title: Prostate cancer stratification using molecular profiles [Stockholm genotype]

status: Public on Sep 16 2015

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

summary: Background   Understanding the heterogeneous genotypes and phenotypes of prostate cancer is fundamental to improving the way we treat this disease.  As yet, there are no validated descriptions of prostate cancer subgroups derived from integrated genomics linked with clinical outcome.    Methods  In a study of 482 tumor, benign and germline samples from 259 men with primary prostate cancer, we used integrative analysis of copy number alterations (CNA) and array transcriptomics to identify genomic loci that affect expression levels of mRNA in an expression quantitative trait loci (eQTL) approach, to stratify patients into subgroups that we then associated with future clinical behavior, and compared with either CNA or transcriptomics alone.      Findings  We identified five separate patient subgroups with distinct genomic alterations and expression profiles based on 100 discriminating genes in our separate discovery and validation sets of 125 and 99 men. These subgroups were able to consistently predict biochemical relapse (p=0.0017 and p=0.016 respectively)  and were further validated in a third cohort with long-term follow-up (p=0.027). We show the relative contributions of gene expression and copy number data on phenotype, and demonstrate the improved power gained from integrative analyses. We confirm alterations in six genes previously associated with prostate cancer (MAP3K7, MELK, RCBTB2, ELAC2, TPD52, ZBTB4) in prostate cancer, and also identify 94 genes not previously linked to prostate cancer progression that would not have been detected using either transcript or copy number data alone. We confirm a number of previously published molecular changes associated with high risk disease, including MYC amplification, and NKX3-1, RB1 and PTEN deletions, as well as over-expression of PCA3 and AMACR, and loss of MSMB in tumor tissue. A subset of the 100 genes  outperforms established clinical predictors of poor prognosis (PSA, Gleason score), as well as previously published gene signatures (p=0•0001). We further show how our molecular profiles can be used for the early detection  of aggressive cases in a clinical setting, and inform treatment decisions.      Interpretation  For the first time this study demonstrates the importance of integrated genomic analyses incorporating both benign and tumor tissue data in identifying molecular alterations leading to generation of robust gene sets that are predictive of clinical outcome in independent patient cohorts.

overall_design: A total of 482 samples from 289 men with prostate cancer from two cohorts were included in this study.  The discovery cohort comprised 125 tumor samples from radical prostatectomy (RP) with 118 matched benign samples, and 85 matched blood samples.  An additional 4 benign samples from men undergoing Holmium laser enucleation of the prostate (HoLEP) and 16 radical prostatectomy samples from men with castrate-resistant prostate cancer, with 13 matched blood samples were also included.  These were assayed on several platforms, including Illumina HT12v4 gene expression arrays, Illumina OMNI2.5M genotyping arrays and Affymetrix SNP6 genotyping arrays.  The validation cohort comprised 103 tumor tissue samples from men with prostate cancer, with 99 matched benign tissue samples and 103 matched blood samples.  This datasheet describes samples in the DISCOVERY COHORT only, with complete, Affymetrix GenomeWideSNP_6 data for 89 tumor samples, 50 matched blood samples and 41 matched benign samples.

first: Helen

last: Ross-Adams

first: Alastair

last: Lamb

first: Silvia

last: Halim

first: Mark

last: Dunning


title: Affymetrix SNP array data for chronic myelomonocytic leukemia samples

status: Public on Dec 01 2015

city: Barcelona

first: Laura

last: Palomo

state: Barcelona

address: Carretera de Can Ruti, Camí de les Escoles, s/n

department: Campus ICO-GTiP

country: Spain

institute: Josep Carreras Leukemia Research Institute

summary: Chronic myelomonocytic leukemia (CMML) is a clonal hematopoietic disorder with heterogeneous clinical, morphological and genetic characteristics. Clonal cytogenetic abnormalities are found in 20-30% of patients with CMML. Patients with low risk cytogenetic features (normal karyotype and isolated loss of Y chromosome) account for approximately 80% of CMML patients and often fall into the low risk categories of CMML prognostic scores. SNP-A were performed in 82 CMML patients with low risk karyotypes and uninformative results for conventional G-banding cytogenetics (CC).

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from bone marrow or peripheral blood samples.
Copy number analysis of Affymetrix array was performed for 82 CMML samples at diagnosis or prior to any treatment,

first: Francesc

last: Solé

first: Lurdes

last: Zamora


title: Prospective biomarker analysis of the randomized CHER-LOB study evaluating the dual anti-HER2 treatment with chemotherapy plus trastuzumab and lapatinib as neoadjuvant therapy for HER2-positive breast cancer [copy number]

status: Public on Oct 06 2015

city: Modena

first: Enrico

last: Tagliafico

state: MO

address: Via Campi 287

department: Center for Genome Research

country: Italy

institute: University of Modena and Reggio Emilia

summary:
The CHER-LOB randomized phase II study showed that the combination of lapatinib and trastuzumab plus chemotherapy increases the pathologic complete remission (pCR) rate as compared to chemotherapy plus either trastuzumab or lapatinib. An extensive biomarker programme was prospectively planned to identify potential predictors of sensitivity to different treatments and evaluate treatment effect on tumor biomarkers.
A mutation in PIK3CA exon 20 or 9 was documented in 20% of the cases. Overall, the pCR rates were similar in PIK3CA wild type and PIK3CA mutated patients (33.3% vs 22.7%; p=0.323). However, for patients receiving trastuzumab plus lapatinib, the probability of pCR was higher in PIK3CA wild type tumors (48.4% vs 12.5%; p=0.06). Ki67, pAKT and apoptosis measured on the residual disease were significantly reduced from baseline. The degree of Ki67 inhibition was significantly higher in patients receiving the dual anti-HER2 blockade. In conclusion, PIK3CA mutations seem to identify patients less likely to benefit from dual anti-HER2 inhibition. p95-HER2 and markers of PI3K pathway deregulation are not confirmed as markers of different sensitivity to trastuzumab or lapatinib.

overall_design: 121 HER2-positive breast cancer patients were randomly assigned to neoadjuvant chemotherapy plus either trastuzumab, lapatinib or both trastuzumab and lapatinib. Pre-treatment, fresh-frozen tissue samples were collected for genomic analyses. 69 samples passed quality control for DNA and were profiled for copy number with Affymetrix technology using the Genome-Wide Human SNP 6.0 Array.

first: Valentina

last: Guarneri

first: Maria

middle: V

last: Dieci

first: Antonio

last: Frassoldati

first: Antonino

last: Maiorana

first: Guido

last: Ficarra

first: Stefania

last: Bettelli

first: Silvio

last: Bicciato

first: Daniele

middle: G

last: Generali

first: Katia

last: Cagossi

first: Giancarlo

last: Bisagni

first: Samanta

last: Sarti

last: Musolino

first: Catherine

last: Ellis

first: Rocco

last: Crescenzo

first: PierFranco

last: Conte


title: Widespread somatic L1 retrotransposition occurs early during gastrointestinal cancer evolution

status: Public on Aug 10 2015

city: Baltimore

first: Szilvia

last: Solyom

state: MD

address: 733 North Broadway

department: Institute for Genomic Medicine

country: USA

institute: Johns Hopkins University School of Medicine

summary: Somatic L1 retrotransposition events have been shown to occur in epithelial cancers1-8. Here, we attempted to determine how early somatic L1 insertions occurred during the development of gastrointestinal (GI) cancers. Using L1-targeted resequencing (L1-seq), we studied different stages of four colorectal cancers arising from colonic polyps, seven pancreatic carcinomas, as well as seven gastric cancers. Surprisingly, we found somatic L1 insertions not only in all cancer types and metastases, but also in colonic adenomas, well-known cancer precursors. Some insertions were also present in low quantities in normal GI tissues, occasionally caught in the act of being clonally fixed in the adjacent tumors. Insertions in adenomas and cancers numbered in the hundreds and many were present in multiple tumor sections implying clonal distribution. Our results demonstrate that extensive somatic insertional mutagenesis occurs very early during the development of GI tumors, probably before dysplastic growth.

overall_design: Here we show Human SNP 6.0 Array experiments on DNAs from four colorectal cancer patients (1BV, 2BV, 3BV, and 4BV) with polyps and metastases. Here we characterize the samples for CNVs and compare the samples' CNV status to their respective somatic L1 retrotransposition profile.

first: Adam

middle: D

last: Ewing

first: Anthony

last: Gacita

first: Laura

last: Wood

first: Florence

last: Ma

first: Dongmei

last: Xing

first: Min-Sik

last: Kim

first: Srikanth

middle: S

last: Manda

first: Gabriela

last: Abril

first: Gavin

last: Pereira

first: Alvin

last: Makohon-Moore

first: Leendert

middle: H

last: Looijenga

first: Ad

middle: J

last: Gillis

first: Ralph

last: Hruban

first: Katharine

middle: E

last: Romans

first: Akhilesh

last: Pandey

first: Christine

middle: A

last: Iacobuzio-Donahue

first: Bert

last: Vogelstein

first: Kenneth

middle: W

last: Kinzler

first: Haig

last: Kazazian


title: Effect of vitrification using the Cryotop method on the gene expression profile of in vitro-produced bovine embryos

status: Public on Aug 03 2015

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

summary: Changes in gene expression induced by the Cryotop vitrification procedure in bovine blastocysts using Agilent EmbryoGENE microarray slides. Bovine in vitro-produced embryos at the blastocyst stage (144 to 156 hours post insemination) were vitrified using the Cryotop system and compared with non-vitrified (control) embryos. After vitrification, the embryos were warmed and cultured for an additional 4 hours. Embryos that re-expanded or developed to the expanded blastocyst stage were used for microarray analysis.

overall_design: Four pools of vitrified embryos were hybridized against four pools of control embryos in a dye-swap design.

first: Ligiane

middle: O

last: Leme

first: Isabelle

last: Dufort

first: José

middle: F

last: Sprícigo

first: Thiago

last: Braga

first: Maurício

middle: M

last: Franco

first: Margot

last: Dode


title: Cellular and molecular response to ruthenium(II)-arene complex with substituted picolinato ligand in HeLa cells

status: Public on Sep 11 2015

city: Belgrade

first: Miljana

last: Tanic

address: Pasterova 14

department: Experimental Oncology

country: Serbia

institute: Institute for Oncology and Radiology of Serbia (IORS)

summary: Ruthenium(II)-arene complexes are promising drug candidates for therapy of solid tumors. We have previously shown that ruthenium(II)-arene complex [Ru(η6-p-cymene)(L7)Cl] (RuT7) exerts cytotoxic effects in a panel of cancer cell lines (J. Organomet. Chem. 2014, 749, 343–349). In this study we analyzed in vitro cellular response and performed whole-transcriptome microarray gene expression analysis in HeLa cells in order to understand the cellular and molecular mechanism of response to RuT7 complex. Results on biological action of ruthenium complex obtained on cellular level were reflected on molecular level as well. Analysis of functional categories and signaling and biochemical pathways that are associated with HeLa cells' response to ruthenium complex revealed that RuT7 complex leads HeLa cells through intrinsic (mitochondrial) apoptotic pathway, via indirect DNA damage made by action of reactive oxygen species and through direct DNA binding of RuT7. Performed molecular toxicity analysis has shown that RuT7 has fewer associated toxicity profiles than cisplatin. Altogether these results provide the basis for development of RuT7 in animal and pre-clinical studies as a potential drug candidate.

overall_design: We hybridized each condition (control, RuT7 and CDDP) at each time point (12 h and 24 h) in triplicate, for a total of 18 samples.

first: Katarina

middle: K

last: Jovanović

last: Tanić

first: Ivanka

last: Ivanović

first: Nevenka

last: Gligorijević

first: Biljana

middle: P

last: Dojčinović

first: Živoslav

last: Lj Tešić

first: Siniša

last: Radulović


title: Expression dynamics in mammalian cells responding to protein misfolding stress

status: Public on Aug 15 2015

city: New York

first: Zhe

last: Cheng

state: New York

address: 12 Waverly Place, 4th Floor

department: Bilogy Department

institute: New York University

summary:
We have employed whole genome microarray expression profiling to track the transcriptome expression change under DTT induced protein misfolding stress.
The relative importance of gene expression regulation at the mRNA versus the protein-level is a matter of ongoing debate. We present an in-depth analysis of a cervical cancer cell line responding to protein misfolding stress induced by dithiothreitol treatment, quantifying the dynamics of mRNA and protein concentrations for >3,500 genes over a time-course 30 hours. While the early phase of the experiment (<two hours) was marked by apoptosis, surviving cells were marked by a strong response to unfolded proteins and stress of the endoplasmatic reticulum, specifically during the intermediate phase (two to eight hours). Using statistical time series analysis, we detected significant changes in the regulatory parameters at the RNA-level, caused by transcription and mRNA degradation, and at the protein-level, caused by translation and protein degradation. mRNA- and protein-level regulation were of equal importance (XX and YYY%, respectively), but displayed different magnitudes and dynamics: mRNA fold changes were much smaller on average than those of the proteins. While our method did not capture immediate changes, we found the strongest regulatory response between two and eight hours after the treatment. mRNA-level regulation showed a spike around this time interval, while protein-level regulation was delayed and continued at slower pace until the end of the experiment.

overall_design: RNA expression in HeLa cell line was measured at 0, 0.5, 1, 2, 8, 16, 24, 30 hrs after exposure to 2.5mM DTT. Two biological replicates were conducted.

first: Sabrina

last: Krueger

first: Tara

last: Rock

first: Christine

last: Vogel


title: Affymetrix SNP array data for high-grade serous ovarian cancer samples

status: Public on Sep 05 2015

city: Mishima

first: Takahide

last: Hayano

state: Shizuoka

address: Yata 1111

department: Division of Human Genetics

country: Japan

institute: National Institute of Genetics

summary: High-grade serous ovarian cancer is the most aggressive histological type of epithelial ovarian cancer, which is characterized by a high frequency of somatic TP53 mutations. To provide a better understanding of the molecular mechanisms involved in the pathogenesis of these cancers and to develop a risk classification system, we conducted profiling of the copy number alterations present in these tumors.

overall_design:
Thirty patients who were diagnosed as high-grade serous ovarian cancer were recruited in this study.
Affymetrix SNP array were performed according to the manufacturer's directions on DNA extracted from high-grade serous ovarian cancer tissues or peripheral blood samples.
The Japanese Serous Ovarian Cancer Study Group


title: Mcl-1 is a key determinant of breast cancer cell survival [copy number]

status: Public on Aug 07 2015

city: North Chicago

first: Xin

last: Lu

state: IL

address: 1 North Waukegan Rd

department: Oncology Discovery

institute: Abbvie

summary: Copy number profile of cultured Breast Cancer cell line measured by Affymetrix SNPs microarrays

overall_design: Whole genome copy number profile of 2 breast cancer cell lines were analyzed using Affymetrix SNP6.0 arrays

first: Yu

last: Xiao

first: Darren

middle: C

last: Phillips


title: Chronic growth factor signaling in Acute Myeloid Leukemia is connected to a specific chromatin signature [Agilent]

status: Public on Jul 03 2015

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

country: Germany

institute: University Medical Center Freiburg

summary: We performed genome-wide DNaseI hypersensitive site in FLT3-ITD and WT patient samples. We report corresponding gene expression, promoter methylation patterns of differential DHSs as well as differentially occupied TF binding motifs using surrounding DNAseI cut profiles. We examined association patterns of FLT3 ITD and WT AMLs and found that FLT3-ITD signaling is associated with common gene expression and chromatin signature.

overall_design: Examination of gene expression patterns in  FLT3 ITD and WT AML via microarray study.

first: Sally

last: James

first: Anetta

last: Ptasinska

first: Joaquin

last: Zacarias-Cabeza

first: Maria

middle: R

last: Imperato

first: Salam

last: Assi

first: Jason

last: Piper

first: Sascha

last: Ott

first: Constanze

last: Bonifer

first: Peter

last: Cockerill


title: TIA proteins drives global and specific translational repression of genes linked to the cell-cycle progression and DNA replication/repair

status: Public on May 19 2015

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

institute: CNB, CSIC

summary: The reduction of T-cell intracellular antigen (TIA) proteins in transformed cells leads to the acquisition of aberrant cellular phenotypes promoting uncontrolled cell proliferation and tumor growth. Here we show that global and specific translational rates are regulatory gene events that contribute markedly to the acquisition of above cellular phenotypes. For example, we observe a significant increase of ribosomal population and translational machinery components in TIA-reduced HeLa cells. Polysomal microarray analysis shows specific changes at both the transcript and translational level following TIA reduction, identifying translationally regulated mRNAs that are not transcriptionally regulated which seem to be prevalent for the adaptation to the new environmental conditions. Validation of microarray data using RT-QPCR and immunological analysis for representative genes were carried out. Up-regulated in this class of mRNA are those involved in cell-cycle progression and DNA replication/repair, including several mRNAs with specific sequences to bind TIA proteins. Our data support a hypothesis that a concerted activation of both global and selective translational rates is relevant for the transition from quiescent to proliferative status in TIA-depleted HeLa cells.

overall_design: Two independent replicates were performed for each experimental condition and hybridized to SurePrint G3 Human GE 8x60K Agilent microarrays.

first: Carmen

last: Sánchez-Jiménez

first: Isabel

last: Carrascoso

first: José

last: Izquierdo


title: Distinctive genotypes in infants with T-cell acute lymphoblastic leukaemia

status: Public on Jul 30 2015

city: Rio de Janeiro

first: Marcela

middle: B.

last: Mansur

state: Rio de Janeiro

address: Rua André Cavalcanti, 37, 2º floor

department: Division of Clinical Research, Research Centre

country: Brazil

institute: Instituto Nacional de Câncer - INCA

summary: Infant T-cell acute lymphoblastic leukaemia (iT-ALL) is a very rare and poorly defined entity with a poor prognosis. We assembled a unique series of 13 infants with T-ALL, which allowed us to identify genotypic abnormalities and to investigate prenatal origins. Matched samples (diagnosis/remission) were analysed by single nucleotide polymorphism-array to identify genomic losses and gains. In three cases, we identified a recurrent somatic deletion on chromosome 3. These losses result in the complete deletion of MLF1 and have not previously been described in T-ALL. We observed two cases with an 11p13 deletion (LMO2-related), one of which also harboured a deletion of RB1. Another case presented a large 11q14·1-11q23·2 deletion that included ATM and only five patients (38%) showed deletions of CDKN2A/B. Four cases showed NOTCH1 mutations; in one case FBXW7 was the sole mutation and three cases showed alterations in PTEN. KMT2A rearrangements (KMT2A-r) were detected in three out of 13 cases. For three patients, mutations and copy number alterations (including deletion of PTEN) could be backtracked to birth using neonatal blood spot DNA, demonstrating an in utero origin. Overall, our data indicates that iT-ALL has a diverse but distinctive profile of genotypic abnormalities when compared to T-ALL in older children and adults.

overall_design:
Copy number analyses of Affymetrix SNP6.0 arrays were performed for 13 infant T-ALL samples.

** Due to privacy concerns, the primary SNP array data for this study is not available with unrestricted access. Individuals wishing to obtain this data for research purposes may request access by contacting the author by email (email address provided below). **

middle: B

first: Frederik

last: van Delft

first: Susan

last: Colman

first: Caroline

middle: L

last: Furness

first: Jane

last: Gibson

first: Mariana

last: Emerenciano

first: Helena

last: Kempski

first: Emmanuelle

last: Clappier

first: Hélène

last: Cave

first: Jean

last: Soulier

last: Pombo-de-Oliveira

first: Anthony

last: Ford

first: Mel

last: Greaves


title: Copy Number Variants at Chromosome 10q11.21, 12p12.1 and 21q22.11 May Be Associated with Hyperlipidemia in Taiwanese Patients

status: Public on May 01 2015

city: Changhua City

first: Wei-Chung

last: Shia

address: 8F., No.235, Xuguang Rd.

department: Cancer Research Center

country: Taiwan

institute: Changhua Christian Hospital

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

summary: Affymetrix SNP array analysis was performed on DNA extracted from whole blood samples of 7 Taiwanese patients with hyperlipidemia. Three copy number variant (CNV) regions associated significantly with hyperlipidemia were identified through genomic segmentation analysis (P<0.001).

overall_design: 7 male Taiwanese hyperlipidemia patients.

first: Wei


title: Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer [SNP]

status: Public on Jun 10 2015

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Basal-like and luminal breast tumors have distinct clinical behavior and molecular profiles, yet the underlying mechanisms are poorly defined. To interrogate processes that determine these distinct phenotypes and their inheritance pattern, we generated somatic cell fusions and performed integrated genetic and epigenetic (DNA methylation and chromatin) profiling. We found that the basal-like trait is generally dominant and it is largely defined by epigenetic repression of luminal transcription factors. Definition of super-enhancers highlighted a core program common in luminal cells but high degree of heterogeneity in basal-like breast cancers that correlates with clinical outcome. We also found that protein extracts of basal-like cells is sufficient to induce luminal-to-basal phenotypic switch implying a trigger of basal-like autoregulatory circuits. We determined that KDM6A might be required for luminal-basal fusions, and identified EN1, TBX18, and TCF4 as candidate transcriptional regulators of luminal-to-basal switch. Our findings highlight the remarkable epigenetic plasticity of breast cancer cells.

overall_design: We investigated the potential contribution of genetic factors to defining cell type-specific gene expression patterns by analyzing allelic inheritance based on Affymetrix SNP6.0 array hybridization of DNA from parental and fusion cells

first: Alexander

last: Gimelbrant

first: Reo

last: Maruyama


title: Gene expression profiling in B lymphocytes from transplanted patients

status: Public on Aug 01 2015

city: Nantes

first: Richard

last: Danger

address: 30 Boulevard Jean Monnet

country: France

institute: CHU Nantes - INSERM- Nantes Universite

summary: The achievement of a drug-free operational tolerance for renal transplanted patients is a major goal in organ transplantation. Previous gene expression profiling in peripheral blood mononuclear cells (PBMC) identified genes associated with operational tolerance. The identification of a common pattern of B cell-related genes associated with tolerance encourage us to analyze gene expression in purified B cell from operationally tolerant patients (TOL=10) compared to renal transplanted patients with stable graft function (STA=12) under immunosuppression and also compared to healthy volunteers (HV=10) who have no immunosuppressive treatment and no graft. Microarray analyses exhibited an absence of gene signature associated with tolerance in purified B cell compared to STA or HV. These results suggest that the B cell signatures observed in PBMC may be due to an increase number of total B cells rather than specific B cell characteristics in operationally tolerant patients.

overall_design: This dataset represents gene expression profiling of purified B cells from 10 renal transplanted patients with operational tolerance (TOL), 12 renal transplanted patients with stable graft function under immunosuppression (STA) and 10 healthy volunteers (HV).

first: Mélanie

last: Chesneau

first: Sophie

last: Brouard


title: Identification of a piscine reovirus-related pathogen in Proliferative Darkening Syndrome infected brown trout (Salmo trutta fario) using a next-generation technology detection pipeline

status: Public on Jun 26 2015

city: Freising

first: Ralph

last: Kuehn

address: Hans-Carl-von-Carlowitz-Platz 2

department: Chair of Zoology

institute: Technical University of Munich

summary: The proliferative darkening syndrome (PDS) is an annually recurring disease that causes species-specific die-off of brown trout (Salmo trutta fario) with a mortality rate of near 100 % in pre-alpine rivers of central Europe. So far the etiology and causation of this disease is still unclear. The objective of this study was to identify the cause of PDS using a next-generation technology detection pipeline. Following the hypothesis that PDS is caused by an infectious agent, brown trout specimens were exposed to water from a heavily affected pre-alpine river with annual occurrence of the disease. Specimens were sampled over the entire time period from potential infection through death. Transcriptomic analysis (microarray) and RT-qPCR of brown trout liver tissue evidenced strong gene expression response of immune-associated genes. Messenger RNA of specimens with synchronous immune expression profiles were ultra-deep sequenced using next-generation sequencing technology (NGS). Bioinformatic processing of generated reads and gap-filling Sanger re-sequencing of the identified pathogen genome revealed strong evidence that a piscine-related reovirus is the causative organism of PDS. The identified pathogen is phylogenetically closely related to the family of piscine reoviruses (PRV) which are considered as the causation of different fish diseases in Atlantic and Pacific salmonid species such as Salmo salar and Onchorhynchus kisutch. This study also highlights that the approach of first screening immune responses along a timeline in order to identify synchronously affected stages in different specimens which subsequently were ultra-deep sequenced is an effective approach in pathogen detection. In particular, the identification of specimens with synchronous molecular immune response patterns combined with NGS sequencing and gap-filling re-sequencing resulted in the successful pathogen detection of PDS.

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design:
Our study design was primarily based on a comparison of brown trout (n=820) exposed to PDS-affected river water and a group exposed to unaffected spring water. The experiment was conducted over a time period of 15 weeks (complete time window from possible first pathogen contact until die-off). Liver tissue from three specimens per group was sampled every day during the whole duration of the experiment and subsequently used for RNA extraction. For pathogen detection and a characterization of the chronology of immune response on mRNA transcriptome level, three different approaches were used: (A) gene expression profiling: Transcriptomic analysis (microarrays) of mRNA from liver tissue was used to monitor the chronology of immune response of individual specimens throughout the whole experiment. This resulted in the identification of immune response candidate genes (IRGs) responding to the infection. RT-qPCRs of IRGs enable sophisticated statistical analysis by using biological and technical replicates to identify specimens with synchronous response pattern; (B) next-generation sequencing and bioinformatics: cDNA from a selection of specimens with synchronous immune response were ultra-deep sequenced on an Illumina HiSeq 2500 next-generation sequencing platform following deep bioinformatics processing. This resulted in identifying the pathogen genetic signal from the comparison between host genome data, the ultra-deep sequencing data of infected specimens and the generated pathogen databases; (C) Sanger re-sequencing and phylogenetic analysis: In order to complete the genetic information of the detected pathogen, primers matching the processed sequence reads were designed for subsequent amplification and Sanger re-sequencing of the gaps in pathogen cDNA. The pathogen was taxonomically and phylogenetically classified by comparing its sequence data with all available pathogen databases.

Detailed description of Transcriptomic analysis (microarrays):
Sampling at both experimental stations started on May 29, 2008, which was also the day on which the fish were first transferred to their exposure tanks (referred to as 0 day post exposure; d.p.e), and ended on the 5th of September 2008. At the treatment station 3 fish, which showed no external signs of PDS (phenotypically healthy, non-Stage 3 individuals), were sampled each day (always at 2pm), whereas at the control station 3 fish were sampled in 7-day intervals (always at 12 noon). Fish were anaesthetized by a blow to the head and organ tissue of interest (liver, kidney, spleen, gill, muscle, stomach and foregut tissue) were immediately harvested from sacrificed fish, snap-frozen in liquid nitrogen and subsequently stored at -80°C. Livers from the three brown trout that were sampled concurrently from both treatment and control group in 7-day intervals starting 7 d.p.e (7, 14, 21, 28, 35, 42, 49, 56, 63, 70, 77, 84, 91 and 98 d.p.e; n=14) were recruited for the use in the microarray analysis.

Microarray analyses were performed using a direct comparison two-channel design in which equimolar amounts of liver sample of one brown trout from both treatment and control group were co-hybridized on the same microarray. For each time point (n=14) microarray co-hybridizations were repeated in triplicate (n=3) and included one dye-swap in order to reduce dye-bias. Thus a total of 42 microarray slides were used in this study (3 biological replicate microarrays x 14 time points = 42 microarrays).

first: Bernhard

last: Stoeckle

first: Marc

last: Young

first: Lisa

last: Popp

first: Jens-Eike

last: Taeubert

first: Michael

last: Pfaffl

first: Juergen

last: Geist


title: Prostate cancer stratification using molecular profiles

first: Chandra

last: Chilamakuri

country: United Kingdom

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

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

overall_design: Refer to individual Series


title: Affymetrix SNP Array data for familial coarctation of the aorta (CoA) II

status: Public on Apr 16 2015

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

institute: Uniklinikum Erlangen

summary: Coarctation of the aorta (CoA) accounts for 5-8% of all congenital heart defects.  CoA can be detected in up to 20% of patients with Ullrich-Turner syndrome (UTS), in which a part or all of one of the X chromosomes is absent. The etiology of non-syndromic CoA is poorly understood. In the present work, we test the hypothesis that rare copy number variation (CNV) especially on the gonosomes, contribute to the etiology of non-syndromic CoA.

overall_design: We performed high-resolution genome-wide CNV analysis using the Affymetrix SNP 6.0 microarray platform for 13 individuals from 3 families with familial CoA.

first: Julia

last: Moosmann

first: Arif

last: Ekici

first: Okan

last: Toka


title: Gene expression from pericytes

status: Public on Apr 08 2015

city: Vienna

first: Klemens

last: Vierlinger

address: Giefinggasse 4

department: HMD

country: Austria

institute: AIT

summary: Background: Blood vessel wall adventitial progenitors may yield a renewable source for therapeutic vasculogenesis in limb and myocardial ischemia models. Donor-related liabilities, epigenetic and expressional changes occurring during stem cell isolation and expansion might result in substantial phenotypic modifications, ultimately impacting on therapeutic activity of the cell product. Methods: Consistency of functional performance was assessed in 15 saphenous vein-derived adventitial progenitor cells (SV-APC) lines, of which 10 derived from leftovers of coronary artery bypass grafts (CABG) and 5 from wastes of varicose SV removal from subjects with no evidence of cardiovascular disease (NC). To correlate the expansion culture data with a clinical outcome, 5 SV-APC lines were transplanted (8x105 cells, im) in mice with limb ischemia (n=5 mice per line). Endpoint measurements of blood flow (BF) by laser Doppler flowmetry, capillary and arteriole density were correlated with epigenetic/expressional markers of transplanted cell populations to predict the outcome of reparative processes in vivo. Results: We report successful expansion in 63% of tested lines, which reached the therapeutic target of 30-50 million viable SVP at passage 8 (P8) in ~10 weeks. Antigenic profile was retained during expansion with stable expression of typical pericyte/mesenchymal markers NG2, PDGFR, CD44, CD90 and CD105 (flow cytometry and immunocytochemistry) and comparative cell line analysis indicated no interference of cardiovascular background. Qualitative differences during expansion show conserved viability and motility capacity and low levels of replicative senescence during expansion in culture. Functional capacity in vitro showed large variability of angiocrine secretion (VEGF-A, Ang1) amongst SV-APC but with no difference based on cardiovascular background and improved network formation with endothelial cell structures on Matrigel. In vivo, SV-APC transplantation induced consistent improvement in BF recovery of ischemic limb, reduced muscle fibrosis and reparative neovascularization. Conclusions: Current protocol generates ready-to-use human SVP in a large number of preparations, with no impact of cardiovascular risk factors on cell product functionality and therapeutic activity.

overall_design: 5 samples characterised by three variables: blood flow, arterial density and capillary density


title: Affymetrix SNP 6.0 array data for ACRG Gastric Cancer Study

status: Public on Apr 17 2015

city: Indianapolis

first: Jason

last: Ting

state: Indiana

address: Lilly Corporate Center

department: Lilly Research Labs - IT

institute: Eli Lilly and Company

summary: Gastric cancer, a leading cause of cancer related deaths, is a heterogeneous disease, with little consensus on molecular subclasses and their clinical relevance. We describe four molecular subtypes linked with distinct patterns of molecular alterations, disease progression and prognosis via: a) Microsatellite Instable: hypermutated intestinal subtype tumors occurring in antrum, best overall prognosis, lower frequency of recurrence (22%), with liver metastasis in 23% of recurred cases; b) Mesenchymal-like: diffuse tumors with worst prognosis, a tendency to occur at an earlier age and highest recurrence (63%) with peritoneal seeding in 64% of recurred cases, low frequency of molecular alterations; c) TP53-inactive with TP53 loss, presence of focal amplifications and chromosomal instability; d) TP53-active marked by EBV infection and PIK3CA mutations. The key molecular mechanisms and associated survival patterns are validated in multiple independent cohorts, to provide a consistent and unified framework for further preclinical and clinical research.

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from 277 stomach cancer samples and 14 matching adjacent stomach normal tissue sample.
PICNIC (Predicting Integer Copy Number In Cancer) analysis was performed on all 291 samples. One normal and six tumor samples failed in PICNIC. Copy number segments were generated for 284 smaples. To access tumor's purity and ploidy, ASCAT (Allele-Specific Copy number Analysis of Tumors) analysis were performa on 277 tumors, with the matching 14 normals. ASCAT analysis successfully completed cauculated tumor's ploidy and purity for 190 tumor samples.

first: Amit

last: Aggarwal


title: Affymetrix SNP Array data for familial coarctation of the aorta (CoA) I

overall_design: We performed high-resolution genome-wide CNV analysis using the Affymetrix SNP 6.0 microarray platform for 70 individuals with sporadic CoA.


title: Tissue-engineered human psoriatic skin as an in vitro model to study the impact of cytokines

status: Public on Apr 11 2015

city: Québec

first: Karine

last: Zaniolo

state: Québec

address: 1050 Chemin Sainte-Foy

department: CUO-Recherche

institute: Centre de recherche du CHU de Québec

summary: Psoriasis is a chronic inflammatory disease of the skin for which no cure has emerged. Its complex etiology requires the development of an in vitro model that appropriately recapitulates the physiopathology of this disease. In this study, we exploited the self-assembly method in order to develop a new tissue-engineered model of psoriatic skin substitutes. To circumvent the addition of immune cells, we supplemented the reconstructed psoriatic substitutes with a cocktail of four cytokines, TNF-α, IL-1α, IL-6 and IL-17, and monitored their impact on global gene expression by DNA microarray. The cytokines-supplemented substitutes have a more irregular epidermis, with protuberances and much thinner areas. Most interestingly, gene profiling on microarrays identified several genes reported as being deregulated psoriasis skin in vivo. Indeed, expression of the S100A12, IL8, DEFB4A and KYNU genes increased dramatically compared to their level in normal skin substitutes (P <0.005 to <0.05). In addition, the ACSBG1 gene, reported to be repressed in psoriasis, was also repressed in the cytokines-supplemented psoriatic substitutes compared to the controls (P <0.005). The product encoded by the genes deregulated in the cytokines-supplemented substitutes belong to biological pathways, such as the inflammatory and the immune responses, that are similarly altered in psoriasis in vivo. In conclusion, addition of cytokines to involved psoriatic substitutes alters the transcriptome of these cells in a manner similar to that observed with psoriasis in vivo. The addition of this pro-inflammatory cocktail, comparable cytokine in vivo psoriasis, prepares us for the next step: the characterization of the model once added immune cells.

overall_design: Tissue-engineered psoriatic human skin (TEPHS) cultivated with (number of replicates: 3) or without (number of replicates: 3) Cytokines (IL-17a, IL-6, IL1a, TNF-a).

first: Claudia

last: Pouliot-Bérubé

first: Jacques

last: Soucy

first: Sylvain

last: Guérin

first: Roxane

last: Pouliot


title: Development of gene expression signatures for miR-340 overexpressing human glioma-initiating cells (GICs)

status: Public on Apr 07 2015

city: Toon

first: Daisuke

last: Yamashita

address: Shitsukawa

department: Neurosurgery

institute: Ehime University Graduate School of Medicine

summary: To identify functional targets of miR-340, we compared the gene expression profiles of miR-340 overexpressing human GICs with the profiles of their parental cells.

overall_design: The precursor form of miR-340 or control miRNA was overexpressed in glioma cells using miRNA lentiviral particles. The cells were incubated with recombinant virus at 37°C for 12 hr and cultured in the presence of puromycin for 3 days.

first: Toru

last: Kondo


title: Gene expression of T47D-MTVL human breast cancer cells upon H1X knock-down

status: Public on Apr 02 2015

city: Badalona

first: Lauro

last: Sumoy

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

institute: IGTP

summary: Gene expression of T47D-MTVL human breast cancer cells expressing Dox-inducible shRNAs against histone H1X

overall_design: Stable breast cancer-derived cell lines expressing an shRNA against the histone H1X isoforms in response to doxycycline (Dox) were grown for six days in the presence or absence of Dox, and serum-starved for the last 48h for synchronization in G1, in duplicate, and RNA extracted for microarray hybridization. Cell lines used: inducible shRNA against H1X, and random shRNA-expression vector as a control.

first: Albert

last: Jordan

first: Regina

last: Mayor


title: Affymetrix SNP array data for NF1-associated glioma risk

status: Public on Feb 20 2015

city: St Louis

first: Joshua

last: Rubin

address: 660 S. Euclid Ave.

department: Pediatrics

institute: Washington University School of Medicine

summary: We performed whole genome SNP profiling on DNA samples from 236 patients with NF1, 123 with glimoa tumors and 113 without; 117 females and 119 males, together with 29 control samples.  To identify polymorphisms in human adenylate cyclase 8 (AC8) which correlate with glioma risk in NF1 in a sex-specific manner, Ac8 SNP were extracted and further analyzed for their sex-specific NF1-associated glioma risk. Three SNPs on ADCY8 were found signficant while other SNPs on CXCR7 and ADCYAP1 were promising.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from blood samples or saliva samples in three separate sets with one processed in Washington University and two in University of Utah. The data included 29 control samples and 236 NF1 patient samples (123 with and 113 without GBM) with 153 blood specimen and 97 saliva specimen.

first: Jingqin

last: Luo


title: Integrated Genomic Profiling, Therapy Response And Survival In Adult Acute Myelogenous Leukemia

status: Public on Mar 01 2015

city: Ann Arbor

first: Sami

middle: N

last: Malek

state: MI

address: 4410 Cancer Center; 1500 E Medical Center Dr

department: Internal Medicine, Hematology-Oncology

institute: University of Michigan

summary: Recurrent gene mutations, chromosomal translocations, acquired genomic copy number aberrations (aCNA) and copy-neutral loss-of-heterozygosity (cnLOH) underlie the genomic pathogenesis of acute myelogenous leukemia (AML).  Genomic lesion types from all of these categories have been variously associated with AML patient outcome.  However, the patterns of co-occurrence of such lesions are only now beginning to be defined, and we seek to further delineate the relative influence of different types of genomic alterations on clinical outcomes in AML. In this study, we performed SNP 6.0 array-based genomic profiling of aCNA/cnLOH along with sequence analysis of 13 recurrently mutated genes on purified leukemic blast DNA from 156 prospectively enrolled non-FAB-M3 AML patients across the clinical spectrum of de novo, secondary, and therapy-related AML.  We identify positive and negative associations of gene mutations, specific aCNA/cnLOH or total aCNA/cnLOH counts with different AML types as well as the associations of specific mutations with overall genomic complexity or genomic stability. Further, we show that NPM1, RUNX1, ASXL1 and TP53 mutations, elevated SNP-A-based genomic complexity, and specific recurrent aCNAs predict response to induction chemotherapy. Finally, results of comprehensive multivariate analyses support a dominant role for TP53 mutations or elevated genomic complexity as predictors of short survival in AML. Integrated genomic profiling of a clinically relevant adult AML population reveals the interplay between gene mutations, recurrent aCNAs, and SNP-A-based genomic complexity and identifies among them the genomic characteristics most associated with types of response to intensive induction therapies and with shortened overall survival.

overall_design: This study is based on 156 patients with previously untreated AML for which paired tumor and normal samples were available. The patients were enrolled into this study at the University of Michigan Comprehensive Cancer Center. The study was approved by the University of Michigan Institutional Review Board (IRBMED #2004-1022) and written informed consent was obtained from all patients prior to enrollment.   Genomic DNA was extracted from purified AML blasts and paired buccal cells.  DNA thus obtained was hybridized to Affymetrix SNP 6.0 arrays.

first: Brian

last: Parkin

first: Peter

last: Ouillette

first: Yildiz

last: Mehmet

first: Saiya-Cork

last: Kamlai

first: Kerby

last: Shedden


title: Lung cell responses to ship diesel exhaust particles

status: Public on Feb 01 2015

city: Munich

first: Sebastian

last: Oeder

address: Biedersteinerstr. 29

department: Center for Allergy and Environment (ZAUM)

institute: Technische Universität München

summary: Human BEAS-2B bronchial epithelial cells were exposed directly at the air-liquid interphase towards exhaust gas and particles of a ship engine. The goal was to compare the responses towards different fuel combustions. The engine run either on diesel fuel (DF) or on Heavy Fuel Oil (HFO).

overall_design: The lung cells were exposed 3 times to each combustion aerosol (DF or HFO). The duration of the exposure was 4h. The cells were seeded into transwell-inserts 24h before exposure.  Within each exposure 3 transwell-inserts were exposed to the complete aerosol and 3 transwell-inserts were exposed to the filtered aerosol. Effects of the complete aerosol were referenced against the filtered aerosol to determine the effects of the aerosol particles.


title: Effect of cajanin stilbene acid and its synthetic derivatives on MCF-7 breast cancer cells

status: Public on Feb 27 2015

city: Mainz

first: Onat

last: Kadioglu

address: Staudinger Weg 5

department: Institute of Pharmacy and Biochemistry

institute: Johannes Gutenberg University

summary: Cajanin stilbene acid (CSA) was previously shown to induce cytotoxicity against cancer cells. We have employed microarray gene expression profiling to identify deregulated genes in MCF-7 breast cancer cells upon treatment with CSA and its synthetic derivatives (CSA6, CSA9, CSA19). TGM2 gene encoding transglutaminase 2 was commonly deregulated after treatment with all four CSA compounds. All compounds revealed strong effects on cell cycle progression and DNA damage response. Promoter motif analysis of the deregulated genes further supported the microarray results emphasizing the relevance of transcription factors regulating cell cycle and proliferation, MYC being among the most pronounced ones. Interestingly, cellular movement was among the top five affected cellular functions after treatment with the four derivatives.

overall_design: Gene expression profiling study with Whole Human Genome RNA chips (8×60K Agilent) was performed in MCF-7 breast cancer cells upon treatment with CSA and its synthetic derivatives (CSA6, CSA9, CSA19). Twelve chips were used; control (x2), CSA (x2), control (x2), CSA6 (x2), CSA9 (x2), CSA19 (x2). MCF-7 cells were treated with the compounds (IC50 concentrations) for 72 hours or left untreated (DMSO control). Two independent experiments were performed for each treatment.

first: Yujie

last: Fu

first: Benjamin

last: Wiench

first: Yuangang

last: Zu

first: Thomas

last: Efferth


title: Genetic diversity of propagating/stem cells in glioblastoma multiforme (GBM)

status: Public on Jan 22 2015

city: Belmont

first: Frederik

last: van Delft

address: 15 Cotswold Road

department: Haemato-oncology

institute: ICR

summary: Glioblastoma multiforme (GBM) is a lethal malignancy whose clinical intransigence has been linked to extensive intra-clonal genetic and phenotypic diversity and therapeutic resistance of cancer stem cells (CSCs). This interpretation embodies an implicit assumption that CSCs are themselves genetically diverse. To test this, we screened neurosphere cultures by SNP arrays to identify copy number alterations (CNA) (minimum of three) that could be visualised in single cells by multi-colour FISH. Interrogation of neurosphere-derived cells (from four patients) and cells derived from secondary transplants of these same cells in Nod/Scid mice allowed us to infer clonal phylogenic architecture and the likely derivation of functional CSCs. This proof-of-principle experiment revealed that more than one sub-clone (but not all) in each GBM had functionally defined, genetically distinct stem cells.

overall_design:
Diagnostic and germ line DNA from 12 patients with GBM was investigated for LOH/CNA using Affymetrix SNP 6.0 arrays. Neurosphere cultures were established from these primary tumors, and intracranially injected into Nod/Scid mice.
Clonal architecture of primary neurospheres and secondary transplants was investigated by multicolour FISH, guided by the LOH/CNA analysis of the primary GBM tumors.

first: Sara

last: Piccirillo

first: Nicola

last: Potter

first: Susan

last: Colman

first: Colin

last: Watts

first: Lyndal

last: Kearney

first: Mel

last: Greaves


title: Functional impact of collagens on the activity directed by the promoter of the a5 integrin subunit gene in corneal epithelial cells

status: Public on Jan 30 2015

first: Karine

last: Zaniolo

summary: Important remodeling of the extracellular matrix is a hallmark of corneal wound healing. Besides the massive secretion of fibronectin (FN) that characterizes the early step of that process, alterations in the secretion of collagens also occurs as part of this wound healingresponse. In this study, we examined whether expression of the gene encoding the α5 subunit from the FN binding integrin α5β1 changes as corneal epithelial cells (CECs) are cultured in the presence of collagens. Responsiveness of the α5 gene toward collagen was determined by transfection of recombinant plasmids bearing the CAT reporter gene under the control of various segments from the human α5 promoter into primary cultured rabbit (RCECs) and human (HCECs) CECs cultured on BSA or on collagens. Electrophoretic mobility shift assays (EMSAs) and Western blot analyses were used to monitor both the DNA binding and expression of the transcription factors required to ensure basal transcription of the α5 gene. The influence collagens on the patterns of genes expressed by HCECs was also studied be gene profiling on microarrays. All collagen types repressed the transcriptional activity directed by the full-length α5 promoter/CAT construct in confluent CECs. A moderate increase in α5 promoter activity was observed in subconfluent RCECs grown on CIV but not on CI. These collagen-dependent regulatory influences also correlated with alterations in either the expression or the DNA binding of the transcription factors Sp1/Sp3, NFI and AP-1 that ensure basal transcription of the α5 gene. Gene profiling on microarray revealed that CI more profoundly alter the pattern of genes expressed by HCECs than what is observed with CIV. Collagens considerably suppressed expression of the α5 gene in CECs at confluence suggesting that the sustained staining for CI and CIV after corneal injury may play a role in controlling adhesion to the temporary FN matrix and further differentiation of CECs into suprabasal epithelial cells through a mechanism involving the α5β1 integrin.

overall_design: Primary cultures of human corneal epithelial cells cultivated on BSA (number of replicates: 2), Collagen type I (number of replicates: 2) and Collagen type IV (number of replicates: 2) matrix.

first: Jennifer

last: Lake

first: Marie-Êve

last: Gingras

first: Christian

last: Salesse

first: Sylvain

last: Guérin


title: Grape berry expression profiling: developmental series and treatment effects

status: Public on Feb 13 2017

city: Glen Osmond

first: Mark

middle: Raymond

last: Thomas

state: SA

address: PO Box 350

department: Plant Industry

country: Australia

institute: CSIRO


title: Comparative transcriptomic profiling of breast-milk isolated total somatic cells from women with mastitis following the consumption of a probiotic containing a Lactobacillus salivarius PS2 strain

status: Public on Jan 21 2015

city: Espinardo

first: María-Teresa

last: García-Conesa

state: Murcia

address: Campus de Espinardo

department: Quality, Safety and Bioactivity of Plant Foods

institute: CEBAS-CSIC

summary: We used Affymetrix microarrays to investigate gene expression changes in somatic cells from breast-milk extracted from women suffering from mastitis and taking a daily dose of three capsules with ~50 mg of a freeze-dried probiotic (~109 CFU of L. salivarius PS2 strain) for 21 days. Healthy women were subjected to the same treatment for comparison.

overall_design:
The aim of this work was to determine whether the daily intake of a probiotic strain for a total of 21 days exerted any modulatory effects, at the level of gene expression, in somatic cells from breast-milk in women with mastitis. Women were divided into 2 groups: mastitis and healthy. Total RNA was extracted from breast-milk isolated cells obtained from 10 participants (7 women from the mastitis group and 3 women from the healthy group) at day 0 (initial) and after 21 days (final) to compare differential gene expression between the groups.
Differential gene expression after 21 days of the study for each group: mastitis and healthy

first: Javier

last: de Andrés

first: Ester

last: Jiménez

first: Juan-Miguel

last: Rodriguez


title: Muscle from patients with mitochondrial myopathies and congenital muscular dystrophies versus normal human muscle

status: Public on Jan 20 2015

city: Barcelona

first: Susana

last: Kalko

state: BARCELONA

address: c/Rosello 153

department: Bioinformatics Platform

institute: IDIBAPS

summary: Global gene expression analysis was performed comparing human skeletal muscle samples from patients with various forms of muscular dystrophy and mitochondrial myopathies in order to  identify specific gene expression changes associated with collagen VI deficiency (leading to Ullrich´s Congenital Muscular Dystrophy) and depletion of mitochondrial DNA relative to other mitochondrial myopathies

overall_design: We analysed the gene expression profile of skeletal muscle from children suffering from mitochondrial myopathies and various forms of muscular dystrophy relative to skeletal muscle from healthy children  using commercially available arrays that represents the complete human genome (Agilent Human SurePrintGE, 8x60K )

first: Cecilia

last: Jimenez-Mallebrera

first: Sonia

last: Paco


title: Mapping of hepatic expression quantitative trait loci (eQTLs) in a Han Chinese population [SNP analysis]

status: Public on Jan 02 2015

city: Shanghai

first: Zhiqiang

last: Li

address: Huashan Road No.1954

department: Bio-X Institutes

country: China

institute: Shanghai Jiao Tong University

summary: Elucidating the genetic basis underlying the variation in hepatic gene expression is of importance to understand disease etiology and drug metabolism variances. To date, no genome-wide eQTL analysis has been conducted in the Han Chinese, the largest ethnic group in the world. We performed a genome-wide eQTL mapping in a set of Han Chinese liver tissue (n=64).

overall_design: Normal (non-diseased) liver tissues were previously collected from 64 Chinese donors who provided informed consent. All samples were stored frozen at -80℃ from collection until processing for RNA and DNA extraction. DNA /Total RNA of the human liver tissue samples were extracted by using the RNA/DNA Mini Kit (Qiagen, Hilden, Germany).each RNA sample were labeled and hybridized to the One-Color Agilent 60-mer Whole Human Genome Microarray (G4112F, GPL4133) at the Agilent Microarray Facility of Shanghai genomePilot Technology, Inc. The genome-wide scan was performed using the Affymetrix Genome-Wide Human SNP Array 6.0. We tested all expression traits for their associations with each of the QC passed SNPs using PLINK's assoc function for quantitative traits, which correlates allele dosage with changes in the trait.

first: Xiaoliang

last: Wang

first: Huamei

last: Tang

first: Mujian

last: Teng

first: Jianguo

first: Junwei

last: Fan

first: Lin

last: Zhong

first: Xing

last: Sun

first: Junming

last: Xu

first: Guoqing

last: Chen

first: Dawei

first: Zhaowen

first: Tonghai

last: Xing

first: Jinyan

last: Zhang

first: Li

last: Huang

first: Shuyun

first: Xiao

last: Peng

first: Shengying

last: Qin

first: Yongyong

last: Shi

first: Zhihai


title: Peripheral regions and central regions from HT-29 tumors

status: Public on Jan 10 2015

city: Chiba

first: Yukie

last: Yoshii

address: Anagawa 4-9-1, Inage

institute: National Institute of Radiological Sciences

summary: Gene expression of peripheral regions and central regions from HT-29 tumors

overall_design: Sample tissues were immediately frozen by liquid nitrogen after isolation. Total RNAs were extracted from samples with a PureLink RNA Mini Kit (Life Technologies). The integrity of total RNAs was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies) was used to prepare Cy3-labelled target cRNA according to the manufacturer's instructions. Labeled cRNAs were hybridized with a SurePrint G3 Human GE 8×60K Microarrays (Agilent Technologies). Three separate hybridizations were performed for each sample. Array images were captured using a DNA Microarray Scanner (Agilent Technologies), and data were analyzed using Feature Extraction Software (Agilent Technologies) to obtain background-corrected signal intensities. Data were further analyzed with GeneSpring GX Software (Version 11.0, Agilent Technologies). After data filtering, mRNAs differentially expressed in target cells versus controls were assessed by Fisher’s exact test, followed by multiple corrections using the Benjamini and Hochberg false discovery rate (FDR) method. Gene sets with a FDR q-value < 0.05 were considered to be significant.


title: Type I interferon regulates the expression of long non-coding RNAs [expression array]

status: Public on Jan 09 2015

city: Pamplona

first: Victor

last: Segura

state: Navarra

address: Avda. Pío XII, 55

department: Unit of Proteomics, Genomics and Bioinformatics

institute: FIMA

summary: Interferons (IFNs) are key players in the antiviral response. IFN sensing by the cell activates transcription of IFN-stimulated genes (ISGs) able to induce an antiviral state by affecting viral replication and release. IFN also induces the expression of ISGs that function as negative regulators to limit the strength and duration of IFN response. The ISGs identified so far belong to coding genes. However, only a small proportion of the transcriptome corresponds to coding transcripts and it has been estimated that there could be as many coding as long non-coding RNAs (lncRNAs). To address whether IFN can also regulate the expression of lncRNAs, we analyzed the transcriptome of HuH7 cells treated or not with IFNα2 by expression arrays. Analysis of the arrays showed increased levels of several well-characterized coding genes that respond to IFN both at early or late times. Furthermore, we identified several IFN-stimulated or -downregulated lncRNAs (ISRs and IDRs). Further validation showed that ISR2, 8, and 12 expression mimics that of their neighboring genes GBP1, IRF1, and IL6, respectively, all related to the IFN response. These genes are induced in response to different doses of IFNα2 in different cell lines at early (ISR2 or 8) or later (ISR12) time points. IFNβ also induced the expression of these lncRNAs. ISR2 and 8 were also induced by an influenza virus unable to block the IFN response but not by other wild-type lytic viruses tested. Surprisingly, both ISR2 and 8 were significantly upregulated in cultured cells and livers from patients infected with HCV. Increased levels of ISR2 were also detected in patients chronically infected with HIV. This is relevant as genome-wide guilt-by-association studies predict that ISR2, 8, and 12 may function in viral processes, in the IFN pathway and the antiviral response. Therefore, we propose that these lncRNAs could be induced by IFN to function as positive or negative regulators of the antiviral response.

overall_design: HuH7 cells were treated with 10000 units/ml of IFN a2 and RNA was isolated 3 days post-treatment

first: Elena

last: Carnero

first: Marina

last: Barriocanal

first: Puri

last: Fortes


title: RNA-Seq Identifies Novel Myocardial Gene Expression Signatures of Heart Failure [microarray]

status: Public on Jan 01 2015

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary: We have utilized the RNA-Seq technology to identify genes with distinct expression patterns between failing and non-failing hearts. In an era of next-generation sequencing studies, our study demonstrates how knowledge gained from a small set of samples with accurately measured gene expressions using RNA-Seq can be leveraged as a complementary strategy to discern the genetics of complex disorders.

overall_design: Identify the signature genes based on RNA-seq come from six Heart Failure and healthy individuals. Validation is based on Affymetrix microarray of a total of 313 individuals with/without Heart Failure.

first: Yichuan

last: Liu

first: Jeffrey

last: Brandimarto

first: Kenneth

last: Margulies

first: Thomas

last: Cappola

first: Mingyao

last: Li


title: Affymetrix SNP array data for adult acute lymphoblastic leukemia samples

city: Tianjin

first: Tian

last: Yuan

address: No.288 Nanjing Road

department: Institute of Hematology and Blood Disease Hospital

institute: Peking Union Medical College

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

summary: Copy number variation (CNV) and loss of heterozygosity (LOH) were investigated in adult Chinese patients with acute lymphoblastic leukemia (ALL), and these patients were screened for adult ALL prognostic genes.The most frequent CNVs are gain at chr13q, loss at chr6 and recurrent LOH at chr17p and 1p33. In Ph- B-ALL patients, the most frequent CNVs are gain at chr7, loss at chr9p and recurrent LOH at chr15q. In T-ALL, the most frequent CNVs are gain at chr20 and 7q, loss at chr2p and recurrent LOH also at chr15q.

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved bone marrow samples.
Copy number analysis of Affymetrix SNP 6.0 arrays was performed for 33 newly diagnosis adult ALL samples, 11 paried complete remission(CR) ALL samples and 1 relapse ALL. There are also 5 healthy donor samples which were used as references for copy number inference.

first: Yuan

last: Tian

first: Mi

last: Yingchang


title: Genes induced during sebocyte differentiation

status: Public on Dec 31 2014

first: Maik

last: Dahlhoff

state: Bavaria

address: Feodor-Lynen-Str. 25

department: Gene Center

institute: LMU Munich

summary: This study was designed to evaluate the transcriptional changes during linoleic acid-induced differentiation and lipid synthesis in a sebocyte cell line (SZ95, Zouboulis et al., J. Invest. Dermatology, 1999).

overall_design: The treatment consisted of adding linoleic acid (10-4 M) or vehicle (ethanol) to the cells for 6, 18, or 36 hours. Two independent experiments were performed at each time point and for each treatment.

first: Marlon

last: Schneider


title: Transcriptomic profiling of granulosa and cumulus cells for prediction of successful embryo implantation in human in-vitro fertilization procedures

city: Ljubljana

first: Ales

last: Maver

address: Slajmerjeva 3

country: Slovenia

institute: Clinical institute of medical genetics Ljubljana Slovenia

summary:
Currently, in vitro fertilization (IVF) is one of the most common approaches towards treating infertility. However, the success of this approach is still relatively low an the outcome of the IVF procedure is challenging to predict. At present, there is no highly successful marker that could reliably predict the pregnancy outcome in the process of assisted reproduction (AR). Currently, multiple embryo transfers are performed to warrant a successful pregnancy outcome, but this commonly results in multiple pregnancies, narrowing the feasibility of this method for a subset of couples affected by infertility. Recently IVF cycles with single-embryo transfers have become an option of interest in AR approaches. Such cycles, however, are significantly less successful and for this reason, there is an incentive to improve the pregnancy chance per IVF cycle by incorporating more criteria for selection of the embryo with the highest implantation potential.  Gene expression in follicular cells, including granulosa cells (GC) and cumulus cells (CC) has previously been considered as a tool to predict the quality of the oocytes in several studies in addition to assessing the morphologic criteria of the embryos. Gene expression estimation in these cells, especially of the CC population, carries along several benefits as their harvesting is non-invasive, they are in direct contact with the oocyte and are usually discarded during the process of intracytoplasmatic sperm injection procedure (ICSI), making them any easily accessible surrogate tissue for gene expression analyses.  Considering that several studies reporting various rates of success in prediction of AR cycle outcome with expression as a biomarker have been published, we attempted to perform the largest study of global gene expression alterations in finding novel biomarkers to outcome of in- vitro fertilization, which would encompass discovery of new biomarker genes and subsequent confirmational study of the selected biomarker set on an independent validation group.
In this experiments 4 samples were hybridized twice, to allow for inspection of technical validity of microarray experiments.

overall_design: Whole genome expression profiling was performed on 64 samples - we have included three different outcomes of IVF, including cases where fertilization was unsuccessful (Unfertilized), those where fertilization was attained but without successful pregnancy (NonPregnant) and those resulting in successful pregnancy outcome (Pregnant). Additionally, we have investigated the extent of expression alterations in two different populations of follicular cells, in order to select the tissue of choice that would have the highest potential for predicting outcome of the IVF process.

first: Tanja

last: Papler

first: Eda

last: Vrtacnik-Bokal

first: Luca

last: Lovrecic

first: Natasa

middle: A

last: Kopitar

first: Borut

last: Peterlin


title: Transcriptome profile of human pancreatic beta cell line (EndoC-βH2 ) following knockdown of RFX6.

status: Public on Dec 22 2014

city: Paris

first: Raphael

last: Scharfmann

state: Paris

address: 123,boulevard de Port-Royal

institute: INSERM-Institut Cochin , Bâtiment Cassini

summary: RFX6 is a key transcription factor for the development of mouse pancreas, however the functional roles of RFX6 in human beta cells are poorly explored. Thus transcriptome analysis was perfomed to determine the functional targets of RFX6 in human beta cells using the recently developed human beta cell-line EndoC-βH2.

overall_design: Transcriptome profile of human beta cell line (EndoC-βH2 cells) following siRNA induced knockdown of RFX6 is compared with siControl (siNT)  treated EndoC-βH2 cells.

first: Vikash

last: Chandra

first: Julie

last: Piccand

first: Gerard

last: Gradwohl


title: Affymetrix SNP copy number data for embryonic stem cell samples

status: Public on Dec 17 2014

city: BALTIMORE

first: William

last: Freed

state: MD

address: 333 CASSELL DRIVE

institute: NIDA NIH

summary: Human pluripotent stem cell (hPSC) lines exhibit repeated patterns of genetic variation, which can alter in vitro properties as well as suitability for clinical use. We examined associations between copy number variations (CNVs) on chromosome 17 and hPSC mesodiencephalic dopaminergic (mDA) differentiation.

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved stem cell samples.
Copy number analysis of Affymetrix Genome-Wide Human SNP Array 6.0 was performed for 17 stem cell samples.


title: Identification of SNPs using genomic DNA and allele specific expression using nascent RNA on snp6 array

first: Ronan

last: Chaligné

address: 26, Rue d'Ulm

institute: Institut Curie

summary: Disappearance of the Barr body has long been considered a hallmark of cancer, although whether this corresponds to epigenetic instability and transcriptional reactivation, or to genetic loss, has remained unclear. Here we show that in breast cancer cell lines as well as primary breast tumors, the inactive X chromosome frequently displays a highly abnormal 3D nuclear organization, with global perturbations in its characteristic heterochromatic state, including apparent gain of euchromatic marks and lessening of repressive marks such as H3K27me3 and promoter DNA methylation. Genome-wide profiling of chromatin and transcription reveal modified epigenomic landscapes in cancer cells accompanied by a significant degree of X-linked gene reactivation, affecting genes previously implicated in cancer, including the histone deacetylase, HDAC8 and transducin (Beta)-Like 1X-Linked, TBL1X. We provide proof of principle that epigenetic deregulation can indeed perturb the dosage of some X-linked factors and demonstrate that many of these genes are reactivated in primary breast tumors. Our study establishes that the inactive X is subject to epigenetic erosion in a cancer context and sets the stage for the use of chromatin marks and X- chromosome genes as potential biomarkers to assess epigenetic changes in cancer.

overall_design: Examination of allele specific expression of genes using nascent RNA on snp6 array by comparing it with snp6 results from genomic DNA.

last: Chaligne

first: Tatiana

last: Popova

first: Marco-Antonio

last: Mendoza-Parra

first: Mohamed-Ashick

last: Saleem

first: David

last: Gentien

first: Kristen

last: Ban

first: Tristan

last: Piolot

first: Olivier

last: Leroy

first: Odette

last: Mariani

first: Hinrich

last: Gronemeyer

first: Anne

last: Vincent-Salomon

first: Marc-Henri

last: Stern

first: Edith

last: Heard


title: Mapping of Hepatic Expression Quantitative Trait Loci (eQTLs) in a Han Chinese Population

first: Zhiqiang

last: Li

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

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

overall_design: Refer to individual Series

first: Xiaoliang

last: Wang

first: Huamei

last: Tang

first: Mujian

last: Teng

first: Jianguo

first: Junwei

last: Fan

first: Lin

last: Zhong

first: Xing

last: Sun

first: Junming

last: Xu

first: Guoqing

last: Chen

first: Dawei

first: Zhaowen

first: Tonghai

last: Xing

first: Jinyan

last: Zhang

first: Li

last: Huang

first: Shuyun

first: Xiao

last: Peng

first: Shengying

last: Qin

first: Yongyong

last: Shi

first: Zhihai


title: The reversed evolution from multicellularity to unicellularity during carcinogenesis

status: Public on Nov 27 2014

city: Guangzhou

first: Han

state: Guangdong

address: Xinggang Rd. Haizhu District

institute: Sun Yatsen University

summary: Using xenograft-based experimental evolution, we characterize the full life history from initiation to metastasis of a tumor at the genomic and transcriptomic levels.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cell lines or xenograft tumor samples.


title: Diverse phospho-signaling networks mediate RTK dependent growth and survival in childhood ALL [copy number]

status: Public on Nov 03 2014

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

institute: University Medical Center Hamburg-Eppendorf

summary: Deregulated RTK activity has been implicated as a causal leukemogenic factor in the context of molecular aberrations that perturb differentiation in the hematopoietic lineage such as in childhood ALL. A deeper understanding of RTK signaling processes on a system-wide scale will be key in defining critical components of signaling networks. To link RTK activity with in vivo output in primary ALL we took a functional approach, which combined SH2 domain binding, mass spectrometry, and transcriptome analyses. Structure and composition of evolving networks were highly diverse with few generic features determined by receptor and cell type. A combinatorial assembly of varying context-dependent and few generic signaling components at multiple levels likely generates output specificity. PAK2 was identified as a phosphoregulated FLT3 target, whose allosteric inhibition resulted in apoptosis of ALL cells. Our studies provide evidence that a functional approach to leukemia signaling may yield valuable information for a network-directed intervention.

overall_design: Primary ALL samples were investigated on Affymetrix SNP 6.0 arrays for copy-number changes related to receptor tyrosine kinases (RTKs). Buffy-Coat samples of healthy persons were used as reference.

first: Kevin

last: Dierck

first: Martin

last: Horstmann


title: The HDAC inhibitor panobinostat acts as a sensitizer for erlotinib activity in EGFR mutated and wildtype NSCLC cells

status: Public on Dec 03 2014

city: Freiburg

first: Gabriele

last: Greve

address: Hugstetter Str 55

department: Department of Internal Medicine 1

institute: University of Freiburg Medical Center

summary:
Background: The receptor tyrosine kinase (RTK) EGFR is overexpressed and mutated in NSCLC. These mutations can be targeted by RTK inhibitors (TKIs) such as erlotinib. Chromatin-modifying agents may offer a novel therapeutic approach by sensitizing tumor cells to TKIs.
Methods: The NSCLC cell lines HCC827 (EGFR mutant, adenocarcinoma), A549 (EGFR wt, adenocarcinoma) andNCI-H460 (EGFR wt, large cell carcinoma) were analyzed by SNP6.0 array. Changes in proliferation after panobinostat (LBH-589, PS) and erlotinib treatment were quantified by WST-1 assay and apoptosis by Annexin V/7-AAD flow cytometry. Abundance of target proteins and histone marks (acH3, H3K4me1/2/3) was determined by immunoblotting.
Results: As expected, the EGFR wt cell lines A549 and NCI-H460 were quite insensitive to the growth-inhibitory effect of single-agent erlotinib (IC50 70-100 μM), compared to HCC827 (IC50 < 0.02 μM). PS treatment diminished growth to <50 % in both EGFR wt cells, and <30 % in HCC827. The combination of both drugs reduced proliferation by >95 % in HCC827, ≥70 % in A549, but not further in NCI-H460. PS alone induced differentiation and expression of p21WAF1/CIP1 and p53 and decreased CHK1 in all three cell lines, with almost no further effect when combined with erlotinib. In contrast, combination treatment additively decreased pEGFR, pERK, pAKT in A549, and synergistically induced acH3 in both adenocarcinoma lines. Surprisingly, we saw an induction of H3K4 methylation marks after erlotinib treatment in HCC827 (and to a lesser extent in A549) that was even further enhanced by combination with PS.
Conclusion: We were able to show that PS synergistically sensitized lung adenocarcinoma cells to the antiproliferative effects of erlotinib. Since single-agent erlotinib has only modest clinical effects in lung adenocarcinoma EGFR wt patients, its combination with an HDACi might offer a promising therapy approach.

overall_design: Copy-number analysis of three NSCLC cell lines HCC827, A549 and NCI-H460 (in unicates) was performed according to protocol by Affymetrix Genome-Wide Human SNP-Array 6.0.

first: Insa

last: Schiffmann

first: Dietmar

last: Pfeifer

first: Milena

last: Pantic

first: Julia

last: Schüler

first: Michael

last: Lübbert


title: Gene expression profiling in blood of patients with chronic respiratory failure

status: Public on Dec 09 2014

city: Nantes

first: Richard

last: Danger

address: 30 Boulevard Jean Monnet

institute: CHU Nantes - INSERM- Nantes Universite

summary: Genes dysregulated in cystic fibrosis (CF) and primary pulmonary arterial hypertension (PAH) at a late stage of pulmonary failure are still largely unknown. Blood samples taken in the frame of the French cohort of lung transplantation COLT offers the opportunity to identify in blood specific gene signatures of each disease and a common gene signature for both pathologies. A microarray analysis was performed with homogeneous groups of CF patients (n=23), PAH (n=13) patients and healthy volunteers (n=28). Blood was collected in a PAXgene® tube to maintain RNA integrity. Total extracted RNA were processed on 60K whole-genome microarrays (Agilent Technologies). Microarrays were analyzed by bioinformatics (GOminer and Ingenuity Pathway Analysis). Three major biological signatures were discovered including (1) genes specifically over-expressed in pPAH and mainly involved in inflammation, vascular remodeling and cell proliferation, (2) genes specifically over-expressed in CF involved in innate immune response and oxidative stress response, and (3) genes under-expressed in both diseases, including genes involved in transcriptional machinery, apoptosis and cell proliferation.

overall_design: RNAs were isolated from blood collected with PAXGene tubes from 13 patients diagnosed with primitive pulmonary arterial hypertension (PAH), 23 patients with cystic fibrosis (CF) and 28 healthy volunteers (HVs).

first: Julie

last: Chesné

first: Sophie

last: Brouard

first: Antoine

last: Magnan


title: DNA copy number changes in malignant mesothelioma

status: Public on Nov 22 2014

city: Nishinomiya

first: Yoshie

last: Yoshikawa

state: Hyogo

address: 1-1 Mukogawa-cho

department: Genetics

institute: Hyogo College of Medicine

summary: Malignant mesothelioma (MM) is an asbestos-related malignancy. Discrimination between MM and reactive mesothelial hyperplasia (RM) is often difficult. MM cells have a broad histological spectrum, and consist mainly of epithelioid, sarcomatoid, and biphasic cell types. The prognosis of MM is generally poor, but better prognosis has been reported with the epithelioid type of MM than the non-epithelioid type. We applied a genome-wide analysis to the identification of new markers that may aid in differentiating the epithelioid type of MM from other histological types and from RM cells.

overall_design: Array-based comparative genomic hybridization analysis was performed on malignant mesothelioma (MM) primary cell cultures, reactive mesothelial hyperplasia (RM) primary cell cultures; early passage of in vitro primary cell cultures to minimize acquisition of additional genomic changes. If available, matched peripheral blood was applied to analysis.

first: Tomoko

last: Hashimoto-Tamaoki


title: Affymetrix SNP array data for lung cancer samples

status: Public on Dec 10 2014

city: Mexico City

first: Alfredo

last: Hidalgo-Miranda

address: Periferico Sur 4124, Torre Zafiro II, piso 6

country: Mexico

institute: National Institute of Genomic Medicine

summary: Lung cancer is the leading cause of death from malignant diseases worldwide, with the non-small cell (NSCLC) subtype accounting for the majority of cases. NSCLC is characterized by frequent genomic imbalances and copy number variations (CNVs), but the epigenetic aberrations that are associated with clinical prognosis and therapeutic failure remain not completely identify. In the present study, a total of 55 lung cancer patients were included and we conducted genomic and genetic expression analyses, immunohistochemical protein detection, DNA methylation and chromatin immunoprecipitation assays to obtain genetic and epigenetic profiles associated to prognosis and chemoresponse of NSCLC patients. Finally, siRNA transfection-mediated genetic silencing and cisplatinum cellular cytotoxicity assays in NSCLC cell lines A-427 and INER-37 were assesed to described chemoresistance mechanisms involved. Our results identified high frequencies of CNVs (60% of cases) in the 7p22.3-p21.1 and 7p15.3-p15.2 cytogenetic regions. However, overexpression of genes, such as MEOX2, HDAC9, TWIST1 and AhR, at 7p21.2-p21.1 locus occurred despite the absence of CNVs and little changes in DNA methylation. In contrast, the promoter sequences of MEOX2 and TWIST1 displayed significantly lower/decrease in the repressive histone mark H3K27me3 and increased in the active histone mark H3K4me3 levels. Finally these results correlate with poor survival in NSCLC patients and cellular chemoresistance to oncologic drugs in NSCLC cell lines in a MEOX2 and TWIST1 overexpression dependent-manner. In conclusion, we report for the first time that MEOX2 participates in chemoresistance irrespective of high CNV, but it is significantly dependent upon H3K27me3 enrichment probably associated with aggressiveness and chemotherapy failure in NSCLC patients, however additional clinical studies must be performed to confirm our findings as new probable clinical markers in NSCLC patients.

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from fresh frozen, and paraffin embedded lung tumor samples
Copy number analysis of Affymetrix 500K SNP arrays was performed for 33 lung tumor samples, including lung precursor metaplasia, lung tumors and cell lines. Six samples were also hybridized on the Affymetrix SNP 6.0 array

first: F

last: Avila-Moreno

first: A

first: J

last: Zuniga-Ramos


title: High-resolution genome-wide copy number analysis of low grade serous ovarian tumours

status: Public on Mar 01 2015

city: Melbourne

first: Sally

last: Hunter

state: VIC

address: 7 St Andrew's Pl

department: Research

institute: Peter MacCallum Cancer Centre

summary:
Integration of genomic copy number analysis (Affymetrix SNP6.0 arrays) and oncogenic RAS/RAF mutation status with clinical features and tumour progression.
This study found that loss of the 9p and the CDKN2A locus with the most significantly enriched copy number aberration distinguishing serous border tumors from low grade serous carcinomas, suggesting this is a key step to tumor progression.

overall_design: Epithelial tissue from 57 serous borderline tumors (SBTs), 19 low grade serous carcinomas (LGSC)(data for 4 of the carcinomas have previously been submitted to GEO - Series GSE19539) and 355 high grade serous carinomas (HGSC)(TCGA, 2011; GSE19539; and 8 new) were analysed for copy number aberrations using Affymetrix SNP6.0 arrays and normalised SNP6.0 data. Stromal tissue from 38 SBT and 1 HGSC were analysed for copy number aberrations using Affymetrix SNP6.0 arrays. Matching lymphocyte DNA was availabe for 54 SBT, 3 LGSC and 1 HGSC. Sanger sequencing of KRAS, BRAF, NRAS, HRAS, ERBB2 and TP53 mutational hotspots was performed on the epithelial and stromal DNA. This information was then correlated with clinical features of the tumors.

first: Ian

middle: G

last: Campbell

first: Kylie

last: Gorringe


title: Identification of a novel E-box binding PI polyamide inhibiting MYC-driven cell-proliferation

status: Public on Dec 27 2014

first: Hiroki

last: Nagase

address: 666-2 Nitona, Chuo-ku

institute: Chiba Cancer Center Research Institute

summary: Gene expression profiling of K562 and P493 cells treated with Myc-5 and Mismatch PI polyamides as well as with DMSO as a control

overall_design: Gene expression in human K562 and P493 cells was measured at 72 hours after treatment with DMSO, MYC-5 and its mismatch PI polyamides.  Four or two replicates  for each sample were hybridized on 8x60K Agilent GE array.


title: SNP6 profiling of metaplastic breast carcinoma

status: Public on Oct 31 2014

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

address: Via Rita Montalcini 4

department: Biomedical Sciences

institute: Humanitas University

overall_design: Metaplastic breast carcinoma (MBC) is a rare and aggressive histologic type of breast cancer, preferentially displaying a triple-negative phenotype (i.e. lacking estrogen receptor, progesterone receptor and HER2 expression). We sought to define the transcriptomic heterogeneity of MBCs on the basis of current gene expression microarray-based classifiers and to determine whether MBCs display gene copy number profiles consistent with those of BRCA1-associated breast cancers.

first: Britta

last: Weigelt

first: Anne

last: Vincent-Salomon

first: Jorge

middle: S

last: Reis-Filho


title: Metaplastic breast carcinomas display genomic and transcriptomic heterogeneity

overall_design:
Refer to individual Series
The SNP and expression datasets represent the same samples (i.e., the 26 SNP6 samples are a subset of the 28 expression samples)


title: Twist1 gain-of-function studied in 2 normal gastric fibroblast lines

status: Public on Oct 28 2014

city: Seoul

first: Chang Ohk

last: Sung

address: Song-Pa gu,Pung-nap dong

department: Pathology

country: South Korea

institute: Asan Medical Center

summary: Primary human gastric normal fibroblast cultures (NL14 and NL32, repectivley) were establised from 2 gastrectomy specimens. Enforced expression (gain-of-function effect) of Twist1 in 2 gastric normal fibroblasts (NL14 and NL32) showed candidate target genes and CAF markers upregulated by Twist1.

overall_design: Experiment design: 2 normal gastric fibroblasts (NL14 and NL32) were establised and studied for Twist1 gain-of-function.

first: Keun-Woo

last: Lee

first: So-Young

last: Yeo

first: Chang

middle: O

first: Seok-Hyung

last: Kim


title: Twist1 is a key regulator for cancer-associated fibroblasts


title: Genome-wide copy number and allele-specific copy number analysis of choroid plexus tumors (I)

status: Public on Nov 01 2014

city: Toronto

first: Diana

middle: M

last: Merino

state: Ontario

address: 686 Bay St.

department: Genetics and Genome Biology

institute: The Hospital for Sick Children

summary: Copy number analysis was performed using genotyping microarrays for 55 choroid plexus tumors. Genomic aberrations were investigated by tumor histological classification and the pattern observed in each subgroup was further refined. Allele specific copy number analysis also allowed us to identify regions of acquired uniparental disomy with neutral copy number values.

overall_design: Fifty-five choroid plexus tumors (23 choroid plexus carcinomas, 23 choroid plexus papillomas, 9 atypical choroid plexus papillomas) were used in this study. These samples were inspected for hybridization quality. No replicates were included.

first: Adam

last: Shlien

first: Anita

last: Villani

first: Margaret

last: Pienkowska

first: Stephen

last: Mack

first: Vijay

last: Ramaswamy

first: David

middle: J

last: Shih

first: Ruth

last: Tatevossian

first: Ana

last: Novokmet

first: Sanaa

last: Choufani

first: Rina

last: Dvir

first: Myran

last: Ben-Arush

first: Brent

middle: T

last: Harris

first: Eugene

middle: I

last: Hwang

first: Rishi

last: Lulla

first: Stefan

last: Pfister

first: Maria

last: Achatz

first: Nada

last: Jabado

first: Jonathan

last: Finlay

first: Rosanna

last: Weksberg

first: Cynthia

last: Hawkins

first: Michael

middle: D

last: Taylor

first: Uri

last: Tabori

middle: W

last: Ellison

first: Richard

last: Gilbertson

last: Malkin


title: Rapid neurogenesis through transcriptional activation in human stem cell (Agilent)

status: Public on Nov 07 2014

city: La Jolla

first: Nathan

last: Lewis

state: CA

department: Pediatrics

institute: University of California, San Diego

summary: Advances in cellular reprogramming and stem cell differentiation now enable ex vivo studies of human neuronal differentiation. However, it remains challenging to elucidate the underlying regulatory programs because differentiation protocols are laborious and often result in low neuron yields. Here, we overexpressed two murine Neurogenin transcription factors in human induced pluripotent stem cells, and obtained neurons with bipolar morphology in four days at greater than 90% purity. The high purity enabled mRNA and microRNA expression profiling during neurogenesis, thus revealing the genetic programs involved in the transition from stem cell to neuron. These profiles were then analyzed to identify the regulatory networks underlying the differentiation of the neurons. The arrays presented here assessed the differences between single neurogenin and dual neurogenin expression.

overall_design: Gene expression profiling (microarray) of iPS cells (PGP1) at X days post- doxycycline induction of juman NEUROG1 and/or NEUROG2, or murine Neurog1 and Neurog2.

first: Volker

last: Buskamp

first: Guye

last: Patrick


title: Twist1 knockdown in two gastric cancer-associated fibroblast lines

first: Chang Ohk

last: Sung

summary: Primary human gastric cancer-associated fibroblast (CAF) cultures (CAF14 and CAF32) were establised from 2 gastrectomy specimens. Silencing the expression (loss-of-function effect) of Twist1 in CAFs showed candidate target genes regulated by Twist1 and abrogated their tumor-promoting properties.

overall_design: Experiment design: two gastric CAFs (CAF14 adn CAF32, respectively) were establised from two gastric cancer patients and Twist1 knockdown studies were performed using shRNA.

first: Keun-Woo

last: Lee

first: So-Young

last: Yeo

first: Chang

first: Seok-Hyung

last: Kim


title: Application of CGH-array and SNP-array for the detection of genomic rearrangements responsible for sindromic mental retardation of unknown cause

status: Public on Oct 17 2014

city: Valencia

first: Francisco

last: Martinez

state: Valencia

address: Avenida Campanar 21

department: Unidad de Genetica

country: Spain

institute: Hospital Universitari i Politecnic La Fe

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


title: Affymetrix SNP array data for 5q- myelodysplastic syndromes

status: Public on Oct 07 2014

city: Badalona

first: Vera

last: Adema

address: Carretera de Can Ruti, Cami de les Escoles s/n

department: MDS Group

institute: Josep Carreras Leukaemia Research Institute

summary: Myelodysplastic syndromes (MDS) are uncommon entities, heterogeneous clinically and cytogenetically. Recently, a new drug, Lenalidomide, has demonstrated to be very effective in patients with MDS and 5q- reaching 70% of hematological responses whereas patients with MDS without 5q- has only 20-30% of hematological responses. The aim of the present study is to determine genetic alteration in this subset of patients, and describe candidate genes related with response or resistance to Lenalidomide.

overall_design:
The aim of the present study is to determine genetic alteration in this subset of patients, and describe candidate genes related with response or resistance to Lenalidomide.
Copy number analysis of Affymetrix GenomeWide SNP 6.0 arrays was performed for 2 patients with MDS an isolated 5q- by conventional cytogenetics. There are also 2 samples from separated CD3+  lymphocytes, which were used as references for copy number and LOH inference.

first: Francesc

last: Solé


title: Application of SNP-array for the detection of genomic rearrangements responsible for sindromic mental retardation of unknown cause

summary: Developmental delay/intellectual disability (DD/ID)affects 2% of our population. However, mostpatients are often leftwithout aspecific diagnosis,with thecorresponding consequences for the patientsand their families.  The application of microarray technology in the study of patients with DD/ID allows whole-genome analysis with a high resolutionand performance. Here we present the results of  a case included in a series of 246 patients with DD/ID, as part of the screening of the genetic causes responsible for their phenotype.

overall_design: SNP-array was performed on Genome-Wide Human SNP_6 (Affymetrix) as recommended by the manufacter. Analysis was performed with Affymetrix reference profile 'GenomeWideSNP_6.hapmap270.na31.r1.a5.ref'.

first: Carmen

last: Orellana

last: Martínez

first: Mónica

last: Rosello

first: Silvestre

last: Oltra

first: Sandra

last: Monfort

first: Sonia

last: Mayo


title: Cyr61 promotes CD204 expression and migration of macrophages via MEK/Erk pathway in the microenvironment of human esophageal squamous cell carcinoma

status: Public on Oct 08 2014

city: Kobe

first: Manabu

last: Shigeoka

address: 7-5-1 Kusunoki-cho, Chuo-ku

institute: Kobe University Graduate School of Medicine

summary: The authors previously suggested that CD204 was a useful marker for tumor-associated macrophages (TAMs) of esophageal squamous cell carcinoma (ESCC). In this study, they discovered that within ESCC microenvironment not only cancer cells but also TAMs expressed cysteine-rich, angiogenic inducer, 61 (Cyr61), induced by conditioned media of ESCC cells. Levels of Cyr61 expression were associated with CD204+ macrophage infiltration in ESCC tissue. Cyr61 promoted CD204 expression and migration of macrophages via MEK/Erk pathway in vitro.

overall_design: To identify the molecules specifically upregulated in TAM-like THP-1 cells, we performed a cDNA microarray analysis using RNAs from THP-1 stimulated with 200 nM TPA or with 200 nM TPA followed by 50% TE-8CM. THP-1 human acute monocytic leukemia cell line was treated with 200 nM 12-O-tetradecanoylphorbol-13-acetate (TPA) for 2 days to induce macrophage-like differentiation, then exposed to 50%Conditioned medium of TE-8 ESCC cell line (TE-8CM) for 2 days. Differentially expressed genes between MΦ-like and TAM-like THP-1 cells were analysed by cDNA microarray. TE-8CM was prepared by plating 5 × 106 tumor cells in 10 mL complete medium in 100-mm dishes for 24 hr, thereafter changing the medium to complete DMEM supplemented with 10% human AB serum  instead of fetal bovine serum. After 2–3 days, the supernatants were harvested, centrifuged and stored in aliquots at −80°C.

first: Hiroshi

last: Yokozaki


title: Characterization of the human a9 integrin subunit gene: promoter analysis and transcriptional regulation

status: Public on Oct 06 2014

city: Québec

first: Karine

last: Zaniolo

address: 1050 Chemin Sainte-Foy

department: CUO-Recherche

institute: Centre de recherche du CHU de Québec

summary: α9b1 is the most recent addition to the integrin family of membrane-bound receptors and consequently remains the one which is the least characterized. To better understand how transcription of the human gene encoding the α9 subunit is regulated at the molecular level, we cloned the α9 promoter and characterized the regulatory elements that are required to ensure its transcription. Transfection of α9 promoter/CAT recombinant plasmids in primary cultured cells and uveal melanoma cell lines demonstrated the presence of both negative and positive regulatory elements along the α9 promoter and positioned the basal α9 promoter to within 118 bp from the α9 mRNA start site. In vitro DNaseI footprinting and in vivo ChIP analyses demonstrated the binding of the transcription factors Sp1/Sp3, c-Myb and NFI to the most upstream α9 negative regulatory element. The transcription factors Sp1/Sp3 and NFI were found to bind the basal α9 promoter individually but Sp1 binding clearly predominates when both transcription factors are present in the same extract. Most of all, addition of tenascin-C (TNC), the ligand of α9β1, to the tissue culture plates prior to cell seeding increased α9 transcription whereas it simultaneously decreased expression of the α5 integrin subunit gene. This dual regulatory action of TNC on the transcription of the α9 and α5 genes suggests that both these integrins must work together to appropriately regulate cell adhesion, migration and differentiation that are hallmarks of tissue wound healing.

overall_design: Primary cultures of human corneal epithelial cells (HCECs; number of replicates: 8), human skin epithelial cells (HSEC; number of replicates: 4), human corneal fibroblast cells (HCFCs; number of replicates: 3), human skin fibroblast cells (HSFCs; number of replicates: 3), human uveal melanocytes (UVM; number of replicates: 3), and various humal uveal melanoma cell lines (T115, T142 and T143; number of replicates: 2-3) were analyzed by gene profiling on microarrays at low culture passages (between passage 2 to 7). HCECs were also cultured on either BSA (number of replicates: 2) or on tenascin-C (number of replicates: 2) and their transcriptome analyzed by gene profiling.

first: Céline

last: Duval

first: Steeve

last: Leclerc

first: Christian

last: Salesse

first: Sylvain

last: Guérin