title: miRNA Profiles in lung cancer patients and controls with other non-cancer lung diseases

status: Public on Sep 24 2015

city: Saarbrücken

first: Christina

last: Backes

address: Campus, Building E 2.1

department: Chair for Clinical Bioinformatics

country: Germany

institute: Saarland University

summary: This project analyzes plasma profiles of patients suffering from lung cancer and controls with other non-cancer lung diseases

overall_design: Analysis of plasma obtained from 26 patients collected at up to 8 time points and from 12 controls

first: Petra

last: Leidinger

first: Andreas

last: Keller


title: Dynamic Transcriptome Analysis Reveal New Prognosis Biomarker in Colorectal Cancer (miRNA)

status: Public on Sep 30 2015

city: Changsha

first: xiayu

last: li

state: Hunan

address: Yuelu district, Tongzipo road #138

department: department of gastroenterology

country: China

institute: Xiangya third hospital

summary: microRNA profile of TNM-specific sequence design and integrated network-based bioinformatic analysis in 20 Colorectal cancer patients(n=5 for each TNM stage) are carried out to find the dynamic miRNA expression pattern specific to TNM stage. Gene microrray experiment of the same samples were also performed. Two different platform of microarray data were analyzed together to uncover the potential biomarker for progression of colorectal cancer.

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

overall_design: Primary tumor and paired distant normal mucosa of 20 colorectal patient were collected to performed the microarray experiment(please refer to the raw data file). Data of five classes including 15 distant normal mucosa,5 stage I, 5 stage II, 5 stage III and 5 stage IV tumor sample (Total of 35 samples) passed the correlation-based data filtering and went for further analysis. microRNA expression pattern in accordance with TNM stage were analyzed to uncover the dynamic microRNA expression pattern. Significant expression pattern with crucial miRNA were uncovered for prognosis prediction and further functional experiment.

first: Xiayu

last: Li


title: Simultaneous amplification and mutation of KRAS: a therapeutic target in a rare subgroup of glioblastoma?

status: Public on Sep 19 2015

city: NICE

first: Thibault

last: FABAS

address: 28 av Valombrose

country: France

institute: CHU Nice

type: Genome variation profiling by genome tiling array

summary: We describe the case of a glioblostoma multiform in a 66 year old female patient showing both amplification and mutation (exon 3; codon 61)  of KRAS.

overall_design: sample was analysed by arrayCGH method using Agilent recommendations. Sample was labeled in Cy5 and co-hybridized with control DNA cy3 labeled.

first: Zoé

last: Pedeutour-Braccini

first: Fabien

last: Almairac

first: Esma

last: Saada-Bouzid

first: Valérie

last: Duranton-Tanneur

last: Kubiniek

first: Florence

last: Pedeutour

first: Fanny

last: Burel-Vandenbos


title: Detecting metastatic tumors after γ-irradiation using longitudinal molecular imaging and gene expression profiling of metastatic tumor nodules

status: Public on Sep 18 2015

city: Seoul

first: SuJin

last: Jang

address: 215-4, Gongneung-dong, Nowon-gu

country: South Korea

institute: KIRAMS

summary:
Microarray analysis in the mouse metastatic tumor after ɣ-irradiation(ɣ-IR): non-irradiated primary tumor vs. radiated primary tumor vs. metastatic tumor after ɣ-irradiation
Metastatic tumors in C6-L (rat glioma cells ) xenografted mice were studied after local treatment with fractionated γ-IR. To accurately detect the metastatic nodules after γ-IR, we observed the effect of γ-IR on distant metastatic tumor growth. Metastatic nodules after γ-IR indicated extensive colonization of C6-L cells in the lungs within 6 weeks after γ-IR. Identified and described the molecular events occurring after γ-IR through gene expression profiling to elucidate genetic changes (differentially expressed genes between the γ-IR primary tumors vs. non-γ-IR primary tumors and metastatic lung nodules vs. γ-IR primary tumors).

overall_design: We investigated the change of gene expression profile in the γ-IR primary tumors vs. non-γ-IR primary tumors and metastatic lung nodules vs. γ-IR primary tumors in rat glioma (C6-L cell) xenograft model.

first: Joo

middle: H

last: Kang

first: Su

middle: J


title: Reverse phase protein arrays (RPPAs) (in vivo)

city: Bethesda

first: Uma

middle: T

last: Shankavaram

state: MD

address: 9000 Rockville Pike

department: NCI

country: USA

institute: NIH

summary: Relative protein levels for each sample were determined by interpolation of each dilution curves from the standard curve antibody slide. All the data points were normalized for protein loading and transformed to a linear value. Linear values were transformed to Log2 value and then median‐centered for hierarchical cluster analysis.

overall_design: In the study presented here, To determine the biological effects of Radiation  on signaling pathways in GBM cells in vivo orthotropic intra cranial(IC)implants (U251 &U87), we profiled the modulation of phosphorylated and non-phosphorylated proteins using RPPA under different doses of radiation treatment (RT).

first: Uday

middle: B

last: Maachani

first: Kevin

last: Camphausen


title: Transferring genomics to the clinic: distinguishing Burkitt and Diffuse large B-cell lymphoma (v3)

city: Leeds

first: Chulin

last: Sha

address: Woodhouse Lane

department: School of Mole&Cell Biology

country: United Kingdom

institute: University of Leeds

summary: Gene expression profiling was carried out for RNA extracted from Formalin-fixed, paraffin embedded (FFPE) biopsies for  76 patients using the Illumina DASL version 3 platform.  The patients were then classified into BL and DLBCL by moleclar classifier proposed in the article.

overall_design: The molecular classification result of the replicate samples are used to evaluated the reproducibility of the classifier, and the clinic diagnosis were used to compare the agreement with the classifier

first: Sharon

middle: L

last: Barrans


title: Dynamic Transcriptome Analysis Reveal New Prognosis Biomarker in Colorectal Cancer (gene expression)

first: xiayu

last: li

summary: Global gene profile of TNM-specific sequence design and integrated network-based bioinformatic analysis in 20 Colorectal cancer patients(n=5 for each TNM stage) are carried out to find the dynamic gene expression pattern specific to TNM stage. microRNA microrray experiment of the same samples were also performed. Two different platform of microarray data were analyzed together to uncover the potential biomarker for progression of colorectal cancer.

overall_design: Primary tumor and paired distant normal mucosa of 20 colorectal patient were collected to performed the microarray experiment. Data of five classes including 12 distant normal mucosa,5 stage I, 4 stage II, 5 stage III and 5 stage IV tumor sample(Total of 31 samples) passed the correlation-based data filtering and went for further analysis. Gene expression pattern in accordance with TNM stage were analyzed to uncover the dynamic gene expression pattern. Significant expression patterns with distinct biological features were uncovered for prognosis prediction and further functional experiment.


title: Genomic copy number aberrations in primary lung squamous cell carcinoma

status: Public on Sep 22 2015

city: Beijing

first: Dongmei

last: Lin

address: Panjiayuannanli 17, Chaoyang District

department: Pathology

institute: Cancer Hospital, CAMS

summary: Chromosomal instability is one of the hallmarks of tumors, which can result in the gain or loss of specific genomic regions or even entire chromosomes.  These copy number aberrations (CNAs) play an important role in carcinogenesis and malignant progression through CNA-induced gene expression alterations and, subsequently, key cancer-specific processes.  In the current study, we applied aCGH analysis to screen out CNAs with potential prognostic value in lung SCC patients.

overall_design: Depending on their survival time, 100 patients with primary SCC were separated into high- or low-risk groups of prognosis, and copy number aberration (CNA) were analyzed by array-comparative genomic hybridization (array-CGH).

first: Yan

last: Cao

first: Yu

last: Liu

first: Xin

last: Yang

first: Liyan

last: Xue

first: Naijun

last: Han

first: Yanning

last: Gao

first: Shujun

last: Cheng

first: Kaitai

last: Zhang


title: Transcriptomic analysis of C. jejuni HPC5 with C. jejuni HPC5 R14, R20, R14A, R14B, R20A, R20B and R20C.

status: Public on Sep 15 2015

city: Leicestershire

first: Amy

last: John

address: Loughborough

institute: University of Nottingham

summary: C. jejuni HPC5 is a Campylobacter strain isolated from chickens. Following bacteriophage CP34 treatment on chickens colonised by C. jejuni HPC5, a series of CP34 insensitive strains like C. jejuni HPC5 R14 and C. jejuni HPC5 R20 were obtained which compromised their ability to colonise chickens. Reintroduction of C. jejuni HPC5 R14 and R20 in to chickens led to reversion of these strains and the MRPs of the revertant strains fell in to different classes termed C. jejuni HPC5 R14A, R14B, R20A, R20B and R20C and these strained were tested positive for colonisation  proficient and bacteriophage sensitive.

platform_organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

overall_design:
There are three biological replicates for each experiment. Seven independent cDNA preps of C. jejuni HPC5 were prepared and they were labelled independently using AF555. The labelled cDNAs were mixed together and this acted as the control. Each daughter strains were considered as sample and they were labelled with AF645. Hybridisations were done between C. jejuni HPC5 and C. jejuni HPC5 as one of the sample and each of the daughter strains in triplicates.
The supplementary files (linked at the foot of this record) contain the summary of the replicate data of the corresponding strain (3 replicates/strain) which have been averaged.

first: Andrew

last: Scott

last: Timms

first: Philippa

last: Connerton

first: Ian


title: Reverse phase protein arrays (RPPAs) (in vitro)

first: Uma

last: Shankavaram

overall_design: In the study presented here, To determine the biological effects of Radiation  on signaling pathways in GBM cells in vitro (U251 &U87), we profiled the modulation of phosphorylated and non-phosphorylated proteins using RPPA under different doses of radiation treatment (RT).

first: Uday

last: Maachani

first: Kevin

last: Camphausen


title: Frequent derepression of the mesenchymal transcription factor gene in acute myeloid leukemia (human)

status: Public on Sep 17 2015

city: Manchester

first: Tim

middle: C

last: Somervaille

state: Lancashire

address: Wilmslow Road

institute: Cancer Research UK Manchester Institute

summary: Bone marrow samples from normal adult male donors were collected into EDTA. Red cells were removed by ammonium chloride lysis. Leukocytes were washed in SM buffer and CD34+ cells were separated from CD34- cells using an AutoMACS device and anti-CD34 immunomagnetic beads (Miltenyi Biotec), according to manufacturer’s instructions. For mature cell populations, CD34- cells were FACS purified according to the following immunophenotypes, with 7-AAD used to exclude dead cells: Neutrophils: side scatter high CD15+ CD16+. Monocytes: side scatter low-intermediate CD14+ CD16- CD15-. See also Huang et al., 2014.

overall_design: Eight exon arrays total; 4 arrays for each cell type; four separate individuals.


title: Real-time quantitative PCR analysis of murine non-ischemic and ischemic wound edge

city: Fort Sam Houston

first: Jaideep

last: Banerjee

state: Texas

address: 3698 Chambers Rd, BHT-1

institute: US Army Inst of Surgical Res.

summary: Wound edges from a murine bipedicle flap ischemic wound model were collected 3 days post wounding. RNA from ischemic and non-ischemic wound edges was isolated by miRVana RNA isolation kit. Mature miRNAs were then profiled by real-time PCR.

overall_design: Wound edges were collected from ischemic (bipedicle flap model) and non-ischemic wounds made in C57Bl6 mice on 3 days post-wounding. RNA was isolated by miRVana RNA isolation kit. Mature miRNAs were profiled by real-time PCR using an Applied Biosystems 7900HT real-time PCR instrument equipped with a 384 well reaction plate. RNA (500 ng) was converted to cDNA by priming with a mixture of looped primers (Mega Plex kit, Applied Biosystems, Foster City, CA). Liquid-handling robots and the Zymak Twister robot were used to increase throughput and reduce error. Real-time PCR was performed using standard conditions

first: T

middle: D

last: Schmittgen

first: Chandan

middle: K

last: Sen


title: Genome analysis of C. jejuni and C. coli isolated from different regions of the same pig

summary: C. coli is the predominant Campylobacter strain that is found in pigs while C. jejuni if present will be 10- 100 folds less. Natural transformation can occur if there is a coexistence of both the strains in the intestine of pigs. Genome analyses were performed on a C. jejuni strain U101 isolated from the upper intestine and two C. coli strains, C101 and L101 isolated from caecum and lower intestine.

sample_organism:
Campylobacter coli
Campylobacter jejuni
Campylobacter jejuni RM1221

overall_design:
Five independent DNA preps of C. jejuni RM1221 were labelled with Cy 5 independently and they were mixed well which was used as the control. C101, U101 and L101 were labelled with Cy 3 independently and equal concentration of the control and sample DNA were used for hybridisation. Three biological replicates were done for each slide.
The supplementary file (linked at the foot of this record) represents a summary of the C101, L101, and U101 replicate data (3 replicates/strain) that have been averaged.


title: DNA microarray analysis of ∆scnAB in Streptomyces chattanoogensis L10

city: HangZhou

first: TanJun

last: Wang

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Biochemistry

institute: Zhejiang University

summary:
scnA (GenBank: ADX66464.1) and scnB (GenBank: ADX66465.1) are ABC transporters located in the biosysnthesis gene cluster of natamycin in Streptomyces chattanoogensis. The two genes are presumbly involved in natamycin efflux. Our goal of this expriment was to investigate the effect of scnA and scnB inactivation on the gene expression in the whole genome.
In ∆scnAB  there were a total of 219 genes displaying at least a two-fold change (P<0.05), including 89 genes with lower and 130 genes with higher expressions

overall_design: In this study, RNA isolated from ∆scnAB or wild type Streptomyces chattanoogensis L10, was used to acquire expression profiles of a total of 8,117 protein-coding genes in S. chattanoogensis L10, leading to the successful construction of different expression profiles between scnA and scnB deletion mutant and wild type S. chattanoogensis L10.

first: Tan

first: Wen

last: Guan

first: Yong

middle: Q

last: Li


title: Rnase1 responsive miRNA

city: Chicago

first: Emanuele

last: Canestrari

address: 900 S. Ashland Ave.(M/C 669)

institute: University of Illinois at Chicago

summary: To determine the importance of RNase1 on cellular miRNA function, we used a lentivirus system to stably express RNase1 in dicer wt and dicer ex5 RKO cells in serum free culture. RNase1 was found to govern miRNA that reside outside the pureview of Dicer. Assignment of RNase1 as miRNA-generating enzyme suggests that, like Dicer, RNaseA enzymes mediate essential physiological functions through regulatory RNA.

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Macacine alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
Saimiriine gammaherpesvirus 2
JC polyomavirus
Human immunodeficiency virus 1
Human betaherpesvirus 6B
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Two-condition experiment, wild-type RNase1 vs mutant (6x) RNase1,in two cell lines RKO dicer wild-type and RKO dicer mutant (ex5). Biological replicates: 2 for each condition and each cell line . One replicate per array.

first: Ken

last: Asada

first: Zain

last: Paroo


title: Detection of differentially expressed genes in Day 30 embryos during gestation in primiparous (PP) sow with different intermittent suckling and breeding strategies

status: Public on Sep 16 2015

city: Edmonton

first: Stephen

last: Tsoi

state: Alberta

address: 4-32G Agriculture/Forestry Cen

department: AFNS

country: Canada

institute: University of Alberta

summary: Transcriptional profiling of Day 30 embryos (D30E) was performed. First parity sows were submitted to an ovulation-induction protocol, intermittent suckling (IS), during lactation. IS consisted of 8 h/d separation from their litters during the last 7d of a 28d lactation. During separation, sows received boar exposure. There were 3 treatments: control (C28, n=19), where piglets were weaned at D28 of lactation and were bred after weaning and two IS treatments: sows were either bred at their first induced estrus during lactation (IS21FE, n=18), or were “skipped” and bred at their second estrus (IS21SE, n= 17) which occurred after final weaning at D28. Sows were slaughtered and embryos were collected on D30 of gestation for DNA PCR sexing. Later, D30E from the same sex with similar weight were pooled for further microarray investigation.

overall_design: Stimulating lactational oestrus then two mating strategies were applied to primiparous sows.  For the microarray experiment, three biological replicates (three sows) were chosen from each treatment group comparing control (C28) to either IS21FE or IS21SE. A pool of females and males D30E were chosen and pooled separately for each comparison.

first: Milena

middle: S

last: Blanes

first: Michael

last: Dyck

first: George

middle: R

last: Foxcroft


title: Gene expression data from mouse squamous cell carcinoma cells

status: Public on Sep 29 2015

city: Edinburgh

first: Adam

last: Byron

address: Western General Hospital, Crewe Road South

department: Edinburgh Cancer Research UK Centre

institute: University of Edinburgh

summary:
We describe a function of focal adhesion kinase (FAK) in driving anti-tumor immune evasion. The kinase activity of nuclear-targeted FAK in squamous cancer cells drives exhaustion of CD8+ T-cells and recruitment of regulatory T-cells by transcriptionally regulating chemokine/cytokine and ligand-receptor networks, including transcription of Ccl5 that is crucial. These changes inhibit antigen-primed cytotoxic CD8+ T-cell activity, permitting growth of FAK-expressing tumors.
To address how FAK activity in squamous cell carcinoma (SCC) cancer cells promotes elevated intra-tumoral regulatory T-cells, we analyzed global transcriptional profiles of SCC cells expressing or not expressing FAK.

overall_design: Total RNA was isolated from three biological replicates each of SCC cells from mice genetically null for Fak (SCC FAK-/-) and cells stably re-expressing FAK (SCC FAK-wt) and hybridized on Affymetrix microarrays.

first: Alan

last: Serrels

first: Tom

last: Lund

first: Bryan

first: Andrew

last: Sims

first: Margaret

last: Frame


title: Phasevarion of non-typeable Haemophilus influenzae R2866

city: Oklahoma City

first: Timothy

middle: M

last: VanWagoner

state: OK

address: 940 SL Young Blvd, BMS340

department: Pediatrics

institute: University of Oklahoma Health Sciences Center

summary: H. influenzae R2866 contains a phase-variable DNA methylase modA10, by virtue of 16 tetrameric repeats present after the start codon. Gain or loss of repeats during replication by slipped-strand mispairing can result in a non-functional reading frame. Microarray analyses of wild-type and insertionally inactivated modA were performed to determine genes affected by phase variable modification.

overall_design: Three replicate cultures were grown in either supplemented brain heart infusion broth (R2866 and R3763) or chemically defined media (R3790 and R3791) to an optical density at 600nm of 0.3 to 0.4 (mid-log phase). RNA was isolated by the method of Jahn et al.

first: T

first: K

last: Nelson

last: Fox

first: H

last: Smith

first: Y

middle: N

last: Srikhanta

first: M

middle: P

last: Jennings

first: J

last: Atack

last: Stull

first: A


title: Gene Expression Analysis Of Plasmablastic Lymphoma Identifies Down Regulation Of B Cell Receptor Signaling and Additional Unique Transcriptional Programs

city: Stanford

last: Gentles

state: CA

address: 1201 Welch Road

institute: Stanford University

summary: Plasmablastic lymphoma is a high grade B cell lymphoma with plasmablastic morphology and a terminally differentiated B cell immunophenotype, usually arising in the setting of immunodeficiency and often demonstrating Epstein Barr Virus positivity.  The molecular and genetic mechanisms underlying the pathogenesis of PBL are largely unknown. To better understand its pathogenesis, herein we have analyzed global gene expression of PBL and compared that to gene expression profiles of diffuse large B cell lymphoma.   While overlaps in transcriptomes between these malignancies were identified, we have shown that the gene expression profile of plasmablastic lymphoma is distinct, demonstrating striking downregulation of B cell receptor signaling genes, BCL6, BCL11A SPI-B, targets of NFKB1, and upregulation of mitochondrial genes, PRMT5, MYC and MYC targets and IL21, implicating these alterations in the pathogenesis of this lymphoma.  In addition we show the usefulness of SWAP-70 immunohistochemistry in the differentiation of immunoblastic diffuse large B cell lymphoma and plasmablastic lymphoma.    Our findings provide justification for considering plasmablastic lymphoma as a specific lymphoma entity and provide insight into the unique transcriptional aberrations occurring in this high-grade lymphoma.

overall_design: Expression profiles of 15 plasmablastic lymphomas and 10 diffuse large B-cell lymphomas were obtained using Afymmetrix U133A2 microarrays.

first: Jennifer

last: Chapman-Fredricks


title: Effects of Intramuscular Administration of Folic Acid and Vitamin B12 on Granulosa Cells Gene Expression in Postpartum Dairy Cow

city: Quebec

first: Annie

last: Gagnon

state: Quebec

address: 2440 boul. Hochelaga

institute: Laval University

summary: The fertility of dairy cows is challenged during early lactation and better nutritional strategies need to be developed to address this issue. Combined supplementation of folic acid and vitamin B12 improves energy metabolism in the dairy cow during early lactation. Therefore, the present study was undertaken to explore the effects of this supplement on gene expression in granulosa cells from the dominant follicle during the postpartum period. Multiparous Holstein cows received weekly intramuscular injection of 320 mg folic acid and 10 mg vitamin B12 (treated group) beginning 24 (SD 4) d before calving until 56 d after calving, whereas the control group received saline. The urea plasma concentration was significantly decreased during the pre-calving period, and the concentration of both folate and vitamin B12 were increased in treated animals. Milk production and dry matter intake were not significantly different between the two groups. Plasma concentrations of folates and vitamin B12 were increased in vitamin-treated animals. Daily dry matter intake was not significantly different between the 2 groups before (13.5 kg SE 0.5) and after (23.6 kg SE 0.9) calving. Average energy-corrected milk tended to be greater in vitamin-treated cows, 39.7 (SE 1.4) and 38.1 (SE 1.3) kg/d for treated and control cows, respectively. After calving, average plasma concentration of BHBA tended to be lower in cows injected with the vitamin supplement, 0.47 (SE 0.04) vs. 0.55 (SE 0.03) for treated and control cows, respectively. The ovarian follicle ? 12 mm in diameter was collected by ovarian pick-up after estrus synchronization. Recovered follicular fluid volumes were greater in the vitamin-treated group. A microarray platform was used to investigate the impact of treatment on gene expression of granulosa cells. Lower expression of genes involved in the cell cycle and higher expression of genes associated with granulosa cell differentiation prior to ovulation were observed. Selected candidate genes were analyzed by reverse transcription quantitative polymerase chain reaction. Although the effects of intramuscular injections of folic acid and vitamin B12 on lactational performance and metabolic status of animals were limited, Ingenuity Pathway Analysis of gene expression in granulosa cells suggests a stimulation of cell differentiation in vitamin-treated cows, which may be the result of an increase in LH secretion.

overall_design: Two conditions experiment (Control and Treated). Granulosa cells from the 66h post second PGF2alpha injection. Biological replicates: 3 from each time point. Two technical replicates for each comparison (dye-swap).

first: Daulat

last: Khan

first: Marc-André

last: Sirard

first: Christiane

last: Girard

first: Jean-Paul

last: Laforest

first: Francois

last: Richard


title: Microarray-based Gene Expression Analysis in the Silkworm Bombyx mori After Parasitization by Tachinid Flies

city: Tsukuba

first: Yuki

last: Nakamura

state: Ibaraki

address: 1-2 Owashi

country: Japan

institute: National Institute of Agrobiological Sciences

summary: We identified genes regulated by parasitization of the silkworm Bombyx mori by three tachinid parasitoid species, Exorista japonica, Drino inconspicuoides and Pales pavida, using oligonucleotide microarrays. The numbers of genes and their intensity of expression varied with the species of parasitoid, within silkworm hemocytes and fat body.

overall_design: Bombyx mori hemocyte, silkgland and fat body samples parasitizated by Exorista japonica, Drino inconspicuoides and Pales pavida were prepared. Gene expression was compared in these two groups: control and parasitized.

last: Kalyebi

last: Kadono-Okuda


title: Dynamic Transcriptome Analysis Reveal New Prognosis Biomarker in Colorectal Cancer

city: Changsha

first: xiayu

last: li

address: Yuelu district, Tongzipo road #138

institute: Xiangya third hospital

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

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

overall_design: Refer to individual Series


title: Genome-wide selection and testing of superior reference genes for quantitative gene expression normalization in tobacco (Nicotiana tabacum)

status: Public on Sep 26 2015

city: Guiyan

first: Ruiyuan

last: Li

state: Guizhou

address: No. 116 Baoshanbei Road, Yuanyan District;

institute: Guizhou Normal University

summary: To diversify the pool of reliable reference genes in tobacco, the expression stability of 44,873 tobacco genes (ESTs) were measured using a custom-designed microarray in a diverse set of 21 samples, representing various tissue types and developmental stages. A total of 14 genes were selected as candidate reference genes because they appeared to be the most stable. These genes were compared with two widely used housekeeping genes (L25 and EF-1a) for further validation by qRT-PCR

first: Xueliang

last: Ren

first: Yushuang

last: Guo


title: Global expression profiling reveals shared and distinct transcript signatures in arrested act2(-) and CDPK4(-) Plasmodium berghei gametocytes

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: Gametocytogenesis and gametogenesis in malaria parasites are complex processes of cell differentiation and development likely involving many gene products. Gametocytes develop in the blood of the vertebrate host but mature gametocytes are not activated until taken up by the mosquito vector. Several distinct mutants have been described that block gametogenesis but the detailed molecular causes for the mutant phenotypes are not understood. To investigate whether a block in gametogenesis also results in a changed transcriptional profile, we studied two gene deletions mutants; act2(-) lacking stage-specific actin II and CDPK4(-) lacking calcium-dependent protein kinase 4. Whole-genome microarray analysis was performed from RNA of mature gametocytes to compare the transcriptomes of the mutants with wild-type Plasmodium berghei. The microarray analysis identified ~12% of all genes being differentially expressed in either or both mutants compared to normal gametocytes, as defined by at least two-fold change in transcript abundance. A large proportion of differentially expressed genes in both mutants overlapped consistent with the developmental gametocyte arrest. Distinct profiles in each mutant were also observed.

overall_design: Microarray experiments were performed as dual-color hybridizations on Agilent-024169 custom whole genome Plasmodium berghei 44K arrays. To compensate for dye-specific effects, a dye-reversal color-swap was applied.

first: Maria

last: Andreadaki

first: Inga

last: Siden-Kiamos

first: Kai

last: Matuschewski

first: Hans


title: Identification of the different miRNA expression in Hep-12 Cells compared with Hep-11 cells

city: Peiking

first: haibo

last: Han

address: 52 Fucheng Road, Haidian District

department: Department of Cell Biology

institute: Peking University School of Oncology

summary: To find miRNAs that regulate the stemness of LTICs, we took advantage of the TIC-enriched Hep-12 and the non-tumorigenic Hep-11 cell lines by genome-wide profiling of miRNA expression with miRNA microarray analysis.

overall_design: Two samples are analyzed.

first: Haibo

first: Zhiqian

last: Zhang


title: Maize plants (Zea may) : WT (Alice) vs. Yellow stripe mutants (ys1 or ys3)

status: Public on Sep 20 2015

city: Tokyo

first: Tomoko

last: Nozoye

address: 1-1-1 yayoi bunkyo-ku

institute: The University of Tokyo

summary: Transcriptional profiling of Yellow stripe 1 (ys1) and ys3 mutants. ys1 and ys3 are recessive mutants of maize (Zea mays L.) that result in symptoms typical of Fe deficiency, i.e., interveinal chlorosis of the leaves. The objective of the present work was to identify the genes involved in the ys1 and ys3 phenotypes, so as to extend our understanding of Fe homeostasis in maize.

overall_design: Root or shoot of WT vs. ys1 or ys3 mutants under Fe sufficient or Fe deficient conditions respectively.


title: Reverse phase protein arrays (RPPAs)

city: Bethesda

first: Uma

last: Shankavaram

address: 9000 Rockville Pike

institute: NIH


title: Genome analysis of C. jejuni and C. coli isolated from different regions of the same chicken

city: Leicestershire

first: Amy

last: John

address: Loughborough

institute: University of Nottingham

summary: The gut of chicken is mostly colonised with Campylobacter jejuni and with 100 fold less C. coli. The competitive ability of C. coli OR12 over C. jejuni OR1 has been examined in experimental broiler chickens following the observation that C. coli replaced an established C. jejuni intestinal colonisation within commercial chicken flocks reared outdoors (El-Shibiny, A., Connerton, P.L., Connerton, I.F., 2005. Enumeration and diversity of campylobacters and bacteriophages isolated during the rearing cycles of free-range and organic chickens. Applied Environmental Microbiology. 71, 1259-1266).

overall_design:
Five independent DNA preps of C. jejuni RM1221 were labelled with Cy 5 independently and they were mixed well which was used as the control. OR1 and OR12 were labelled with Cy 3 independently and equal concentration of the control and sample DNA were used for hybridisation. Three biological replicates were done for each slide.
The supplementary file (linked at the foot of this record) represents the averaged normalised values for each experimental condition (3replicates/experimental condition).

first: Ayman

last: El-Shibiny

first: Andrew

last: Timms

first: Philippa

last: Connerton

first: Ian


title: Microarray based differential transcriptomics study to understand arsenic-thiourea interaction in rice.

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: In our earlier study, thiourea has been shown to improve the growth of rice and reduce the arsenic load from aerial parts of the seedlings. We have also shown the applicability of thiourea to delineate the redox regulatory mechansisms under arsenic stress in rice. To move further, present microarray was performed to reveal the involvement of overall gene and regulatory netwrok under arsenic with/without thiourea treatment in rice.

overall_design: Agilent custom one-color experiment,Organism:Oryza sativa, Whole Genome Rice 8x60k (AMADID: 064722) designed  by Genotypic Technology Private Limited.

first: A

last: Srivastava

first: P

last: Jadhav

first: G

last: Sablok

first: S

last: Suprasanna


title: microRNA expression signatures and parallels between monocyte subsets and atherosclerotic plaque in humans

city: Aachen

first: Lin

last: Gan

address: Pauwelsstr. 30

department: IZKF

institute: University Hospital Aachen

summary: Small non-coding microRNAs (miRs) have emerged to play critical roles in cardiovascular biology. Monocytes critically drive atherosclerotic plaque formation, and can be subdivided into a classical and non-classical subset. Here we scrutinized the miR signature of human classical and non-classical monocytes, and compared miR expression profiles of atherosclerotic plaques from human carotid arteries and healthy arteries.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: This study includes cell samples from human sorted classical and non-classical monocyte subset, as well as pooled sample from carotid artery plaque and Ae. mammaria.

first: Kiril

last: Bidzhekov

first: Bernd

last: Denecke

first: Mihail

last: Hristov

first: Thomas

middle: A

last: Koeppel

first: Alma

last: Zernecke

first: Christian

last: Weber


title: Effects of pubertal exposure to dietary soy on estrogen receptor pathway in the breast of cynomolgus macaques

status: Public on Sep 11 2015

city: Winston-Salem

first: Jeff

last: Chou

state: NC

address: Medical Center Blvd

institute: Atrium Health Wake Forest Baptist

summary: We evaluated mammary gland responses over time in pubertal female cynomolgus macaques fed diets containing either casein/lactalbumin or soy protein that contained a human-equivalent dose of 120 mg isoflavones/day for ~4.5 years spanning menarche. We assessed estrogen receptors (ERs) expression, and markers of ER activity and estrogen metabolism. Promoter methylation of ERs and their downstream targets was also evaluated. As we found that pubertal soy exposure resulted in transient effects on mammary ER-a transcription after menarche with subtle effects on differentiation and ER activity, a gene expression microarray was performed on a subset of samples as an exploratory approach to investigate potential pathways and gene sets that may be of importance during this post-menarchal breast development.

overall_design: Gene expression profiles were assessed from breast biopsy samples from a subset of soy-fed and casein/lactalbumin-fed cynomolgus monkeys (n=4/diet group) from two timepoints, which are 7-12 months and 19-24 months after menarche.

first: Fitriya

last: Dewi

first: Charles

middle: E

last: Wood

first: Cynthia

last: Willson

last: Register

last: Lees

first: Timothy

last: Howard

first: Zhiqing

last: Huang

first: Susan

last: Murphy

first: Janet

last: Tooze

first: Lance

last: Miller

middle: W

first: J

last: Cline


title: MeDIP-chip from 3 pairs of gastric cancer and adjacent tissues

status: Public on Sep 14 2015

city: Beijing

first: Jia

last: Yu

address: Dong Dan San Tiao 5

department: Department of Biochemistry and Molecular Biology Institute of Basic Medical Sciences

institute: Peking Union Medical College & Chinese Academy of Medical Sciences

type: Methylation profiling by genome tiling array

summary:
Methylated modifications of genome are common events in carcinogenesis and is involved in the tumorigenesis and progression of various cancers including gastric cancer
Methylated DNA immunoprecipitation (MeDIP) combined with a human miRNA tiling microarray analysis demonstrated that there are much methylation differention between gastric cancers and adjacent controls

overall_design: microRNA gene methylation comparison of 3 pairs of gastric cancer and controls

first: Lei

last: Dong


title: Genome-wide ParB2-DNA and RctB-DNA interaction analyses in Vibrio cholerae

first: Jonghwan

last: Baek

address: 37 Convent Dr

type: Genome binding/occupancy profiling by array

summary: Replication and segregation are the two main processes that maintain chromosomes in growing cells. In bacteria, replication and transcription have been proposed to provide motive force in chromosome segregation.  Recently, ParB2, a segregation protein, encoded by V. cholerae chromosome II (chrII) was also found to influence chrII replication. V. cholerae chrII replication is primarily controlled by its specific initiator protein, RctB. Here, we have screened for ParB2 and RctB binding sites using a genome-wide DNA binding analysis (ChIP-chip). We report the identification of a new region containing additional RctB and ParB2 binding sites, and suggest the mechanisms to coordinate replication initiation with segregation of chromosomes.

sample_organism: Vibrio cholerae O1 biovar El Tor str. N16961

overall_design: ParB2 binding DNA (Cy5) vs total DNA (input, Cy3) in wildtype (CVC209), RctB binding DNA (Cy5) vs total DNA (input, Cy3) in wildtype (CVC209),  RctB binding DNA (Cy5) vs total DNA (input, Cy3) in MCH1 (CVC2099, rctB-deleted strain), Biological replicates: 3 or 2

first: Peter

last: FitzGerald

first: Dhruba

last: Chattoraj


title: Effects of agouti overexpression in the brain and skin transcriptome of zebrafish

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary: Twenty transgenic fish overexpressing agouti-signaling protein (ASIP, Ceinos et al., Pigment Cell and Melanoma Research 28:196-209, 2015) and wild type (WT) zebrafish were placed in 6-liter tanks and acclimated during 30 days prior to sampling to minimize physiological differences. Animals were sacrificed and the brain+pituitary and the skin dissected under the stereo microscope, placed in trizol and stored at -80C until RNA extraction. Six biological replicates (3 females and 3 males) of each tissue  (skin and brain) of each group (ASIP vs WT) were analyzed in a total of 6 slides containing 4 microarrays in the 4 × 44 k format. Global gene expression analyses were performed to search for both sex-dependent and transgene-dependent effects as well as the interaction between both factors (sex x phenotype) on the brain+pituitary and skin transcriptome.

overall_design: Wild type (Tu) or transgenic zebrafish overexpression agouti-signaling protein (ASIP) were reared in similar conditions. Brain+pituitary and skin were sampled from 6 ASIP (3 males + 3 females) and WT (3 males + 3 females) zebrafish. Samples were individually hybridized in a total of 6 slides containing 4 microarrays in the 4 × 44 k format. Microarrays included 60-mer probes to the unique transcripts from Ensembl and Unigene which were annotated by functional categories of GO and pathways of KEGG with bioinformatics package STARS

first: Cerdá

last: Reverter

first: Jose

last: Miguel

first: Josep

last: Rotllant


title: On the relevance of technical variation due to building pools in microarray experiments [Honey bee]

city: Bochum

first: Henrik

last: Rudolf

address: Universitätsstr. 150

department: Medical computer science, Biometry and Epidemiology

institute: Ruhr-Universität Bochum

summary:
The objective of the study was to assess the technical error due to blending of individual samples into pools in different experimental data sets.
The blending error variance component corresponds to random effects for inaccuracies, which were modeled on the logarithmic scale of normalized gene expression. It's estimation based on a linear mixed model, fitted for each transcript.

overall_design: Honey bees showing hygienic behavior towards Varroa-parasitized brood were compared with controls and among each other. Tissues from mushroom body, antennal lobe and Antennae of honey bees were processed for microarray analysis. They were measured as single samples as well as pooled samples from 2 or 4 individuals.

first: T

last: Gempe

first: G

last: Leboulle

first: H


title: Breastfeeding infants transmit influenza virus to the mammary glands during feeding [Dataset Part II]

status: Public on Sep 10 2015

city: Toronto

first: Stephane

middle: G

last: Paquette

state: Ontario

address: 101 College Street

department: Experimental Therapeutics

institute: University Health Network

summary: Influenza virus transmission between mothers and nursing-infants has not been investigated although mothers and infants often develop severe disease.  Ferrets are considered the most appropriate model for influenza studies. We investigated influenza transmission in infant and nursing-mother ferrets. Influenza infected infants transmitted virus to mother mammary glands leading to live virus excretion in milk and influenza virus positive mammary gland epithelial cells.  Global gene expression analysis showed down-regulation of milk production and induction of breast involution and oncogenesis pathways.  Our results provide insight into influenza transmission between mothers and infants which may impact fields of infectious disease, maternal/infant health and neoplasm etiology.

overall_design: Total RNA was obtained from ferret lungs at days 3 and 6 post-intranasal infection with 10^5 EID50 A/California/07/2009 (H1N1) (n = 3/time-point).  Total RNA was also collected from uninfected control lung tissues (n = 3).  Changes in gene expression relative to uninfected tissue controls were then investigated.

first: David

last: Kelvin


title: Breastfeeding infants transmit influenza virus to the mammary glands during feeding


title: Expression data from rat tumors formed by 9L.EV or 9L.EGFRvIII cells

status: Public on Sep 08 2015

city: Philadelphia

first: Matthew

middle: J

last: Lazzara

address: 220 South 33rd Street

institute: University of Pennsylvania

summary: Analysis of rat tumor xenografts revealed genes that are upregulated in tumors expressing EGFRvIII

overall_design: 12 rats received intracranial injections of 9L cells expressing EGFRvIII or an empty vector control.  Three weeks after implantation and subsequent growth, tumors were aseptically removed, processed for RNA extraction, and analyzed for gene expression profiling using the RatRef12 Illumina chip array.  We compared the average expression of all the transcripts between EGFRvIII-expressing and empty vector control tumors.

first: Alice

last: Walsh

first: Gurpreet

last: Kapoor

first: Yingtao

last: Bi

first: Ramana

middle: V

last: Davuluri

first: Donald

last: O'Rourke


title: Genome-wide identification of N6-methyladenosine by microarray

city: Cambridge

first: Yue

last: Li

state: Massachusetts

address: 32 Vassar Street, 32-D528

institute: Massachusetts Institute of Technology

type: Expression profiling by genome tiling array

summary: Although internal PolyA RNA modification N6-methyladenosine (m6A) plays essential roles in diverse biological processes, technology to detect precise m6A sites at transcriptome-wide scale is lacking. Here, we discovered that m6A interferes A (Adenine) – U (Uracil) or A-T (Thymidine) pairing. Based on differential hybridization between methylated vs. unmethylated RNAs to a DNA probe, we developed tiling microarray to pinpoint m6A sites in mouse transcriptome. We validated some of the identified sites and provided evidence to suggest that one functional mechanism of m6A is to block small RNA targeting to methylated mRNA.

overall_design: We designed a custom tiling array with  to examine the precise location of m6A within meRIP-seq peaks from mouse embryonic stem cells determined in our previous publication (Wang et al., 2014). Each custom two-channel Agilent tiling array harbors 947,952 probes. Each probe is 25 nucleotides (nt), and any two adjacent probes in the genomic coordinate overlap each other by 19 nt. The Cy5 or red channel corresponds to Mettl14 knockout (M14) or DZA mutant mESC cell line, and Cy3 or green channel is associated with wild type cell line treated with scramble hairpin (SCR). Thus, in principle a higher Cy5/Cy3 signal for each probe reflects an increased hybridization to the oligonucleotide due to de-methylation of a particular RNA molecule in M14 or DZA condition relative to the SCR control. Moreover, we employed additional arrays with both channels dedicated for M14 as an external control for technical difference between the Cy5 and Cy3 dye (details below). For each comparison, we have three biological replicates, and therefore there are 9 tiling arrays in total (i.e., 3 arrays for M14 vs SCR, 3 arrays for DZA vs SCR, and 3 arrays for M14 vs M14).

first: Yang

last: Wang

first: Zhaolei

last: Zhang

first: Alicia

last: Montes de Oca

first: Jing

last: Zhao


title: Quantitative proteomic analysis reveals maturation as a mechanism underlying glucocorticoid resistance in B lineage ALL and JNK inhibitors as a re-sensitising therapy

status: Public on Sep 02 2015

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

summary:
Glucocorticoids (GC) are pivotal in the treatment of childhood acute lymphoblastic leukaemia (ALL) but resistance is a continuing clinical problem with the underlying mechanisms still unclear. An isobaric tag proteomic approach was used to compare protein profiles of the B lineage ALL GC-sensitive cell line, PreB 697, and its GC-resistant sub-line, R3F9, before and after dexamethasone exposure. Two transcription factors involved in B- cell differentiation, PAX5 and IRF4, were differentially regulated in the PreB 697 compared to the R3F9 cell line in response to GC. PAX5 basal protein expression was less in R3F9 compared to its GC-sensitive parent and was confirmed to be lower in other GC-resistant sub-lines of Pre B697 and was associated with a decreased expression of the PAX5 transcriptional target, CD19. Gene set enrichment analysis of microarray data from the cell lines showed that increasing GC-resistance was associated with differentiation from preB-II to an immature B-lymphocytes stage. GC resistant sub lines were shown to have a higher levels of p-JNK compared to the parent line and JNK inhibition caused re-sensitisation to GC. Reduced CD19 levels accompanying GC resistance was also apparent in some clinical samples, with high levels of MRD persisting after GC containing induction chemotherapy. Thus, quantitative proteomic analysis reveals a role for PAX5 and maturation as a recurrent mechanism underlying glucocorticoid resistance in ALL and identifies JNK inhibitors as a possible re-sensitising therapy.
Gene expresion profiling of GC-sensitive and resistant precursor B-ALL cells.

overall_design: Gene set enrichment analysis (GSEA) was used to analyse the state of differentiation of GC-resistant sub-lines and genes were ranked according to the correlation of gene expression with dexamethasone IC50 values for the individual sub-lines.

first: Lindsay

last: Nicholson

first: Caroline

last: Evans

first: Elizabeth

last: Matheson

first: Lynne

last: Minto

first: Christopher

last: Keilty

first: Maryna

last: Sanichar

first: Marian

last: Case

first: Claire

last: Schwab

first: Daniel

last: Williamson

first: Christine

last: Harrison

first: Reinhard

last: Kofler

first: Andrew

last: Hall

last: Redfern

first: Anthony

last: Whetton

first: Julie

last: Irving


title: Gene expression in Xenopus laevis embryogenesis

status: Public on Sep 05 2015

city: Tsukuba

first: Yuzuru

last: Ito

address: Central 6, Higashi 1-1-1

department: Biotechnology Research Institute for Drug Discovery

institute: National Institute of Advanced Industrial Science and Technology (AIST)

summary: Analysis of whole body of unfertilized eggs and two-cell stage, 16-cell stage, stage 8, stage 9, stage 10.5, stage 12, stage 15, stage 20, stage 25, stage 30, stage 35 and stage 40 embryos. Results provide insight into the global molecular changes in Xenopus embryogenesis.

overall_design: Gene expressions in intact whole unfertilized eggs and whole embryos at two-cell stage, 16-cell stage, stage 8, stage 9, stage 10.5, stage 12, stage 15, stage 20, stage 25, stage 30, stage 35 and stage 40.

first: Yasuko

last: Onuma


title: Breastfeeding infants transmit influenza virus to the mammary glands during feeding [Dataset Part I]

first: Stephane

last: Paquette

overall_design: Total RNA was obtained from nursing mother ferret mammary glands at days 3/4 and 6/7 post-intranasal kit infection with 10^5 EID50 A/California/07/2009 (H1N1).  Total RNA was also collected from uninfected control nursing mother mammary gland tissues (n = 3).  Changes in gene expression relative to uninfected tissue controls were then investigated.

first: David

last: Kelvin


title: Loss of Karma transposon methylation underlies oil palm somaclonal mantling

status: Public on Sep 09 2015

city: St. Louis

first: Steve

middle: W.

last: smith

state: MO

address: 4041 Forest Park Ave

department: Bioinformatics

institute: Orion Genomics

summary:
The oil palm fruit abnormality, mantled, is a somaclonal variant arising from tissue culture that drastically reduces yield, and has largely halted efforts to clone elite hybrids for breeding and oil production.  Widely regarded as epigenetic, mantling had defied explanation, and has become an icon of unsustainability in environmentally sensitive tropical plantation crops.  We identified the MANTLED gene using Epigenome Wide Association analysis of genetically identical palms from multiple clonal lineages.  Hypomethylation of a LINE retrotransposon related to rice Karma, found in the intron of the homeotic gene DEFICIENS, is common to all mantled clones and is correlated with alternative splicing and loss of small RNA.  DNA methylation is regained in spontaneous revertants accounting for non-Medelian inheritance of the Good Karma and Bad Karma epialleles.  Thus epigenetic regulation of transposable elements results in somaclonal variation and provides a means to cull mantled nursery palms before committing limiting plantation resources to clonal propagation.
DNA methylation profiling was performed using the McrBC DNA methylation dependent fractionation and microarray hybridization method as described in Lippman, Z., Gendrel, A. V., Colot, V. & Martienssen, R. Profiling DNA methylation patterns using genomic tiling microarrays. Nat Methods 2, 219-224 (2005).

overall_design: DNA methylation profiling was performed on 54 parthenocarpic mantled ramet, 43 normal ramet and 1 ortet adult leaf samples.   For each sample, two independent fractionations of total genomic DNA and DNA methylation-depleted DNA were performed.  Each total DNA/methylation-depleted DNA pair was differentially labeled and hydrized to a custon Nimblegen microarray in a dye-swapped design (4 array hybridizations per sample).

first: Meilina

last: Ong-Abdullah

first: Jared

last: Ordway

last: Jiang

first: Siew–Eng

last: Ooi

first: Sau-Yee

last: Kok

first: Norashikin

last: Sarpan

first: Nuraziyan

last: Azimi

first: Ahmad

middle: T

last: Hashim

first: Zamzuri

last: Ishak

first: Samsul

last: Rosli

first: Fadila

last: Malike

first: Nor

last: Bakar

first: Marhalil

last: Marjuni

first: Norziha

last: Abdullah

first: Zulkifli

last: Yaakub

first: Mohd

last: Amiruddin

first: Rajanaidu

last: Nookiah

first: Rajinder

last: Singh

first: Eng-Ti

last: Low

first: Steven

last: Smith

first: Blaire

last: Bacher

first: Muhammad

last: Budiman

last: Van Brunt

first: Corey

last: Wischmeyer

first: Melissa

last: Beil

first: Nathan

last: Lakey

first: Chin-Ching

last: Lim

first: Xaviar

last: Arulandoo

first: Chin-Nee

last: Choo

first: Wei-Chee

last: Wong

first: Yen-Yen

last: Kwan

first: Sharifah

last: Alwee

first: Ravigadevi

last: Sambanthamurthi

first: Robert

last: Martienssen


title: Comparing transcriptome by means of DNA microarrays of Streptococcus pneumoniae D39 grown with a mix of sugars (mannose, N-acetylglucosamine, galactose) to cells grown with the same mix after a 1 hr pulse with glucose

status: Public on Sep 01 2015

city: Groningen

first: Tomas

last: Kloosterman

address: Nijenborgh 7

department: Natural Sciences

country: Netherlands

institute: University of Groningen

summary:
Streptococcus pneumoniae is a strictly fermentative human pathogen that relies on carbohydrate metabolism to generate energy for growth. The nasopharynx colonised by the bacterium is poor in free sugars, but mucosa lining glycans can provide a source of sugar. In blood and inflamed tissues glucose is the prevailing sugar. As a result during progression from colonisation to disease S. pneumoniae has to cope with a pronounced shift in carbohydrate nature and availability. Thus, we set out to assess the pneumococcal response to sugars found in glycans and the influence of glucose (Glc) on this response at the transcriptional, physiological and metabolic levels. Galactose (Gal), N-acetylglucosamine (GlcNAc) and mannose (Man) affected the expression of 8 to 14% of the genes covering cellular functions including central carbon metabolism and virulence. The pattern of end-products as monitored by in vivo 13C-NMR is in good agreement with the fermentation profiles during growth, while the pools of phosphorylated metabolites are consistent with the type of fermentation observed (homolactic vs. mixed) and regulation at the metabolic level. Furthermore, the accumulation of   -Gal6P and Man6P indicate metabolic bottlenecks in the metabolism of Gal and Man, respectively.

Glc added to cells actively metabolizing other sugar(s)was readily consumed and elicited a metabolic shift towards a homolactic profile. The transcriptional response to Glc was large (over 5% of the genome). In central carbon metabolism (most represented category), Glc exerted mostly negative regulation. The smallest response was observed on a sugar mix, suggesting that exposure to varied sugars improves the fitness of S. pneumoniae. The expression of classical virulence factors was negatively controlled by Glc in a sugar-dependent manner. Overall, our results shed new light on the link between carbohydrate metabolism, adaptation to host niches and virulence.

overall_design: Two conditions with the same strain (D39), including a dye swap


title: Comparing transcriptome by means of DNA microarrays of Streptococcus pneumoniae D39 grown with mannose to cells grown with the same sugar after a 1 hr pulse with glucose


title: Chromatin immunoprecipitation and RNA-seq analysis in purified quiescent yeast cells to identify the genomic RNA polymerase II and histone H3 methylation occupancy profiles and the transcriptome

city: Dublin 2

first: Darren

middle: John

last: Fitzpatrick

state: Ireland

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

type: Genome binding/occupancy profiling by genome tiling array

summary: A defining characteristic of quiescent cells is their low level of gene activity compared to growing cells.  Using a yeast model for cellular quiescence, we compared the genome-wide profiles of multiple histone modifications between growing and quiescent cells, and correlated these profiles with the presence of RNA polymerase II and its transcripts.  Quiescent cells retained several forms of histone methylation normally associated with transcriptionally active chromatin and had many transcripts in common with growing cells. Quiescent cells also contained high levels of RNA polymerase II, but only low levels of the canonical initiating and elongating forms of the polymerase.  The data suggest that the transcript and histone methylation marks in quiescent cells were either inherited from growing cells or established early during the development of quiescence and then retained in this non-growing cell population.  This might ensure that quiescent cells can rapidly adapt to a changing environment to resume growth.

overall_design: Immunoprecipitation experiments were carried out for Pol II, H3K36me3, H3K4me3, H3K79me3 and H3 separately using both Log-phase and Quiescent cells. Each ChIP-chip assay was conducted using a control (IN) and in all instances, at least one replicate experiment was performed.

first: Conor

last: Young

first: Cory

last: Hillyer

first: Karsten

last: Hokamp

first: Nikifor

last: Konstantinov

first: Jacqueline

last: Welty

first: Scott

last: Ness

first: Margaret

last: Werner-Washburne

first: Alastair

middle: B

last: Fleming

first: MaryAnn

last: Osley


title: Comparing transcriptome by means of DNA microarrays of Streptococcus pneumoniae D39 grown with N-acetylglucosamine to cells grown with the same sugar after a 1 hr pulse with glucose


title: Ikzf1 alterations contribute to the pathogenesis of BCR-ABL1 positive acute lymphoblastic leukemia (400K CGH)

status: Public on Sep 04 2015

city: Memphis

first: Charles

last: Mullighan

state: TN

address: 262 Danny Thomas Place

institute: St Jude Children's Research Hospital

summary:
Alterations of IKZF1, encoding the lymphoid transcription factor IKAROS, are a hallmark of high risk acute lymphoblastic leukemia (ALL), however the role of IKZF1 alterations in ALL pathogenesis is poorly understood. Here we show that in mouse models of BCR-ABL1 leukemia, Ikzf1 and Arf alterations synergistically promote the development of an aggressive lymphoid leukemia. Ikzf1 alterations were associated with acquisition of stem cell-like features, including self-renewal and increased bone marrow stromal adhesion. Rexinoid receptor agonists reversed this phenotype, in part by inducing expression of IKZF1, resulting in abrogation of adhesion and self-renewal, cell cycle arrest and attenuation of proliferation without direct cytotoxicity. Retinoids potentiated the activity of dasatinib in mouse and human BCR-ABL1 ALL, providing a new therapeutic option in IKZF1-mutated ALL.
Significance: The outcome of therapy for high-risk acute lymphoblastic leukemia remains suboptimal despite contemporary chemotherapy and the advent of targeted therapeutic approaches. Recent genomic studies have identified deletions or mutations of IKZF1 as a hallmark of high-risk ALL, but an understanding of how IKZF1 alteration contribute to leukemia development are lacking. Here we show that IKZF1 alterations drive lymphoid lineage, a stem cell-like phenotype, abnormal bone marrow adhesion, and poor responsiveness to tyrosine kinase inhibitor (TKI) therapy. Using a high-content screen, we show that retinoids reverse this phenotype in part by inducing expression of wild type IKZF1, and increase responsiveness to TKIs. These findings provide new insight into the pathogenesis of high-risk ALL and potential new therapeutic approaches.

overall_design: Mouse Ikzf1+/- BCR-ABL1 tumor and B220+ B cell normal DNA was analyzed

first: Michelle

middle: L

last: Churchman

first: Yong-Dong

last: Wang

first: Jing

last: Ma


title: STAT2 and IRF9-dependent IFN-I signaling restores ISRE-mediated transcription and anti-viral activity independent of STAT1 (mouse)

city: Poznań

first: Hans

last: Bluyssen

address: Umultowska 89

department: Department of Human Molecular Genetics

country: Poland

institute: Faculty of Biology, University of Adam Mickiewicz

summary: Type I Interferons (IFN-I) mediate cellular responses to virus infection. IFN-I induces IFN-stimulated gene (ISG) expression by phosphorylating STAT1 and STAT2, and together with interferon regulatory factor (IRF9), form the transcription complex ISGF3 that binds to the interferon-stimulated response element (ISRE) in ISG promoters. As a component of ISGF3, it is clear that STAT2 plays an essential role in the transcriptional responses to IFN-I with a strong dependence on STAT1. Previously, we showed that STAT2 also forms homodimers that interact with IRF9 (STAT2-IRF9) to activate transcription of ISRE-containing ISGs in response to IFN-I. Indeed, evidence is accumulating for the existence of a STAT1-independent IFN-I signaling pathway, where STAT2-IRF9 can substitute the role of ISGF3. Here, we provide further insight in the transcriptional regulation and the biological implications of STAT2-IRF9 dependent IFN-I signaling. In human STAT1 KO cells overexpressing human STAT2 (U3C-STAT2), we observed that in response to IFN-I, STAT2 homodimers interact with IRF9 to regulate ISG transcription. The IFN-I-induced phosphorylation profile of STAT2 in U3C-STAT2 was prolonged as compared to WT cells (2fTGH), which corresponded with the expression pattern of OAS2 that also depended on IRF9. Subsequent microarray analysis of IFN-I treated 2fTGH and U3C-STAT2 extended our initial observations and identified more than 60 known antiviral ISGs commonly up-regulated in both cell types. The expression profile of these ISGs was delayed and prolonged in U3C-STAT2 as opposed to the early and transient response in 2fTGH. Moreover, U3C-STAT2 were able to restore an antiviral response upon EMCV and VSV infection that was comparable to the response in 2fTGH. Together, our results strongly suggest that an alternative IFN-I-mediated, STAT2-IRF9 dependent signaling pathway exists that can generate an antiviral response without STAT1 and could be beneficial for example against viruses that directly block STAT1 and impair the formation of ISGF3.

overall_design: Overall, 16 samples were analyzed. MEF wild type cells were treated with IFNalpha at 0h, 4h, 8h, and 24h in duplicates. MEF ST1 KO mST2 cells stably overexpressing mouse STAT2 were treated with IFNalpha at 0h, 4h, 8h, 24h in duplicates. Time point 0h was used as a reference sample.

first: Katarzyna

last: Blaszczyk

first: Adam

last: Olejnik

first: Stefan

last: Chmielewski

first: Kaja

last: Kostyrko

first: Joanna

last: Wesoly

first: Chien-Kuo

last: Lee


title: Patterns of somatic uniparental disomy identify novel tumor suppressor genes in colorectal cancer

city: Barcelona

first: Jordi

last: Camps

state: Catalonia

address: c/Rosselló 149-153 4th floor, Center Esther Koplowitz

department: Gastroenterology

country: Spain

institute: IDIBAPS / Hospital Clinic

summary: The aim of this study is to establish an integrative profiling of recurrent UPDs/UPPs, CNAs and genome-wide methylation status in sporadic CRC. Our results indicate that regions showing high frequencies of UPDs/UPPs mostly coincide with regions typically involved in genomic losses such as chromosome arms 1p, 5q, 8p, 14q, 17p, 18q, 20p, and 22q. Of these, chromosome arms 5q, 14q, 17p, and 20p preferentially showed UPDs/UPPs over genomic losses suggesting that tumor cells must maintain the disomic state of certain genes to favor cellular fitness. A meta-analysis using over 300 samples from The Cancer Genome Atlas confirmed our findings. In addition, the genes CSPG2, FLT4, SFRP1, DLK1, and GAS7 were frequently involved in regions of UPDs/UPPs and showed high levels of methylation revealing that UPDs/UPPs can result in the duplication of hypermethylated inactive genes.

overall_design:
A total of 32 primary tumors from the colon and rectum were collected from the Hospital Clinic of Barcelona under the supervision of an experienced pathologist. DNA was extracted and bisulfited according to manufacturer's protocols. Matched patient DNA from normal mucosa  was used as a reference for these experiments.
This dataset includes methylation data for 29 colorectal cancers (only including those with good QC).

first: Keyvan

last: Torabi

first: Rosa

last: Miró

first: Nora

last: Fernández-Jiménez

first: Isabel

last: Quintanilla

first: Laia

last: Ramos

first: Esther

last: Prat

first: Javier

last: del Rey

first: Núria

last: Pujol

first: Jonathan

middle: K

last: Killian

first: Paul

last: Meltzer

first: Pedro

last: Fernández

first: Thomas

last: Ried

first: Juan

last: Lozano

first: Immaculada

last: Ponsa


title: Circulating miRNA signature in serum of pateints with primary sclerosing cholangitis (PSC), cholangiocarcinoma (CC) and healthy controls.

city: Hannnover

first: Shashi

middle: Kumar

last: Gupta

address: Carl-Neuberg Strasse 1

department: IMTTS

institute: Hannover Medical School

summary: RNA was isolated from serum of pateints with PAS, CC and healthy controls. Global microRNA profiling was done using miRNome microRNA Profiler QuantiMir Human PCR Array (#RA660A-1, version 15; BioCat, Heidelberg, Germany)

overall_design: miRNA arrays were performed on pooled RNA samples from six patients for PSC and CC each and a comparison was performed to healthy control patients. MiRNAs with Ct value above 32 were discarded.

first: Jasmin

last: Fetisch

last: Thum


title: Genomic alterations during the progress of pulmonary hypertension

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary: Pulmonary hypertension (PH), a rare disorder is a complication of a number of  cardiopulmonary, unrelated systemic diseases, drug toxicity and genetic mutations. Major advances have been made in the field, but the pathogenesis of PH is not yet understood.  Several experimental models such as monocrotaline (MCT) and hypoxia have been used to understand the mechanism underlying the pathogenesis of PH. We have recently shown that that the addition of hypoxia to MCT injected rats accelerates the disease process leading to neointima formation. We have profiled the lungs of adult male Sprague-Dawley rats kept for 4 weeks in normal atmospheric conditions or in hypobaric hypoxia (380 mmHg) w/o subcutaneous injection with 40 mg/kg MCT or just saline. While MCT and hypoxia altered expression of few genes when applied separately, together they induced a substantial alteration of the transcriptome. The most profoundly altered pathways by the combined effect of hypoxia and MCT were: endocytosis, apoptosis, HIF-1 signaling pathway and vascular smooth muscle contraction.

overall_design: Two-condition (C = normal atmospheric conditions (control) vs H = hypobaric hypoxia) + two treatment (M = with MCT, O = without MCT) experiment. Four biological replicas of each combination: CO, HO, CM, HM. Differently labeled biological replicates were cohybridized with each array. Results of similarly labeled different conditions were compared then averaged for the two fluorescent labels. For instance: CO1 & CO3 were compared with CM1 & CM3, CO2 & CO4 were compared  with CM2 & + CM4, and the results of the comparisons averaged. This design uses 100% of the resources, has a better normlaiztion and allows all possible comparisons among the conditions.

first: Rajamma

last: Mathew

first: Jing

last: Huang

first: Abraham

last: Sangeap

first: Sanda


title: Transcriptional and metabolic effects of glucose on S. pneumoniae sugar metabolism

first: Tomas

last: Kloosterman

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

overall_design: Refer to individual Series


title: Circulating miRNA signature in bile of pateints with primary sclerosing cholangitis (PSC) vs  cholangiocarcinoma (CC)

summary: RNA was isolated from bile of pateints with PAS or CC and global microRNA profiling was done using miRNome microRNA Profiler QuantiMir Human PCR Array (#RA660A-1, version 15; BioCat, Heidelberg, Germany)

overall_design: Three arrays were performed for the PSC group with pooled RNA from n = 5 patients each and two arrays for the CC group with pools of RNA from n = 4 patients each

first: Sabrina


title: Tumor microRNA expression profiling identifies circulating microRNAs for earlier breast cancer detection

status: Public on Sep 03 2015

city: Madrid

first: Nerea

last: Matamala

address: Calle de Pedro Rico, 6

institute: IDIPAZ

summary: Due to their role in tumorigenesis and remarkable stability in body fluids, microRNAs (miRNAs) are emerging as a promising diagnostic tool. The aim of this study was to identify tumor miRNA signatures for the discrimination of breast cancer and the intrinsic molecular subtypes, and the study in plasma of the status of the most significant ones in order to identify potential circulating biomarkers for breast cancer detection.

overall_design: MiRNA expression profiling of 1919 human miRNAs was conducted in 122 FFPE breast tumors (31 luminal A, 33 luminal B, 27 Her2 and 31 triple negative) and 11 normal breast tissues using LNA based miRNA microarrays. Breast tumors were divided into a training (n=61) and a test set (n=61). Both series comprised a similar number of samples from each molecular subtype. Differential expression analysis was performed and microarray classifiers were developed with samples from the training set and validated in samples from the test set. The most relevant miRNAs were validated by quantitative PCR and analyzed in plasma from 36 pretreated patients, 47 postreated patients and 26 healthy individuals. In addition, further validation in 114 pretreated patients and 116 healthy individuals was performed.

first: Javier

last: Benítez


title: Comparing transcriptome by means of DNA microarrays of Streptococcus pneumoniae D39 grown with mannose to cells grown with glucose as carbon source


title: Comparing transcriptome by means of DNA microarrays of Streptococcus pneumoniae D39 grown with galactose to cells grown with glucose as carbon source


title: Comparing transcriptome by means of DNA microarrays of Streptococcus pneumoniae D39 grown with N-acetyl glucosamine to cells grown with glucose as carbon source


first: Jordi

last: Camps

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

summary:
The aim of this study is to establish an integrative profiling of recurrent UPDs/UPPs, CNAs and genome-wide methylation status in sporadic CRC. Our results indicate that regions showing high frequencies of UPDs/UPPs mostly coincide with regions typically involved in genomic losses such as chromosome arms 1p, 5q, 8p, 14q, 17p, 18q, 20p, and 22q. Of these, chromosome arms 5q, 14q, 17p, and 20p preferentially showed UPDs/UPPs over genomic losses suggesting that tumor cells must maintain the disomic state of certain genes to favor cellular fitness. A meta-analysis using over 300 samples from The Cancer Genome Atlas confirmed our findings. In addition, the genes CSPG2, FLT4, SFRP1, DLK1, and GAS7 were frequently involved in regions of UPDs/UPPs and showed high levels of methylation revealing that UPDs/UPPs can result in the duplication of hypermethylated inactive genes.
This dataset includes the array CGH of 30 colorectal cancers.

overall_design: A total of 30 primary tumors from the colon and rectum were collected from the Hospital Clinic of Barcelona under the supervision of an experienced pathologist. DNA was extracted and labeled according to manufacturer's protocols. Matched patient DNA from normal mucosa  was used as a reference for these experiments.

first: Keyvan

last: Torabi

first: Rosa

last: Miró

first: Nora

last: Fernández-Jiménez

first: Isabel

last: Quintanilla

first: Laia

last: Ramos

first: Esther

last: Prat

last: del Rey

first: Núria

last: Pujol

first: Jonathan

middle: S


title: DNA methylation at transcription start sites blocks TBP binding and transcription onset by RNApolII [MeDIP]

city: Montreal

first: Moshe

last: Szyf

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

institute: McGill University

summary: We measured the methylation levels of gene promoters of cerebral cortex of mice. We used MeDIP-array,  immunoprecipitating genomic DNA with an antibody against methylated DNA and measuring methylation levels using custom arrays. The input DNA was used as control.

overall_design: triplicates of frontal cortex DNA pools of 3 mice

first: Renaud

last: Massart

first: Matthew

last: Suderman


title: Comparing transcriptome by means of DNA microarrays of Streptococcus pneumoniae D39 grown with galactose to cells grown with the same sugar after a 1 hr pulse with glucose


title: The effects of ibuprofen on the transcriptome of a euryhaline fish

city: Davis

first: Ken

last: Jeffries

address: One Shields Avenue

institute: UC Davis

summary: Ibuprofen is one of the most commonly detected pharmaceuticals in wastewater effluent; however the effects of ibuprofen on aquatic organisms are poorly understood. This study presents the transcriptome-wide response of the inland silverside, Menidia beryllina, to chronic 14 d exposures to ibuprofen.

overall_design: Twenty-four samples were run on twenty-four arrays, there were six replicates for each of three ibuprofen exposure concentrations and a control group.

middle: M

first: Susanne

last: Brander

first: Monica

last: Britton

first: Nann

last: Fangue

first: Richard

last: Connon


title: Integrated miRNA and gene expression analysis of prostate cancer associated fibroblasts supports a prominent role for interleukin-6 in fibroblast activation [miRNA]

city: Milan

first: Maurizio

last: Callari

address: Via Amadeo, 42

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

summary: Tumor microenvironment coevolves with and simultaneously sustains cancer progression. Reactive fibroblasts found in prostate cancer (PCa), known as cancer associated fibroblasts (CAF), have been indeed shown to fuel tumor development and metastasis by mutually interacting with PCa cells. Little is known about the molecular mechanisms that lead to activation of CAFs from tissue-resident fibroblasts, circulating marrow-derived fibroblast progenitors or mesenchymal stem cells. Through integrated gene and microRNA expression profiling, here we showed that transcriptome of CAFs isolated from prostate tumors strictly resembles that of normal fibroblasts stimulated in vitro with interleukin-6 (IL6), thus confirming the capability of the cytokine to promote acquisition of an activated and cancer-promoting phenotype, and, for the first time, proving that IL6 is able per se to induce all the complex transcriptional changes characteristic of patient-derived CAFs. Comparison with publicly available datasets, however, suggested that prostate CAFs may be alternatively characterized by IL6 and TGFβ-related signatures, indicating that either signal, depending on the context, tumor stage and etiology, may concur to fibroblast activation. Our analyses also highlighted pathways relevant for induction of reactive stroma, including genes the role of which in fibroblast activation is still to be explored. In addition, we revealed a role for muscle-specific miR-133b as a soluble factor secreted by activated fibroblasts to support paracrine activation of non-activated fibroblasts or promote tumor progression.  Overall, in this study we provided insights on the molecular mechanisms driving fibroblast activation in prostate cancer, thus contributing to identify novel hits for the development of therapeutic strategies targeting the crucial interplay between tumor cells and their microenvironment.  Tumor microenvironment coevolves with and simultaneously sustains cancer progression. Reactive fibroblasts found in prostate cancer (PCa), known as cancer associated fibroblasts (CAF), have been indeed shown to fuel tumor development and metastasis by mutually interacting with PCa cells. Little is known about the molecular mechanisms that lead to activation of CAFs from tissue-resident fibroblasts, circulating marrow-derived fibroblast progenitors or mesenchymal stem cells. Through integrated gene and microRNA expression profiling, here we showed that transcriptome of CAFs isolated from prostate tumors strictly resembles that of normal fibroblasts stimulated in vitro with interleukin-6 (IL6), thus confirming the capability of the cytokine to promote acquisition of an activated and cancer-promoting phenotype, and, for the first time, proving that IL6 is able per se to induce all the complex transcriptional changes characteristic of patient-derived CAFs. Comparison with publicly available datasets, however, suggested that prostate CAFs may be alternatively characterized by IL6 and TGFβ-related signatures, indicating that either signal, depending on the context, tumor stage and etiology, may concur to fibroblast activation. Our analyses also highlighted pathways relevant for induction of reactive stroma, including genes the role of which in fibroblast activation is still to be explored. In addition, we revealed a role for muscle-specific miR-133b as a soluble factor secreted by activated fibroblasts to support paracrine activation of non-activated fibroblasts or promote tumor progression.  Overall, in this study we provided insights on the molecular mechanisms driving fibroblast activation in prostate cancer, thus contributing to identify novel hits for the development of therapeutic strategies targeting the crucial interplay between tumor cells and their microenvironment.  Tumor microenvironment coevolves with and simultaneously sustains cancer progression. Reactive fibroblasts found in prostate cancer (PCa), known as cancer associated fibroblasts (CAF), have been indeed shown to fuel tumor development and metastasis by mutually interacting with PCa cells. Little is known about the molecular mechanisms that lead to activation of CAFs from tissue-resident fibroblasts, circulating marrow-derived fibroblast progenitors or mesenchymal stem cells. Through integrated gene and microRNA expression profiling, here we showed that transcriptome of CAFs isolated from prostate tumors strictly resembles that of normal fibroblasts stimulated in vitro with interleukin-6 (IL6), thus confirming the capability of the cytokine to promote acquisition of an activated and cancer-promoting phenotype, and, for the first time, proving that IL6 is able per se to induce all the complex transcriptional changes characteristic of patient-derived CAFs. Comparison with publicly available datasets, however, suggested that prostate CAFs may be alternatively characterized by IL6 and TGFβ-related signatures, indicating that either signal, depending on the context, tumor stage and etiology, may concur to fibroblast activation. Our analyses also highlighted pathways relevant for induction of reactive stroma, including genes the role of which in fibroblast activation is still to be explored. In addition, we revealed a role for muscle-specific miR-133b as a soluble factor secreted by activated fibroblasts to support paracrine activation of non-activated fibroblasts or promote tumor progression.  Overall, in this study we provided insights on the molecular mechanisms driving fibroblast activation in prostate cancer, thus contributing to identify novel hits for the development of therapeutic strategies targeting the crucial interplay between tumor cells and their microenvironment.

overall_design: In the present study, patient derived-CAFs and HPFs activated in vitro with either TGFβ or IL6 were comparatively analyzed for gene and microRNA (miRNA) expression profiles, with the aim to define transcriptional pathways responsible for fibroblast activation and establish whether different subpopulations of CAFs may exist in PCa.

first: Valentina

last: Doldi

first: Elisa

last: Giannoni

first: Francesca

last: D'Aiuto

first: Massimo

last: Maffezzini

first: Riccardo

last: Valdagni

first: Paola

last: Chiarugi

first: Paolo

last: Gandellini

first: Nadia

last: Zaffaroni


title: Discovery of a drug targeting microenvironmental support for lymphoma cells by screening using patient-derived xenograft cells

status: Public on Aug 31 2015

city: Otsu-shi

first: keiki

last: sugimoto

state: Shiga

address: 1-11-1, Karasaki

department: Fujii Memorial Research Institute

institute: Otsuka Pharmaceutical

summary: Cell lines have been used for drug discovery as useful models of cancers; however, they do not recapitulate cancers faithfully, especially in the points of rapid growth rate and microenvironment independency. Consequently, the majority of conventional anti-cancer drugs are less sensitive to slow growing cells and do not target microenvironmental support, although most primary cancer cells grow slower than cell lines and depend on microenvironmental support. Here, we developed a novel high throughput drug screening system using patient-derived xenograft (PDX) cells of lymphoma that maintained primary cancer cell phenotype more than cell lines. The library containing 2613 known pharmacologically active substance and off-patent drugs were screened by this system. We could find many compounds showing higher cytotoxicity than conventional anti-tumor drugs. Especially, pyruvinium pamoate showed the highest activity, and its strong anti-tumor effect was confirmed also in vivo. We extensively investigated its mechanism of action and found that it inhibited  glutathione supply from stromal cells to lymphoma cells, implying the importance of the stromal protection from ox 1 idative stress for lymphoma cell survival and a new therapeutic strategy for lymphoma. Our system introduces a primary cancer cell phenotype into cell-based phenotype screening and sheds new light on anti-cancer drug development.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Global gene expression profiles of PDX cells showed high similarity to those of original primary cells. The correlation coefficient of gene expression profiles between PDX cells and the originalprimary cells was 0.814-0.890.

first: Sugimoto

last: Keiki


title: High dietary protein decreases fat deposition induced by high-fat and high-sucrose diet in rats

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: High-protein diets are known to reduce adiposity in the context of high carbohydrate and Western diets. However, few studies have investigated the specific high-protein effect on lipogenesis induced by a high-sucrose (HS) diet or fat deposition induced by high-fat feeding. We aimed to determine the effects of high protein intake on the development of fat deposition and partitioning in response to high-fat and/or HS feeding. A total of thirty adult male Wistar rats were assigned to one of the six dietary regimens with low and high protein, sucrose and fat contents for 5 weeks. Body weight (BW) and food intake were measured weekly. Oral glucose tolerance tests and meal tolerance tests were performed after 4th and 5th weeks of the regimen, respectively. At the end of the study, the rats were killed 2 h after ingestion of a calibrated meal. Blood, tissues and organs were collected for analysis of circulating metabolites and hormones, body composition and mRNA expression in the liver and adipose tissues. No changes were observed in cumulative energy intake and BW gain after 5 weeks of dietary treatment. However, high-protein diets reduced by 20 % the adiposity gain induced by HS and high-sucrose high-fat (HS-HF) diets. Gene expression and transcriptomic analysis suggested that high protein intake reduced liver capacity for lipogenesis by reducing mRNA expressions of fatty acid synthase (fasn), acetyl-CoA carboxylase a and b (Acaca and Acacb) and sterol regulatory element binding transcription factor 1c (Srebf-1c). Moreover, ketogenesis, as indicated by plasma β-hydroxybutyrate levels, was higher in HS-HF-fed mice that were also fed high protein levels. Taken together, these results suggest that high-protein diets may reduce adiposity by inhibiting lipogenesis and stimulating ketogenesis in the liver.

overall_design: Adult male Wistar rats were fed diets with varying amounts of protein, carbohydrates and fat for 5 weeks. At the end of the experiment, rats were killed and tanscriptome analysis was performed on pooled liver samples.

first: Catherine

last: Chaumontet

first: Patrick

last: Even

first: Jessica

last: Schwarz

first: Angélique

last: Simonin-Foucault

first: Julien

last: Piedcoq

first: Gilles

last: Fromentin

first: Daniel

last: Tomé

first: Dalila

last: Azzout-Marniche


title: Aberrant differentiation of glioma stem cells: Implications for therapeutic targeting (GSCs)

city: Austin

first: Brian

middle: D

last: Vaillant

department: Neurology

institute: Seton Brain and Spine Institute

summary:
SUMMARY  Terminal differentiation has been proposed as a therapeutic strategy for glioblastoma (GBM). Culturing of GBM derived tumor initiating glioma stem cells (GSCs) in fetal bovine serum containing media is a proposed mode of differentiation that is thought to induce loss of stem cell characteristics, promote neural lineage differentiation and a parallel loss of tumor initiation capacity. Here we show that GSCs retained both neurosphere formation and tumor initiation abilities after short or long term serum exposure. Under serum induced differentiating conditions, GSCs expressed both neural lineage and stem cell markers, highlighting the aberrant pseudo-differentiation state. GSCs maintained under adherent differentiating conditions continued to proliferate and initiate tumor formation with efficiencies similar to GSCs maintained under proliferating (neurosphere) conditions. Proneural (PN) GSCs under serum exposure showed an induction of mesenchymal (MES) gene expression signatures. Our data indicate that the tumor initiation ability of GSCs is independent of their differentiation state and that terminal differentiation as a therapeutic approach may not effectively negate tumorigenicity of GSCs.
SIGNIFICANCE  Terminal differentiation has been proposed as a therapeutic strategy for glioblastoma (GBM). Culturing of GBM derived tumor initiating glioma stem cells (GSCs) in fetal bovine serum containing media is a proposed mode of differentiation that is thought to induce loss of stem cell characteristics, promote neural lineage differentiation and a parallel loss of tumor initiation capacity. Here we show that GSCs retained both neurosphere formation and tumor initiation abilities after short or long term serum exposure. Under serum induced differentiating conditions, GSCs expressed both neural lineage and stem cell markers, highlighting the aberrant pseudo-differentiation state. GSCs maintained under adherent differentiating conditions continued to proliferate and initiate tumor formation with efficiencies similar to GSCs maintained under proliferating (neurosphere) conditions. Proneural (PN) GSCs under serum exposure showed an induction of mesenchymal (MES) gene expression signatures. Our data indicate that the tumor initiation ability of GSCs is independent of their differentiation state and that terminal differentiation as a therapeutic approach may not effectively negate tumorigenicity of GSCs.

overall_design: Gene expression data for 17 isolated Glioma Stem Cells

first: Veerakumar

last: Balasubramaniyan

first: Shuzhen

last: Wang

first: Joy

last: Gumin

first: M

last: Butalid

first: Ke

last: Sai

first: Se

middle: H

last: Kim

first: H

last: Boddekke

first: Frederick

last: Lang

first: Kenneth

last: Aldape

first: Erik

middle: P

last: Sulman

first: Krishna

last: Bhat

first: Howard

last: Colman


title: Aberrant differentiation of glioma stem cells: Implications for therapeutic targeting (shift)

overall_design: Gene expression data for 4 Glioma stem cells lines grown long-term growth in fetal bovine serum (comparison files in Fig1A)

middle: E

middle: W


title: Aberrant differentiation of glioma stem cells: Implications for therapeutic targeting [Xenograph]

overall_design: GSC 20 and 23, grown in basal GSC media with bFGF and EGF or fetal bovine serum, then injected into brains of immunocompromised mice, then tumor harvested for Gene expression


title: CLL exosomes modulate the transcriptome and behaviour of recipient stromal cells and are selectively enriched in miR-202-3p [mirBase 13]

city: Liverpool

first: Mosavar

last: Farahani

address: Daulby Street

department: Molecular and Clinical Cancer Medicine

institute: University of Liverpool

summary: Bi-directional communication with the microenvironment is essential for homing and survival of cancer cells with implications for disease biology and behaviour. In chronic lymphocytic leukemia (CLL) the role of the microenvironment on malignant cell behaviour is well described. However, how CLL cells engage and recruit nurturing cells is poorly characterised. Here we demonstrate that CLL cells secrete exosomes that are nanovesicles originating from the fusion of multivesicular bodies with the plasma membrane, to shuttle proteins, lipids, microRNAs (miR) and mRNAs to recipient cells. We characterise and confirm the size (50 - 100 nm) and identity of the CLL-derived exosomes by Electron microscopy (EM), Atomic force microscopy (AFM), flow cytometry and western blotting using both exosomes-specific and CLL-specific markers. Incubation of CLL-exosomes, derived either from cell culture supernatants or from patient plasma, with human stromal cells shows that they are readily taken up into endosomes, and induce expression of genes such as c-fos and ATM as well as enhance proliferation of recipient HS-5 cells. Furthermore, we show that CLL exosomes encapsulate abundant small RNAs and are enriched in certain miRs and specifically hsa-miR-202-3p. We suggest that such specific packaging of miR-202-3p impacts on the expression of 'suppressor of fused' (Sufu), a Hedgehog (Hh) signalling intermediate, in the parental CLL cells. Thus, our data show that CLL cells secrete exosomes that alter the transcriptome and behaviour of recipient cells. Such communication with microenvironment is likely to have an important role in CLL disease biology.

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Macacine alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
Herpesvirus saimiri (strain 11)
JC polyomavirus
Human immunodeficiency virus 1
Human betaherpesvirus 6B
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: miR analysis was carried out on 3 exosomal samples and 3 corresponding cellular samples from CLL patients.  Exosomes are a discrete population of small (50-100 nm diameter) EVs of endosomal origin with a lipid membrane bilayer and a cup-shaped morphology. We used common reference design which allows visualization of variations between the samples.  Each sample equals one array and each sample compared with common reference (Pool).  The pool or common reference was a collection of 23 RNA samples isolated from 23 CLL cases. We hypothesised that CLL derived exosomes should contain unique miRs that are reflective of CLL cell content and additionally relevant for disease biology.

first: Carlos

last: Rubbi

first: Lu-Ning

last: Liu

first: Joseph

middle: R

last: Slupsky

first: Nagesh

last: Kalakonda


title: miR-1246 association with distant metastasis and poor prognosis in breast cancer patients

city: Milano

first: Elena

last: Landoni

address: Via Vanzetti 5

summary: Circulating microRNAs have recently emerged as a new class of promising non-invasive cancer biomarkers. The purpose of this study was the identification by a high-throughput approach (miRNA microarray) of circulating miRNAs associated with breast cancer-derived distant metastasis. To achieve this goal, we resorted to archival plasma samples collected from patients in the control arm of a randomized clinical trial on stage I breast cancer. We compared plasma miRNA levels in patients that developed distant metastasis after a radical or conservative surgery and in those long-term disease-free. Microarray results were technically and independently validated by Real Time PCR. Subsequent in vitro, in vivo and in silico analyses were performed to investigate the miRNA biological/clinical significance in relation with breast cancer progression. We demonstrated that high circulating miR-1246 levels were associated to distant metastasis and that high tissue expression of this miRNA was correlated with unfavorable outcome in ER+HER2- breast cancer patients. In addition, miR-1246 expression was also found to be related with stem-like features.

overall_design: 64 samples (32 patients with metastasis and 32 patients with no metastasis) were considered from a total of 208 hybridized samples collected between 1987 and 2004 (including 94 paired samples according to tumor ER status, age at drawing, drawing year, time from surgery, 7 additional samples from 'no evidence of disease' (NED) patients, 10 references, 1 healthy donor and 2 replicated samples)

first: Maurizio

last: Callari


title: Aberrant differentiation of glioma stem cells: Implications for therapeutic targeting

first: Brian

last: Vaillant


title: CLL exosomes modulate the transcriptome and behaviour of recipient stromal cells and are selectively enriched in miR-202-3p


title: Negative Regulation of Filamentous Growth in Candida albicans by Dig1p

first: Hannah

last: Regan

address: 7141 Sherbrooke Street West

department: Biology

institute: Concordia University

summary: Candida albicans is an opportunistic fungal pathogen capable of causing superficial and systemic infections in humans. The ability of C. albicans to switch between various morphological forms depending on its host environment is thought to contribute to its virulence. Filamentous growth states are associated with tissue invasion, biofilm formation, evasion of innate host defences and mating. Although the mechanisms of activation of filamentous growth pathways are well understood, less is known about which factors control the negative regulation of filamentation. In this study, we have identified a previously uncharacterized Orf that shares sequence similarity with Saccharomyces cerevisiae Dig1p and Dig2p. Deletion of the gene encoding this Orf triggers invasive growth in C. albicans and so we have retained the yeast designation of Dig1 (for Down-regulation of Invasive Growth).  Mutants lacking CaDIG1 form cultures of hyperpolarized cells, form robust biofilms, are highly invasive in vitro but not in vivo and are constitutively activated for the pheromone response. Deletion of key transcription factors that act downstream of Dig1p provide evidence to suggest that CaDig1 regulates filamentation and mating through multiple signalling pathways.

overall_design: Transcriptional analysis of the C. albicans dig1Δ/dig1Δ homozygous mutant versus the wild type (SN148) in the MTLa/alpha background.  Four biological replicates of the mutant and the wild type were included in the analysis.  Samples were grown at 30 °C in YPD medium plus uridine

first: Yuan

last: Sun

first: Yaolin

last: Chen

first: Malcolm

last: Whiteway


title: Transcriptional response to histone deacetylase inhibitors

city: Birmingham

first: John

last: Halsall

address: Medical School, Vincent Drive

department: Cancer and Genomic Sciences

institute: University of Birmingham

summary:
Histone deacetylase inhibitors are a class of drug which rapidly induce hyperacetylation of histone proteins. Here, we aimed to study the association between HDACi-induced histone acetylation and changes in gene expression.
To study the early responses to HDACi treatment we treated cells with three different concentrations of two HDACi, sodium valproate (VPA) and suberoylanilide hydroxamic acid over a short timecourse.

overall_design: AH LCL cells were treated with 0.2mM, 1mM or 5mM valproic acid (VPA) or 0.5, 2.5 or 12.5µM suberoylanilide hydroxamic acid (SAHA). GM12878 cells were treated with 1mM VPA. Samples were collected at 0, 30, 60 and 120 minutes. All experiments were carried out in triplicate. One replicate of AH LCL, 0.2mM VPA, 30min and one replicate of AH LCL, 5mM VPA, 30min were eliminated as outliers

middle: A

last: Turan

first: Bryan

last: Turner


title: Detection of chromothripsis-like patterns from custom array platform for chronic lymphocytic leukemia diagnosis (qchip Hemo custom array v3)

first: Itziar

last: Salaverria

address: Rossello 153

institute: Hospital Clínic

summary:
Chronic lymphocytic leukemia (CLL) is the most frequent leukemia in Western countries. The main genetic alterations associated to this disease are loss of 13q14, loss of 11q23, trisomy 12 and, less frequently, 17p13 losses, and are routinely studied using fluorescence in situ hybridization. These genomic aberrations have been demonstrated to be important independent predictors of disease progression in CLL and their detection currently has a direct implication in the treatment strategy of the patients.
It has been widely demonstrated that array-based karyotyping clearly detects DNA gains and losses and allows the identification of CLL abnormalities not included in the standard FISH panel.
We have here established and tested an oligonucleotide-based array platform for the diagnosis of CLL that interrogates the most relevant chromosomal regions related with the disease and may help in the differential diagnosis between CLL and other small B-cell leukemias and may be used as a powerful prognosis tool to stratify the CLL patients.

overall_design: Copy number analysis using Custom Agilent 60K was performed on 47 chronic lymphocytic Leukemia patients with sex-matched control DNAs

first: Lluís

last: Armengol

first: Elias

last: Campo

first: Silvia

last: Beà