significantly down-regulated by exogenous miR-200c. Tissue microarray analysis further revealed that CFL2 expression in primary breast cancer tissue correlated with tumor grade. To our knowledge, this study is the first systematic screening of functional miRNA target genes in aggressive breast cancer cells. The results obtained from this study may improve our understanding of the role of these candidate miRNAs and their target genes in relation to breast cancer aggressiveness and ultimately lead to the identification of novel biomarkers associated with prognosis.

overall_design: Affymetrix Gene 1.0 ST arrays were performed according to the manufacturer's directions on RNA extracted from breast cancer cell lines which are treated with miRNA mimic

first: Daya

last: Luo

first: Nikki

last: Harvel


title: Expression profile of MCF7, CCD18 and Ramos human cell lines

status: Public on May 31 2013

city: Pamplona

first: Victor

last: Segura

state: Navarra

address: Avda. Pío XII, 55

department: Unit of Proteomics, Genomics and Bioinformatics

country: Spain

institute: FIMA

summary: To uncover the chromosome 16 associated proteome and to take advantage of the generated knowledge to make progress in human biology in health and disease, a consortium of 15 groups was organized in four working groups: SRM and protein sequencing, antibody and peptide standard, clinical healthcare and biobanking and bioinformatics. According to a preliminary in silico study integrating knowledge from Ensembl, UniProt and GPM, Ramos B lymphocyte cells, MCF-7 epitelial cells and CCD18 fibroblast were selected as it is theoretically expected that any chromosome 16 protein coding gene is expressed in at least one of them. To define in detail the transcriptome of the above mentioned cell lines Affymetrix microarray based analyses were performed.   Upon hybridization in Human ST 1.0 arrays, raw data were processed with RMA algorithm for background correction and normalization. Chromosome 16 gene expression pattern was then defined in each cell line and comparative analysis was done with R package statistics. Biological functions involving chromosome 16 genes were analysed with GO and functional networks were studied with Ingenuity Pathway Analysis. Expressed genes were compared with data from shotgun proteomic experiments to find the degree of correlation mRNA-protein. Expression of genes coding for proteins with weak or none MS evidence is shown. The integration of this information in decision-making process of the mass spectrometry group is discussed.

overall_design: Expression profiles of MCF7, CCD18 and Ramos human cell lines.

first: Fernando

middle: J

last: Corrales

first: Juan

middle: P

last: Albar

first: Alberto

last: Medina


title: Expression data from mock- or LMO3 silenced differentiating adipose stem cells

summary:
In this study we aimed to gain further insight on the role of GCs in adipocyte differentiation. For the future drugability of candidate targets it is of utmost importance to find factors relevant to human biology. Thus, we analyzed the transcriptome of GC induced primary human adipose stem cells (hASC) to identify novel factors downstream of GC action
We used microarrays to detail the global programme of gene expression following glucocorticoid treatment and identified distinct classes of up- and downregulated genes during this process.

overall_design: Human preadipocytes (human adipose stem cells) were obtained from lipoaspirates by enzamytic digestions, followed by several steps of centrifugations (Mikkelsen et. al Cell. 2010 Oct 1;143(1):156-69.). Following isolation, human adipose stem cells were transfected with a control siRNA (siCtrl) or two different siRNA oligos targeting the gene LMO3 (siLMO3_oligo1 or siLMO3_oligo2). 40Hrs later, the transfected human adipose stem cells were induced to differentiate into mature adipocytes with a adipogenic cocktail (FullMix) and RNA isolated at day 0 or day6 after induction of differentiation.


title: Keratinocyte and fibroblast gene expression in skin and keloid scar tissue

status: Public on May 28 2013

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary: Keloids are scars that extend beyond original wounds and are resistant to treatment.  In order to improve understanding of the molecular basis of keloid scarring, we have assessed the genomic profiles of keloid fibroblasts and keratinocytes.

overall_design: Skin and scar tissues were obtained for isolation of primary keratinocytes and fibroblasts.  Keloid scars were excised from patients undergoing scar excision surgery, normal skin samples were isolated from patients undergoing elective plastic surgery.  Primary culters were prepared for keratinocytes and fibroblasts, and were harvested for analysis up to passage three.  Nine keloid scars, for adjacent non-lesional keloid skin samples, and three normal skin samples were obtained and cultured.  RNA was isolated using RNeasy, and quality verified using an Agilent 2100 Bioanalyzer.  Labeling and hybridization to Affymetrix Human Gene 1.0 ST microarray chips was performed by the Vanderbilt Genome Sciences Resource at Vanderbilt University Medical Center.

first: Dorothy

last: Supp

first: Bruce

last: Aronow


title: Expression data from human induced pluripotent stem cell-derived teratomas and embryoid bodies

city: Jerusalem

first: Uri

last: Ben-David

address: Givat-Ram

department: Genetics

country: Israel

institute: Hebrew University

summary: The tumorigenicity of human pluripotent stem cells (hPSCs) is a major safety concern for their application in regenerative medicine. Here we identify the tight-junction protein Claudin-6 as a specific cell surface marker of hPSCs that can be used to selectively remove Claudin-6-positive cells from mixed cultures. We show that Claudin-6 is absent in adult tissues but highly expressed in undifferentiated cells, where it is dispensable for hPSC survival and self-renewal. We use three different strategies to remove Claudin-6-positive cells from mixed populations: an antibody against Claudin-6; a cytotoxin-conjugated antibody that selectively targets undifferentiated cells; and clostridium perfringens enterotoxin, a toxin that binds several Claudins, including Claudin-6, and efficiently kills undifferentiated cells, thus eliminating the tumorigenic potential of hPSC-containing cultures. This work provides a proof of concept for the use of Claudin-6 to eliminate residual undifferentiated hPSCs from culture, highlighting a strategy that may increase the safety of hPSC-based cell therapies.

overall_design: total RNA was isolated from teratomas or from embryoid bodies differentiated from human induced pluripotent stem cells

first: Neta

last: Nudel

first: Nissim

last: Benvenisty


title: LMO3 is a novel regulator of adipogenesis

first: Markus

last: Jeitler

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

overall_design: Refer to individual Series


title: Expression data from HUVEC adenovirally overexpressing MEF2C

first: Caterina

last: Sturtzel

address: Lazarettgasse 19

department: Dep f Vasc Bio

institute: Medical Univ Vienna

summary:
The transcription factor MEF2C is specifically induced by VEGF in endothelial cells. To delineate target genes of MEF2C in endothelial cells, which might be important during angiogenesis also, MEF2C was overexpressed adenovirally in human umbilical vein endothelial cells (HUVECs) over a period of 8 to 32 hours.
Expression data should be compared to control infected cells, to discriminate against virally induced genes, and should be further compared to HUVECs infected with an adenovirus encoding for a dominant-negative form of MEF2.

overall_design: HUVECs of the same batch, passage 3 were infected with Ad.con, Ad.MEF2C or Ad.DNMEF2 for 8, 16 or 32 hours for RNA extraction and hybridization on Affymetrix microarrays.

first: Martin

last: Bilban


title: Distinct, non-overlapping gene panels of peripheral blood gene expression predict response to infliximab therapy in rheumatoid arthritis and Crohn's disease

status: Public on Jun 25 2013

city: Debrecen

first: Bertalan

last: Mesko

address: Egyetem tér 1.

department: Department of Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

summary: We used microarrays to identify markers predicting responder status in infliximab treatment in 19 rheumatoid arthritis and 20 Crohn's disease patients at week 0 and week 2 of treatment.

overall_design: Peripheral blood samples were obtained at week 0 and week 2 of inxliximab treatment and global gene expression profiling identified markers of responder status.

first: Szilard

last: Poliska

first: Andrea

last: Vancsa

first: Zoltan

last: Szekanecz

first: Karoly

last: Palatka

first: Zsolt

last: Hollo

first: Attila

last: Horvath

first: Laszlo

last: Steiner

first: Gabor

last: Zahuczky

first: Janos

last: Podani

last: Nagy


title: Expression data from dexamethsone-treated human adipose stem cells

overall_design: Human preadipocytes (human adipose stem cells) were obtained from lipoaspirates by enzamytic digestions, followed by several steps of centrifugations (Mikkelsen et. al Cell. 2010 Oct 1;143(1):156-69.). Following isolation, human adipos estemm cells were treated with Dexamethasone (100nM) for various times.


title: Gene expression data from immortal and arsenite-transformed malignant prostate epithelial cells

status: Public on May 18 2013

city: Tucson

first: Paul

last: Severson

state: AZ

address: 1515 N Campbell Ave

department: Pharmacology and Toxicology

institute: University of Arizona

summary: The aim of this study was to determine how gene expression is changed after arsenite-induced malignant transformation of prostate epithelial cells.

overall_design: Gene expression from three distinct passages of untreated, immortal RWPE-1 cells was compared to three timepoints of arsenite-exposed RWPE-1 cells (CAsE-PE) that have undergone malignant transformation.

middle: L

first: Lukas

last: Vrba

first: Erik

last: Tokar

first: Michael

last: Waalkes

first: Bernard

middle: W

last: Futscher


title: PKC Activation Induces Inflammatory Response and Cell Death in Human Bronchial Epithelial Cells

status: Public on May 27 2013

city: Toronto

first: Ricardo

last: Zamel

state: Ontario

address: 101 College St.

country: Canada

institute: University Health Network

summary: A variety of airborne pathogens can induce inflammatory responses in airway epithelial cells, which is a crucial component of host defence. However, excessive inflammatory responses and chronic inflammation also contribute to different diseases in the respiratory system.  We hypothesized that the activation of protein kinase C (PKC) is one of the essential mechanisms of inflammatory responses in airway epithelial cells.  In the present study, we stimulated human bronchial lung epithelial (BEAS-2B) cells with phorbol ester Phorbol 12, 13-dibutyrate (PDBu), and examined gene expression profile with microarray analysis. Bioinformatics suggested that PKC activation induced dramatic changes in gene expression related to multiple cellular functions. The top two functional networks of genes were centered on NFκB and TNF-α, which are two commonly known pathways for cell death and inflammation.  Subsequent tests confirmed the decrease in cell viability and increase in the production of various cytokines. Interestingly, each of the increased cytokines was differentially regulated at mRNA and/or protein levels by different sub-class of PKC isozymes.  We conclude that many pathogen-induced cell death and cytokine production in airway epithelial cells may be mediated through PKC related signaling pathways. These findings suggest that PKCs can be new targets for treatments of lung diseases.

overall_design: Three groups of BEAS-2B cells were prepared: control, 0.5 hour of PDBu stimulation, and 4 hours of PDBu stimulation. Each group consisted of three biological replicates.

first: Hyunhee

last: Kim

first: Xiaohui

last: Bai

first: Mingyao

last: Liu


title: Gene expression alterations in human colon cancer xenograft treated with anti-VEGF antibody

status: Public on May 25 2013

city: Hamamatsu

first: Hirotoshi

last: Kikuchi

address: 1-20-1 Handayama, Higashi-ku

department: Second Department of Surgery

country: Japan

institute: Hamamatsu University School of Medicine

summary:
Recent randomized clinical trial revealed the additional effect of bevacizumab, a humanized monoclonal antibody against vascular endothelial growth factor (VEGF)-A, to conventional chemotherapy on survival of patients with metastatic colorectal cancer. However, a number of preclinical reports indicate resistant mechanisms to anti-angiogenic therapy in several tumor models.
We investigated the  phenotypic alterations of colorectal cancer xenograft during antiangiogenic therapy.

overall_design: TK-4, a solid tumor strain derived from human colon cancer, was orthotopically implanted into cecal walls of nude mice and treated with anti-VEGF antibody or control IgG for 35 days. Gene expression was analyzed using microarrays (Human Gene 1.0ST Array, Affymetrix).

first: Shinichiro

last: Miyazaki

first: Ichirota

last: Iino

first: Takashi

last: Uehara

first: Tomohiko

last: Setoguchi

first: Takeshi

last: Fujita

first: Yoshihiro

last: Hiramatsu

first: Manabu

last: Ohta

first: Kinji

last: Kamiya

first: Kyoko

last: Kitagawa

first: Masatoshi

first: Satoshi

last: Baba

first: Daniel

middle: C

last: Chung

first: Hiroyuki

last: Konno


title: Retained heterodisomy is associated with high gene expression in hyperhaploid inflammatory leiomyosarcoma

status: Public on May 22 2013

city: Lund

first: Karolin

middle: H

last: Nord

address: BMC C13

department: Dept of Clinical Genetics

country: Sweden

institute: Lund University

type:
Expression profiling by array
Genome variation profiling by SNP array


title: Expression data from blood and biopsies of BKV viremia and nephropathy transplant patients

status: Public on May 23 2013

city: Bronx

first: Pilib

last: Ó Broin

state: NY

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

summary:
We study the global gene expression profiles of BKV viremia and nephropathy patients using microarrays in order to better understand the immunologic response to polyomavirus BK (BKV).
BKV has become increasingly prevalent since the introduction of more potent immunosuppressive agents. It has been shown that as many as 30% of renal transplant recipients develop asymptomatic viral shedding in the urine shortly after transplant, 10-20% have viremia, and as many as 1-10% can go on to develop overt nephropathy (BKVN) that might lead to graft loss. To date, the genomics of BKV viremia and BKVN have not been investigated thoroughly by microarray.

overall_design: Patients who were enrolled in the IRB-approved Immune Monitoring Study had blood PAXGene samples taken at post-transplant visits and had clinically indicated biopsy samples were used for analysis. A total of 17 biopsy samples were used for gene expression profiling microarrays, three with histopathologic diagnosis of BKVN, 3 patients with evidence of BK viral replication in peripheral blood, but normal biopsy and 11 patients with normal biopsies or mild IFTA, and stable graft function. Blood PAXGene samples from 40 patients were used for gene expression profiling by microarrays, 14 patients with stable graft function and without BK viremia, 19 patients' blood samples at the time of BKV viremia, and 7 patients blood samples taken 1-2 months prior to development of BK viremia.

first: Enver

last: Akalin


title: Gene expression data from human NSCLC cell line (U-1810 cells) treated with miRNA-214 antagomir or non-targeting antagomir

city: Stockholm

first: Hogir

last: Salim

address: KBC Z5:01

department: Oncology-Pathology

institute: Karolinska Institutet

summary: Prognosis of non small cell lung cancer (NSCLC) is very poor mainly because it often has metastasized to distant organs already at the time of diagnosis. Therefore biomarkers which can predict metastasis are urgently needed. miRNAs have been shown to play important roles in the regulation of different tumor cell processes including those involved in metastasis. We recently showed that miRNA-214 is linked to a radioresistant phenotype of NSCLC. Interestingly, altered miRNA-214 expression has in breast, cervical and melanoma been linked to metastasis. We therefore examined the role of miRNA-214 in the metastasis of NSCLC cells. We found that down regulation of miRNA-214 increased invasive potential of NSCLC cells and conversely, overexpression of miRNA-214 in NSCLC cells with low endogenous level of miRNA-214, decreased invasiveness. Gene expression analyses of NSCLC cells with low and high levels of miRNA-214, followed by bioinformatics analyses identified a number of target genes which were linked to metastasis including pregnancy associated plasma protein A (PAPP-A), alpha protein kinase 2 (ALPK2), cyclin-dependent kinase 6 (CDK6) and tumor necrosis-factor alpha-induced protein 3 (TNFAIP3). These targets were validated on mRNA and protein level.

overall_design: U-1810 cells with high endogenous level of miRNA-214 were treated with miRNA-214 antagomir (3 biological replicates) or non-targeting antagomir (3 biological replicates) and then RNA was extracted and applied to Affymetrix gene array platform.

first: Kristina

last: Viktorsson


title: Predicting multi-class responses to preoperative chemoradiotherapy in rectal patients

status: Public on May 14 2013

first: Jungsoo

middle: Ieden

last: Gim

state: Gwanak gu

address: Gwanak ro 1

institute: Seoul National University

summary: The treatment strategy of rectal cancer has substantially changed in recent decades. Historically postoperative chemoradiotherapy (CRT) was considered to be the first-line therapy for stage II and III rectal cancers. However, the preoperative CRT is now considered to be the optimal therapy regimen for locally advanced rectal ancer due to its improved local control, reduced toxicity, and increased rate of sphincter preservation. Our study established a clinically practical multi-class prediction model by adopting a novel strategy that applies two separate prediction models (MI and TO predictor) sequentially to a patient to predict the response. For promising clinical practice, we validated our model in a published dataset, which is completely independent dataset from ours. This study suggests a clinically plausible prediction model that correctly infers the preoperative CRT response of patients with high accuracy based on 163 gene signatures we identified.

overall_design: Total RNAs were isolated from primary rectal tumor tissues of 69 patients who underwent chemoradiation therapy (CRT). These patients are classified into four different CRT responses: minimal response (MI), moderate response (MO), near total response (NT) and total response (TO). All the RNAs were subjected to microarray analysis using Affymetrix GenChip arrays.

first: Yong

middle: B

last: Cho

first: Hey

middle: K

last: Hong

first: Hee

last: Kim

first: Seong

last: Yun

first: Ho-Kyung

last: Chun

first: Hong-Gyun

last: Wu

first: Seung-Yong

last: Jeong

first: Taesung

last: Park

first: Woong-Yang

first: Woo

middle: Y

last: Lee


title: Expression data from human umbilical vein endothelial cells (HUVEC) treated with DMSO, telmisartan, or telmisartan and amlodipine

city: New Haven

first: Mauro

last: Siragusa

address: 10 Amistad Street

institute: Yale University School of Medicine

summary:
Objective – Telmisartan, an angiotensin II type 1 (AT1) receptor blocker, and amlodipine, a calcium channel blocker, are antihypertensive agents clinically used as monotherapy or in combination. They exert beneficial cardiovascular effects independently of blood pressure lowering and classic mechanisms of action. In this study, we investigate molecular mechanisms responsible for the off-target effects of telmisartan and telmisartan-amlodipine in endothelial cells (EC), using an unbiased approach.
Approach and Results – In human umbilical vein endothelial cells, microarray analysis of gene expression followed by pathway enrichment analysis and qRT-PCR validation revealed that telmisartan modulates the expression of key genes responsible for cell cycle progression and apoptosis. Amlodipine’s effect was similar to control. EC exposed to telmisartan, but not amlodipine, losartan or valsartan, exhibited a dose-dependent impairment of cell growth and failed to enter the S-phase of the cell cycle. Similarly, telmisartan inhibited proliferation in COS-7 cells lacking the AT1 receptor. In telmisartan-treated EC, phosphorylation and activation of Akt as well as MDM2 was reduced, leading to accumulation of p53 in the nucleus, where it represses the transcription of cell cycle promoting genes. Phosphorylation of GSK3β was also reduced, resulting in rapid proteolytic turnover of CyclinD1. Telmisartan induced downregulation of proapoptotic genes and protected EC from serum starvation- and 7-ketocholesterol-induced apoptosis.
Conclusions – Telmisartan exerts antiproliferative and antiapoptotic effects in EC. This may account for the improved endothelial dysfunction observed in the clinical setting.

overall_design: HUVEC were treated with 100 µmol/L telmisartan or 5 µmol/L amlodipine or both in dimethyl sulfoxide (DMSO) or an equivalent volume of DMSO alone, as control, for 24 hours. Microarray analysis was carried out on two biological replicates per group (total of six samples). See PROTOCOL section for experimental details.

first: William

last: Sessa


title: Retained heterodisomy is associated with high gene expression in hyperhaploid inflammatory leiomyosarcoma (Expression)

first: Karolin

last: Nord

summary: Global gene expression analysis of inflammatory leiomyosarcoma (ILMS) and conventional leiomyosarcoma (LMS).

overall_design: RNA was extracted from frozen tumor biopsies (3 ILMS and 15 LMS) and hybridized onto Affymetrix Human Gene 1.0 ST arrays. LMS_18b is the same sample as LMS_18a, analyzed at a different time point. LMS_18b data are not included in the final gene expression analysis; and therefore, there is no Sample data table. This sample was instead used in a previous analysis to show that a normalization method (the ComBat algorithm) was successful in removing batch effects and keeping biological variation.

first: Kajsa

last: Paulsson

first: Srinivas

last: Veerla

first: Johan

last: Wejde

first: Otte

last: Brosjö

first: Nils

last: Mandahl

first: Fredrik

last: Mertens


title: Carcinoma-associated fibroblasts’ transcriptomic program predicts clinical outcome in stage II/III colorectal cancer

status: Public on May 10 2013

city: L'Hospitalet de Llobregat

first: david

middle: g

last: mollevi

address: Av Gran Via 197-203

institute: IDIBELL

summary:
We obtained fibroblast cultures from fresh surgical specimen ressected from patients with primary colorectal carcinoma: normal colonic fibroblasts (NCF=9) from the normal colonic mucosa at least 5-10cm from the surgical margin, carcinoma-associated fibroblasts from the primary tumor (CAF-PT=14) and carcinoma-associated fibroblasts (CAF-LM=11) from fresh surgical specimens of liver metastases. We identified 277 probes, in common between the three types of fibroblasts, whose expression level is sequentially deregulated according to cancer progression (NCF→CAF-PT→CAF-LM; fold change Log2 normalized expression>1.5 in each step). Prediction Analysis of Microarrays was applied to obtain a 25-gene signature that better characterizes each fibroblast class. The signature is able to classify patients carrying primary tumors according to prognosis. This fact was exploited to obtain a 19-gene signature (from the 277 deregulated probes) predicting recurrence with high accuracy in stage II/III colorectal cancer patients. Signature validation has been carried out in two independent datasets and in a meta-cohort of 336 stage II/III patients.
Since the 25-gene signature was obtained regardless of gene expression data of tumor specimens or patient’s clinical data, the prognostic power of this signature provides strong evidence of the link between the tumor stroma and cancer progression. Furthermore, the 19-gene signature was able to identify low-risk patients with very high accuracy, especially relevant for those high-risk stage-II patients.

overall_design: We hybridised fibroblast RNA in Affymetrix GeneChip 1.0 st arrays

first: D

middle: G

last: Mollevi

first: M

last: Berdiel


title: Expression data from primary tissue, human oral mucosa (mRNA data)

status: Public on May 06 2013

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

institute: University Clinic of Schleswig Holstein

summary: The experiment aims to identify regulatory miRNA networks influencing mRNA profiles in oral lichen planus (OLP). RNA and miRNA were extracted simultaniously using miRVana (Ambion, Life Technologies). Sample and array processing was carried out according to the manufacturer's guidelines. Affymetrix raw data was processed using AGCC Expression Console 1.1 (Affymetrix), employing RMA normalization. Linking miRNA and mRNA was performed with a correlation analysis, while a false discovery rate was used to exclude false-positive correlations between miRNAs and their predicted targets.

overall_design: 7 cases (OLP) and 7 controls (healthy individuals). Genome wide mRNA and miRNA screening, linking both datasets (see summary).

last: Häsler


title: Expression data from primary tissue, human oral mucosa

platform_organism:
Homo sapiens
synthetic construct


title: Analysis of proposed human B1 cells

status: Public on May 01 2013

city: Leuven

first: Leentje

last: Van Lommel

address: Herestraat 49 bus 901

department: Molecular cell biology

country: Belgium

institute: KULeuven

summary: The recent discovery of the human B1 cells, identified by the expression of CD20, CD27 and CD43 in absence of expression of CD70 and CD69 has been subject of debate. Some studies have raised the possibility that these cells are B cells differentiating towards the plasmablast and plasma cell stage rather than being the human counterpart of murine B1 cells. No further in depth studies have been performed. Therefore, a functional comparison was made between, the proposed B1 cells and plasmablasts. We observed that for several functional characteristics (distribution of isotypes of spontaneously producted antibodies, production of antigen-specific antibodies after vaccination with both T-cell dependent as well as T-cell independent antigen, the proposed B1 cells behaved similar to plasmablasts. In addition, we were able to differentiate the proposed B1 cells in vitro, indicating that they are not from a distinct lineage as the murine B1 cells. Gene expression analysis revealed that these cells cluster between memory B cells and plasmablasts, contradicting them being the genuine human counterpart of murine B1 cells, rather revealing a preplasmablast phenotype.

overall_design: Different B cells subsets were isolated from PBMC from healthy donors by a combination of magnetic and fluorescence activated cell sorting

first: Kris

last: Covens

first: Bert

last: Verbinnen

first: Nick

last: Geukens

first: Isabelle

last: Meyts

first: Frans

last: Schuit

first: Marc

last: Jacquemin

first: Xavier

last: Bossuyt


title: MiR-378 dysregulated genes

status: Public on Apr 30 2013

city: San Francisco

first: Kevin

last: Blansit

state: Ca

address: UCSF Helen Diller Family Comprehensive Cancer Center

institute: UCSF

summary: Dysregulated Genes between miR-378 vs. negative control ovarian cancer cells

overall_design: We transfected ovarian cancer cell lines with miR-378 or negative control

first: Daniela

last: Matei

first: Tuyen

last: Kiet

first: Joan

last: Hilton

first: John

last: Chan


title: The transcriptomic effect of induced LRIG1 expression in NPC cells

status: Public on May 02 2013

city: Zhunan Miaoli County

first: Chia

middle: Huei

last: Lee

address: 35, Keyan Rd.

department: National Institute of Cancer Research

country: Taiwan

institute: Taiwan National Health Research Institute

summary: As LRIG1 known to be a negative regulator of EGFR, we postulate that restored LRIG1 expression will change the transcription profile through the regulation of EGFR as well as its downstream signal cascades. Thus, we conducted a time-course microarray study to examine the effect of restored LRIG1 expression in NPC line, TW01-LG1/a, which the LRIG1 expression is under the control of a promoter with Doxycycline response element.

overall_design: We established stable transfectants of the LRIG1 gene in the TW01 cells which the expression of LRIG1 protein was barely detectable. To control the expression of LRIG1, the coding sequences were placed under the control of a promoter with doxycycline (Dox)-response element using the Tetoff system. Thus the LRIG1 expression could be turn on by removing Dox from the culture medium. Cellular total RNA were harvested along a time course of 12, 24, 36, and 48 hr following LRIG1 turn on expression, and then subjected to exon array analysis (Affymatrix Human Gene 1.0 ST), using the LRIG1 non-expressing sample (with Dox) as control for all comparison. For each time-point, a biological replicate was included.

first: C

first: Jim

last: Sheu


title: Transcriptional profiling of Ewing's sarcoma derived exosomes

city: München

first: Olivia

last: Prazeres da Costa

state: Bavaria

address: Trogerstr. 30

department: Medical Microbiology, Immunology and Hygiene

institute: Technische Universität München

summary: Exosomes are small RNA and protein containing vesicles that can mediate hetero- and homotypic intercellular communication between normal and malignant cells. Especially, tumor-derived exosomes are believed to mediate reprogramming of the tumor-associated stroma to favor tumor growth and metastasis. In this study we isolated exosomes from three different Ewing’s sarcoma (ES) cell lines by ultracentrifugation. Microarray analysis of ES-derived exosomes and their parental cells was performed to gain insight into the spectrum of transcripts they contain and the functions in which these transcripts might be involved in.

overall_design: In total we analyzed six different samples consisting of three pairs of exosomal and cellular RNA of different Ewing's sarcoma cell lines.

first: Isabella

middle: V

last: Miller

last: da Costa

first: Guenther

last: Richter

first: Stefan

last: Burdach

first: Thomas

last: Grunewald


title: Dynamically regulated miRNA-mRNA networks revealed by exercise

city: Moscow

first: Maxim

last: Shkurnikov

address: 2 bld. 85, Ugreshkaya st.

country: Russia

institute: SRC Bioclinicum

summary:
MiRNAs are essential mediators of many biological processes. The aim of this study was to investigate the dynamics of miRNA-mRNA regulatory networks during exercise and subsequent recovery period.
Here we monitored the transcriptome changes by microarray analysis of the whole blood of eight highly trained athletes after 30 min of moderate exercise followed by 30 min and 60 min of recovery period. We combined expression profiling and bioinformatics and analysed metabolic pathways enriched with differentially expressed mRNAs and then mRNAs which are known to be validated targets of differentially expressed miRNAs. Finally we revealed four dynamically regulated networks comprising differentially expressed miRNAs and their known target mRNAs with anti-correlated expression profiles over time. The data suggest that hsa-miR-21-5p regulated TGFBR3, PDGFD and PPM1L mRNAs. Hsa-miR-24-2-5p was likely to be responsible for MYC and KCNJ2 genes and hsa-miR-27a-5p for ST3GAL6. The targets of hsa-miR-181a-5p included ROPN1L and SLC37A3. All these mRNAs are involved in processes highly relevant to exercise response, including immune function, apoptosis, membrane traffic of proteins and transcription regulation.
We have identified four miRNA-mRNA networks dynamically regulated following exercise. This work is the first study to monitor miRNAs and mRNAs in parallel into recovery period. The results provide a novel insight into the regulatory role of miRNAs in stress adaptation.

overall_design: Each subject performed a treadmill test with an incremental step protocol until exhaustion. Blood samples were taken from the antecubital vein using indwelling catheter before (T1), immediately after ramp test to exaustion (T2) and after 30 min of recovery (T3). Two weeks later, athletes participated in the main exercise, consisting of running at 80% VO2 peak for 30 min on a treadmill. Blood samples were taken from the antecubital vein using indwelling catheter before (T4), immediately after running at 80% VO2 peak for 30 min on a treadmill (T5), after 30 min (T6) and 60 min (T7) of recovery.

first: Alexander

last: Tonevitsky

first: Diana

last: Maltseva

first: Timur

middle: R

last: Samatov

first: Dmitry

last: Sakharov

middle: U

first: Anatoly

middle: I

last: Grigoriev


title: Gene expression profiling of Capan-1 and Pt45P1 cells treated or not with alternatively spliced tissue factor (asTF)

status: Public on Apr 10 2013

city: Cincinnati

first: Dusten

middle: John

last: Unruh

address: 3125 Edan Ave

department: Hematology/Oncology

institute: University of Cincinnati

summary: The effects of alternatively spliced tissue factor (asTF) were measured by gene expression profiling of Capan-1 and Pt45P1 cells.

overall_design: 4 samples: Capan-1 cells +/- asTF, Pt45P1 cells +/- asTF.

first: Bruce

last: Aronow

first: Vladimir

last: Bogdanov

first: Ramprasad

last: Srinivasan


title: Stress-Independent Activation of XBP1s and/or ATF6 Reveals Three Functionally Distinct ER Proteostasis Environments [HEK293DYG]

status: Public on Apr 23 2013

city: La Jolla

first: R.

middle: Luke

last: Wiseman

state: CA

address: 10550 N. Torrey Pines Rd. MEM 220

department: Molecular & Experimental Medicine

institute: The Scripps Research Institute

summary:
The unfolded protein response (UPR) maintains endoplasmic reticulum (ER) proteostasis through the activation of transcription factors such as XBP1s and ATF6. The functional consequences of these transcription factors for ER proteostasis remain poorly defined. Here, we describe methodology that enables orthogonal, small molecule-mediated activation of the UPR-associated transcription factors XBP1s and/or ATF6 in the same cell independent of stress. We employ transcriptomics and quantitative proteomics to evaluate ER proteostasis network remodeling owing to the XBP1s and/or ATF6 transcriptional programs. Furthermore, we demonstrate that the three ER proteostasis environments accessible by activating XBP1s and/or ATF6 differentially influence the folding, trafficking, and degradation of destabilized ER client proteins without globally affecting the endogenous proteome. Our data reveal how the ER proteostasis network is remodeled by the XBP1s and/or ATF6 transcriptional programs at the molecular level and demonstrate the potential for selectively restoring aberrant ER proteostasis of pathologic, destabilized proteins through arm-selective UPR-activation.
The unfolded protein response adapts endoplasmic reticulum (ER) proteostasis via stress-responsive transcription factors including XBP1s and ATF6. Here, R. Luke Wiseman and colleagues implement technology for the orthogonal, ligand-dependent activation of XBP1s and/or ATF6 in a single cell. They characterize how XBP1s and/or ATF6 activation impacts ER proteostasis pathway composition and function. Adapted ER environments influence the proteostasis of destabilized protein variants without affecting the endogenous proteome. The work informs the development of proteostasis environment-adapting therapeutics for protein misfolding-related diseases. In order to activate both XBP1s and ATF6 in the same cell, we incorporated DHFR.ATF6 and tet-inducible XBP1s into a HEK293T-REx cell line stably expressing the tet-repressor.  The HEK293DYG control cell line expresses tet-inducible eGFP and DHFR.YFP and is used as a control to demonstrate that the addition of doxycycline (dox) and trimethoprim (TMP) do not induce UPR genes.

overall_design: HEK293DYG cells were treated for 12 h with vehicle or 1 μg/mL dox and 10 μM TMP in biological triplicate. Cells were harvested and RNA was extracted using the RNeasy Mini Kit (Qiagen). Genomic DNA was removed by on-column digestion using the RNase-free DNase Set (Qiagen). Data from HEK293DYG cells showed no significant overlap in the ligand-treated transcriptomes obtained from HEK293DAX  cells.

first: Matthew

middle: D

last: Shoulders

first: R


title: Stress-Independent Activation of XBP1s and/or ATF6 Reveals Three Functionally Distinct ER Proteostasis Environments

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

overall_design: Refer to individual Series


title: Stress-Independent Activation of XBP1s and/or ATF6 Reveals Three Functionally Distinct ER Proteostasis Environments [HEK293DAX]

summary:
The unfolded protein response (UPR) maintains endoplasmic reticulum (ER) proteostasis through the activation of transcription factors such as XBP1s and ATF6. The functional consequences of these transcription factors for ER proteostasis remain poorly defined. Here, we describe methodology that enables orthogonal, small molecule-mediated activation of the UPR-associated transcription factors XBP1s and/or ATF6 in the same cell independent of stress. We employ transcriptomics and quantitative proteomics to evaluate ER proteostasis network remodeling owing to the XBP1s and/or ATF6 transcriptional programs. Furthermore, we demonstrate that the three ER proteostasis environments accessible by activating XBP1s and/or ATF6 differentially influence the folding, trafficking, and degradation of destabilized ER client proteins without globally affecting the endogenous proteome. Our data reveal how the ER proteostasis network is remodeled by the XBP1s and/or ATF6 transcriptional programs at the molecular level and demonstrate the potential for selectively restoring aberrant ER proteostasis of pathologic, destabilized proteins through arm-selective UPR-activation.
The unfolded protein response adapts endoplasmic reticulum (ER) proteostasis via stress-responsive transcription factors including XBP1s and ATF6. Here, R. Luke Wiseman and colleagues implement technology for the orthogonal, ligand-dependent activation of XBP1s and/or ATF6 in a single cell. They characterize how XBP1s and/or ATF6 activation impacts ER proteostasis pathway composition and function. Adapted ER environments influence the proteostasis of destabilized protein variants without affecting the endogenous proteome. The work informs the development of proteostasis environment-adapting therapeutics for protein misfolding-related diseases. In order to activate both XBP1s and ATF6 in the same cell, we incorporated DHFR.ATF6 and tet-inducible XBP1s into a HEK293T-REx cell line stably expressing the tet-repressor. Selection of a single colony resulted in the HEK293DAX cell line in which XBP1s is induced by doxycycline and DHFR.ATF6 is activated by trimethoprim (TMP; TMP-dependent DHFR.ATF6 activation in HEK293DAX cells will henceforth be referred to as ATF6 activation for simplicity).

overall_design: HEK293DAX  cells were treated for 12 h with vehicle, 1 μg/mL dox, 10 μM TMP, or both in biological triplicate. Cells were harvested and RNA was extracted using the RNeasy Mini Kit (Qiagen). Genomic DNA was removed by on-column digestion using the RNase-free DNase Set (Qiagen). Data from HEK293DYG cells showed no significant overlap in the ligand-treated transcriptomes obtained from the control HEK293DYG cells.

middle: L


title: Characterisation of nuclear architectural alterations during in vitro differentiation of human stem cells of myogenic origin

status: Public on Apr 06 2013

city: Poznań

first: Tomasz

middle: Jan

last: Kolanowski

address: Strzeszyńska 32

department: Biology of Reproduction and Stem Cells

country: Poland

institute: Institute of Human Genetics PAS

summary:
Cell differentiation is based on a synchronised orchestra of complex pathways of intrinsic and extrinsic signals that manifest in the induced expression of specific transcription factors and pivotal genes within the nucleus. One cannot ignore the epigenetic status of differentiating cells, comprising not only histones and DNA modifications but also the spatial and temporal intranuclear chromatin organisation, which is an important regulator of nuclear processes. In the present study, we investigated the nuclear architecture of human primary myoblasts and myocytes in an in vitro culture, with reference to global changes in genomic expression. Repositioning of the chromosomal centromeres, along with alterations in the nuclear shape and volume, was observed as a consequence of myotube formation. Moreover, the microarray data showed that during in vitro myogenesis cells tend to silence rather than induce gene expression. The creation of a chromosome map marked with gene expression changes that were at least 2-fold confirmed the observation. Additionally, almost all of the chromosomal centromeres in the differentiated cells preferentially localised near the nuclear periphery when compared to the undifferentiated cells. The exceptions were chromosomes 7 and 11, in which we were unable to confirm the centromere repositioning.
In our opinion, this is the first reported observation of the movement of chromosomal centromeres along differentiating myogenic cells. Based on these data we can conclude that the myogenic differentiation with global gene expression changes is accompanied by the spatial repositioning of chromosomes and chromatin remodelling, which are important processes that regulate cell differentiation.

overall_design: Six samples from human skeletal muscle stem cells populations before and after differentiation were analysed

first: Natalia

last: Rozwadowska

first: Ewa

last: Wiland

first: Marcin

last: Siatkowski

first: Piotr

last: Pawlak

first: Agnieszka

last: Malcher

last: Mietkiewski

first: Marta

last: Olszewska

first: Maciej

last: Kurpisz


title: TGF-beta1-Induced Gene Expression Changes in HepG2 Cells

city: Aachen

first: Ralf

last: Weiskirchen

state: NRW

address: Pauwelsstr. 30

department: Institute of Clinical Chemistry and Pathobiochemistry

institute: RWTH University Hospital Aachen

summary: We here compared gene expression profiles in HepG2 cells upon stimulation with 1 ng/ml TGF-beta1 for 20 min, 1 hour, 2 hours, 4 hours, and 24 hours with untreated control cells. Experiments were done in three independent replicates. The goal of this study was to determine genes regulated by TGF-beta1.HepG2 cells were obtained from DSMZ (Braunschweig, Germany) and cell identity confirmed by STR profiling using the AmpFlSTR Identfiler Direct PCR Amplification kit (Life Technologies, Darmstadt, Germany). Gene expression profiles were compared at indicated time points after stimulation with TGF-beta (1 ng/ml) using the Human Gene 1.0 ST arrays (Affymetrix). In total 18 hybridizations are included in this series.

overall_design: 18 samples were hybridized to Affymetrix Human Gene 1.0 ST Array

first: Steffen

last: Meurer

first: Gudrun

last: Walenda

first: Khalid

last: Abnaof

first: Sylvia

last: Joussen

first: Qiong

last: Lin

first: Martin

last: Zenke

first: Kurt

last: Hoffmann

first: Wolfgang

last: Wagner

first: Holger

last: Fröhlich


title: Effects of TCDD on differentiating NHEKs

status: Public on Apr 05 2013

city: Memphis

first: Lawrence

middle: H

last: Kennedy

state: TN

address: 3700 Walker Ave

department: Biological Sciences

institute: University of Memphis

summary: TCDD increased expression of numerous differentiation specific genes and decreased expression of numerous genes involved in mitochondrial health and redox homeostasis

overall_design: 8 total samples - 4 control (100% density) 4 TCDD (100% density)

first: Thomas

last: Sutter

first: Carrie

first: Quynh

last: Tran


title: Fanconi anemia proteins interact with CtBP1 and modulate the expression of the Wnt antagonist Dickkopf-1

city: Quebec

first: Ezequiel

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

institute: CRCHUL

summary: Fanconi anemia (FA) is a genetic disorder characterized by congenital abnormalities, bone marrow failure and increased susceptibility to cancer. Of the fifteen FA proteins, Fanconi anemia group C (FANCC) is one of eight FA core complex components of the FA pathway. Unlike other FA core complex proteins, FANCC is mainly localized in the cytoplasm, where it is thought to function in apoptosis, redox regulation, cytokine signaling and other processes. Previously, we showed that regulation of FANCC involved proteolytic processing during apoptosis. To elucidate the biological significance of this proteolytic modification, we searched for molecular interacting partners of proteolytic FANCC fragments. Among the candidates obtained, the transcriptional corepressor protein C-terminal binding protein-1 (CtBP1) interacted directly with FANCC and other FA core complex proteins. Although not required for stability of the FA core complex or ubiquitin ligase activity, CtBP1 is essential for proliferation, cell survival and maintenance of chromosomal integrity. Expression profiling of CtBP1-depleted and FA-depleted cells revealed that several genes were commonly up- and down-regulated, including the Wnt antagonist Dickkopf-1 (DKK1). These findings suggest that FA and Wnt signaling via CtBP1 could share common effectors.

overall_design: HeLa cell line was grown in DMEM media supplemented with 10% FBS and were incubated in 5% CO2 at 37°C. A four-plasmid (pRSV-Rev, pMDLg/pRRE, pMD2.G and pLKO.1) expression system was used for lentiviral production. Different pLKO.1 plasmids carrying shRNAs targeting FANCA, FANCD2, CtBP1 or CtBP2  or a lentiviral control vector pLKO.1-scrambled were used. Lentiviral particles were produced via calcium phosphate-mediated transient transfection of the four plasmids into HEK293T cells. Cells were exposed to appropriate lentiviral particles. In each experiment, HeLa cells were transduced for 6 hours with filtered supernatant containing recombinant lentiviral particles. After transduction, the cells were cultured for 72 hours. Total RNA extracts from 3 different samples of each scrambled, CtBPs and FANCD2 shRNA treated HeLa cells were subjected to gene expression profiling via microarray analysis. Gene expression profiles were determined with Affymetrix GeneChip® Human Gene 1.0.

first: Caroline

last: Huard

first: Cédric

middle: S

last: Tremblay

first: Kathrin

last: Helsper

first: Marie-Chantal

last: Delisle

first: Detlev

last: Schindler

first: Georges

last: Lévesque

first: Madeleine

last: Carreau


title: Differentiation of human fetal multipotential neural progenitor cells to astrocytes reveals susceptibility factors for JC Virus

status: Public on Apr 09 2013

city: Bethesda

first: Kory

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: Viral infections of the CNS are of increasing concern, especially among immunocompromised populations. Rodent models are often inappropriate for studies of CNS infection, as many viruses, including JC Virus (JCV) and HIV, cannot replicate in rodent cells. Consequently, human fetal brain-derived multipotential CNS progenitor cells (NPCs) that can be differentiated into neurons, oligodendrocytes, or astrocytes, have served as a model for CNS studies. NPCs can be non-productively infected by JCV, while infection of progenitor-derived astrocytes (PDAs) is robust. We profiled cellular gene expression at multiple times during differentiation of NPCs to PDAs. Several activated transcription factors show commonality between cells of the brain in which JCV replicates and lymphocytes in which JCV is likely latent. Bioinformatic analysis determined transcription factors that may influence the favorable transcriptional environment for JCV in PDAs. This study attempts to provide a framework for understanding the functional transcriptional profile necessary for productive JCV infection.

overall_design: 19 Human samples: 4 Human Fetal Brain NPC 0h, 4 Human Fetal Brain NPC in Serum 1h, 4 Human Fetal Brain NPC in Serum 1d, 4 Human Fetal Brain NPC in Serum 7d, 3 Human Fetal Brain NPC in Serum 30d.

first: M

middle: W

last: Ferenczy

first: K

first: L

middle: J

last: Marshall

middle: C

last: Monaco

first: E

middle: O

last: Major


title: Gene expression in the mitochondrial syndrome of coenzyme Q deficiency

city: Sevilla

first: Daniel Jose

last: Moreno Fernandez-Ayala

address: Carretera de Utrera, Km. 1

institute: Universidad Pablo de Olavide

summary:
Coenzyme Q10 deficiency syndrome includes a clinically heterogeneous group of mitochondrial diseases characterized by low content of CoQ10 in tissues. The only currently available treatment is supplementation with CoQ10, which improves the clinical phenotype in some patients but does not reverse established damage.
Incubation with CoQ10 restored respiration and apoptotic pathways but did not affect lipid metabolism, cell growth, and undifferentiated phenotype presented by CoQ10 deficient cells. We conclude that the mitochondrial dysfunction caused byCoQ10 deficiency induces a stable survival adaptation of somatic cells from patients, thus explaining their incomplete recovery after treatment.

overall_design: We compared the gene expresion of human dermal fibroblast from healthy people (group 1) with fibroblast from diferent patient diagnosed with the human syndrome of coenzyme Q10 deficiency, which were treated (group 3) or not (group 2) with coenzyme Q10 to recovery ATP levels.

first: Daniel

last: Fernández-Ayala

first: Ignacio

last: Guerra

first: Maria

last: Cascajo

first: Angela

last: Gavilán

first: Salvatore

last: DiMauro

first: Michio

last: Hirano

first: Leonardo

last: Salviati

first: Rafael

last: Artuch

last: de Cabo

first: Plácido

last: Navas


title: Genome-wide expression study of human carotid atheroma

status: Public on Apr 01 2013

city: Lyon

first: Catherine

last: Cerutti

address: 8 avenue Rockefeller

country: France

institute: Université Lyon 1 & Hôpital Nord-Ouest

summary: The aim of this study was to identify new biomarkers and to investigate pathways involved in the progression of human carotid atheroma.

overall_design: The study was conducted from pieces of carotid endarterectomy collected in 32 hypertensive patients. The samples contained media and neo-intima without adventitia. They were paired, including for each patient one sample of the atheroma plaque (stage IV and over of the Stary classfication) containing core and shoulders of the plaque, and one sample of distant macroscopically intact tissue (stages I and II). In addition, clinical, biological and histological data were collected.

first: Giampiero

last: Bricca

first: Hanene

last: Ayari

first: Liliana

last: Legedz


title: Rapid and efficient transdifferentiation into functional myocytes from human induced pluripotent stem cells (hiPSCs).

city: Kyoto

first: Hidetoshi

last: Sakurai

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

institute: Center for iPS Cell Research and Application

summary: HiPSCs and human myoblast cells were differentiated into myocytes, and the global gene expression profile were analyzed.

overall_design: Comparison of gene expressions among 8 experiments, 3 were derived from hiPSCs(cell line; 253G1), 1 was derived from hiPSCs(cell line; 253G4), 1 was derived from hiPSCs(cell line; 201B7), 2 were from human myoblast cell line (Hu5/E18) and 1 was undifferentiated hiPSCs.


title: Expression data from multiple sclerosis patients in remission and relapse

city: Donostia - San Sebastián

first: Aritz

last: Irizar

address: Pº Dr. Beguiristain, s/n

department: Neuroscience Area

institute: Biodonostia Research Institute

summary: Whole-genome expression of peripheral blood leukocytes was measured in 22 patients and 24 controls using the Human Gene 1.0 ST array by Affymetrix

overall_design: 22 Multiple Sclerosis patients with samples both in remission and relapse (2 samples for each patient; 44 blood samples in total) and 24 healthy controls were included in the study, for a total of 68 samples.

first: Haritz

first: David

last: Otaegui


title: Mitosis is the main pathway altered in cervical cancer and is a source of potential markers for screening and survival, and therapeutic targets.

status: Public on Mar 31 2013

city: Distrito Federal

first: Ana María

last: Espinosa

state: Cuauhtemoc

address: Dr. Balmis No. 148

department: Unidad de Medicina Genómica

country: Mexico

institute: Hospital General de México O.D.

summary: The effect of preventive vaccination against Human Papillomavirus (HPV) in reducing the burden of cervical cancer (CC) will not be seen before 30 years. It is still necessary to improve the procedures of screening and treatment against CC. Current methods for screening have low sensitivity (Pap test) or specificity (HPV tests) to detect high-grade cervical intraepithelial neoplasias (CIN) and CC (CIN2+). The objective of this study was the identification and characterization of cellular targets present in most CC and absent in normal cervical tissue that can be considered as potential markers for screening or therapeutic targets.   Methods and Findings.   A pyramidal strategy was used. Initially the expression of 8,638 genes was compared between 43 HPV16-positive CC and 12 healthy cervical epitheliums using the HG-Focus microarray. The expression intensity of 8,370 genes was validated in 24 samples with a second microarray (HG-ST1.0). A total of 997 genes were deregulated in CC and the 21 best ranked were validated and confirmed by qRT-PCR in 67 CC and 25 controls. According to the ROC analysis and the fold change (FC), the best (AUC ≥ 0.97 and FC ≥ 10) six genes (CCNB2, CDC20, PRC1, SYCP2, NUSAP1, CDKN3) belong to the mitosis pathway. They were further explored by qRT-PCR in 29 CIN1 and 21 CIN2/3 lesions to investigate whether they could differentiate CIN2+ from CIN1 and healthy cervical epitheliums (CIN1-). Three of these genes were associated exclusively with invasive tumors (CCNB2, PRC1, SYCP2) and three (CDC20, NUSAP1, CDKN3) also with CIN2/3. The sensitivity and specificity of CDKN3 and NUSAP1, along with CDKN2A, to detect CIN2+ was around 90%. The protein codified by these genes was confirmed by immunohistochemistry in CC. The effect of these markers on the survival was investigated in 40 CC patients followed by 42 months. Only high-expression level of CDKN3 was associated with a poor survival (20%; p = 2 x 10-4, Long-rank test) and it was independent from FIGO staging.  Conclusions.  CDKN3 and NUSAP1, together with CDKN2A, may be potential targets for development of screening methods. However, further studies are needed from a screening population to define the optimal trade-off between sensitivity and specificity for detection of CIN2+. CDKN3 may be also considered as a survival marker. Inhibition of mitosis is a well-known strategy to combat cancers. Therefore, CDKN3 may be a potential therapeutic target in CC. However, it´s still necessary to demonstrate whether it´s indispensable for tumor growth.

overall_design: cervical cancer vs. healthy cervix

first: Ana

middle: M

first: Ingrid

last: Martinez

first: Jaime

last: Berumen


title: Comparing gene-expression profiles between bone-metastatic vs. non bone-metastatic human prostate cancer cells

status: Public on Mar 30 2013

city: Philadelphia

first: Alessandro

last: Fatatis

state: PA

address: 245 N. 15th Street - MS488

department: Pharmacology and Physiology & Pathology and Laboratory Medicine

institute: Drexel University

summary: Disseminated prostate cancer cells colonize the skeleton to progress into macroscopic lesions only if they successfully adapt to the bone microenvironment. We previously reported that the ability of prostate cancer cells to generate skeletal tumors in animal models correlated with the expression of the alpha-receptor for Platelet-Derived Growth Factor (PDGFRa). In this study we aimed to identify PDGFRa-regulated genes responsible for the acquisition of a bone-metastatic prostate phenotype. We performed genome-wide expression comparative analyses of human prostate cancer cell lines that differ for PDGFRa expression and propensity to establish tumors in the skeleton of animal models. We investigated the genes that were differentially regulated in the highly bone-metastatic PC3-ML cells and their low-metastatic counterpart PC3-N cells, and the genes differentially regulated between PC3-N and PC3-N with overexpression of PDGFRa (PC3NRa).  We have previously shown that DU-145 cells lack PDGFRa and fail to survive longer than three days as disseminated tumor cells after homing to the mouse bone marrow. Interestingly, and in contrast to PC3-N cells, the exogenous expression of PDGFRa did not promote metastatic bone-tropism of DU-145 cells in our model. Thus, we examined the genes that were differentially regulated between DU-145 and DU-145(Ra) and excluded them from our candidate genes. Finally, to refine our findings and compensate for PC3 and DU-145 genetic disparity,  we performed a comparative analysis of the genes differentially regulated between two bone metastatic single-cell progenies that were derived from PC3-ML cells.

overall_design: Seven human prostate cancer cell lines were analyzed in total for this study. Each cell line was analyzed in duplicate from two different passages in culture.

first: Qingxin

last: Liu


title: Expression data from human primary fibroblasts (IMR90) stably expressing H-RasV12 and treated with Metformin or vehicle

city: Montréal

first: Xavier

last: Deschênes-Simard

state: Québec

address: 3655 Sir William Osler

department: Medicine

institute: McGill University

summary:
Metformin reduces the incidence of cancer in diabetics or in animal models. At the cellular level, the effects of metformin include the inhibition of complex I of the mitochondrial electron transport chain, a reduction in ATP levels and the activation of the energy sensor AMP kinase. Metformin also prevents the production of reactive oxygen species in primary human cells expressing oncogenic ras and the DNA damage associated to the process.
We used microarrays to characterize the gene expression changes induced by metformin in primary human fibroblasts expressing oncogenic ras.

overall_design: Primary human fibroblasts were infected with a retroviral vector that expresses oncogenic ras. The cell population was then divided in two groups and one of them was treated with 5 mM metformin for 6 days. Then RNA was extracted from three independent replicas of this experiment and compared with cells treated with vehicle. Total RNA was send to Genome Quebec service for hybridization with Affymetrix microarrays.

first: Olga

last: Moiseeva

first: Gerardo

last: Ferbeyre

first: Michael

last: Pollak


title: Interleukin-27 is a potent inhibitor of cis HIV-1 replication in Monocyte-derived Dendritic Cells via a Type I Interferon-independent pathway

status: Public on Mar 29 2013

city: Frederick

first: Richard

middle: A

last: Lempicki

address: PO Box B

department: Clinical Services Program

institute: Leidos Biomedical Research, Inc.

summary: IL-27 treated DCs were shown to be highly potent inhibitors of cis HIV-1, particularly of CCR5 tropic strains. Microarray studies of IL-27 treated DCs showed no up-regulation of Type I (IFN) gene expression. Neutralization of the Type-I IFN receptor had no impact on the HIV inhibition. Lastly, IL-27 mediated inhibition was shown to act post-viral entry and prior to completion of reverse transcription. These results show for the first time that IL-27 is a potent inhibitor of cis HIV-1 infection in DCs by a Type I IFN independent mechanism.

overall_design: Gene expression microarrays from 3 samples of immature dendritic cells (iDCs) were compared with 3 samples of iDCs treated with IL-27

first: Qian

last: Chen

first: Tomozumi

last: Imamichi

first: Sanjay

last: Swaminathan


title: Interleukin-27 treated human macrophages induce the expression of novel miRNAs which may mediate anti-viral properties (affy)

first: Xiaojun

last: Hu

address: 1050 Boyles St.

department: CSP

institute: SAIC_Frederick, INc

summary: In this study, we hypothesized that IL-27 could induce the expression of novel miRNAs in macrophages which may have functional relevance in terms of anti-viral activity. In this study, primary monocytes were differentiated into macrophages using M-CSF (M-Mac) or with a combination of M-CSF and IL-27 (I-Mac) for seven days. Following this, total RNA was extracted from these cells and deep sequencing was performed, in parallel with gene expression microarrays. Using the novel miRNA discovery software, miRDeep, seven novel miRNAs were discovered in the macrophages, four of which were expressed higher in I-Mac (miRNAs 2.1, 8.1, 9.1 and 14.2) whilst three were detected in both M-Mac and I-Mac (miRNAs 9.3, 13.6 and 15.8). The expression of six of the seven novel miRNAs was highly correlated with qRT-PCR using specific primer/probes designed for the novel miRNAs. Gene expression microarray further demonstrated that a number of genes were potentially targeted by these differentially expressed novel miRNAs.

overall_design: Gene expression microarrays from 3 samples of microphage treated with M-CSF (M-MAC)  were compared with 3 samples of micropahge treated with M-CSF + IL-27 (I-MAC)

first: Dawei

last: Huang

first: Jun

last: Yang


title: Expression profiling comparisons of human PBMC treated with class I/IIb or class IIa HDAC inhibitors

status: Public on Mar 24 2013

city: Cambridge

first: Scott

last: Davis

state: MA

address: 200 Technology Square, Suite 602

department: Tempero DPU

institute: GSK

summary: The aim of this study was to identify differential gene expression resulting from the inhibition of class IIa HDACs in human PBMC.

overall_design:
Human PBMC were cultured ex vivo with a mitogenic stimulus (1 ug/ml phytohemagglutinin, PHA) for 60 hours concurrent with exposure to vehicle (DMSO), vorinostat (3 uM), or TMP195 (3 uM).  In addition to the whole PBMC populations, a portion of the cultures treated with DMSO or TMP195 were used for FACS purification of mutually exclusive CD3+ (T cell), CD19+ (B cell), and CD14+ (monocyte) populations. All samples were then processed for RNA extraction, labeling, and hybridization to Affymetrix arrays.
Vehicle vs. vorinostat vs. TMP195 treatments in PBMC; Vehicle vs. TMP195 treatment in CD3+, CD19+ or CD14+ cells

last: Nolan

first: Quentin

middle: G

last: Wright

first: Mercedes

last: Lobera


title: Expression status of mRNA for sex hormone receptors in human dental pulp cells and the response to sex hormones in the cells

status: Public on Mar 28 2013

city: Chiyoda-ku

first: Tomoko

last: Kobayashi

state: Tokyo

institute: The Nippon Dental University

summary: Objectives: Sex hormone receptors are reported to be present in human dental pulp (HDP) cells. The purpose of this study was to examine the biological significance of estrogen and androgen receptors (ER and AR, respectively) in HDP cells.  Design: We isolated HDP cells expressing ER- and AR-mRNAs and investigated the expression status of the receptors and the response to sex hormones in the cells.   Results: HDP cells expressing ER- and/or AR-mRNAs had the ability to form alizarin red S-positive nodules in which calcium and phosphorus were deposited in vitro and to differentiate into odontoblasts-like cells and dentin-like tissue in vivo.  Individual clones isolated from HDP cells exhibited a different expression pattern of mRNA for ER and AR.  Some clones expressed ERα- and/or ERβ-mRNAs and the others coexpressed ER- and AR-mRNAs.  Using the Ingenuity software, we found that 17β-estradiol (E2) and dihydrotestosterone (DHT) could act directly on HDP cells through ER- or androgen signaling-mediated mechanisms.  E2 or DHT stimulated the mRNA expression for genes related to odontogenesis of dentin-containing teeth and odontoblast differentiation, suggesting that ER and AR in HDP cells may be involved in dentinogenesis.  Conclusions: Our findings provide new insights into the biological significance of sex hormone receptors in HDP cells.

overall_design:
Gene expression profiles of human dental pulp cells derived from one male patient were compared between cells treated with 10^-6 M 5alpha-dihydrotestosterone and cells treated with vehicle.  Each sample has one replicate.
Gene expression profiles of human dental pulp cells derived from one female patient were compared between cells treated with 10^-9 M 17beta-estradiol and cells treated with vehicle.  Each sample has one replicate.

first: Takeki

last: Tsutsui


title: GENOMICS TO IDENTIFY HLA IDENTICAL RENAL TRANSPLANT TOLERANCE SIGNATURES

first: Sunil

last: Kurian

address: 10550 N Torrey Pines Road

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

type:
Third-party reanalysis
Expression profiling by array

summary: Immunosuppression is needed in HLA identical sibling renal transplantation.  We conducted a tolerance trial in this patient cohort using Alemtuzumab induction, donor hematopoietic stem cells, tacrolimus/mycophenolate immunosuppression converted to sirolimus, planning complete drug withdrawal by 24 months post-transplantation.  After an additional 12 months with no immunosuppression, normal biopsies and renal function, recipients were considered tolerant.  Twenty recipients were enrolled.  Of the first 10 (>36 months post-transplantation), 5 had immunosuppression successfully withdrawn for 16-36 months (tolerant), 2 had disease recurrence and 3 had subclinical rejection in protocol biopsies (non-tolerant). Microchimerism disappeared after 1 year, and CD4+CD25highCD127-FOXP3+ T cells and CD19+IgD/M+CD27- B cells increased to 5 years post-transplantation in both groups, whereas immune/inflammatory gene expression pathways in the peripheral blood and urine were differentially downregulated in tolerant compared to non-tolerant recipients. Therefore, in this HLA identical renal transplant tolerance trial, absent chimerism, Treg and Breg immunophenotypes were indistinguishable between tolerant and non-tolerant recipients, but global genomic changes indicating immunomodulation were observed only in tolerant recipients.

overall_design: A total of 46 PBMC samples representing blood draws from four time points in the first 9 recipients were processed for microarray analysis (The Scripps Research Institute, La Jolla, CA). The analyzed time points were: immediately pre-operatively in the absence of immunosuppression (n=9); post-operatively at 1 year (n=8, range 11-13 months); at 2 years (n=12, range 18-25 months); >3 years (n=17, range 32-48 months).  (At year 2 and at > 3 years, repeated samples were obtained from individual subjects, and at one year, one subject had a technically unsatisfactory sample.)  To discount the effects of immunosuppression on gene expression, microarray data were included on whole blood from 18 healthy human subjects (controls: GSE40586; NCBI Gene Expression Omnibus [GEO] repository).


title: Expression data from early human B-cell development

status: Public on Mar 26 2013

city: Seoul

first: Seung-Tae

last: Lee

state: - None -

address: 50 Iron-Dong KanangmGu

department: Laboratory Medicine & Genetics

institute: Samsung Medical Center

summary:
A global DNA methylation and gene expression analysis of early human B-cell development reveals a demethylation signature and transcription factor network. Nucleic Acids Res. 2012 Dec;40(22):11339-51.
We examined DNA methylation and RNA expression status during early B-cell development by sorting multiple replicates of four separate stages of pre-B cells derived from normal human fetal bone marrow and applied high-dimension DNA methylation scanning and expression arrays.
We identified a distinct development-dependent demethylation signature which has gene expression regulatory properties for pre-B cells, and provide a catalog reference for the epigenetic changes that occur in pre-B-cell leukemia and other B-cell-related diseases.

overall_design: Human fetal bone marrow was obtained, and using flow cytometry antibodies, four populations of B-cell developmental stages including stage 1 (S1; predominantly multipotent progenitors before lineage commitment and common lymphoid progenitors), stage II (S2; pre-B-I cells), stage 3 (S3; pre-B-II cells) and stage 4 cells (S4; immature B cells). For 8 indibiduals, DNAs and RNAs were isolated and the methylation and expression changes during early B-cell development were identified using the Illumina HumanMethylation450 Beadchip (Illumina) and GeneChip Human Gene 1.0 ST Array (Affymetrix).

first: Yuanyuan

last: Xiao

first: Joseph

last: Wiemels


title: Expression data of human coronary artery perivascular adipocytes and subcutaneous adipocytes

status: Public on Mar 15 2013

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary:
Inflammatory crosstalk between perivascular adipose tissue and and blood vessel wall may contribute to atherosclerosis pathogenesis, and exhibits more pro-inflammatory than adipogenic phenotype than subcutaneous adipocytes.
To identify a genomic basis for biologic differences, we performed genome-wide expression to identiy expression genes differentially regulated between perivascular and subcutaneous adipocytes.for biologic differences.

overall_design: We performed global gene expression analyses on in vitro differentiated adipocytes from human left coronary artery perivascular adipose tissue and subcutaneous adipose tissues derived from unrelated donors who were non-obese and did not have any known metabolic or atherosclerotic disease.

first: Tapan

last: Chaterjee

first: Bruce

last: Aronow


title: Gene-expression change along with differentiation stage from human iPS cells to astrocytes

status: Public on Mar 22 2013

first: Haruhisa

last: Inoue

state: Kyoto

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

institute: Kyoto University

summary:
gene-expression change along with differentiation stage from human iPS cells to astrocytes is unkown.
We used microaray to investigate gene-expression change along with differentiation stage from human iPS cells to astrocytes, and to confirm similarity between human primary astrocyte and iPSC-derived astrocytes.

overall_design: comparison along with differentiation stage from human iPS cells to astrocytes

first: Takayuki

last: Kondo


title: Gene expression from human pancreatic islet

city: Malmö

first: Joao

last: Fadista

address: Jan Waldenströms gata 35

institute: Lund University Diabetes Centre

summary: Expression profiling of cell cycle genes in human pancreatic islets with and without type 2 diabetes

overall_design: Islets from cadaver donors were provided by the Nordic Islet Transplantation Programme (www.nordicislets.org), Uppsala University. The microarrays were performed using GeneChip® Human Gene 1.0 ST whole transcript according to Affymetrix standard protocol.

first: João

first: Jalal

last: Taneera


title: Gene expression data from iPSC-derived neural cells, comparison between APP wild and E693delta mutation

summary:
Oligomeric forms of amyloid-beta peptide (Abeta) are presumed to play a pivotal role in the pathogenesis of Alzheimer’s disease (AD). However, it is still unclear how Abeta oligomers contribute to AD pathogenesis in patient neural cells. We generated induced pluripotent stem cells (iPSCs) from a familial AD patient and differentiated them into neural cells. Abeta oligomers were accumulated in neural cells of AD bearing amyloid precursor protein (APP)-E693delta mutation.
To uncover Abeta oligomers in AD(APP-E693delta) neural cells, we analyzed gene expression profiles of control and the AD neural cells

overall_design: comparison between control (n=3) and AD (n=3)


title: Microarray Analysis in Vestibular Schwannomas

status: Public on Mar 01 2013

city: Badalona

first: Miguel

last: Torres-Martin

state: Barcelona

address: Carretera de Canyet, s/n

department: Clinical Genomics Unit

institute: Hospital Universitari Germans Trias i Pujol

summary: Vestibular Schwannomas are benign neoplasms that arise from the vestibular nerve. The hallmark of these tumors is the biallelic inactivation of NF2. Transcriptomic alterations, such as the Nrg1/ErbB2 pathway, have been described in Schwannomas. Here, we have performed a whole transcriptomic analysis in 31 vestibular Schwannomas and 9 control nerves in the Affymetrix Gene 1.0ST platform, validated by quantitative Real-Time PCR using TaqMan Low Density Arrays. We performed a mutational analysis of NF2 by PCR/dHPLC and MLPA as well as a microsatellite marker analysis of the loss of heterozygosity of chromosome 22q. The microarray analysis showed that 1516 genes were deregulated, and 48 of the genes were validated by qRT-PCR. At least two genetic hits (allelic loss and/or gene mutation) in NF2 were found in 16 tumors, seven cases showed one hit and eight tumors showed no NF2 alteration. As conclusion, MET and associated genes such as ITGA4/B6, PLEXNB3/SEMA5 and CAV1 showed a clear deregulation in vestibular Schwannomas. In addition, androgen receptor (AR) downregulation may denote a hormonal effect or cause in this tumor. Furthermore, the osteopontin gene (SPP1), which is involved in Merlin protein degradation, was upregulated, which suggests that this mechanism may also exert a pivotal role in Schwannoma Merlin depletion. Finally, no major differences were found between tumors of different sizes, histological types or NF2 status, which suggests that at the mRNA level all Schwannomas, regardless of molecular and clinical characteristics, may share common features that can be used in the fight against them.

overall_design: In order to find target to fight against vestibular schwannoma, we performed an analysis of gene expression by microarrays.

first: Luis

last: Lassaletta

first: Jose

last: de Campos

first: Alberto

last: Isla

first: Javier

last: Gavilan

first: Barbara

last: Melendez

last: Castresana

first: Rommel

middle: R

last: Burbano

first: Jesus

last: San-Roman-Montero

first: Giovanny

last: Pinto

first: Juan

last: Rey


title: Expression data from Che-1 (AATF) depleted HCT 116 cell line

status: Public on Mar 12 2013

city: rome

first: maurizio

last: fanciulli

address: via e chianesi 53

department: molecular medicine

country: Italy

institute: regina elena cancer institute

summary:
Che-1 is a RNA Polymerase II binding protein involved in the regulation of gene transcription. Che-1 emerges as an important adaptor that connects transcriptional regulation, cell-cycle progression, checkpoint control, and apoptosis.
We have observed that Che-1 depletion sensitizes cells to chemotherapy. We used microarrays analysis to investigate classes of genes regulated by Che-1.

overall_design: Total RNA was extracted from control and Che-1 depleted HCT 116 cells 48 hours after transient transfection of siRNA.

first: T

last: Bruno

first: B

last: Benassi


title: Expression data from HCT116 colorectal cancer cells.

city: Aurora

first: Matthew

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

summary:
To define the contribution of CDK8 versus CDK19 to gene expression control, we performed a series of microarray assays for cells where each kinase was stably knocked down.
Toward this end, we subjected HCT116 cells to three different stress stimuli: 5-fluorouracil (5FU), glucose deprivation, and hypoxia. We found that CDK8, but not CDK19, functions as a widespread coactivator of HIF1A target genes in hypoxia.

overall_design: Total RNA from HCT116 cells harvested using an RNeasy kit (Qiagen) was used for gene expression analysis on Affymetrix HuGene 1.0 ST arrays following the manufacturer’s instructions. Differential gene expression was determined with Partek software using one-way ANOVA.


title: Expression data between FOXP3 wild type and 2T>C(mut)

status: Public on Mar 08 2013

city: Milan

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

institute: OSR - San Raffaele Scientific Institute

summary:
Investigation of the role of FOXP3 in CD4+ T effector cells. FOXP3 is transiently upregulated in T effector cells under activation. This temporary expression in Teff cells is insufficient to suppress expression of reported targets of FOXP3 repressor activity. The role of FOXP3 in T effector cells remains unclear.
We used microarray analysis to detail the differentially expressed genes between FOXP3 wild type and 2T>C(mut) clones and identified classes of up-regulated or down-regulated genes based upon FOXP3 expression.

overall_design: We used T effector cells from one IPEX disease carrier mother that consist of a mixed population ofFOXP3 wild type and 2T>C(mut) clones. We activated them using anti-CD3, anti-CD28. We compareFOXP3 wild type and 2T>Cl clones at different stages: resting phase and activated phase at 72hrs.

first: Alicia

last: McMurchy

first: Megan

middle: K

last: Levings


title: Expression data MCF10A/ErbB2 RB-proficient and RB-deficient cells cultured in 3-D cell culture

city: PHILADELPHIA

first: Adam

last: Ertel

address: 233 S 10TH ST

department: Cancer Biology

institute: Thomas Jefferson University

summary: Gene expression analysis for structural components in Rb-deficient and RB-proficient ErbB2-overexpressing immortalized breast cell line using 3-D cell culture model to analyze structural and organizational changes of epithelial cells.

overall_design: Cells were cultured in a reconstituted membrane for 7 days. Cells were extracted with the use RNA-STAT-60 method.

first: Dayana

middle: B

last: Rivadeneira

first: Isabelle

last: Mercier

first: Jeffry

last: Dean

first: A

last: McClendon

first: Sankar

last: Adyak

first: Agnieszka

last: Witkiewicz

first: Federica

last: Sotgia

first: Michael

middle: P

last: Lisanti

first: Erik

last: Knudsen


title: Lipoprotein lipase in chronic lymphocytic leukemia - strong biomarker with lack of functional significance

status: Public on Feb 13 2013

city: Vienna

first: Stefanie

last: Tauber

address: Dr. Bohr-Gasse 9

department: CIBIV

institute: MFPL

summary:
LPL co-deregulated genes after LPL specific siRNA knock-down
In chronic lymphocytic leukemia (CLL), lipoprotein lipase (LPL) mRNA overexpression is an established poor prognostic marker, its function, however, is poorly understood. Measuring extracellular LPL enzymatic activity and protein, we found no difference between levels in CLL patients and those of controls, both before and after heparin treatment in vivo and in vitro. Investigating LPL knock down effects, we determined five potential downstream targets, of which one gene, STXBP3, reportedly is involved in fatty acid metabolism.

overall_design: While possibly reflecting an epigenetic switch towards an incorrect transcriptional program, LPL overexpression by itself does not appear to significantly influence CLL cell survival.

first: Edit

last: Porpaczy

first: Katrina

last: Vanura


title: Affymetrix Control Samples

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

summary: Control samples from Affymetrix

overall_design: various control samples


title: Expression data from human peripheral blood lymphocytes stimulated with anti-CD3 and anti-CD28 antibodies.

status: Public on Feb 25 2013

city: Munich

first: Jacek

last: Puchałka

address: Lindwurmstrasse 2a

department: University Children's Hospital

country: Germany

institute: Munich University Hospital

summary: Peripheral blood lymphocytes were separated in the Ficoll gradient and subjected for stimulation with anti-CD3 and anti-CD28 antiobodies upon time (6h, 12h and 18h). Next, total RNA was isolated and trenscriptional analysis of stimulated cells was performed.

overall_design: 11 total samples were analysed. Analysis was performed using samples from two healthy donors and one sample from patient. Unstimulated samples were used as a controls.

first: Christoph

last: Klein

first: Dietmar

last: Pfeifer


title: Probing off-target effect of LMNA siRNA and pro-siRNA in HeLa-d1EGFP cell line

status: Public on Feb 06 2013

city: Boston

first: Linfeng

last: Huang

state: Massachusetts

address: 200 Longwood Avenue

department: PCMM

institute: Boston Children's Hospital

summary: We have develped a novel method of making siRNAs (named pro-siRNA for prokaryotic siRNA). To evaluate off-targeting of pro-siRNA, we compared mRNA expression profile of HeLa-d1EGFP cells transfected with 4 nM LMNA siRNAs and pro-siRNAs by microarray.

overall_design: We used microarray to study off-target effect of siRNAs in HeLa-d1EGFP cell line. After transfection of siRNAs for 24 hrs, RNA were extracted using Trizol. RNA samples were sent to Microarray Core at Dana-Farber Cancer Institute (http://macf-web.dfci.harvard.edu/index.php?option=com_frontpage&Itemid=1) to be probed using Human Gene 1.0 ST (Affymetrix).

first: Judy

last: Liebmerman


title: The clinical and genomic significance of donor-specific antibody (DSA) positive/C4d negative and DSA negative/C4d negative transplant glomerulopathy

status: Public on Feb 07 2013

city: New York

first: Bin

last: Ye

state: NY

address: 1301 Morris Park Ave

department: Genetics

institute: Albert Einstein College of Medicine

summary: We investigated the clinical, histopathologic and genomic features of donor-specific antibody (DSA) +/C4d- and DSA-/C4d- transplant glomerulopathy (TGP) using microarrays. Comparison of the gene expression profiles of DSA-/C4d- TGP biopsies with ptc+g score > 1  to normal and IFTA (Interstitial Fibrosis and Tubular Atrophy) biopsies by microarrays revealed increased expression of quantitative cytotoxic T cell--associated transcripts (QCAT). However, CAMR (chronic antibody-mediated rejection) and DSA+/C4d- TGP had increased expression of QCAT, interferon-gamma and rejection induced, constitutive macrophage-associated, natural killer cell-associated, and DSA selective transcripts. B cell and endothelial cell associated transcripts expression were upregulated only in CAMR biopsies. Our results suggest that while DSA+/C4d- TGP should be classified under CAMR, DSA-/C4d- TGP with ptc+g score > 1 probably develops through a chronic cellular immune response.

overall_design: Total of 57 arrays included in this study. G1. Normal transplant kidney biopsies (N= 12); G2. Non-specific IFTA (N= 17); G3. TGP DSA-/C4d- (N=8); G4. TGP DSA+/C4d- (N= 9); G5. CAMR/TGP C4d+/DSA+ (N= 11)

first: Enver

last: Akalin


title: H3K4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence (expression)

status: Public on Jan 31 2013

city: Cold Spring Harbor

first: Agustin

last: Chicas

address: One Bungtown Road

institute: Memorial Sloan Kettering

summary: Cellular senescence is a tumor-suppressive program that involves chromatin reorganization and specific changes in gene expression that trigger an irreversible cell-cycle arrest. We have examined the effect of suppressing the histone demethylases Jarid1a and Jarid1b on the senescence-associated gene expression signatures.

overall_design: Human fibroblast (IMR90) cells were infected with retroviral vectors expresssing shRNA targeting Jarid1a, Jarid1b or both, and triggered to undergo quiescence by removal of serum or senescence by over-expression of activated ras (Hrasv12).

first: Scott

last: Lowe

first: Xiaowo

last: Wang


title: HIV-1 Tat protein promotes neuronal dysfunction through disruption of microRNAs.

status: Public on Feb 12 2013

city: Philadelphia

first: Bassel

middle: E

last: Sawaya

address: 3307 N. Broad Street

department: Neurology

institute: Temple University

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

summary: Over the last decade, small noncoding RNA molecules such as microRNAs (miRNAs) have emerged as critical regulators in the expression and function of eukaryotic genomes. It has been suggested that viral infections and neurological disease outcome may also be shaped by the influence of small RNAs. This has prompted us to suggest that HIV infection alters the endogenous miRNA expression patterns, thereby contributing to neuronal deregulation and AIDS dementia. Therefore, using primary cultures and neuronal cell lines, we examined the impact of a viral protein (HIV-1 Tat) on the expression of miRNAs due to its characteristic features such as release from the infected cells and taken up by noninfected cells. Using microRNA array assay, we demonstrated that Tat deregulates the levels of several miRNAs. Interestingly, miR-34a was among the most highly induced miRNAs in Tat-treated neurons. Tat also decreases the levels of miR-34a target genes such as CREB protein as shown by real time PCR. The effect of Tat was neutralized in the presence of anti-miR-34a. Using in situ hybridization assay, we found that the levels of miR-34a increase in Tat transgenic mice when compared with the parental mice. Therefore, we conclude that deregulation of neuronal functions by HIV-1 Tat protein is miRNA-dependent.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
synthetic construct
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design:
Using primary cultures and neuronal cell lines, we examined the impact of a viral protein (HIV-1 Tat) on the expression of miRNAs and mRNAs.
Human fetal neurons were chosen to examine the impact of HIV-1 Tat protein on gene expression [GSM1173253-GSM1173256]

first: J

last: Chang

first: R

last: Mukerjee

first: A

last: Bagashev

first: L

last: Del Valle

first: T

last: Chabrashvili

first: B

last: Hawkins

last: He


title: identification of miRNA differential expression patterns in a new model of acquired letrozole resistance

status: Public on Jan 30 2013

city: Lyon

first: Julie

last: Vendrell

state: Select a State or Province

address: 8 avenue Rockefeller

department: INSERM U1052

institute: ISPBL - Faculté de Pharmacie de Lyon

summary: Since differential miRNA expression patterns associated with acquired AI resistance have been poorly investigated, the aim of this study was to delineate the deregulation of miRNA expression associated with aromatase inhibitor (AI) response failure in new cellular models of AI resistance. For this purpose, we generated and characterized novel cellular models of acquired resistance to letrozole (Res-Let cells) and to anastrozole (Res-Ana cells) and performed microarray experiments to identify miRNAs whose expression was either deregulated between control (MCF-7aro) and resistant cells (Res-Let or Res-Ana). With the aim to select relevant miRNAs, two independent cell culture replicates were performed for each experimental condition.

overall_design: MCF-7aro and Res-Let cells were grown in the presence of androstenedione (AD) combined or not with letrozole. Two independent cell culture replicates for each experimental condition were used to generate total RNA. Total RNA was extracted from cell culture using a Qiagen RNA extraction kit and RNA quality was assessed using the BioAnalyzer 2100? (Agilent Technologies). Complex probes were produced from these RNA, then hybridized to GeneChip® miRNA 3.0 array according to the manufacturer's recommendations (Affymetrix).  Res-Ana cells were grown in the presence of androstenedione (AD). Two independent cell culture replicates for each experimental condition were used to generate total RNA. Total RNA was extracted from cell culture using a Qiagen RNA extraction kit and RNA quality was assessed using the BioAnalyzer 2100 (Agilent Technologies). Complex probes were produced from these RNA, then hybridized to GeneChip® miRNA 3.0 array according to the manufacturer's recommendations (Affymetrix).

first: P

last: Cohen

last: Vilquin