title: A Myc transcriptional program that is independent of EMT drives a poor prognosis tumor-propagating phenotype in HER2+ breast cancer

city: Sydney

first: Daniel

last: Roden

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute

summary: The HER2 (ERBB2) and MYC genes are commonly amplified genes in breast cancer, yet little is known about their molecular and clinical interaction. Using a novel chimeric mammary transgenic approach and in vitro models, we demonstrate markedly increased self renewal and tumour propagating capability of cells transformed with Her2 and c-Myc. Co-expression of both oncogenes in cultured cells led to a pronounced activation of a c-Myc transcriptional signature and acquisition of a self renewing phenotype independent of an EMT programme or regulation of cancer stem cell markers. We show that HER2 and c-MYC are frequently co-amplified in a clinical breast cancer cohort and that co-amplification is strongly associated with aggressive clinical behaviour and poor outcome. Lastly, we show that in patients receiving adjuvant chemotherapy (but not targeted anti-HER2 therapy), MYC amplification is associated with a poor outcome in HER2+ breast cancer patients. These findings demonstrate the importance of molecular context in oncogenic transformation and acquisition of a malignant stem-like phenotype and have important diagnostic and therapeutic consequences for the clinical management of HER2+ breast cancer.

overall_design: Gene expression analysis of Her2, Myc, and Her2 + Myc over expression on MCF10A cells, with MCF10A vector control comparison

first: Radhika

last: Nair

first: Wee

middle: S

last: Teo

first: Andrea

last: McFarland

first: Simon

last: Junakar

first: Sunny

last: Ye

first: Akira

last: Nguyen

first: Jessica

last: Yang

first: Iva

last: Nikolic

first: Adrienne

last: Morey

first: Jaynish

last: Shah

first: Christina

last: Selinger

first: Laura

last: Baker

last: Cowley

first: Matthew

last: Naylor

first: Christopher

last: Ormandy

first: Sunil

last: Lakhani

first: Warren

last: Kaplan

first: Sandra

last: O'Toole

first: Alexander

last: Swarbrick


title: Gene expression profiling of BIX01294-treated human neuroblastoma cell line BE(2)-C

status: Public on Oct 23 2013

city: Augusta

first: Justin

last: Choi

state: GA

address: 1410 Laney Walker Blvd.

department: Cancer Center

country: USA

institute: Georgia Regents University

summary: Increased activation of the serine-glycine biosynthetic pathway is an integral part of cancer metabolism that drives macromolecule synthesis needed for cell proliferation. Whether this pathway is under epigenetic control is unknown. Here we show that the histone H3 lysine 9 (H3K9) methyltransferase G9A is required for maintaining the pathway enzyme genes in an active state marked by H3K9 monomethylation and for the transcriptional activation of this pathway in response to serine deprivation. G9A inactivation depletes serine and its downstream metabolites, triggering cell death with autophagy in cancer cell lines of different tissue origins. Higher G9A expression, which is observed in various cancers and is associated with greater mortality in cancer patients, increases serine production and enhances the proliferation and tumorigenicity of cancer cells. These findings identify a G9A-dependent epigenetic program in the control of cancer metabolism, providing a rationale for G9A inhibition as a therapeutic strategy for cancer.

overall_design: Affymetrix microarray assays were performed according to the manufacturer's directions on total RNA isolated from three independent samples of BE(2)-C cells treated either with 0.05% DMSO or with 5 µM BIX01294 (B9311, Sigma-Aldrich) for 24 hours.

first: Han-Fei

last: Ding

first: Jane


title: Gene expression changes in group 2 sigma factor mutant, ΔsigCDE, in standard growth conditions and after high-light treatment

status: Public on Sep 20 2013

city: Turku

first: Taina

last: Tyystjarvi

address: Pharmacity/Itäinen Pitkäkatu 4 C, 6th floor

department: Biochemistry

country: Finland

institute: University of Turku

summary: Adjustment of gene expression during acclimation to stress conditions, such as bright light, in the cyanobacterium Synechocystis sp. PCC 6803 depends on four group 2 σ factors (SigB, SigC, SigD, SigE). A ∆sigCDE strain containing the stress responsive SigB as an only functional group 2 σ factor appears twice as resistant to photoinhibition of photosystem II (PSII) as the control strain. Microarray analyzes of the ∆sigCDE strain indicated that 77 genes in standard conditions and 79 genes in high light were differently expressed compared to the control strain. Analysis of possible photoprotective mechanisms revealed that high carotenoid content and up-regulation of the photoprotective flavodiiron operon flv4-sll0218-flv2 protected PSII in ∆sigCDE, while up-regulation of pgr5-like, hlipB or isiA genes in the mutant strain did not offer particular protection against photoinhibition. The photoinhibition resistance was lost if ∆sigCDE was grown in high CO2 where carotenoid and Flv4-Sll0218-Flv2 contents were low. Additionally, photoinhibition resistance of the ∆rpoZ strain (lacking the omega subunit of RNA polymerase) with very high carotenoid but only low Flv4-Sll0218-Flv2 content supported the importance of carotenoids in PSII protection. Carotenoids likely protect mainly via quenching of singlet oxygen but efficient non-photochemical quenching in ∆sigCDE might offer some additional protection. Comparison of photoinhibition kinetics in control, ∆sigCDE and ∆rpoZ strains showed that protection by the flavodiiron operon was most efficient during the first minutes of high-light illumination.

overall_design: Cells from cyanobacteria Synechocystis sp. PCC 6803 named as control strain (CS) and group 2 sigma factor mutant ΔsigCDE (A730=1, 40 mL) were harvested directly from standard growth conditions (continuous illumination at the PPFD of 40 µmol m-2s-1, 32°C, ambient CO2) or after 30-min illumination a PPFD 750 µmol m-2s-1. From three to four independent experiments were performed at each conditions.

first: Kaisa

last: Hakkila

first: Hans

middle: C

last: Matthijs


title: Microarray data of human leukemia cells MV4;11 with or without IKK inhibitor treatment.

status: Public on Sep 19 2013

city: Stanford

first: HSU-PING

last: KUO

state: CA

address: 265 Campus Dr.

institute: Stanford University

summary: MLL fusion proteins in leukemia induce aberrant transcriptional elongation and associated chromatin perturbations, however the upstream signaling pathways and activators that recruit or retain MLL oncoproteins at initiated promoters are unknown. Through functional and comparative genomic studies, we identified an essential role for NF-kB signaling in MLL leukemia. Suppression of NF-kB led to robust anti-leukemia effects that phenocopied loss of functional MLL oncoprotein or associated epigenetic cofactors. The NF-kB subunit RELA occupies promoter regions of crucial MLL target genes and sustains the MLL-dependent leukemia stem cell program. IKK/NF-kB signaling is required for wild-type MLL and fusion protein retention and maintenance of associated histone modifications providing a molecular rationale for enhanced efficacy in therapeutic targeting of this pathway in MLL leukemias.

overall_design: MV4;11 cells were treated with 1µM IKK inhibitor or vehicle. Each group contains triplicate samples

first: Hsu-Ping

last: Kuo

first: Zhong

last: Wang

first: Dung-Fang

last: Lee

first: Masayuki

last: Iwasaki

first: Jesus

last: Duque-Afonso

first: Stephen

middle: H

last: Wong

first: Maria

middle: E

last: Figueroa

first: Jie

last: Su

first: Ihor

middle: R

last: Lemischka

first: Michael

middle: L

last: Cleary


title: Expression data from peripheral blood  - blood draws at Pre and Post time points of Allergen inhalation challenge (ER and DR)

city: Vancouver

first: Scott

last: Tebbutt

state: BC

address: Room 166, 1081 Burrard Street

department: Medicine

country: Canada

institute: University of British Columbia

summary: To determine differential gene expression in peripheral blood of asthmatic individuals undergoing allergen inhalation challenge between early responders (ERs) and dual responders (DRs) following allergen inhalation challenge

overall_design:
Blood was collected immediately prior to, and two hours after challenge
The change in gene expression (post expression minus pre expression) in ERs was compared with the change in gene expression in DRs using age and sex as covariates
Preprocessing and probeset filtering were applied to the entire dataset (28 CEL files) using the Factor Analysis for Robust MicroArray Summarization (farms) package in R
The Linear Models for MicroArrays (limma) package was used to determine differential gene expression using a Benjamini Hochberg FDR of 10%.

first: Amrit

last: Singh

first: Masatsugu

last: Yamamoto

first: Sarah

last: Kam

first: Jian

last: Ruan

first: Gail

middle: M

last: Gauvreau

first: Paul

last: O'Byrne

first: J

last: FitzGerald

first: Louis-Philippe

last: Boulet

first: Gabriella

last: Wojewodka

first: Cynthia

last: Kanagaratham

first: Juan

middle: B

last: De Sanctis

first: Danuta

last: Radzioch

middle: J


title: microRNA expression in heart tissue

status: Public on Sep 17 2013

city: Lodnon

first: Xiufen

last: Zheng

state: Ontario

address: 339 windermere Road,LHSC-UC, B4-235

department: Pathology

institute: university of Western Ontario

summary:
Ischemia reperfusion (I/R) injury is an unavoidable event occurring during heart transplantation, leading to graft failures and lower long-term survival rate of the recipient. microRNAs are major regulators of genes. IR causes  apoptosis/death of cardiomyocytes, resulting from up-regulation of apoptotic genes and down-regulation of anti-apoptotic genes which are regulated by microRNA.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

overall_design: We perserved donor hearts with university of  Wisconsin solution for 18h at 4C degree before being implanted into recipients to create ischemia reperfusion injury. The preserved hearts were implanted into a syngeneic recipient mice. 24h after transplantation, heart grafts were harvested for microRNA extraction.


title: Expression data from kidney biopsies of liver disease patients

city: Bronx

first: Pilib

last: Ó Broin

state: NY

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

summary:
Glomerular abnormalities have been demonstrated in kidney biopsies of patient after orthotopic liver transplantation (OLT). We hypothesize that these changes exist prior to OLT and may play a role in the development of renal failure after OLT. We use gene expression microarrays to investigate the mechanism of kidney disease in patients listed for OLT.
Gene expression profiles of biopsies of cirrhotic patients were compared with pre-implantation living donor biopsies. Glomerular abnormalities were seen in 92% of the biopsies, the most common being increase in mesangial matrix. Electron microscope showed effacement of podocytes (93%) and duplication (35%) and widening of glomerular basement membrane (45%). Gene Ontology analysis revealed significant up-regulation of genes implicated in immune response, including T-cell, leucocyte and platelet activation and differentiation. Pathogenesis-based transcripts analysis revealed significantly increased expression of cytotoxic T-cell, macrophage, B-cell, natural killer cell, and endothelial cell associated transcripts, indicating an ongoing inflammatory immune response.

overall_design:
Eight patients with cirrhotic livers listed for transplantation were referred to the kidney transplant clinic at Montefiore Medical Center, Bronx, New York, for evaluation of renal dysfunction between April 2010 and March 2013. Patients consented prior to clinically indicated kidney biopsy for enrollment into the study. Information and lab results were collated for each patient including: age, sex, race, etiology of liver disease, history of diabetes mellitus (DM) and hypertension (HTN), metabolic profile, liver function tests, glycosylated hemoglobin (HgbA1c), C3 and C4 complement concentrations, antinuclear antibody titers and spot urine protein to creatinine ratio. Patients completed a 24-hr urine collection for protein and creatinine, which was used to assess proteinuria and creatinine clearance. eGFR was calculated using the Modified Diet of Renal Disease (MDRD) formula. Hematuria was defined as presence of any red cells in urine analysis. Proteinuria was defined as protein excretion of greater than 100mg in 24 hour. HTN and DM were defined by use of anti-hypertensive and insulin or oral hypoglycemic agents respectively in past or at time of kidney biopsy. Biopsies from cirrhotic patients were then compared to nine pre-implantation biopsies from living kidney donors.

The de-identified patient clinical characteristics are provided in each sample records;
For Hematuria, HTN, MM (mesangial matrix expansion), MC (mesangial cell increase), II (interstitial inflammation), podocyte, BM (basement membrane thickening), the value 0 and 1 represents 'ABSENT' and 'PRESENT', respectively.
For C3 and C4, the value 0 and 1 represents NORMAL and LOW C3 (or C4) LEVELS, repectively.
For TA (tubular atrophy), IF (interstital fibrosis), AS (arteiosclerosis), the value 0, 1, and 2 represents ABSENT, PRESENT MILD, and PRESENT MODERATE, respectively.
For IgG, IgA, IgM, C, and EmPE, the values represent 1 (ABSENT), 1 (MILD STAINING), 2 (MODERATE), 3 (SEVERE), NA (NOT AVAILABLE), P (PENDING).
For BMWId, BMd, and EDD, the values represent 0 (ABSENT), 1 (PRESENT), NA (NOT AVAILABLE), P (PENDING).

first: Enver

last: Akalin

first: Graciela

last: de Boccardo


title: Gene expression analysis of RB1 knockdown in bone in response to radiation

status: Public on Sep 14 2013

city: Melbourne

first: Maya

last: Kansara

state: Victoria

address: St Andrews Place

department: Research

institute: Peter MacCallum Cancer Centre

summary: The role of RB1 in response to radiation was examined in human osteoblasts.  We demonstrate that RB1 induced SASP genes, a response which was attenuated in RB1 knockdown osteoblasts.

overall_design: Subconfluent hOB shEV and shRB1 cells were irradiated at 4 Gy using a 137Cesium source at a dose rate of 1.7 min/Gy and cell pelllets collected 0, 2, 4, 8, 16  and 24 hrs after irradiation.

first: David

last: Thomas


title: Expression data from Adipose Stem Cells (ASC) from morbidly obese and non-obese individuals

city: Barcelona

first: Lina

last: Badimon

address: St Antoni M Claret, 167

department: ICCC-Cardiovascular Program

country: Spain

institute: Research Institut- HSCSP

summary:
The adipose tissue is an endocrine regulator and a risk factor for atherosclerosis and cardiovascular disease when by excessive accumulation induces obesity. Although the adipose tissue is also a reservoir for stem cells (ASC) their function and “stemcellness” has been questioned. Our aim was to investigate the mechanisms by which obesity affects subcutaneous white adipose tissue (WAT) stem cells.
We used microarrays to analyze differences in transcriptomic profiles between the adipose stem cells from morbidly obese and non-obese individuals.

overall_design: Subcutaneous white adipose tissues that were obtained during bariatric surgery (Obese) or liposuction (Lean) were donated by patients after obtaining informed consent. Three cases with BMI>40 kg/m2 (ASCmo) and three controls with BMI<25 kg/m2 (ASCn) were selected and processed extracting total RNA, processing and hybridizating on microarrays.

first: Blanca

last: Oñate

first: Gemma

last: Vilahur

first: Sandra

last: Camino-López

first: Alberto

last: Díez-Caballero

first: Carlos

last: Ballesta-López

last: Ybarra

first: Fabrizio

last: Moscatiello

first: Javier

last: Herrero


title: Transcriptional profiling of breast cancer stem cell xenografts and their metastatic derivatives

status: Public on Sep 15 2013

city: Roma

first: alfredo

last: pagliuca

state: RM

address: viale regina Elena 299

department: EOMM

country: Italy

institute: ISS

summary:
Breast cancer stem cell (BCSC) line #1 and #4 were grown in either stem cell medium or medium favoring the differentiation. Cells were genetically labeled with fluorescent protein expression cassettes and xenotransplanted into immunocompromised mice, giving rise to tumors. Tumors were explanted, dissociated and kept in culture so as to isolate growing cells. Cells were then sorted for fluorescent protein expression and RNA was extracted.
Breast cancer stem (BCSC) and differentiated (dBCCs) cells, grown in opportune conditions, were transfected with lentiviral vector encoding luciferase/enhanced green fluorescent protein (Luc/EGFP-BCSCs) or luciferase/red fluorescent protein (Luc/RFP-dBCCs) reporter genes and orthotopically injected in defined ratios (1:1) into immunocompromised mice. Primary tumor growth and the onset of distant metastases was then observed in time. Following primary and metastatic lesions resection,  labeled dBCCs, BCSCs and metastatic derivatives, thereafter referred to as fat pad differentiated cells (FPD), fat pad stem cells (FPS) and metastases (Ms) respectively, were consequently isolated from through fluorescent-activated cell sorting and RNA extracted.

overall_design: 14 samples, with at least 2 biological replicates for each category

first: Alfredo

last: Pagliuca

first: Monica

last: Bartucci


title: Comparative gene expression analysis of the human periodontal ligament in deciduous and permanent teeth

status: Public on Sep 06 2013

city: Seoul

first: Seong-Oh

last: Kim

address: 250 Seongsanno, Seodaemun-gu

department: Pediatric dentistry

country: South Korea

institute: Yonsei University College of Dentistry

summary: There are histological and functional differences between human deciduous and permanent pediodontal ligament (PDL) tissues. The purpose of this study was to determine the differences between these two types of tissue at the molecular level by comparative gene expression analysis.

overall_design: PDL samples were obtained from permanent premolars (n=38) and anterior deciduous teeth (n=31) extracted from 40 healthy persons. Comparative cDNA microarrary analysis revealed several differences in gene expression between the deciduous and permanent PDL tissues.


title: Mesenchymal Stem/Progenitors and Other Endometrial Cell Types from Women with Polycystic Ovary Syndrome (PCOS) Display Inflammatory and Oncogenic Potential

status: Public on Sep 30 2013

city: San Francisco

first: Linda

last: Giudice

address: 513 Parnassus Ave. HSE 1619

department: OBGYN and RS

institute: University of California, San Francisco

summary: Context: Endometrium in polycystic ovary syndrome (PCOS) presents altered gene expression indicating progesterone resistance and predisposing to reduced endometrial receptivity and endometrial cancer.  Objective: We hypothesized that an altered endocrine/metabolic environment in PCOS may result in an endometrial “disease phenotype” affecting the gene expression of different endometrial cell populations, including stem cells and their differentiated progeny.   Design and setting: A prospective study conducted at an academic medical center.  Patients and Main Outcome Measures: Proliferative phase endometrium was obtained from 6 overweight/obese PCOS (NIH criteria) and 6 overweight/obese controls. Microarray analysis was performed on fluorescence-activated cell sorting (FACS)-isolated endometrial epithelial cells (eEP), endothelial cells (eEN), stromal fibroblasts (eSF) and mesenchymal stem cells (eMSC). Gene expression data were validated using microfluidic Q-RT-PCR and immunohistochemistry (IHC).   Results: The comparison between eEPPCOS and eEPCtrl showed dysregulation of inflammatory genes and genes with oncogenic potential (CCL2, IL-6, ORM1, TNAIFP6, SFRP4, SPARC). eSFPCOS and eSFCtrl showed upregulation of inflammatory genes (C4A/B, CCL2, ICAM1, TNFAIP3). Similarly, in eMSCPCOS vs. eMSCCtrl the most upregulated genes were related to inflammation and cancer (IL-8, ICAM1, SPRR3, LCN2). IHC scoring showed increased expression of CCL2 in eEPPCOS and eSFPCOS compared to eEPCtrl and eSFCtrl and IL-6 in eEPPCOS compared to eEPCtrl.    Conclusions: Isolated endometrial cell populations in women with PCOS showed altered gene expression revealing inflammation and pro-oncogenic changes, independent of BMI, especially in eEPPCOS and eMSCPCOS, compared to controls. The study reveals an endometrial  “disease phenotype” in women with PCOS with potential negative effects on endometrial function and long-term health.

overall_design:
Proliferative phase endometrium was obtained from 6 overweight/obese PCOS (NIH criteria) and 6 overweight/obese controls. Microarray analysis was performed on fluorescence-activated cell sorting (FACS)-isolated endometrial epithelial cells (eEP), endothelial cells (eEN), stromal fibroblasts (eSF) and mesenchymal stem cells (eMSC).
Tissue samples were obtained through the National Institute of Health (NIH)/University of California, San Francisco (UCSF), Human Endometrial Tissue and DNA Bank in accordance with the guidelines of the Declaration of Helsinki. Informed consent was obtained from all participants in the UCSF Center for Reproductive Health, and the study was approved by the UCSF Committee on Human Research. The clinical summary of the study participants is shown in Table 1. Eleven proliferative phase endometrial biopsies (Pipelle, Cooper Surgical Shelton, Connecticut) and one curettage specimen were collected from over-weight (Body Mass Index [BMI, kg/m2] ≥ 27 < 29.9; n=1) and obese (BMI ≥ 30; n=5) women with PCOS (age 30.5± 2.1 yrs, BMI 34.13± 2.2, NIH criteria  (17) and overweight (n=2) and obese (n=4) control women (age 36.50±1.70 yrs, BMI 35.73±3.96). All PCOS subjects had normal 17-hydroxyprogesterone, prolactin and thyroid hormone levels. Control samples were obtained from healthy volunteer and women undergoing benign gynecological surgery. All controls reported menstrual cycles with regular interval (25-35 days) and no clinical evidence of having PCOS. Neither PCOS nor control subjects were exposed to hormonal medications for at least 2 months prior to tissue sampling and were confirmed not pregnant.

first: Terhi

middle: T

last: Piltonen

first: Joseph

last: Chen

middle: W

last: Erikson

first: Trimble

last: Spitzer

first: Fatima

last: Barragan

last: Rabban

first: Heather

middle: G

last: Huddleston

first: Juan

last: Irwin


title: Potential biomarkers of non-obstructive azoospermia identified in microarray gene expression analysis

status: Public on Sep 16 2013

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

summary: We analyzed gene expression profiles of human testicular biopsies in men with idiopathic nonobstructive azoospermia. Using new generation oligonucleotide microarray platform GeneChip® Human Gene 1.0 ST,  we identified genes which could be potential biomarkers of azoospermia and molecular indicators that could determine a particular stage of impaired spermatogenesis. Thus, we shed light on genes which were had so far been weakly characterized and which were had never related to infertility before. These studies also included the comparative analysis of the hierarchical clustering of gene expression profile with histopathological data provided for azoospermic patients.

overall_design: We analyzed 31 testicular biopsy samples with Affymetrix Human Gene 1.0 ST microarrays. 27 of them were obtained from patients with various types of NOA and 4 with normal spermatogenesis.

first: A

last: Malcher

first: N

last: Rozwadowska

first: T

last: Kolanowski

first: P

last: Jedrzejczak

first: W

last: Zietkowiak

first: M

last: Kurpisz


title: Genome-wide DNA methylation profiling in cultured eutopic and ectopic endometrial stromal cells (expression)

status: Public on Sep 07 2013

city: Ube

first: Yoshiaki

last: Yamagata

state: Yamaguchi

address: Minamikogushi 1-1-1

department: Obstetrics and Gynecology

country: Japan

institute: Yamaguchi University School of Medicine

summary: Transcriptome profiles were investigated in isolated endometrial stromal cells (ESCs) from eutopic and ectopic endometrium. The profiles were quite different between eutopic ESC and ectopic ESC, whereas no clear dfference was recognized between eutopic ESC with and without endometriosis.

overall_design: Total RNA from three cultured endometrial stromal cells (ESCs) from eutopic endometria without endometriosis, three ESCs with endometriosis and three ESCs from chocolate cysts were hybridised to the Affymetrix Human Gene 1.0 ST Array.

first: Koichiro

last: Nishino

first: Eiichi

last: Takaki

first: Shun

last: Sato

first: Ryo

last: Maekawa

first: Akira

last: Nakai

first: Norihiro

last: Sugino


title: Genome-wide DNA methylation profiling in cultured eutopic and ectopic endometrial stromal cells

type:
Methylation profiling by array
Expression profiling by array

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

overall_design: Refer to individual Series


title: Genome-wide expression profiling of 30 uM curcumin treatment of immortalized prostate fibroblasts (PShTert-AR)

city: Adelaide

first: Lauren

last: Giorgio

state: SA

address: Basil Hetzel Institute, 28 Woodville Rd Woodville South

institute: University of Adelaide

summary: Identifying the effect of the natural agent curcumin on global transcriptional activity of PShTert-AR prostate fibroblast cells over time with a view to understanding mechanisms of action over time. Treatment of PShTert-AR cells for 4, 8, 12 and 16 hours in PShTert-AR cells significantly altered the expression of approximately 1200 genes. Through non-hierarchical cluster analysis, these genes were classified into 3 distinct groups depending on their pattern of temporal response.

overall_design: PShTert-AR cells were treated with vehicle control (16 hours DMSO) or 30 uM curcumin (4, 8, 12 or 16 hours). Total RNA was extracted. Triplicate RNA samples were pooled and hybrydised to Affymetrix Human Gene 1.0 ST array chips.

first: Grant

last: Buchanan


title: Comparing gene expression in stem/progenitor cells from patients with CML in chronic, accelerated and blastic phase with normal volunteers

city: Glasgow

first: david

last: irvine

address: 21 shelly road

department: MVLS

country: United Kingdom

institute: University of Glasgow

summary: A comparison of global gene expression between rigorously defined stem and progenitor cells from patients with chronic myeloid leukaemia (CML) in chronic (CP), accelerated (AP) and blastic (BC) phase and similar populations isolated from normal volunteers.

overall_design: Cryopreserved CD34+ enriched cell populations obtained from patients with CML in CP, AP or BC at diagnosis prior to treatment -- or from normal volunteers -- were thawed and flow sorted into rigorously defined sub-populations (HSC, MPP, CMP, GMP and MEP -- using surface phenotype as described below). Total RNA was obtained and global gene expression measured following hybridisation to Affymetrix HuGene-1_0-st-v1 gene-chips. In total, 3 normal patient samples were compared with 6 CP, 4 AP and 2 BC samples. HSC, CMP, GMP and MEP populations were obtained from all specimens, MPP populations were obtained from normal, AP and BC specimens but not CP specimens.

last: Copland

first: D

middle: A

last: Irvine


title: Comparative gene expression profiling of the EBV-positive NPC cell line C666.1 and normal primary tonsillar epithelial cells

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

institute: Durham University

summary: In this study, we have performed comparative gene expression profiling of primary tonsil epithelial cells with the EBV-positive NPC cell line C666.1 using a human gene array.

overall_design: Differences in cellular gene expression was compared using RNA isolated from C666-1 cells and primary tonsil epithelial cells grown in serum-free keratinocyte growth medium (performed in triplicate). RNA isolated from each sample was processed according to the Genechip WT sense target labelling protocol. 1μg of RNA was hybridised to human gene 1.0 ST array chips.

first: Chunfang

last: Hu

first: John

last: Arrand

first: Christopher

last: Dawson


title: Gene expression analysis of OVCAR-3 and CDK2 resistant sublines

status: Public on Sep 01 2013

city: East Melbourne

first: Dariush

last: Etemadmoghadam

address: St Andrew's Place

summary: Cyclin E1 (CCNE1) is amplified in various tumor types including high-grade serous ovarian cancer where it is associated with poor clinical outcome. We have demonstrate that suppression of the Cyclin E1 partner kinase, CDK2, induces apoptosis in a CCNE1 amplicon-dependent manner. Little is known of mechanisms of resistance to CDK inhibitors. We therefore generated OVCAR-3 sublines with reduced sensitivity to CDK2 inhibitors and profiled by gene expression microarrays.

overall_design: Arrayed samples included parental OVCAR-3 cells (n = 4 replicates) and five independently derived sublines resistant to PHA-533533 (OVCAR3-533533-R1, -R3, -R5, -R6, -R7). The resistant cell lines were arrayed after drug selection (P5) and after continued passage in the absence of inhibitor (P10+).

first: David

last: Bowtell


title: Analysis of transcripts in PNA-A(15) oligo treated  human HEK-293 cells

status: Public on Sep 03 2013

city: Bangkok

first: Chatchawit

last: Aporntewan

address: Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University

country: Thailand

institute: Chulalongkorn University

summary: Mononucleotide A and T repeats are abundant in human genome. Many of A repeats are bound by Argonaute proteins (AGOs). To evaluate the role of AGOs and A repeats in gene regulation, HEK293 cells were treated with 8-amino-3,6-dioxaoctanoic acid added peptide nucleic acid (PNA) AAAAAAAAAAAAAAA oligo (OO-A(15)).

overall_design: Matched two sets of two individual HEK293 cells were transfected with OO-A(15) and scramble OO-PNA oligo, and were analyzed as biological duplicates. Cells were grown in DMEM (Gibco-BRL) according to the manufacturer’s protocol. OO-A(15) and scramble oligo were dilute with dH2O to reach 10μM. Cells were transfected in 6-well plates, seed 6 x 105 cells per well with 50 nM OO-A(15) and scramble oligo using  TransIT-siQUEST transfection reagent (Mirus). The transfected cell lines were cultured for 48 h post-transfection and harvested total RNA by Trizol reagent (Invitrogen). All RNA integrity assays were performed and hybridized on beadchip according to the protocol.

first: Nachol

last: Chaiyaratana

first: Piyapat

last: Pin-on

first: Apiwat

last: Mutirangura


title: Epigenome analysis of uterin leiomyoma and myometrium with or without leiomyoma [Expression data]

first: Ryo

last: Maekawa

address: Minami-Kogushi 1-1-1

department: Department of Obstetrics and Gynecology

summary: Profiles of genome-wide DNA methylation were investigated in leiomyomas and in myometrium with and without leiomyomas.  Profiles of DNA methylation in the myometrium with and without leiomyomas were quite similar while those in leiomyomas were distinct.

overall_design: Total RNA from the three uterine leiomyoma, three myometrium with leiomyoma and three myometrium without leiomyoma were analyzed with the Affymetrix GeneChip Mouse Gene 1.0 ST Array.

first: Shun

last: Sato

first: Yoshiaki

last: Yamagata

first: Hiromi

last: Asada

first: Isao

last: Tamura

first: Maki

last: Okada

first: Hiroshi


title: Expression data from human olfactory neurosphere derived cells (hONS) established from adult donors treated with coated and uncoated ZnO nanoparticles

status: Public on Sep 11 2013

city: North Ryde

first: Megan

last: Osmond-McLeod

address: 11 Julius Avenue

institute: CSIRO

summary:
ZnO nanoparticles can elicit a range of cytotoxic responses in different cells in vitro that may reflect either Zn2+ dissolution or nanoparticle-specific effects.  Coating the ZnO nanoparticles may mitigate their cytotoxicity.
We aimed to capture whole genome transcriptional profiles (up and down regulated) at time-points associated with distinct cytotoxic responses in cells treated with two types of uncoated (Nanosun, Z-COTE) or two types of coated (HP1, MAX) ZnO nanoparticles, compared to untreated cells.

overall_design: hONS cells were incubated with 25ug/ml ZnO nanoparticles (uncoated: Nanosun and Z-COTE; coated: MAX, HP1) for 2h and 6h and their expression profiles were compared to time-matched untreated cells.

last: Osmond

first: Yalchin

last: Oytam

first: Maxine

last: McCall


title: Gene expression and copy number analysis of OVCAR-3 and CDK2 resistant sublines

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


title: Clinical Monoclonal B lymphocytosis versus Rai 0 Chronic Lymphocytic Leukemia: a comparison of the cellular, molecular, cytogenetic features and clinical course in a prospective multicenter study [mRNA]

status: Public on Aug 30 2013

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

summary: Prospective series of 136 clinical monoclonal B lymphocytosis (cMBL) and 216 chronic lymphocytic leukemia (CLL) Rai 0 patients, were investigated in this study. While the distribution of CD38 and ZAP-70 positivity was similar, IGHV-mutated cases were more frequent among cMBL (P = 0.005). A Cox multivariate analysis on the whole patient cohort showed that cMBL condition was predictive of longer PFS, while CD38 expression and IGHV-unmutated status and CD38 expression correlated significantly with a shorter PFS in cMBL and Rai0-CLL, respectively. Trisomy 12, 11q- and 17p- abnormalities were scanty and of no predictive value in both conditions. Notably, gene and miRNA expression profiling showed no significant differences between cMBL and Rai0-CLL. Furthermore, similar gene and miRNA expression signatures were found in cMBL and Rai0-CLL according to the IGHV gene mutational status: that is, unmutated cases had different signatures from mutated cases, irrespectively of the cMBL or CLL condition. Overall, our study based on a prospective series of patients indicates that no major biological differences exist in cMBL compared to Rai0-CLL, suggesting that this two entities mainly differ for the initial size of the monoclonal cell population which may reflect in the longer time for clonal expansion.

overall_design: This series of microarray experiments contains the gene expression profiles of purified B-cell chronic lymphocytic leukemia (B-CLL) cells obtained from 160 patients (Binet stage A) including 45 cMBL and 115 Rai0-CLL. Peripheral blood mononuclear cells from CLL patients were isolated by Ficoll-Hypaque (Seromed, Biochrom KG, Berlin, Germany) density-gradient centrifugation. For gene and miRNA expression profiling experiments CLL cells were enriched by negative selection with the EasySep-Human B cell enrichment kit without CD43 depletion (Stem Cell Technologies) using the fully automated protocol of immunomagnetic cell separation with RoboSepTM (Stem Cell Technologies).

first: Morabito

last: Fortunato

first: Mosca

last: Laura

first: Cutrona

last: Giovanna

first: Tuana

last: Giacomo

first: Ferracin

last: Manuela

first: Zagatti

last: Barbara

first: Fabris

last: Sonia

first: Matis

last: Serena

first: Gentile

last: Massimo

first: Recchia

last: Anna

first: Bossio

last: Sabrina

first: D

first: Ilariucci

last: Fiorella

first: Musolino

last: Caterina

first: Molica

last: Stefano

last: Francesco

first: Tassone

last: Pierfrancesco

first: Negrini

first: Ferrarini

last: Manlio

first: Neri

last: Antonino


title: Gene expression data from 8 pairs of CD138+/- myeloma cell lines

status: Public on Sep 05 2013

city: IOWA CITY

first: Fenghuang

last: Zhan

state: IA

address: 285 Newton Rd, 3269A CBRB

institute: University of Iowa

summary:
8 pairs of myeloma cell lines were sorted by MACS CD138-microbead, and the each cell lines were divided into two fraction CD138+ and CD138-.
We used microarrays to detail the global programme of gene expression in these 8 pairs of CD138+/- myeloma cell lines

overall_design: CD138- fraction in myeloma are thought to be myeloma stem cells fraction, and we compared the gene expression profile between CD138- and CD138+ fraction.

first: Hongwei

last: Xu

first: Ye

last: Yang


title: Transcription profiles of cumulus cells from GnRH agonists and GnRH antagonists treated oocytes at different maturity stages

status: Public on Sep 13 2013

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

summary:
Affymetrix gene expression profiling in cumulus cells (CC) retrieved from patients undergoing GnRH agonists and GnRH antagonists IVF treatment.
Oocytes from three different maturity stages were considered: metaphase I oocytes (MI), nonfertilized metaphase II (MII) oocytes (MII-NF) and MII oocytes developed to blactocyst stage embryo (MII-BL).

overall_design: From 4 GnRH agonist treated patients, CC MI, CC MII-NF and CC MII-BL samples were collected; from 5 GnRH agonist and 6 GnRH antagonist treated patients, CC MII-NF and CC MII-BL samples were collected; and from 2 GnRH agonist and 4 GnRH antagonist treated patients, CC MI and CC MII-BL were collected. Altogether, 10 CC MI, 15 CC MII-NF and 21 CC MII-BL were collected and considered for transcriptome analysis.

first: Rok

last: Devjak

first: Klementina

last: Fon Tacer

first: Irma

last: Virant Klun

first: Damjana

last: Rozman

first: Eda

last: Vrtačnik Bokal


title: Agilent 244K CGH data for esophageal squamous cell carcinoma (ESCC)

city: beppu

first: sawada

last: genta

address: tsurumihara

institute: kyushu university

type: Genome variation profiling by genome tiling array

summary: Copy number analysis of primary esophageal squamous cell carcinoma (ESCC) from 40 patients in Japan. Integrative analysis of gene expression profiles and genomic alterations obtained from array-CGH and NGS provided us new insight into the pathogenesis of ESCC.

overall_design: 40 tumor samples were prepared for aCGH analysis. For genome profiling, labeling and hybridization of genomic DNA onto the Agilent-014693 Human Genome Microarray Kit 244K (Agilent Technologies) was performed according to the manufacturer's instructions.

first: Koshi

last: Mimori

first: Masaki

last: Mori


title: Genome-wide expression profiling of Hic-5 and TGFB in WPMY fibroblasts

status: Public on Aug 26 2013

first: damien

last: leach

address: woodville road

institute: the university of adelaide

summary: Identifying the effect of the co-regulator Hic-5 (TGFB1I1) and TGFB on the transcriptional profile of WPMY human prostate fibroblast cells with view to further elucidating the broader biological role of Hic-5 and TGFB on fibroblast.

overall_design: Isogenic WPMY-1 fibroblasts stably transfected with short-hairpin RNA against Hic-5 or transfected with non-specific negative control short-hairpin RNA, were kept in 5% hormone stripped FBS RPMI for 48 hours and subsequently treated with either ethanol vehicle control or TGFB for 16hr.  Total RNA was extracted. Five independent vehicle and five TGFB siSCR and siHic5 samples were hybrydised to Affymetrix Human Gene 1.0 ST array chips.

first: Damien

last: Leach

first: Grant

last: Buchanan


title: Gene expression data from MCF-7 cells treated with Lacciac Acid A

city: Iowa City

first: Thomas

last: Bair

address: 335 EMRB

summary: Lacciac Acid A was indentified as an inhibitor of DMNT1. MCF-7 cells were treated with Lacciac Acid A (200 uM) for 5 days. Changes in gene expression were identified by using Affymetrix Human gene ST1.0 arrays. We used microarrays to determine global changes in gene expression upon treatment with Lacciac Acid A an inhibitor of DMNT1.

overall_design: MCF-7 cells near mid passage were treated with Lacciac Acid A for 5 days. RNA was extracted and hybridized on Affymetrix microarrays. Treated and untreated cells were from the same cell passage. Two sample sets from the same passage and the third set from the previous passage were used.

first: Lori

last: Wallrath

first: Diane

last: Cryderman

first: Charles

last: Brenner

first: Rebecca

last: Fagan

first: Bo-uan

last: Wu


title: CytoScanHD array Data for Colerectal Tumor and Normal Samples

city: Riyadh

first: Sathish

last: Periyasamy

state: Select a State or Province

department: Bioinformatics

country: Saudi Arabia

institute: NGHA

summary: Genomic abnormalities leading to colorectal cancer (CRC) include somatic events causing copy number aberrations (CNAs) as well as copy neutral manifestations such as loss of heterozygosity (LOH) and uniparental disomy (UPD). We studied the causal effect of these events by analyzing high resolution cytogenetic microarray data of 15 tumor-normal paired samples. We detected 144 genes affected by CNAs. A subset of 91 genes are known to be CRC related yet high GISTIC scores indicate 24 genes on chromosomes 7, 8, 18 and 20 to be strongly relevant. Combining GISTIC ranking with functional analyses and degree of loss/gain we identify three genes in regions of significant loss (ATP8B1, NARS, and ATP5A1) and eight in regions of gain (CTCFL, SPO11, ZNF217, PLEKHA8, HOXA3, GPNMB, IGF2BP3 and PCAT1) as novel in their association with CRC. Pathway analysis indicates TGF-β signaling pathway to be affected by the cytogenetic events causing CRC as evidenced by the action of genes impacted by CNAs on SMAD family of proteins. Finally, LOH and UPD collectively affected nine cancer related genes. Transcription factor binding sites on regions of >35% copy number loss/gain influenced 16 CRC genes. Our analysis shows patient specific CRC manifestations at the genomic level and that these different events affect individual CRC patients differently.

overall_design: Copy number analysis of Affymetrix CytoScanHD arrays was performed for 15 Tumors and 15 Adjacent Normals from Colorectal Tissue was used as reference for the study.

first: Hisham

last: Eldai

first: Mohammad

last: Aziz

first: Saeed

last: Al Qarni

first: Maha

last: Al Rodayyan

first: Sabeena

last: Mustafa

first: Ebtehal

last: Al Sheikh

first: Mohammed

last: Khan

first: Mishal

last: Johani

first: Zeyad

last: Yousef


title: Clinical Monoclonal B lymphocytosis versus Rai 0 Chronic Lymphocytic Leukemia: a comparison of the cellular, molecular, cytogenetic features and clinical course in a prospective multicenter study

first: Luca

last: Agnelli

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


title: Morphological, genomic, and transcriptomic characterization of heterogeneity in chordoma cells

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

summary: The classical sacrococcygeal chordoma tumor presents with a typical morphology of lobulated myxoid tumor tissue with cords, strands and nests of tumor cells consisting of small non-vacuolated cells, intermediate cells with a wide range of vacuolization and large heavily vacuolated (physaliferous) cells. Because of its rare incidence, lack of suited model systems and technical limitations analysis was only performed on bulk tumor mass neglecting its heterogeneous composition.  We aimed at elucidating the differences between small non-vacuolated and large physaliferous cells on the genomic and transcriptomic level. Secondly, we intended to clarify whether the observed cell types are derived from genetically distinct clones or rather represent different phenotypes.  Using the chordoma cell line MUG-Chor1 we monitored morphological changes via time lapse experiments. We isolated pure fractions of each phenotype by means of laser microdissection or micromanipulation allowing phenotype-specific analysis. Pools of 100 cells each were genetically profiled after whole genome amplification by array comparative genomic hybridization. For expression analysis 20 cells each were subjected to whole transcriptom amplification, forwarded to RNA microarray analysis and qRT-PCR.  Time lapse analysis unveiled small non-vacuolated cells to develop into large physaliferous cells via intermediate cells containing an increasing amount of vacuoles. Furthermore, we showed small and large physaliferous cells to proliferate at the same rate but intermediate cells to be the most proliferating cell phenotype.  Small non-vacuolated and large physaliferous cells showed identical copy number variations. Despite their obvious morphological disparities we detected only modest changes in over all gene expression. However, verification of candidate genes yielded significant up-regulation of ALG11 (700-fold), PPP2CB (18.6-fold), and UCHL3 (18.7-fold) in large physaliferous cells.

overall_design: Of two different cell types (large and small MUG-Chor1 cells) we analysed each in triplicates. In total 6 cell pools were analysed.

first: Amin

last: El-Heliebi

first: Thomas

last: Kroneis

first: Dagmar

last: Kolb-Lenz

first: Julia

last: Feichtinger

first: Gerhard

last: Thallinger

first: Franz

last: Quehenberger

first: Bernadette

last: Liegl-Atzwanger

first: Beate

last: Rinner


title: mRNA microarray analysis on HepG2 cells exposed to Grpahene oxide (GO) and reduced graphene oxide (rGO) Nanomaterials

status: Public on Aug 21 2013

city: seoul

first: jinhee

last: choi

address: 90 Jeonnong-dong, Dongdaemun-gu

department: College of Urban Science

institute: University of Seoul

summary:
In order to evaluate the identification of genes and pathways, the global gene expression profiles were assessed in response to GO and rGO on Human hepatoma (HepG2) cells. We performed whole genome DNA microarray experiments using HepG2 cells exposed to GO and rGO for 24h.
We used whole genome microarrays to screen for global changed in HepG2 transcription profiles and with subsequent quantitative analysis conducted on selected genes.

overall_design: 24h GO and rGO exposed HepG2 cells were used for total RNA extraction and hybridization on Affymetrix microarrays.

first: Jinhee

last: Choi

first: Nivedita

last: Chatterjee


title: Microarray analysis of monoclonal K562 lines transfected with pEF1a or pEF1a-Pu.2

status: Public on Aug 23 2013

city: Sydney

first: Ka Sin

last: Mak

address: High Street

institute: UNSW

summary:
Ectopic expression of the novel Pu.1 isoform Pu.2 in K562 was performed to investigate the biological function and importance of this novel protein
Affymetrix microarrays were performed on RNA from K562 cells transfected with pEF1a or pEF1a-Pu.2

overall_design: Three monoclonal lines derived from K562 expressing pEF1a and three monoclonal lines of K562 expressing pEF1a-Pu.2

first: Ka

first: Alister

last: Funnell

first: Merlin

last: Crossley


title: Expression data of SW480 cells with TFAP2E overexpression and without TFAP2E (empty vector control)

status: Public on Aug 09 2013

city: Munich

first: Marc

last: Taenzer

address: Ismaningerstr 22

country: Germany

institute: MRI

summary:
AP2 transcription factors play important roles in development and cancer, we tried to clarify the role of the so far uncharacterised TFAP2E in colorectal cancer.
We used GENE ST 1.0 Arrays to detail up and downregulated target genes of this AP-2 transcription factor.

overall_design: We used the ptarget mammalian expression vector (Promega) to overexpress the TFAP2E gene in the SW480 CRC line.

first: Matthias

last: Ebert


title: Low-dose actinomycin D preferentially disrupts EWS-FLI1DNA binding.

city: Plantagenet

first: Madeleine

middle: E.

last: Lemieux

state: ON

address: 275 Main St., Suite 252

institute: Bioinfo

summary: Fusion of the EWS gene to FLI1 produces a fusion oncoprotein that drives an aberrant gene expression program responsible for the development of Ewing sarcoma. We used a homogenous proximity assay to screen for compounds that disrupt the binding of EWS-FLI1 to its cognate DNA targets. A number of DNA-binding chemotherapeutic agents were found to non-specifically disrupt protein binding to DNA. In contrast, actinomycin D was found to preferentially disrupt EWS-FLI1 binding by comparison to p53 binding to their respective cognate DNA targets in vitro. In cell-based assays, low concentrations of actinomycin preferentially blocked EWS-FLI1 binding to chromatin, and disrupted EWS-FLI1-mediated gene expression. Higher concentrations of actinomycin globally repressed transcription. These results demonstrate that actinomycin preferentially disrupts EWS-FLI1 binding to DNA at selected concentrations. Although the window between this preferential effect and global suppression is too narrow to exploit in a therapeutic manner, these results suggest that base-preferences may be exploited to find DNA-binding compounds that preferentially disrupt subclasses of transcription factors.

overall_design: Using proximity assays in A673 Ewing Sarcoma cells, we screened 7 bioactive-enriched small molecule libraries, totaling 5,200 compounds to identify compounds that could disrupt the binding of EWS-FLI1 to its cognate DNA binding sequence. We defined a set of EWS-FLI1-regulated genes by shRNA depletion of EWS-FLI1in the same cell line. Duplicate knock down experiments were carried out and compared to duplicate scrambled shRNA controls. This signature was used to interrogate the effects in duplicate experiments of low- and high-dose actinomycin D treatment in A673 cells as compared to DMSO and untreated controls (2 each).

first: Andrew

last: Kung


title: Lymphotoxin-beta receptor activation in HBV-infected HepaRG cells

status: Public on Aug 15 2013

city: München

first: Florian

last: Reisinger

address: Schneckenburgerstr. 8

institute: Helmholtz-Zentrum München

summary: The objective of this experiment was to test the effect, at a transcrptomic level, of lymphotoxin-beta receptor activation in HBV-infected differentiated HepaRG cells

overall_design: 4 biological replicates per condition were analyzed

first: Ke

last: Zhang

first: Julie

last: Lucifora

first: Thorsten

last: Buch

first: Ulrike

last: Protzer

first: Mathias

last: Heikenwälder


title: Addiction of t(8;21) and inv(16) AML to native RUNX1 [Gene Expression data]

status: Public on Aug 18 2013

city: Rehovot

first: Yoram

last: Groner

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: Weizmann institute

summary: Cancer cells maintain a sensitive balance between growth-promoting oncogenes and apoptosis inhibitors. We show that WT RUNX1 is required for survival of t(8;21)-Kasumi-1 and inv(16)-ME-1 AML cell lines. The malignant AML phenotype is sustained by a delicate AML1-ETO/RUNX1 balance that involves competition for common DNA binding sites regulating a subset of AML1-ETO/RUNX1 targets.

overall_design: Genome  expression was profiled after performing knockdown of RUNX1 and AML1-ETO in Kasumi-1 cells using specific siRNA-oligo nucleotides, and analyzed using Affymetrix Gene 1.0 ST arrays.

first: Oren

last: Ben Ami

first: Dan

last: Friedman


title: Gene expression profiling of lung adenocarcinomas and normal lung tissue

status: Public on Aug 06 2013

city: Houston

first: Humam

last: Kadara

state: TX

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

summary:
Lung cancer is still the leading cause of cancer-related deaths in the US and worldwide. Understanding the global molecular profiles or transcriptome of lung cancers would strengthen our understanding of the biology of this malignancy.
We performed gene expression profiling using the Human Gene 1.0 ST platform of 80 lung adenocarcinomas and 30 normal lung tissues to better understand the biology of this significant fraction of non-small cell lung carcinomas (NSCLCs)

overall_design: Lung adenocarcinomas were comrpised of never-smoker (n=40) and smoker (n=40) adenocarcinomas. Normal lung tissue (n=30) were paired to 30 of the never-smoker cases. Gene expression profiling was performed on the samples to identify differentially expressed profiles between lung adenocarcinomas and normal lung tissues.

first: Ignacio

middle: I

last: Wistuba


title: Expression data from blood and biopsies of Donor-Specific Antibody positive patients

city: Bronx

first: Pilib

last: Ó Broin

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

summary:
The presence of Donor-Specific anti-HLA Antibodies (DSA) is associated with an increased risk of both acute and chronic antibody-mediated rejection (AMR) in kidney allografts.  AMR has remained challenging in kidney transplantation and is the major cause of late allograft loss. However, not all patients with DSA develop AMR, leading to the question of whether this represents accommodation, if other protective mechanisms exist or if this is actually a state of pre-rejection.
Clinical and histological features, and gene expression profiles of kidney biopsy and blood samples of donor-specific antibody (DSA)+ patients without rejection were compared to antibody-mediated rejection (AMR) patients to elucidate the mechanisms involved in prevention of AMR. Of the 71 DSA+ patients, 46 had diagnosis of AMR and 25 did not show rejection. 50 DSA- patients without rejection were used as control. A subgroup of patients with available biopsy (n=61) and blood samples (n=54) were analyzed by microarrays.  Both, DSA+/AMR+ and DSA+/AMR- biopsies showed increased expression of gene transcripts associated with cytotoxic T, natural killer cells, macrophages, interferon-gamma and rejection compared to DSA- biopsies. Regulatory T cell transcripts were up-regulated in DSA+/AMR+ and B cell transcripts in DSA+/AMR- biopsies. Whole blood gene expression analysis showed increased immune activity in only DSA+/AMR+ patients. There were no differentially expressed tolerant genes studied (n=14) in the blood or biopsy specimens of DSA+/AMR- patients. During a median 36 months follow-up, 4 DSA+/AMR- patients developed AMR, 12 continued to have DSAs but 9 lost DSAs. Gene expression profiles did not predict the development of AMR or persistence of DSAs. These results indicate increased immune activity in DSA+/AMR- biopsies despite lack of histologic findings of rejection.

overall_design: All clinically indicated kidney transplant biopsies performed at our institution after January 2009 were reviewed and 263 patients with anti-HLA antibody testing at the time of biopsy were identified. There were 71 DSA+ and 192 DSA- patients (Figure 1). Of the 71 DSA+ patients, 46 had biopsy diagnosis of acute AMR (n=9) or chronic AMR (n=37), and 25 had normal histopathology or minimal non-specific interstitial fibrosis/tubular atrophy (IFTA). Of the 192 DSA- patients, 50 patients with normal histology and/or mild non-specific IFTA were used as a control group. Clinical and histopathological findings of these 3 groups (DSA+/AMR+, DSA+/AMR- and DSA-) were analyzed.   A subgroup of patients who were enrolled in the Institutional Review Board-approved “Immune Monitoring Study” who had clinically indicated biopsy (n=61) and whole blood samples (n=54) stored were used for genomic analysis. Twenty-eight biopsy and blood samples from DSA+/AMR+ patients, 13 biopsy and 14 blood samples from DSA+/AMR- patients, and 20 biopsy and 12 blood samples from DSA- patients,  were available for microarray analysis.

first: Enver

last: Akalin


title: Induction of IL-17+ T-cells by HIV-Tat protein is mediated via Vascular Endothelial Growth Factor Receptor-2

status: Public on Aug 02 2013

city: Bethesda

first: Kory

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: Anti-retroviral therapy (ART) has transformed human immunodeficiency virus (HIV) infection from a fatal illness to a chronic condition by controlling viral replication and restoring immune function. However, chronic T-cell activation can be observed in 20-35% of individuals on ART, resulting in an immune reconstitution inflammatory syndrome (IRIS) [1-3]. IRIS involving the CNS can result in permanent disability and death [4]. Tat is a viral protein produced in HIV-infected cells and released into the extracellular space [5]. We show that the secreted-Tat protein activated uninfected T-cells in an antigen-independent manner without inducing proliferation. Notably, Tat induced the secretion of IL-17 from T-cells and increased the percentage of T-cells with a Th17 phenotype.  T-cell activation was independent of the T-cell receptor but dependent on endocytosis of Tat and activation of vascular endothelial growth factor receptor 2 (VEGFR2).  Tat induced global changes in histone acetylation and increased HIV infection in non-replicating T-cells. Furthermore, in an individual with CNS IRIS, Tat expressing infiltrates and secretion of IL-17 was detected in the absence of viral replication in the brain.  Thus Tat can induce T-cell activation in a paracrine and autocrine manner resulting in propagation of inflammation and increased virulence.

overall_design: 12 Human samples in 6 pairs: 6 Human T cell HIV tat exposed 0hrs, 6 Human T cell HIV tat exposed 24hrs

first: Tory

middle: P

first: Karan

last: Patel

first: Peter

last: Calabresi

first: Rodrigo

last: Hasbun

first: Avindra

last: Nath


title: The gene expression analysis of paracrine/autocrine factors in patients with spermatogenetic failure compared to normal spermatogenesis

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

institute: University of Bergen

summary: The role of paracrine/autocrine factors in inflammation, immune response and tumor development is well established. There is also an evidence that some of the cytokines there involved may participate in the regulation of the male gonads. However, their  involvement in pathogenesis of male infertility has not been well defined yet. The aim of the present study was to examine the expression levels of  IL-1 family members, IL-6, IL-10, TNF family, SCF and c-kit in infertile patients with idiopathic non-obstructive azoospermia (NOA) compared to men with normal spermatogenesis

overall_design: We analyzed testicular biopsy specimens obtained from 16 patients with non-obstructive azoospermia (NOA) and 4 with normal spermatogenesis using Affymetrix Human Gene 1.0 ST.

first: A

last: Malcher

first: N

last: Rozwadowska

first: T

first: P

last: Jedrzejczak

first: W

last: Zietkowiak

first: M

last: Kurpisz


title: Gene expression analysis in human colon cancer cells and liver cancer cells with FoxA knockdown.

status: Public on Aug 01 2013

city: Worcester

first: Junhao

last: Mao

state: MA

address: 364 Plantation Street, LRB 417

department: Cancer Biology

institute: University of Massachusetts Medical School

summary: FoxA transcription factors are involved in development and tumorigenesis of the gastrointestinal tract. However, the downstream programs controlled by FoxA factors remain poorly understood. The goal of this study is to understand the transcriptional responses regulated by FoxA proteins in liver and colon cancer cells.

overall_design: Human liver cancer cell line HepG2 and colon cancer cell line LS174T infected with lentivirus expressing shRNAs targeting human FoxA1 and FoxA2.

first: Jiayi

last: Wang


title: Transcriptional responses of human colon and liver cancer cells to TCF inhibition.

summary: Dysregulation of Wnt/TCF signaling is closely associated with cancers arising from the gastrointestinal tract, inlcluding colon cancer and liver cancer. The goal of this study is to understand the transcriptional programs underlying Wnt/TCF activation in gastrointestinal cancers. We examined the transcriptional responses to TCF inhibition in cultured human colon cancer cells and liver cancer cells that are characteristic of Wnt pathway activation.

overall_design: Human liver cancer cell line HepG2 and colon cancer cell line LS174T with or without expression of a dominant negative form of TCF4


title: Macrophages in T cell/histiocyte rich B cell lymphoma strongly express metal-binding proteins and show a bi-activated phenotype

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

summary: In a supervised principal component analysis, histiocytes from TCHRBCL were most closely related to epithelioid cells from NLPHL, with both types of cells expressing genes related to proinflammatory and regulatory macrophage activity.

overall_design: 39 microdissected histiocyte samples were compared with 9 sorted monocyte samples

first: Sylvia

last: Hartmann


city: Tuebingen

first: Michael

last: Bonin

state: BW

address: CAlwerstr. 7

department: Medical Genetics

institute: University Tuebingen

summary: HIF-1 is an important transcription factor for immune responses to bacterial infection. We wanted to analyze the HIF-1 dependent gene expression upon S. aureus infection and analyzed the gene expression of HepG2 nt and HepG2 HIF-1-/- cells four hours upon infection using affymetrix human gene 1.0 st. gene arrays.

overall_design: triplicates of HepG2 nt and HepG2 HIF-1-/- cells were infected with S. aureus 8325-4 (4 h, MOI: 20), triplicates of uninfected cells were used as control

first: Christiane

last: Beerlage

first: Volkhard

last: Kempf


title: Expression data from H295R cells where NRSF/REST or SF-1 were knocked down

city: Valbonne

first: Enzo

last: LALLI

address: 660 route des Lucioles

department: CNRS UMR 7275

country: France

institute: IPMC

summary:
SF-1 is a nuclear receptor transcription factor playing a key role in adrenogonadal development and in adrenocortical tumorigenesis when overexpressed. NRSF/REST is a transcriptional repressor that represses expression of neuronal genes in non-neural tissues. Some data suggest that SF-1 and NRSF/REST can functionally interact in adrenocortical cancer cells.
We studied gene expression profiles using Affymetrix microarrays in the H295R/TR SF-1 adrenocortical cancer cell line. In this cell line, SF-1 expression can be increased in a doxycycline-dependent manner (Mol. Endocrinol. 21: 2968–2987, 2007). The effects of a control siRNA and sRNAs specific for SF-1 and for NRSF/REST (in basal or increased SF-1 expression conditions) on gene expression were measured.

overall_design: In H295R/TR SF-1 cells SF-1 and NRSF/REST (in conditions of basal and increased SF-1 dosage) expression were knocked down by Amaxa nucleofection. RNA was extracted and hybridized to Human Gene 1.0 ST Affymetrix microarrays.

last: Lalli


title: Cyclin D1 determines estrogen dependent signaling in human breast cancer cell line MCF7

status: Public on Jul 18 2013

first: Mathew

middle: Casimiro

last: Casimiro

state: United States

address: 233 South 10th St, Rm 1035

department: 233 South 10th St, Rm 1035

institute: Thomas Jefferson University

summary: The CCND1 gene, which is frequently overexpressed in cancers, encodes the regulatory subunit of a holoenzyme that phosphorylates the retinoblastoma protein (pRb). It is known that cyclin D1 regulates ERα transactivation using heterologous reporter systems, the significance of this observation to E2 dependent gene activation is unknow. E2 stimulated MCF7 cells treated with cyclin D1 siRNA in order to analyze the genes regulated by estradiol in a cyclin D1 dependent manner. Hormone deprived MCF7 cells were treated with cyclin D1 siRNA or control siRNA and stimulated with E2 or vehicle

overall_design: Four separate 10cm plates of MCF7 cells treated with control siRNA were compared to four 10cm plates of MCF7 cells treated with cyclin D1 siRNA. 2 plates in each group treated with vehicle and two plates treated with E2.

first: Richard

last: Pestell


title: Clonal Genetic and Hematopoietic Heterogeneity among Human Induced Pluripotent Stem Cell lines

status: Public on Jul 26 2013

city: Philadelphia

first: Jason

last: Mills

state: PA

address: 3501 Civic Center Blvd, CTRB, RM5100

department: Laboratory Medicine

institute: The Children's Hospital of Philadelphia

summary: Induced pluripotent stem cells hold great promise for modeling human hematopoietic diseases. However, intrinsic variability in the capacities of different iPSC lines for hematopoietic development complicates comparative studies and is currently unexplained.

overall_design: We created and analyzed three separate iPSC clones from fibroblasts of three different normal individuals using a standardized approach that included excision of integrated reprogramming genes by Cre-Lox mediated recombination. Gene expression profiling and hematopoietic differentiation assays showed that independent lines from the same individual were generally more similar to each other than those from different individuals.

first: Kai

first: Prasuna

last: Paluru

first: Lei

last: Ying

first: Lin

last: Lu

first: Aline

last: Galvão

first: Dongbin

last: Xu

first: Yu

last: Yao

first: Spencer

middle: K

last: Sullivan

first: Lisa

first: Helen

last: Mac

first: Amel

last: Omari

first: Jyh-Chang

last: Jean

first: Steve

last: Shen

first: Adam

last: Gower

first: Avi

last: Spira

first: Gustavo

last: Mostoslavsky

first: Darrell

middle: N

last: Kotton

first: Deborah

last: French

first: Mitchell

last: Weiss

first: Paul

last: Gadue


title: Expression data from aldosterone-producing adenomas (APAs) with a somatic mutation in either KCNJ5, CACNA1D, or ATP1A1

status: Public on Jul 14 2013

city: Cambridge

first: Elena

middle: Aisha Binti

last: Azizan

state: Cambridgeshire

address: Box 110, Addenbrooke's Hospital

department: University of Cambridge

institute: Clinical Pharmacology Unit

summary:
Analysis of aldosterone-producing adenoma (APA) samples from patients with primary hyperaldosteronism. These APAs have a somatic mutation in either KCNJ5, CACNA1D, or ATP1A1. Results provide insight into the different mechanisms each mutation may cause leading to elevated aldosterone production in APA.
In this dataset, we include expression data from aldosterone-producing adenomas (APAs) with a somatic mutation in either KCNJ5, CACNA1D, or ATP1A1. These data are used to obtain differentially expressed genes between KCNJ5 mutant APAs and CACNA1D/ATP1A1 mutant APAs.

overall_design: A total of 13 samples were analyzed (8 KCNJ5 mutant APAs and 5 CACNA1D/ATP1A1 mutant APAs).  43 genes had a false discovery rate (FDR) <0.5% and were >2-fold different between KCNJ5 mutant APAs and 5 CACNA1D/ATP1A1 mutant APAs. The two sets of genotypes were separated on unsupervised hierarchical clustering of 1475 genes correlating >0.6 with CYP11B2.

first: E

first: M

last: Brown


title: Expression data of myeloma CD138+ and CD138- populations

status: Public on Jul 17 2013

city: Singapore

first: Renji

last: Reghunathan

address: KentRidge Road

country: Singapore

institute: National University Hospital

summary: Comparison of gene expression profiles between CD138+ and CD138- populations from human myeloma cell lines RPMI-8226 and NCI-H929. We used Affymetrix human gene 1.0ST array and analyzed with GeneSpring GX.

overall_design: CD138+ and CD138- subsets of cells were separated using FACS and clonogenecity of both population were compared. The RNA was extracted and hybridized with Affymetrix Human Gene 1.0ST array.

first: Bi

last: Chonglei


title: CGH array: Sprague-Dawley rat (SDR) vs Hirosaki hairless rat (HHR)

status: Public on Jul 13 2013

city: Aomori

first: Naoki

last: Nanashima

state: Aomori

address: 58-1 Mase, Hamadate

department: Department of Nutrition

institute: Aomori University of Health and Welfare

summary: Profiling of gain and loss of DNA fragments in HHR comparing control SDR.

overall_design: Two analyses were performed; sample 1, SDR (male) vs HHR (male) and sample 2,  SDR (female) vs HHR (female).

first: Toshiyuki

last: Yamada

first: Shigeki

last: Tsuchida


title: Expression data from C33-A cell line

city: Sevilla

first: Jose

middle: C.

last: Reyes

address: Av. Américo Vespucio

department: Genome biology

institute: CABIMER

summary:
C33-A is a Homo sapiens cervix carcinoma cell line. In this experiment we determine the level of gene expression under exponentially growing conditions.
The final goal of the experiment is to correlate other epigenetic characteristics from other experiments with gene expression levels.

overall_design: C33-A cells from three independent exponentially growing cultures were recovered and processed for RNA extraction and hybridization on Affymetrix microarrays

first: María

last: Ceballos-Chavez

middle: C


title: Comparison of  WAT EPCs  vs WAT ASCs

status: Public on Jul 05 2013

city: Milan

first: Giuliana

last: Gregato

address: Via ripamonti 435

department: Anatomy pathology

institute: IEO

summary: Human adipose tissue contains two populations of progenitors (EPCs and ASCs) with cooperative roles in breast cancer. EPCs (CD45-CD34+CD31+CD13-CCRL2+) can generate endothelial cells. ASCs (CD45-CD34+CD31-CD13+CD140b+) are mesenchymal progenitors which generated pericytes.

overall_design: CD13+ cells and CD13- cells from 7 Lipotransfer aspirate

first: Stefania

last: Orecchioni

first: Ines

last: Martin-Padura

first: Francesca

last: Reggiani

first: Paola

last: Braidotti

first: Patrizia

last: Mancuso

first: Angelica

last: Calleri

first: Giancarlo

last: Pruneri

first: Stefano

last: Martella

first: Jean-Yves

last: Petit

first: Mario

last: Rietjens

first: Francesco

last: Bertolini


status: Public on Jul 01 2013

first: Rivka

last: Dikstein

address: 2 Hertzl st.

institute: The Weizmann Institute of Science

summary:
HEK293T cells were transfected with the Rbp1-amr or slow (R729H-amr) α-amanitin resistant subunit of RNA Pol II and selected with α-amanitin 24 hours after transfection for additional 24 hours. Total RNA was extracted and global changes in gene expression were determined using microarray chips.
MiRNAs are transcribed by RNA pol II but the transcriptional features influencing their synthesis are poorly defined. Here we report that a TATA-box in miRNA and a subset of protein-coding genes is associated with increased sensitivity to a slow rate of transcription elongation. We also show that promoters driven by TATA-box or NF-κB elicit high transcription re-initiation rate, but paradoxically lower levels of miRNA. Interestingly, miRNA synthesis was converted to a more productive mode by decreasing initiation rate, but less productive when the re-initiation rate increased. This phenomenon was found to be associated with a delay in miR-146a induction by NF-κB. We also demonstrate that miRNAs are remarkably strong pause sites. Our findings suggest that lower efficiency of miRNA synthesis directed by the TATA-box or NF-κB is a consequence of frequent transcription initiation that lead to Pol II crowding at pause sites, thereby increasing the chance of collision and premature termination. These findings highlight the importance of the transcription initiation mechanism for miRNA synthesis, and have implications for TATA-box promoters in general.

overall_design: HEK293T cells were transfected with plasmids directing the expression of α-amanitin-resistant variants of Pol II (Rpb1-amr and R749H-amr). α-amanitin was added and RNA was prepared 24 and 48 h later, respectively. The data provided is from 3 Rpb1-amr  vs 3 R749H-amr (6 samples).

first: Nadav

last: Marbach-Bar

first: Amitai

last: Ben-Noon

first: Ana

last: Harush

first: Tali

last: Avnit-Sagi

first: Michael

middle: D

last: Walker


title: Expression profiling of skin fibroblast and iPSC from Werner Syndrome

status: Public on Jul 11 2013

first: Hoi Hung

last: Cheung

address: 49 Convent Dr, Rm.2C08 Bldg.49

country: USA

institute: NICHD

summary: The premature aging disorder Werner Syndrome (WS) is characterized by early onset of aging phenotypes resembling natural aging. In most WS patients there are mutations in the DNA helicase WRN, an enzyme important in maintaining genome stability and telomere replication. Interestingly, its clinical manifestations reflect a severe degree of deterioration for connective tissue, whereas the central nervous system is less affected. We suggest that the varied vulnerability to aging is regulated by an unknown mechanism that protects specific lineages of stem cells from premature senescence. To address this problem, we reprogrammed patient skin fibroblasts to induced pluripotent stem cells (iPSC). The expression profile for the differentiated normal and WS fibroblasts and undifferentiated iPSC were compared. A distinct expression profile was found between normal and WS fibroblasts, however, few changes of gene expression were found in iPSC. Our findings suggest an erasure of aging phenotype associated with WS in reprogrammed iPSC.

overall_design: Human normal and WS skin fibroblasts were reprogrammed to induced pluripotent stem cells (iPSC). These samples, before and after reprogramming, were analyzed for the change of gene expression profile.

first: H

middle: H

first: L

last: Thouennon

first: O

middle: M

last: Rennert


title: The influence of resveratrol on rheumatoid fibroblast-like synoviocytes based on a gene chip transcription analysis

status: Public on Jul 31 2013

city: graz

first: margherita

last: breisach

address: Auenbruggerplatz 5

institute: Medical university of graz

summary: The aim of our study is to increase understanding of the antiproliferative and pro-apoptotic potency of resveratrol by identifying genes which underlie involved pathological pathways and biological process. Therefore, we performed a gene Chip Transcription Analysis with subsequent Protein ANalysis THrough Evolutionary Relationships (PANTHER) analysis to evaluate which transcripted genes are significantly influenced by resveratrol.

overall_design: To determine the transcriptional profile of resveratrol, three biological replicates were processed on Affymetrix Gene Chip Human 1.0 ST.

first: Mathias

last: Glehr

first: Margherita

last: Breisach

first: Birgit

last: Lohberger

first: Sonja

last: Walzer

first: Florentine

last: Fuerst

first: Beate

last: Rinner

first: Gerald

last: Gruber

first: Winfried

last: Graninger

first: Andreas

last: Leithner

first: Reinhard

last: Windhager


title: SNAI1-mediated epithelial-mesenchymal transition confers chemoresistance and cellular plasticity on MCF10A cells by regulating signaling pathways involved in apoptosis and stem cell maintenance

city: Cologne

first: Soyoung

last: Lim

address: Kerpener Str. 62

department: Institute of Pathology

institute: Cologne medical school

summary: Stable expression of SNAI1 in MCF10A cells enhanced resistance to cell death and cellular plasticity by regulating signalling pathways involved in apoptotis and stem cell maintenance.

overall_design: To identify changes on gene expression upon SNAI1-induced epithelial-mesenchymal transition, total RNA was purified from MCF10A cells and MCF10A cells stably expressing SNAI1. Three biololgical replicates were used.

first: Jutta

last: Kirfel


title: Expression data from normal and Malignant hematopoietic cells

status: Public on Jul 06 2013

city: Baltimore

first: Yezhou

last: Sun

address: 620 W. Lexington St.

institute: U. of Maryland, Baltimore

summary:
This data was used to determine levels of BRCA1 and BRCA2 in primary human leukemia samples.  Samples were determined to be high BRCA1 and/or BRCA2 or low BRCA1 and/or BRAC2.
This data was used to determine levels of BRCA1 and BRCA2 in primary human leukemia samples.  Samples were determined to be high BRCA1 and/or BRCA2 or low BRCA1 and/or BRAC2.

overall_design: AML cell lines and patient samples, B ALL cell lines and Patient samplest, T ALL cell lines and patient samples, norma B cells, normal granulocytes, normal monocytes, normal T cells and normal CD34+ cells were used for RNA extraction and hybridization on Affymetrix microarrays. All the AML, B ALL, T ALL cell lines were cultured in vitro under appropriate culture conditons and harvested in their log phase growth for RNA extraction. AML, B ALL, and T ALL patient samples were collected...(I assume these are the PBMCs from eitehr peripheral blood or bone marrow from patients, please confirm). Normal B cells, granulocytes, monocytes, and T cells were purified from human peripheral blood of normal healthy donors.

first: Curt

last: Civin


title: The molecular basis of the renal and vascular consequences of Uremia

status: Public on Jun 30 2013

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

institute: IARC WHO

summary:
Background. Chronic renal failure is characterized by progressive renal scarring and accelerated cardiovascular disease. In animal models, this is thought to be due to non-dialyzable uremic toxins – small, protein-bound molecules normally secreted via Organic Anion Transporters (OATs) in the proximal renal tubule,rather than filtered at the glomerulus. The best studied of these is indoxyl sulfate (IS).
Methods. We examined global gene expression responses in cultured normal human renal tubular cells incubated with control plasma (n=5) or pre- and post-dialysis uremic plasma (n=10).
Results. GeneSpring analysis of microarrays revealed significantly altered expression of 2016 genes. The expression of 537 genes “normalized” in post-dialysis plasma, suggesting removal of “low molecular weight uremic toxins” by dialysis. The expression of the majority of dysregulated genes (1479) was not normalized in post-dialysis plasma. These likely represent the effects of substances not effectively removed by dialysis (“protein-bound uremic toxins”). Addition of  indoxyl sulfateto control plasma simulated most effects (81.1%) of uremic plasma, while the addition of probenecid, an OAT inhibitor, to uremic plasma reversed most changes in gene expression. Analysis of molecular programs with the Gene Set Enrichment Analysis and the DAVID database revealed patterns common to indoxyl sulfate-treated control plasma, pre-dialysis, and post-dialysis uremic plasma.  These included increased cell cycle, pro-inflammatory, and pro-fibrotic molecular programs, particularly genes in the TGF-β pathway.
Conclusion: These findings provide insight into the role of non-dialyzable, protein-bound uremic toxins in the pathogenesis of renal scarring and uremic vasculopathy. The GSEA patterns confirm that inflammatory and fibrotic programs are active.

overall_design:
Transcriptomic remodeling in response to external stimulus
RNA from non-immortalized cultured renal cortical cells incubated with plasma samples from 5 controls, 10 uremics pre-dialysis, 10 uremics post-dialysis, 5 controls with indoxyl sulfate added, 5 uremics pre-dialysis with probenecid added, 5 uremics post-dialysis with indoxyl sulfate added

first: Sachin

middle: R

last: Jhawar

first: Jerome

last: Lowenstein

last: Zavadil

first: Prabhjot

last: Singh

first: Daniel

last: Torres

first: Francisco

last: Ramirez-Valle

first: Hania

last: Kassem

first: Trina

last: Fernandez


title: Profile of mRNAs associated with Ago (Argonaute) 1 in normoxic and hypoxic endothelial cells

city: La Jolla

first: Zhen

last: Chen

address: 9500 Gilman Dr.

institute: UCSD

summary:
Messenger RNAs that are bound to Ago1 is to be transcriptionally or translational suppressed. Therefore the changes in Ago1-associated transcripts indicate the changes of suppression of these genes.
We used microarrays to detail changes of mRNA transcripts that are associated with Ago1 in endothelial cells under normoxia and hypoxia conditions.

overall_design: Human umbilical vein endothelial cells pooled from 8 different sources were subjected to normoxia (21% oxygen, Nx) or hypoxia (2% hypoxia, Hx) for 24 hr. Ago1 was immunoprecipitated with mouse anti-human Ago1 using a lysis buffer containing 0.1% NP-40. The associated RNA was extracted and hybridized on Affymetrix Human Gene 1.0 ST arrays.

first: John

middle: Y

last: Shyy


title: Sarcoptes scabiei Mites Modulate Gene Expression In Human Skin Equivalents

status: Public on Jul 03 2013

city: Dayton

first: Michael

last: Markey

state: OH

address: 3640 Colonel Glenn Hwy.

department: Biochemistry and Molecular Biology

institute: Wright State Unviersity

summary: The purpose of this study was to identify genes in keratinocytes and fibroblasts in human skin equivalents that changed expression in response to the burrowing of live scabies mites.

overall_design: Four biological replicates for the uninfested control condition and five biological replicates for the treatment conditions (live mites, mite extract) were processed for gene expression analysis using Affymetrix Human Gene 1.0 ST arrays.


title: PAX5 overexpression is not enough to reestablish the mature B-cell phenotype in classical Hodgkin lymphoma

status: Public on Jul 30 2013

city: Berlin

first: Lora

last: Dimitrova

state: Berlin

address: Hindenburgdamm 30

institute: Charité-University Medicine Berlin

summary: In lymphomas derived from mature B cells the expression of the transcription factor PAX5 is maintained whereas classical Hodgkin lymphoma displays significantly reduced PAX5 expression despite its derivation from mature B cells. To elucidate the functional role of PAX5 in classical Hodgkin lymphoma, we re-established the PAX5 expression in the Hodgkin cell line L428 with and without epigenetic modulation. To this end, we stably transfected the Hodgkin cell line L428 with an inducible PAX5 expression construct. Although the overexpressed PAX5 was transcriptionally active as demonstrated by synthetic reporter constructs, no induction of the B-cell phenotype was achieved. PAX5 chromatin immunoprecipitation with subsequent next generation sequencing in B-cell lines and the PAX5 overexpressing L428 cell line showed different binding patterns. Since epigenetic restrictions might affect PAX5 binding, combined DNA demethylation and histone acetylation was performed. However, no re-expression of B-cell genes was observed also under these conditions. Thus, PAX5 is not sufficient for the re-activation of the B-cell program in Hodgkin cells despite epigenetic opening of the chromatin. This clearly indicates that the repression of the B-cell identity of the Hodgkin cells is caused and secured by complex molecular mechanisms.

overall_design: 2 Burkitt lymphoma cell lines (Raji, Namalwa), the Hodgkin lymphoma cell line L428 and the PAX5-producing L428 (L428-PAX5) with or without 5-aza-2′-deoxycytidine/Trichostatin A treatment were analysed in triplicate.

first: Volkhard

last: Seitz

first: Jochen

last: Hecht

first: Dido

last: Lenze

first: Peter

last: Hansen

first: Monika

last: Szczepanowski

first: Liya

last: Ma

first: Elisabeth

last: Oker

first: Anke

last: Sommerfeld

first: Franziska

last: Jundt

first: Wolfram

last: Klapper

last: Hummel


title: Expression data from prostate cancer cell lines C4-2B (docetaxel sensitive) and  TaxR (docetaxel resistant) cells

city: Sacramento

first: allen

last: Gao

state: California

address: 4645 2nd Ave Research 3

institute: UC Davis

summary:
Prostate cancer C4-2B cells were cultured in docetaxel in a dose-escalation manner. After nine months selection, cells were able to divide freely in 5 nM docetaxel, with a specific sets of genes been deregulated.
We performed global gene expression analysis by cDNA microarrays to  identify genes responsible for docetaxel resistance in TaxR cells.

overall_design: Docetaxel resistant TaxR cells were selected from C4-2B cells during long time docetaxel treatment. Genes responsible for docetaxel resistance were identified using C4-2B vs. TaxR RNA extraction and hybridization on Affymetrix microarrays.

first: Yezi

last: Zhu

first: Allen


title: Changes in gene expression in HOS and U2-OS cell lines after exposure to 600 μg/mL OGE

status: Public on Jun 26 2013

city: Taichung

first: Jer-Yuh

last: Liu

address: Hsueh-Shih Road

department: Graduate Institute of Cancer Biology

country: Taiwan

institute: China Medical University

summary:
Osteosarcoma (Osteosarcoma) is a type of bone cancer. Eighty percent of this tumor will be metastatic to the lungs or liver, and as a result, patients generally need chemotherapy to improve survival possibility. Recently, anti-tumor activity has been reported in Ocimum gratissimum aqueous extract (OGE), which has been the focus of recent extensive studies on therapeutic strategies due to its antioxidant properties.
We used microarrays to identify potential and novel target genes responsive to the anticancer effect in OGE treatment in osteosarcoma cells,

overall_design: We performed pharmacogenomics analyses for the effect of OGE on human osteosarcoma U2-OS and HOS cell growth. Cell viability, Western blot and flow cytometry analysis were performed before performing pharmacogenomics analyses for the effect of OGE on human osteosarcoma U2-OS and HOS cell growth, including cDNA microarray and RT-PCR assays.


title: Designed Oligooxopiperazines as Modulators of Hypoxia-Inducible Factor Signaling

city: Los Angeles

first: Bogdan

last: Olenyuk

state: CA

address: 1985 Zonal Ave. PSC B15-C

department: Pharmacology and Pharmaceutical Sciences

institute: University of Southern California

summary: We performed gene expression profiling of oligooxopiperazines (OPs) targeting the hypoxia-inducible transcription factor complex.  Treatment of cells with OPs inhibited hypoxia-inducible gene expression in A549 cells.

overall_design: Hypoxic A549 cells were treated with transcriptional inhibitors BB2-162, BB2-125, BB2-282 or vehicle and their expression profiles were compared to normoxic A549 cells treated with vehicle.

middle: Z

first: Paramjit

middle: S

last: Arora


title: Frequent truncating mutations of STAG2 in bladder cancer

city: San Francisco

first: David

middle: A.

last: Solomon

address: 513 Parnassus Ave, HSW 450

department: Pathology

institute: University of California, San Francisco

summary:
Here we report the discovery of truncating mutations of the gene encoding the cohesin subunit STAG2, which regulates sister chromatid cohesion and segregation, in 36% of papillary non-invasive urothelial carcinomas and 16% of invasive urothelial carcinomas of the bladder. Our studies suggest that STAG2 has a role in controlling chromosome number but not the proliferation of bladder cancer cells. These findings identify STAG2 as one of the most commonly mutated genes in bladder cancer.

Affymetrix CytoScan HD Arrays were performed according to the manufacturer's directions on genomic DNA extracted directly from 12 snap-frozen human urothelial carcinoma primary tumors with somatic mutations of the STAG2 gene.

overall_design: Copy number analysis using Affymetrix CytoScan HD Arrays was performed for 12 human urothelial carcinomas of the bladder with truncating mutations of the STAG2 gene.

middle: A

first: Todd

last: Waldman

first: Abdel

last: Elkahloun


title: Expression data from the rat knee articular cartilage at different developmental stages

city: Taiyuan City

first: Xiao Chun

last: Wei

state: Shanxi Shanxi

address: No.382, Wuyi Road,Taiyuan City.

department: Department of Orthopaedics

country: China

institute: the Second Hospital of Shanxi Medical University

summary:
Age as the primary rise factor could be play an important role in incidence and development of osteoarthritis. Several studies have confirmed some tissue specific microRNA were associated with development of osteoarthritis. But if age related microRNA or miRNA cluster would be involved in pivotal post-transcriptional gene regulation in osteoarthritis is unclear. In view of this, we have an idea that several age-related miRNAs would be screened from the rat knee cartilage at different development ages by miRNAs Microarray analysis.
We used microarrays to detail the global programme of gene expression underlying the rat knee cartilage and identified distinct classes of age-related miRNAs during this process.

overall_design:
The rat knee articular cartilage were selected at successive stages of the rat developmental for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous populations of cartilage at each developmental stage in order to increase the temporal resolution of expression profiles. To that end, we hand-selected cartilage according to the rat developmental stages, i.e. seven time-points: newborn (T0), childhood (T1), youth(T2), adult (T3), middle-aged (T4) early-stage elderly(T5) and latter-stage elderly(T6).
The objective of the study is to identify miRNA profile of knee articular cartilage at different developmental ages in rats. Total RNA were extracted from the knee articular cartilage of Sprague-Dawley rats at postnatal day 0(T0), week1(T1), week 4(T2), mon3(T3), mon 6(T4), mon 12(T5), and mon 18(T6). The microRNA profile in the specimens was detected with the Affymetrix GeneChipÂ® miRNA 3.0 Array.

first: XiaoChun

first: YongPing

last: Li


title: Protein Domain Mimetics as In Vivo Modulators of Hypoxia-Inducible Factor Signaling

status: Public on Jun 18 2013

summary: We performed gene expression profiling of hydrogen-bond surrogate that targets hypoxia-inducible transcription factior complex and results in inhibition of hypoxia-inducible genes with relatively minimal perturbation of non-targeted signaling pathways.

overall_design: Hypoxic HeLa cells were treated with transcriptional inhibitors HBS 1, HBS 2 or vehicle and their expression profiles were compared to normoxic HeLa cells.


title: Molecular phenotyping of the idiopathic interstitial pneumonias identifies two Subtypes of idiopathic pulmonary fibrosis.

status: Public on Jun 21 2013

city: Aurora

last: Schwartz

state: CO

address: Anschutz Medical Campus

department: Medicine

institute: University of Colorado, Anschutz Medical Campus

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series

first: Ivana

middle: V

last: Yang

first: Chris

last: Coldren

first: Sonia

last: Leach

first: Elissa

last: Murphy

first: Jia

last: Lin

first: Rachel

last: Burton

first: Steve

last: Groshong

first: Carlyne

last: Cool

first: Gregory

last: Cosgrove

last: Lynch

first: Kevin

last: Brown

first: Marvin

middle: I

last: Schwarz

first: Tasha

middle: E

last: Fingerlin


title: The dual pathway inhibitor rigosertib is effective in direct-patient tumor xenografts of head and neck squamous cell carcinomas

status: Public on Jun 13 2013

city: Salt Lake City

first: Aik Choon

last: Tan

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: Huntsman Cancer Institute

summary:
Rigosertib treatment of head and neck squamous cell cancer
The dual pathway inhibitor rigosertib inhibits phosphoinositide 3-kinase (PI3K) pathway activation as well as polo-like kinase 1 (PLK1) activity across a broad spectrum of cancer cell lines. The importance of PIK3CA alterations in head and neck squamous cell cancer (HNSCC) has raised interest in exploring agents targeting PI3K, the product of PIK3CA. The genetic and molecular basis of rigosertib treatment response was investigated in a panel of 16 HNSCC cell lines, and direct patient tumor xenografts from 8 HNSCC patients (4 HPV16-positive). HNSCC cell lines and xenografts were characterized by pathway enrichment gene expression analysis, exon sequencing, gene copy number, western blotting, and IHC. Rigosertib had potent antiproliferative effects on 11 of the 16 HPV- HNSCC cell lines. Treatment sensitivity was confirmed in two cell lines using an orthotopic in vivo xenograft model. Growth reduction after rigosertib treatment was observed in 3/8 HNSCC direct patient tumor lines. The responsive tumor lines carried a combination of a PI3KCA activating event (amplification or mutation) and a p53 inactivating event (either HPV16-mediated or mutation-mediated TP53 inactivation). In this study, we evaluated the in vitro and in vivo efficacy of rigosertib in both HPV+ and HPV- HNSCCs focusing on inhibition of the PI3K pathway. Although consistent inhibition of the PI3K pathway was not evident in HNSCC, we identified a combination of PI3K/TP53 events necessary, but not sufficient for rigosertib-sensitivity.

overall_design: Sixteen HNSCC lines data were profiled at baseline to find differentially expressed genes and pathways sensitive to rigosertib.

first: Aik

first: Antonio

last: Jimeno

first: Ryan

last: Anderson


title: Expression analysis of Escherichia coli MG1655 K-12 WT and ∆fnr mutant

status: Public on Jun 20 2013

city: Madison

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

summary: Investigation of whole genome gene expression level changes in a Escherichia coli MG1655 K-12 ?fnr mutant, compared to the wild-type strain. The mutations engineered into this strain produce a strain lacking the FNR protein. WT strains were grown under aerobic and anaerobic growth conditions.

sample_organism: Escherichia coli str. K-12 substr. MG1655star

overall_design: A six chip study using total RNA recovered from two separate cultures of Escherichia coli MG1655 K-12 WT (aerobic and anaerobic) and two separate cultures of the ?fnr mutant strain (anaerobic). Each chip measures the expression level of 4,661 genes from Escherichia coli MG1655 K-12 with eight 60-mer probes per gene, with each probe represented twice on the array.

first: Huihuang

last: Yan

first: Irene

last: Ong

first: Dongjun

last: Chung

first: Kun

last: Liang

first: Frances

last: Tran

first: Sunduz

last: Keles

first: Robert

last: Landick

first: Patricia

last: Kiley


title: Molecular phenotyping of the idiopathic interstitial pneumonias [mRNA]

first: David

last: Schwartz

summary:
Rationale: The fibrosing idiopathic interstitial pneumonias (IIPs) are classified based on clinical, radiographic, and pathologic criteria. The separation into phenotypic subgroups is useful in predicting outcome and therapeutic strategy; however a large degree of ambiguity remains. Gene expression profiling may contribute to traditional criteria in IIPs by characterizing the dynamic biology that more accurately distinguishes subtypes of these diseases or their prognoses.
Methods: We collected transcriptional and miRNA profiles on lung tissue from 167 subjects with IIP and 50 non-diseased controls.  Differential expression of individual transcripts and miRNAs was identified using an ANCOVA model incorporating the clinical diagnosis of each subject as well as age, gender, and smoking status.  Validation was performed in an independent cohort of 131 IIPs and 39 non-diseased controls.
Results: Our results demonstrate a substantial degree of overlap in mRNA and miRNA signatures of clinical subtypes of IIP.  However, we identify two subtypes of IPF/UIP based on a strong molecular signature associated with expression of cilium genes.  We demonstrate that elevated expression of cilium genes is associated with more extensive microscopic honeycombing, more fibroblastic foci, higher expression of the airway mucin gene MUC5B, and better survival in an independent cohort of IPF/UIP patients.  Moreover, we identify miRNAs involved in the regulation of cilium-associated gene expression that contribute to novel molecular subphenotypes of IPF.
Conclusions: While subtypes of IIP are related biologically with similar transcriptional profiles, expression of cilium genes appear to identify two unique clinical presentations of IPF/UIP.

overall_design: 167 subjects with IIP and 50 non-diseased controls with no replicates

first: Ivana

last: Yang

first: Chris

last: Coldren

first: Sonia

last: Leach

first: Elissa

last: Murphy

first: Jia

last: Lin

first: Rachel

last: Burton

first: Steve

last: Groshong

first: Carlyne

last: Cool

middle: P

last: Cosgrove

middle: K


title: Comparison of gene expression profiles between human DFAT cells and ADSCs derived from the same donors

status: Public on Jun 12 2013

city: Itabashi

first: Yuji

last: Iribe

state: Tokyo

address: 30-1 Ohyaguchikamicho

department: Department of Medical Science

institute: Nihon University School of Medicine

summary: Dedifferentiated fat (DFAT) cells, established in vitro from mature adipocytes, exhibit certain properties of multipotent mesenchymal stem/stromal cells (MSCs), such as the ability to differentiate into multiple mesenchymal lineages. Although DFAT cells exhibit properties of proliferative progeny, at present there is only limited knowledge about their MSC-specific characteristics because those cells are considered to be potential artifacts of cell culture. To elucidate the identity of DFAT cells, we compared gene expression profiles of human DFAT cells and adipose-derived stem/stromal cells (ADSCs) established using adipose tissue from the same donors. Microarray analysis showed that global mRNA expression profiles of human DFAT cells were very similar to those of ADSCs, a representative MSC, despite being committed adipocyte progenitors.

overall_design: Subcutaneous adipose tissues that were obtained during surgical operation for non-malignant disease were donated by 3 patients after obtaining informed consent. Three sets of DFAT cells and ADSCs, each derived from adipose tissue from the same donor were used for RNA extraction and subsequent microarray analysis.

first: Taro

last: Matsumoto